title: 1098561_Hudep2_CTCF

description: HUDEP2 CTCF

data_processing:
Reads were mapped to hg38 using BWA mem (v0.7.16a).
Duplicated and multi-mapped reads were removed using samtools (v0.17)
Genome signal tracks (.bw files) were generated using DeepTools bamCoverage (v3.2.0)
Assembly: hg38
Supplementary files format and content: bigWig

source_name: umbilical cord blood

extract_protocol:
Approximately 2.5 × 10^7 cells were used for each immunoprecipitation. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with rotation, and the reaction was quenched with glycine at a final concentration of 125 mM. Cross-linked cells were then lysed and resuspended in 2 mL of RIPA buffer and sonicated for 12 cycles with a Branson 250 sonifier (10 s on/90 s off for a total of 2 min of pulses with 20% output from the micro-tip) to obtain fragments of chromatin approximately 200–300 bp in size. Supernatants were precleared by incubation with 200 µL of protein A/G agarose bead slurry (Thermo Fisher Scientific, cat. #15918014) overnight at 4°C with rotation. Meanwhile, 12.5 µg of IP antibody was incubated with 50 µL of protein A/G agarose bead slurry in 1 mL of PBS overnight at 4°C with rotation. Saved precleared chromatin (20 µL) was used as the input sample. Precleared chromatin was incubated with the antibody–bead complex for 7 h at 4°C with rotation. Cross-linking of DNA was reversed by incubation with RNase A (1 µg/µL), proteinase K (0.2 mg/mL), and 0.25 M NaCl overnight at 65°C.
Immunoprecipitated DNA was purified using the Qiagen PCR Extraction Kit and eluted with 20 µL of EB elution buffer. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, cat. #E7645) with homemade TruSeq adaptors. Libraries were sequenced using an Illumina HiSeq 4000 system.

value: umbilical cord blood

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 2, abbreviated HUDEP2, expresses beta-globin upon induced differentiation

tag: target

value: CTCF


title: 1172061_H1_Input

status: Public on Apr 10 2023

type: SRA

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

description: HUDEP1 input

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 1, abbreviated HUDEP1, expresses gamma-globin upon induced differentiation


title: H3K9me3_H1_2

description: HUDEP1 H3K9me3


title: XT-GR-36

city: Villejuif

first: Felix

last: Blanc-Durand

address: 114 rue Edouard Vaillant

department: Medical Oncology

country: France

institute: Institut Gustave Roussy

data_processing:
Alignment BWA-MEM v-0.7.12
Alignment correction: Samtools v-1.2; Picard-tools v-1.139
Variant calling: GATK Haplotype v-3.4-46;MutaCaller-1.7
Assembly: hg19
Supplementary files format and content: variants, vcf format

source_name: Tumor Tissue

extract_protocol:
QIAsymphony DSP DNA Kits (QIAGEN)
SureSelect XT HS Target Enrichment System (Agilent Technologies) : large pan-cancer panel

treatment_protocol: FFPE treated and bisulfite-conversion + ddPCR

value: Tumor Tissue

value: Ovarian cancer

tag: cell subtype

value: High-grade serous

tag: genotype

value: Myriad MyChoice CDx Positive

tag: treatment

value: After chemotherapy


title: H3K4me3_H1_2

description: HUDEP1 H3K4me3


title: XT-GR-95

value: Myriad MyChoice CDx Negative


title: XT-GR-50

value: Before chemotherapy


title: H3K27me3_H1_2

description: HUDEP1 H3K27me3


title: XT-GR-75


title: 1111615_Hudep1_CTCF_50bp

description: HUDEP1 CTCF


title: H3K4me1_H1_2

description: HUDEP1 H3K4me1


title: XT-GR-66


title: H3K4me3_H1_1

description: HUDEP1 H3K4me3


title: XT-GR-35


title: XT-GR-8


title: KO Hypoxia 103

city: Boston

first: Vamsi

last: Mootha

state: MA

address: 185 Cambridge Street 6th Floor

institute: Massachusetts General Hospital

description:
unstranded 150bp; 2 lanes 350M raw reads per lane
ercc1_rna-seq.raw_counts.csv.gz
ercc1_rna-seq.sample_metadata.csv.gz
ercc1_rna-seq.gene_metadata.csv.gz

library_source: transcriptomic

data_processing:
Reads were aligned to the mm10 mouse genome assembly with the STAR aligner (v. 2.7.5a).
For reads that aligned equally well to both the mtDNA and a known NUMT, the mtDNA alignment was set as the primary alignment in the BAM file.
Duplicate reads were removed using Picard MarkDuplicates (GATK v4.1.5.0-9-g227bef6-SNAPSHOT, Picard v2.21.9).
Reads were mapped to genes using featureCounts (Subread v2.0.1) with GENCODE vM24 genome annotation for the mm10 assembly, and with options "-t exon -p -M --primary".
The featureCounts output was parsed and assembled into an annotated data matrix (AnnData v0.7.5) for downstream analysis.
Assembly: mm10
Supplementary files format and content: ercc1_rna-seq.raw_counts.csv.gz is a comma-delimited file that contains the raw read count data for each sample and gene. ercc1_rna-seq.sample_metadata.csv.gz is a comma-delimited file that contains the metadata for each sample. Note that sample WT Normoxia 101 was an outlier in PCA and had excessive Cook's distance on many genes based on DESeq2 analysis, so was excluded from our analysis. ercc1_rna-seq.gene_metadata.csv.gz is a comma-delimited file that contains the metadata for each gene, including Ensembl gene ID, the gene common name, and the transcript length as reported in the featureCounts output (for use in TPM normalization of the counts).

molecule: polyA RNA

organism: Mus musculus

source_name: bulk cerebellum

extract_protocol:
RNA was extracted and polyA-selected by Genewiz (now Azenta Life Sciences, South Plainfield, NJ)
Unstranded RNA-seq libraries were prepared by Genewiz (now Azenta Life Sciences, South Plainfield, NJ)

treatment_protocol: Hypoxia treament = at age 4 weeks (time of weaning) mice were placed in continuous 11% oxygen (normobaric at sea level, achived with dilution of air with nitrogen) for the remainder of the experiment. All mice were hybrid C57BL/6 and FVB.

tag: Sex

value: M

value: bulk cerebellum

value: Ercc1 [delta]/-

value: Hypoxia (11%)

tag: time (age_in_weeks)


title: XT-GR-88


title: H3K36me3_H1_2

description: HUDEP1 H3K36me3


title: H3K27ac_H1_2

description: HUDEP1 H3K27ac


title: XT-GR-71


title: H3K9me3_H1_1

description: HUDEP1 H3K9me3


title: XT-GR-53


title: XT-GR-4


title: H3K27ac_H1_1

description: HUDEP1 H3K27ac


title: XT-GR-15


title: H3K36me3_H1_1

description: HUDEP1 H3K36me3


title: XT-GR-37

value: Undifferentiated


title: XT-GR-91


title: 1047946_Hudep1_CTCF

description: HUDEP1 CTCF


title: XT-GR-94


title: XT-GR-86


title: H3K4me3_CD34_2

description: CD34_E H3K4me3

source_name: blood

value: blood

value: CD34+ HSPCs differentiated ex vivo into erythroblasts, abbreviated CD34_E


title: XT-GR-42


title: H3K9me3_CD34_2

description: CD34_E H3K9me3


title: H3K4me1_CD34_2

description: CD34_E H3K4me1


title: XT-GR-29


title: H3K4me1_H1_1

description: HUDEP1 H3K4me1

value: umbilical cord blood


title: XT-GR-84


title: H3K36me3_CD34_2

description: CD34_E H3K36me3


title: WD36

first: Salvador

last: Casani

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
RNA processing: Data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c)[ref], expression was quantified using the –quantMode option in STAR
count matrix in tsv
Assembly: hg38
Supplementary files format and content: in table

molecule: total RNA

source_name: Liposarcoma

growth_protocol: Base Media: RPMI, 15% FBS, 1% penstrep, 1% glutamax.

extract_protocol:
Total RNA was extracted using qiagen rneasy plus mini kit
Libraries were prepared first with Poly-A enrichment using magnetic oligo(dT)-beads, then ligated to RNA adaptors for sequencing.

treatment_protocol: no treatment, DMSO, or 100nM HDM201 as indicated in sample name

value: Liposarcoma

value: No treatment


title: H3K27me3_H1_1

description: HUDEP1 H3K27me3

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 1, abbreviated HUDEP1, expresses gamma-globin upon induced differentiation


title: WD33


title: H3K4me3_CD34_1

description: CD34_E H3K4me3


title: H3K9me3_CD34_1

description: CD34_E H3K9me3


title: WD30


title: WD28


title: WD24


title: H3K36me3_CD34_1

description: CD34_E H3K36me3


title: WD23


title: WD22


title: H3K4me1_CD34_1

description: CD34_E H3K4me1


title: WT2_1

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

country: Germany

institute: UKE Hamburg-Eppendorf

description: bulk RNA-seq

data_processing:
Quality control was done with FastQC (Barbraham Bioinformatics). Raw reads were trimmed using TrimGalore! (Barbraham Bioinformatics) and mapped with Tophat to hg19 using Galaxy Freiburg.
Read counts extracted with htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample

source_name: Podocyte

growth_protocol: Conditionally immortalized human podocytes were let to proliferate at 33°C in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS), Penicillin/Streptomycin, ITS and non-essential amino acids.

extract_protocol:
Total RNA of cells was isolated using the Phenol/Chloroform method as previously described.
All steps were performed according to standard protocol of Iluminalibrary preparation.
RNA sequencing was performed by GATC, Germany.

treatment_protocol: Conditionally immortalized human podocyte WT and CRISPR/CAS9 GLA KO cell lines were differentiated at 37 °C at 70% confluency for 10 to 14 days.

value: Immortalized podocyte cell line

tag: group

value: WT

value: Replicate 1


title: N34

extract_protocol:
Total RNA was extracted using qiagen rneasy plus mini kit
Libraries were prepared by ligating Illumina TrueSeq adapters adpators followed by 14 cycles of amplification


title: KO_5AA1_2

description: bulk RNA-seq

value: CRISPR/CAS9 GLA KO

value: Replicate 2


title: WT2_2

description: bulk RNA-seq


title: WD14


title: WD19


title: N33


title: N31


title: KO_5AA1_1

description: bulk RNA-seq


title: CRISPRa_C1_Rep2

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

description:
CRISPRa_C1_Rep2
CRISPRa.TPM.txt

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15).
The Fastq files were aligned to the reference genome (hg38) using Hisat2 (v2.1.0).
Reads mapped to tRNA and rRNA are removed.
Stringtie (v2.0.6) was used to calculate the TPM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: CRISPRa.TPM.txt

source_name: HEK 293T

growth_protocol: The HEK293T-Cas9 cells were harvested on days 3 after transfection and cultured in endotoxin-free DMEM medium with 10% (v/v) fetal bovine serum (FBS, Gibco).

extract_protocol:
The cDNA was processed with the Fluidigm C1 Single-Cell Auto Prep System
RNA libraries were prepared with TruePrep DNA Library Prep Kit V2 for Illumina according to manufacture's instruction

treatment_protocol: Cells were transfected with plasmid.

tag: cell line

value: HEK 293T

tag: transfection

value: plasmid transfection


title: WD34


title: N30


title: N22


title: DD36


title: DD31


title: N15


title: DD30


title: WD15


title: DD35


title: CRISPRa_C1_Rep1

description:
CRISPRa_C1_Rep1
CRISPRa.TPM.txt


title: WD13


title: 4R128-L2-T1_Day15_Control

city: Irvine

first: Timothy

last: Downing

state: CA

address: University of California, Irvine

department: Biomedical Engineering

institute: University of California, Irvine

data_processing:
HCS 3.4.0.38 Software was used for basecalling.
RNA-seq reads were aligned to hg38 and Transcipts per Million (TPM) produced using Salmon 1.2.0 Software.
Read normalization and differential gene expression analysis were conducted with DESeq2 1.26.0 Software
Genome_build: hg38
Supplementary_files_format_and_content: excel file includes non-normalized TPM for each sample

source_name: hiF-Ts

growth_protocol: hiF-T cells were grown and reprogrammed using protocol from Cacchiarelli et. al,, Cell, 2015. Briefly, cells were grown in media containing 10% ES-FBS and reprogrammed in media containing 20% KSR with or without lentivirus expressing shRNA vectors. Reprogramming was performed for 15 days in the presence of LSD1i.

extract_protocol:
Reprogramming cells underwent MEF depletion using magnetic bead separation (Miltenyi Biotec). Then total RNA was extracted from remaining cells using Direct-zol RNA Miniprep Kit (Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols. Biological replicates of each sample sequenced in separate flow cell, except for Day -1.

treatment_protocol: Reprogramming cells were treated with or without lentivirus expressing shRNA vectors targeting SHROOM3 or LacZ, a non-targeting control.

value: hiF-Ts

tag: reprogramming timepoint (day)

tag: gene knockdown

tag: passage


title: 4R128-L2-T1_Day15_Shroom3


title: 4R128-L3-T2_Day15_Control


title: 4R128-L3-T2_Day15_Shroom3


title: DD20


title: 4R128-L3-T2_Day15_LacZ

value: LacZ


title: N19


title: 4R128-L3-T2_Day12_Shroom3


title: WD5


title: N12


title: 4R128-L2-T1_Day12_Shroom3


title: N14


title: 4R128-L2-T1_Day12_Control


title: 4R128-L3-T2_Day12_LacZ


title: 4R128-L3-T2_Day12_Control


title: N10


title: DD2


title: 4R128-L3-T2_Day9_LacZ


title: 4R128-L3-T2_Day9_Shroom3


title: 4R128-L2-T1_Day9_Shroom3


title: DD15


title: 4R128-L2-T1_Day15_LacZ


title: DD10


title: 4R128-L2-T1_Day9_Control


title: 4R128-L3-T2_Day9_Control


title: 4R128-L3-T2_Day6_Shroom3


title: LPS853 t6_2


title: LPS853 t6_1


title: DD1


title: 4R128-L2-T1_Day6_Shroom3


title: WD4


title: LPS853 t4_2


title: 4R128-L3-T2_Day6_LacZ


title: WD10


title: WD12


title: 4R128-L2-T1_Day6_LacZ


title: LPS853 t4_1


title: 4R128-L2-T1_Day12_LacZ


title: LPS853 t2_2


title: 4R128-L3-T2_Day6_Control


title: LPS853 t2_1


title: LPS853 t0_2


title: LPS853 t0_1


title: 4R128-L2-T1_Day3_Shroom3


title: 4R128-L2-T1_Day9_LacZ


title: 4R128-L3-T2_Day3_Shroom3


title: 4R128-L3-T2_Day3_LacZ


title: 4R128-L2-T1_Day3_LacZ


title: LPS853_2


title: Tumor_expression


title: 4R128-L3-T2_Day3_Control


title: 4R128-L2-T1_Day3_Control


title: LPS141_1


title: 4R128-L3-T2_Day0_Shroom3


title: T778_rna_seq


title: T449_rna_seq


title: 220401_U2OS_rep_2_untreated_input_S24

data_processing:
ChIP processing:ChIP-Seq data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c), including parameters --alignIntronMax 1 --alignEndsType EndToEnd. Tag directories of the mapped reads were created using homer (v4.11.1 using hg38 v6.4), and peaks were called using the findPeaks function.
Assembly: hg38

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
Libraries were prepared by ligating Illumina TrueSeq adapters adpators followed by 14 cycles of amplification

tag: chip antibody

value: Untreated


title: 4R128-L2-T1_Day0_Shroom3


title: 4R128-L2-T1_Day0_LacZ


title: 220401_U2OS_rep_2_untreated_H3K27ac_S23

data_processing:
ChIP processing:ChIP-Seq data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c), including parameters --alignIntronMax 1 --alignEndsType EndToEnd. Tag directories of the mapped reads were created using homer (v4.11.1 using hg38 v6.4), and peaks were called using the findPeaks function.
Supplementary_files_format_and_content: peak files in bed format
Assembly: hg38


title: 220401_U2OS_rep_2_untreated_P53_S22


title: 220401_U2OS_rep_2_untreated_MDM2_S21


title: 4R128-L2-T1_Day-1_Control


title: 4R128-L3-T2_Day0_LacZ


title: 4R128-L2-T1_Day6_Control


title: 4R128-L3-T2_Day0_Control


title: 220324_U2OS_untreated_P53_S18


title: 220324_U2OS_untreated_MDM2_S17


title: 220324_U2OS_untreated_H3K27ac_S19


title: 220401_HCT116_rep_3_untreated_input_S26


title: 220401_HCT116_rep_2_untreated_P53_S18


title: 220401_HCT116_rep_2_untreated_input_S20


title: NKC1.73

description: single cell

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15).
The Fastq files were aligned to the reference genome (hg38) using Hisat2 (v2.1.0).
Reads mapped to tRNA and rRNA are removed.
Stringtie (v2.0.6) was used to calculate the TPM of each gene to represent their mRNA expression level.
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: bone marrow

growth_protocol: The K-562-Cas9 cells were harvested on days 14 after lentivirual infection and cultured in endotoxin-free DMEM medium with 10% (v/v) fetal bovine serum (FBS, Gibco).

treatment_protocol: Cells were infected with lentivirus (MOI=0.3).

value: lentiviral infection


title: NKC1.69

description: single cell


title: NKC1.70

description: single cell


title: NKC1.71

description: single cell


title: NKC1.68

description: single cell


title: 220401_HCT116_rep_3_untreated_P53_S25


title: 220401_HCT116_rep_2_untreated_MDM2_S17


title: 220324_U2OS_untreated_input_S20


title: NKC1.66

description: single cell


title: 4R128-L2-T1_Day0_Control


title: NKC1.67

description: single cell


title: NKC1.65

description: single cell


title: 220401_HCT116_rep_2_untreated_H3K27ac_S19


title: 220317_HCT116_untreated_MDM2_S19


title: NKC1.63

description: single cell


title: 220317_HCT116_untreated_H3K27ac_S20


title: NKC1.62

description: single cell


title: NKC1.64

description: single cell


title: NKC1.61

description: single cell


title: LPS853_nutlin_1uM_K27ac_1_S10

value: Nutlin


title: LPS853_nutlin_1uM_input_1_S12


title: NKC1.60

description: single cell


title: NKC1.72

description: single cell


title: LPS853_DMSO_input_1_S6

value: DMSO


title: NKC1.59

description: single cell


title: 220317_LPS853_DMSO_cell_signaling_YY1


title: NKC1.58

description: single cell


title: NKC1.57

description: single cell


title: LPS853_DMSO_MDM2_1_S5


title: NKC1.56

description: single cell


title: LPS853_200910_nutlin_201208_MDM2_S11


title: NKC1.55

description: single cell


title: 220317_HCT116_untreated_input_S21


title: LPS853_200910_nutlin_201208_K27ac_S12


title: LPS853_200910_DMSO_201208_input_S10


title: LPS853_200910_DMSO_201208_K27ac_S8


title: NKC1.52

description: single cell


title: NKC1.54

description: single cell


title: NKC1.53

description: single cell


title: NKC1.50

description: single cell


title: LPS853_200903_nutlin_201208_p53_S22


title: NKC1.51

description: single cell


title: NKC1.49

description: single cell


title: NKC1.48

description: single cell


title: 210308_LPS853_nutlin_p53_S14


title: 210308_LPS853_nutlin_cJun_S15

value: cJun


title: 210308_LPS853_nutlin_RUNX2_S16


title: LPS853_200903_DMSO_201208_p53_S21


title: 210308_LPS853_nutlin_MDM2_S13


title: NKC1.47

description: single cell


title: NKC1.46

description: single cell


title: NKC1.45

description: single cell


title: NKC1.44

description: single cell


title: LPS853_200910_nutlin_201208_p53_S9


title: 210308_LPS853_nutlin_H3K27ac_S12


title: NKC1.43

description: single cell


title: 210308_LPS853_DMSO_p53_S8


title: NKC1.42

description: single cell


title: 210308_LPS853_DMSO_input_S18


title: NKC1.41

description: single cell


title: LPS853_200910_DMSO_201208_MDM2_S7


title: 210308_LPS853_DMSO_cJun_S9


title: NKC1.40

description: single cell


title: 210308_LPS853_DMSO_RUNX2_S10


title: 210308_LPS853_nutlin_input_S19


title: 210308_LPS853_DMSO_MDM2_S7


title: NKC1.39

description: single cell


title: 210308_LPS853_DMSO_H3K27ac_S6


title: 210223_LPS853_Nutlin_p53_S12


title: NKC1.34

description: single cell


title: NKC1.35

description: single cell


title: NKC1.33

description: single cell


title: NKC1.36

description: single cell


title: 210223_LPS853_Nutlin_cJun_S13


title: 210223_LPS853_DMSO_p53_S9


title: 210223_LPS853_Nutlin_RUNX2_S14


title: 210223_LPS853_DMSO_input_S20


title: NKC1.31

description: single cell


title: 210223_LPS853_DMSO_cJun_S10


title: NKC1.32

description: single cell


title: 210204_LPS853_input_S18


title: NKC1.30

description: single cell


title: NKC1.29

description: single cell


title: NKC1.28

description: single cell


title: 210204_LPS853_cJun_S14


title: 210202_LPS853_input_S11


title: NKC1.26

description: single cell


title: NKC1.25

description: single cell


title: NKC1.38

description: single cell


title: NKC1.37

description: single cell


title: 210202_LPS853_RUNX2_S9


title: NKC1.24

description: single cell


title: LPS141, HDM201, 100nM, 6hr, rep1, S13

description:
lps141_rna_countMatrix.txt
column 7 in txt file
lps141_rna_countMatrix.txt

data_processing:
RNA processing: Data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c)[ref], expression was quantified using the –quantMode option in STAR
Supplementary files format and content: counts table
Assembly: hg38

value: liposarcoma cell

tag: timepoint


title: LPS141, HDM201, 100nM, 6hr, rep2, S14

description:
lps141_rna_countMatrix.txt
column 8 in txt file
lps141_rna_countMatrix.txt


title: NKC1.23

description: single cell


title: LPS141, HDM201, 100nM, 4hr, rep2, S12

description:
lps141_rna_countMatrix.txt
column 6 in txt file
lps141_rna_countMatrix.txt


title: LPS141, HDM201, 100nM, 4hr, rep1, S11

description:
lps141_rna_countMatrix.txt
column 5 in txt file
lps141_rna_countMatrix.txt


title: LPS141, HDM201, 100nM, 2hr, rep2, S10

description:
lps141_rna_countMatrix.txt
column 4 in txt file
lps141_rna_countMatrix.txt


title: NKC1.21

description: single cell


title: NKC1.22

description: single cell


title: NKC1.20

description: single cell


title: NKC1.19

description: single cell


title: LPS141, DMSO, rep1, S7

description:
lps141_rna_countMatrix.txt
column 1 in txt file
lps141_rna_countMatrix.txt


title: NKC1.18

description: single cell


title: NKC1.16

description: single cell


title: LPS141, untreated, rep2, input

data_processing:
ChIP processing:ChIP-Seq data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c), including parameters --alignIntronMax 1 --alignEndsType EndToEnd. Tag directories of the mapped reads were created using homer (v4.11.1 using hg38 v6.4), and peaks were called using the findPeaks function.
For some of the ChIP-seq samples we do not have any quantitative data; the bed files were generated to address peaks. The ones for which we generated quantitative data, bigWig files are provided.
Supplementary files format and content: input - no processed data
Assembly: hg38

value: Non treated


title: NKC1.17

description: single cell


title: 210204_LPS853_RUNX2_S16


title: NKC1.27

description: single cell


title: LPS141, DMSO, rep2, S8

description:
lps141_rna_countMatrix.txt
column 2 in txt file
lps141_rna_countMatrix.txt


title: NKC1.15

description: single cell


title: NKC1.14

description: single cell


title: LPS141, untreated, rep2, MDM2

data_processing:
ChIP processing:ChIP-Seq data were mapped to the GRCh38 reference genome using STAR aligner (v2.6.0c), including parameters --alignIntronMax 1 --alignEndsType EndToEnd. Tag directories of the mapped reads were created using homer (v4.11.1 using hg38 v6.4), and peaks were called using the findPeaks function.
For some of the ChIP-seq samples we do not have any quantitative data; the bed files were generated to address peaks. The ones for which we generated quantitative data, bigWig files are provided.
Supplementary files format and content: peak files in bed format
Assembly: hg38


title: LPS141, untreated, rep2, P53


title: LPS141, untreated, rep2, H3K27ac


title: NKC1.12

description: single cell


title: LPS141, untreated, rep1, input


title: NKC1.13

description: single cell


title: NKC1.11

description: single cell


title: LPS141, untreated, rep1, MDM2


title: LPS141, untreated, rep1, P53


title: NKC1.9

description: single cell


title: NKC1.10

description: single cell


title: LPS141, HDM201, 100nM, 2hr, rep1, S9

description:
lps141_rna_countMatrix.txt
column 3 in txt file
lps141_rna_countMatrix.txt


title: LPS141, 2h, rep2, input


title: LPS141, untreated, rep1, H3K27ac


title: NKC1.7

description: single cell


title: LPS141, 2h, rep2, P53


title: LPS141, 2h, rep2, H3K27ac


title: LPS141, 2h, rep1, input


title: NKC1.6

description: single cell


title: LPS141, 2h, rep1, P53


title: NKC1.4

description: single cell


title: LPS141, 2h, rep1, MDM2


title: NKC1.5

description: single cell


title: NKC1.2

description: single cell


title: NKC1.3

description: single cell


title: LPS141, 2h, rep1, H3K27ac


title: LPS141, 24h, rep2, input


title: LPS141, 24h, rep2, P53


title: NKC1.1

description: single cell


title: LPS141, 24h, rep2, MDM2


title: LPS141, 24h, rep2, H3K27ac


title: NKC1.8

description: single cell


title: LPS141, 24h, rep1, input


title: LPS141, 24h, rep1, P53


title: LPS141, 2h, rep2, MDM2


title: LPS141, DMSO, input, 5


title: LPS141, 24h, rep1, H3K27ac


title: LPS141, DMSO, cJun, rep2


title: LPS141, 24h, rep1, MDM2


title: LPS141, DMSO, input, 4


title: LPS141, DMSO, RUNX2, rep2


title: LPS141, DMSO, input, 3


title: LPS141, DMSO, MDM2, rep3


title: LPS141, DMSO, H3K27ac, rep2


title: LPS141, DMSO, input, 2


title: LPS141, DMSO, MDM2, rep2


title: MCF7_mono24w+_rep3

type: RNA

city: Washington

first: Ayesha

last: Shajahan-Haq

state: District of Columbia

address: 3970 Reservoir Road, NW, NBR E404

institute: Georgetown University Medical Center, Lombardi Comprehensive Cancer Center

description: Gene expression for MCF7 cells after 24+ week 500nM mono palbociclib treatment

hyb_protocol: Cyanine 3 labeled cRNA was hybridized to the Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray kit (catalog number G4851C, design ID 072363) at 65 °C. After 17 hours, the array was washed with Agilent Gene Expression Wash Buffer 1 and Agilent Gene Expression Wash Buffer 2 (pre-warmed at 37 °C overnight), followed by scanning with Agilent Microarray Scanner System G2505C (s/n US123023249). The array data was generated by using Feature Extraction software v11.5.1.1

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan.

data_processing: The scanned images were analyzed with limma R package to obtain background subtracted and normalized signal intensities.

source_name: MCF7 cells, palbociclib 500nM 24w+, replicate 3

label_protocol: 100ng RNA was labeled with cyanine 3-dUTP using Low RNA Input Linear Amplification PLUS kit (Agilent) and purified with RNAeasy column purification (QIAGEN, Valencia, CA) Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF7 cells used in this study were obtained from Georgetown University Medical Center Tissue Culture Shared Resources. Cells were cultured in phenol red free IMEM (Improved Minimum Essential Medium), supplemented with 10% charcoal-stripped calf serum (CCS; Life Technologies, Grand Island, NY) and 10nM 17-beta-estradiol (E2). Cells were grown for indicated times with treatments at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Direct-zol RNA MiniPrep kit from ZYMO Research was used for the RNA extraction. The qualities of RNAs  were checked by Agilent 2100 Bioanalyzer. The RNAs with RIN number were > 8 were used for microarray analysis.

treatment_protocol: There are four treatment conditions: (1) parental MCF7 cells; vehicle treated with 0.04% DMSO, (2) cells treated with palbociclib monotherapy at 750nM for 10 weeks, (3) alternating treatment  with palbociclib at 750nM for 1 weeek  and then switched to ICI182,780 at 750nM for 1 week, for 10 weeks total, and (4) cells cultured for >6 months in palbociclib (500nM). All media (with specified drugs) were replenished every 3 days. Four biological replicated were collected for each treatment condition.

value: breast cancer

value: palbociclib 500nM 24w+


title: MCF7_alt10w_rep4

description: Gene expression for MCF7 cells after 10 week 750nM palbociclib (1w)->750nM ICI (1w)  treatment

source_name: MCF7 cells, palbociclib 750nM 1w -> ICI 750nM 1w, replicate 4

value: palbociclib 750nM 1w -> ICI 750nM 1w


title: LPS141, DMSO, K27ac, rep1


title: MCF7_mono10w_rep3

description: Gene expression for MCF7 cells after 10 week 750nM mono palbociclib treatment

source_name: MCF7 cells, mono palbociclib 750nM, replicate 3

value: mono palbociclib 750nM


title: MCF7_mono24w+_rep1

source_name: MCF7 cells, palbociclib 500nM 24w+, replicate 1


title: MCF7_mono24w+_rep4

source_name: MCF7 cells, palbociclib 500nM 24w+, replicate 4


title: MCF7_alt10w_rep3

source_name: MCF7 cells, palbociclib 750nM 1w -> ICI 750nM 1w, replicate 3


title: MCF7_alt10w_rep1

source_name: MCF7 cells, palbociclib 750nM 1w -> ICI 750nM 1w, replicate 1


title: MCF7_alt10w_rep2

source_name: MCF7 cells, palbociclib 750nM 1w -> ICI 750nM 1w, replicate 2


title: MCF7_mono10w_rep2

source_name: MCF7 cells, mono palbociclib 750nM, replicate 2


title: MCF7_mono10w_rep1

source_name: MCF7 cells, mono palbociclib 750nM, replicate 1


title: MCF7_mono24w+_rep2

source_name: MCF7 cells, palbociclib 500nM 24w+, replicate 2


title: MCF7_rep3

description: Gene expression for MCF7 cells

source_name: MCF7 cells, no treat, replicate 3

value: no treat


title: SC3

city: Ithaca

first: Cédric

last: Feschotte

state: NY

address: 216 Biotechnology Building

institute: Cornell University

data_processing:
Quality control assessment using FastQC v0.11.9
Read alignment to Danio rerio reference genome (GRCz11) using STAR v2.7.5a.
Read counting using Tetranscripts v2.2.1’s Tecount tool

organism: Danio rerio

source_name: Whole embro

growth_protocol: Tübingen strain zebrafish were maintained at 28°C on a 14/10hr light/dark schedule. Individual breeding pairs of male and female fish were separated overnight to induce naturally synchronized spawning and fertilization the following morning.

extract_protocol:
Embryos were collected at shield stage, and stored at -20°C immediately after collection. Total RNA extraction was perfomed using the Qiagen Rneasy kit.
Strand-specific libraries were prepared by Novogene Inc. using poly-A enrichment.
Strand-specific 150bp paired-end RNA-seq

treatment_protocol: Fertilized zygotes were injected with 4.5ng of either a custom FiNZ-ZNF translation blocking morhoplino, or a scrambled 25N control.

value: Whole embro

tag: strain

value: Tuebingen

tag: collection date

tag: treatment group

value: control

value: 25N scrambled control morpholino

tag: time

value: 6 hours post fertilization (shield stage)


title: MCF7_mono10w_rep4

source_name: MCF7 cells, mono palbociclib 750nM, replicate 4

tag: cell type


title: MCF7_rep1

description: Gene expression for MCF7 cells

source_name: MCF7 cells, no treat, replicate 1


title: MCF7_rep2

description: Gene expression for MCF7 cells

source_name: MCF7 cells, no treat, replicate 2


title: MCF7_rep4

description: Gene expression for MCF7 cells

source_name: MCF7 cells, no treat, replicate 4


title: LPS141, DMSO, p53, rep1


title: SC1

tag: tissue


title: FM3

value: treatment

tag: treatment


title: FM2


title: FM1


title: LPS141, DMSO, cJun, rep1


title: LPS141, DMSO, RUNX2, rep1


title: smartseq2_BL_UA_13days_proximal_136152

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs arm regenrating blastema time points (13 dpa proximal BL CT cells).

data_processing:
Smart-seq2 processing pipeline was adapted for axolotl genome from nf-core/rnaseq.
The raw reads were trimmed with trim_galore (v0.6.2) and mapped to axolotl genome (AmexG_v6,  Schloissnig et al., 2021) using hisat2 (v2.1.0).
Read counts at gene levels were quantified by featureCounts in subread (v2.0.1).
To identify segment-specific genes in mature samples, the read counts were normalized and pairwise comparisons were done with DESeq2 (v1.26.0)
Bigwig files were made with deeptools (v3.1.2)
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

organism: Ambystoma mexicanum

source_name: Connective tissue cells

extract_protocol:
RNA was harvested using a total RNA isolation kit (in-house kit provided by Molecular Biology Services in Vienna BioCenter). Sequencing libraries were prepared by VBC NGS-Facility.
Smart-seq version 2

value: Connective tissue cells

tag: genotype

value: Arm amputation and regeneration

value: 13 dpa


title: smartseq2_BL_UA_13days_proximal_136146


title: smartseq2_BL_UA_13days_distal_136153

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs arm regenrating blastema time points (13 dpa distal BL CT cells).


title: SC2


title: LPS141, DMSO, input, 1

value: DMSO


title: smartseq2_BL_UA_13days_distal_136147


title: Control MCF7 xenograft-5M cells-Replicate 3

city: Baltimore

first: Dipali

last: Sharma

state: Maryland

address: 1550 Orleans Street

department: School of Medicine

institute: The Johns Hopkins University

data_processing:
Single-end 75nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to NCBI Homo sapiens sequence GRCh38.p12 April-'18, with CLCGenomicsServer 9.1.1 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 10.0.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: NCBI GRCh38.p12
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples. Raw FPKM values of 0 are represented as Nulls in log space.

source_name: Xenograft/Human cancer cell line in mice

growth_protocol: MCF7 cells were seeded in 10% serum supplemented DMEM media and allowed to grow for 24 hours. Cells were then treated with 100 ng/ml of BFT in 2% serum supplemented DMEM. Medium in the control group was changed to 2% serum supplemented DMEM. 3 days post tretment, cells were harvested in 0.25% trypsin/EDTA, neutralized with 10% FBS supplemented DMEM and centrifuged. Pellets were resuspended in serum free media and equal volume of matrigel was added to the cell suspension. 5 million cells were implanted on to the 4th mammary fat pad of SCID-NOD mice on either side with E2 supplementation. Tumors were allowed to grow for 8 weeks and monitored after which tumors were resected. The resecetd tumors were dissociated and tumor cells were isolated and subjected to in vivo limiting dilution; cells ranging from 5000 to 500000 were implanted in different mammary fat pads of SCID-NOD mice and tumors were allowed to grow. At the end of 8 weeks, resulting tumors were resected and RNA sequencing was performed.

extract_protocol:
RNA extracted on the QIAGEN QIAcube devise using their RNeasy Mini-QIAcube kit following manufacturer's protocol.
Using the Illumina TruSeq Stranded Total RNA kit, quality-controlled total RNA was purified to mRNA with poly-T magnetic beads, fragmented, and then reverse transcribed into cDNA.  Fragments of 150~200bp were selected and the library PCR amplified.

tag: tag

value: Tumors obtaind from untreated cells

value: Tumor

tag: bacterial treatment

value: untreated

tag: xenograft cell count


title: Control MCF7 xenograft-5M cells-Replicate 2


title: linc-mipep scMultiome 6d brains - WT scRNA AGN002631

city: New Haven

first: Antonio

last: Giraldez

state: CT

address: 333 Cedar street

department: Genetics

institute: Yale

data_processing:
The raw 10x Genomics Multiome data of scRNA-seq and scATAC-seq were processed using the 10x Genomics cellranger-arc pipeline (v1.0.1) with the genome zebrafish GRCz11.
Assembly: GRCz11
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz

source_name: brain

extract_protocol:
Brains at peak daytime activity levels (Zeitgeber Time 4, i.e. 4 hours after lights on) were dissected from 6 dpf zebrafish from one linc-mipep-/- heterozygous incross (n=12 per sample) in ice-cold Neurobasal media supplemented with B-27 (Thermo Fisher Scientific), snap-frozen in a dry ice/methylbutane bath (to preserve nuclear structure), and stored at -80℃ until use. Trunks of linc-mipep fish from the heterozygous cross were genotyped, then wild type or linc-mipep-/- brains as confirmed by genotyping were pooled together before proceeding with scMulitome.
Single Cell Multiome ATAC + Gene Expression 10x Genomics:
Flash-frozen pooled brains were prepared based on Protocol CG000366 – Rev D (Protocol 2) from 10x Genomics (available at https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sample-prep/nuclei-isolation-from-embryonic-mouse-brain-tissue-for-single-cell-multiome-atac-plus-gene-expression-sequencing). It is critical to keep samples cold and/or on ice for all steps. Briefly, all samples were processed identically and simultaneously, to minimize batch effects. Chilled 0.1X Lysis Buffer (500μl) was immediately added to frozen samples, and samples were homogenized using a glass dounce tissue grinder with glass pestle. Samples were incubated on ice for 5 minutes, gently pipetted 10x, then incubated again for 5 minutes. Chilled Wash Buffer (500μl) was gently added to samples. After pipetting the mix 5x, the samples were passed through 70μm-porosity Flowmi tips into new ice-cold low-bind 1.5ml tubes. Each suspension was subsequently passed through a 40μm-porosity Flowmi tip into a new ice-cold low-bind 1.5ml tube. Samples were centrifuged at 500 rcf 5 minutes at 4°C. The supernatant was gently removed, without disturbing the nuclei pellet. Chilled Wash Buffer (1ml) was added, and the nuclei were gently resuspended 5x. This wash and resuspension step was repeated one more time. On the final step, nuclei were resuspended in Diluted Nuclei Buffer. Quality and number of nuclei (as assessed by >90% Trypan Blue staining) for each sample was assessed using a hemocytometer, and were immediately used for tagmentation step using the 10x Genomics platform.

value: brain

value: linc-mipep WT


title: LPS141, DMSO, MDM2, rep1

tag: cell line

value: liposarcoma cell


title: linc-mipep scMultiome 6d brains - WT scATAC AGN002630


title: smartseq2_BL_UA_9days_136151

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs arm regenrating blastema time points (9 dpa BL CT cells).

value: 9 dpa


title: linc-mipep scMultiome 6d brains - linc-mipepMut scRNA AGN002629

value: linc-mipep MUT


title: Control MCF7 xenograft-5M cells-Replicate 1


title: smartseq2_BL_UA_5days_136150

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs arm regenrating blastema time points (5dpa BL CT cells).

value: 5 dpa


title: female, iron deficient + choline, rep4

city: Minneapolis

first: Phu

middle: V

last: Tran

state: MN

address: 516 Delaware St., SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
Raw reads were processed with CHURP-PURR pipeline (https://doi.org/10.1145/3332186.3333156). Each library was searched for contamination from ribosomal RNA using a representative rRNA sequence list from the SILVA database release 132. Reads were summarized with FastQC, adapter-trimmed (Trimmomatic) and aligned to the reference genome with HISAT2.
Alignments were processed with the featureCounts tool from the subread package. Fragments were counted in a strand-specific manner. Both mates of a read pair were required to map to a feature to be counted.
Assembly: Rnor_6.0
Supplementary files format and content: Tab delimited text files with raw counts. Column names correspond to samples and row names to genes.

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
RNeasy Midi Kit (Qiagen)
RNA quantity and quality were assessed using the RiboGreen RNA Assay kit (Invitrogen) and capillary electrophoresis (Agilent BioAnalyzer 2100). Barcoded libraries were constructed for each sample with the TruSeq RNA v2 kit (Illumina) using RNA with a RIN score > 8.0

value: Sprague-Dawley

value: Hippocampus

tag: Sex

value: female

tag: diet

value: IDch

tag: age (days)

tag: seq batch

value: II


title: Control MCF7-Replicate 3

source_name: Cell culture/Human cancer cell line

value: MCF7 untreated


title: smartseq2_BL_UA_9days_136145

value: Connective tissue cells

value: Arm amputation and regeneration


title: smartseq2_BL_UA_5days_136144


title: linc-mipep scMultiome 6d brains - linc-mipepMut scATAC AGN002628


title: Control MCF7-Replicate 2


title: smartseq2_Mature_UA_136149

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs arm regenrating blastema time points (intact Upper arm CT cells).

value: Mature arm before amputation

value: 0 dpa


title: female, iron deficient + choline, rep3


title: atac_Embryo_Stage40_137330

description: To find ACRs in the developmental limb buds, whole limb buds (stage 40/41) were isolated and used for ATAC-seq library preparation with in-house Tn5.

data_processing:
The pair-ended ATAC-seq reads were trimmed with cutadapt (v1.18) and aligned to axolotl genome (AmexG_v6) with bowtie2 (v2.3.5.1).
Multimappers and duplicated reads in the aligned bam files were discarded respectively with samtools (v1.10) and picard (v2.20.6). ATAC-seq narrow peaks were called by macs2 (v2.2.5) with default parameters.
The processing workflow was wrapped with nextflow. For the purpose of reproducibility, peaks were retained only if they were called in at least two biological replicates with p-value < 10^-6;
they were merged into a list of peak consensuses for all samples. Read counts were quantified within those peaks with feature counts from subread (v2.0.1).
After low-signal peaks were filtered with less than 50 read counts, the read counts within peaks across all samples were normalized using the scaling factors from DESeq2 (v1.26.0). These scaling factors were also used to make bigwig files with deeptools (v3.1.2) for the data visualization.
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

source_name: Whole limb buds

extract_protocol:
The sample was performed from 20,000 cells isolated from transgenic animals. Limb connective tissue cells were used for FACS, and then used for library preparation immediately.
We performed ACR profiling analysis using data obtained from ATAC-seq libraries of developmental limb buds (stage 40/41, stage 46 proximal and distal parts), and mature limb at different segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa (13 dpa blastema data have two different positions like proximal and distal parts) regenerating arm blastema.

value: Whole limb buds

value: d/d strain

value: Cells were isolated and FAC-sorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: atac_Embryo_Stage40_137329


title: Control MCF7-Replicate 1

value: untreated


title: atac_BL_UA_9days_136166

description: To find ACRs in arm regenerating blastema cells (9 dpa blastema cells), ATAC-seq libray with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: UA 9 dpa BL

value: UA 9 dpa BL

value: Cells were isolated and FACSorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: female, iron deficient + choline, rep2


title: BFT treated MCF7 xenograft-5000 cells-Replicate 4

value: Tumors obtaind from BFT pre-treated cells

value: Tumor

value: BFT pre-treated


title: atac_BL_UA_5days_136165

description: To find ACRs in arm regenerating blastema cells (5 dpa blastema cells), ATAC-seq libray with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: UA 5 dpa BL

value: UA 5 dpa BL


title: female, iron deficient + choline, rep1

value: Sprague-Dawley

value: Hippocampus

value: female

value: IDch


title: atac_BL_UA_5days_136160

value: Connective tissue cells


title: female, iron deficient, rep4

value: ID

value: II


title: atac_BL_UA_13days_distal_136163

description: To find ACRs in arm regenerating blastema cells (only distal part of 13 dpa blastema cells), ATAC-seq libray with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: UA 13 dpa BL distal part

value: UA 13 dpa BL distal part


title: BFT treated MCF7 xenograft-5000 cells-Replicate 3


title: atac_BL_UA_13days_proximal_136162

description: To find ACRs in arm regenerating blastema cells (only proximal part of 13 dpa blastema cells), ATAC-seq libray with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: UA 13 dpa BL proximal part

value: UA 13 dpa BL proximal part


title: atac_BL_UA_13days_proximal_136167


title: BFT treated MCF7 xenograft-5M cells-Replicate 3


title: female, iron deficient, rep3


title: smartseq2_Mature_UA_136143

value: Mature arm before amputation

value: 0 dpa


title: BFT treated MCF7 xenograft-5000 cells-Replicate 2


title: atac_Mature_LA_177596

description: To find ACRs in mature limb cells, ATAC-seq library with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: Mature LA

value: Mature LA


title: BFT treated MCF7 xenograft-5M cells-Replicate 2


title: female, iron deficient, rep1


title: atac_HEAD_177597

source_name: Head without lower jaw

value: Head without lower jaw

value: Cells were isolated and FACSorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: atac_BL_UA_13days_distal_136168


title: female, iron deficient, rep2


title: atac_HEAD_177595


title: atac_Mature_UA_136164

source_name: Mature UA

value: Mature UA


title: BFT treated MCF7 xenograft-5000 cells-Replicate 1

value: Tumors obtaind from BFT pre-treated cells

value: Tumor

value: BFT pre-treated


title: female, iron sufficient + choline, rep4

value: Sprague-Dawley

value: Hippocampus

value: ISch


title: atac_BL_UA_9days_136161

value: UA 9 dpa BL

value: Connective tissue cells


title: atac_Mature_UA_136159


title: BFT treated MCF7 xenograft-5M cells-Replicate 1


title: female, iron sufficient + choline, rep3

value: female

value: II


title: female, iron sufficient + choline, rep2


title: BFT treated MCF7-Replicate 3

value: MCF7 cells BFT treated

value: BFT treated


title: atac_Mature_Hand_161522

source_name: Mature Hand

value: Mature Hand


title: atac_Mature_LA_177598

value: Mature LA


title: female, iron sufficient + choline, rep1


title: CT_H3K4me1_mHand_186066

description: mature Hand H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).

data_processing:
library strategy: CUT&Tag
The pair-ended reads were trimmed with cutadapt (v1.18) and aligned to axolotl genome (AmexG_v6) with bowtie2 (v2.3.5.1).
Multimappers and duplicated reads were discarded respectively with samtools (v1.10) and picard (v2.20.6).
The bigwig files were generated from aligned bam files with deeptools (v3.1.2).
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

extract_protocol: See the used antibodies in our study. Tagmented genomic DNA was purified with Proteinase K treatment and PCR purification with magnetic-based beads. The library was amplified with 12 PCR cycles.

treatment_protocol: The sample was performed from 20,000 cells isolated from transgenic animals. Limb connective tissue cells were used for FACS, and then frozen at the deep-freezer until preparation starts.

tag: chip antibody

value: H3K4me1 (Abcam #ab8895)


title: female, iron sufficient, rep4

tag: strain

value: IS


title: BFT treated MCF7-Replicate 1


title: CT_H3K4me1_mLA_186063

description: mature LA H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K27me3_mLA_186064

description: mature LA H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).

value: H3K27me3 (Active Motif #39155)


title: atac_Mature_UA_166903

value: Mature UA

value: Cells were isolated and FACSorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: female, iron sufficient, rep3


title: female, iron sufficient, rep1


title: CT_H3K27me3_mUA_186061

description: mature UA H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_BL13days.dist_185788

description: UA 13 dpa BL distal region H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).

value: H3K4me3 (Abcam #ab8580)


title: CT_H3K4me1_BL13days.dist_185785

description: UA 13 dpa BL distal region H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: WM35-3

city: Tampa

first: Olga

last: Vera

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: Moffitt Cancer Center

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a.
Uniquely mapped reads were counted by htseq-count (Anders et al. 2015) (version 0.6.1) using Gencode v25 primary annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: Melanoma

growth_protocol: The human immortalized melanocytes cell lines were cultured in RPMI media supplemented with 10% FBS, 10ng/mL hSCF, 200nM TPA, 200pM Cholera Toxin and 10nM Endothelin-1 at 37˚C in a humidified atmosphere containing 10% CO2. BRAF-V600E melanocytes cell line was cultured in RPMI media supplemented with 10% FBS, 10ng/mL hSCF, 200pM Cholera Toxin and 10nM Endothelin-1 at 37˚C in a humidified atmosphere containing 10% CO2. All melanoma cell lines were cultured in RPMI containing 5% FBS at 37˚C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA from cells was isolated using RNA isolation kit (Qiagen) and analyzed for RIN.
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

treatment_protocol: pLGH (control) and BRAFV600E-expressing human melanocytes cell lines were derived by infecting Hermes1 with a BRAFV600E lentivirus (provided by L. Wan) for six hours in the presence of 8µg/mL Polybrene. Transduced cells were selected in 100nM of Hygromycin (Invivogen, Cat # ant-hg-1) for seven days in the absence of TPA. Prior to RNA isolation, TPA was withdrawn from media of melanocytes cell lines and melanoma cells were cultured in RPMI 10% FBS for 24 hours.

value: skin

tag: infection

value: WM35-no treatment


title: WM793-2

value: WM793-no treatment


title: WM793-1


title: CT_IgG_mUA_186059

description: mature UA IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_mUA_186060

description: mature UA H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_BL13days.dist_185784

description: UA 13 dpa BL distal region IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K27me3_mHand_186067

description: mature Hand H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: BFT treated MCF7-Replicate 2


title: adult testes modulo mutant, rep 3, lane 3 [Exp.3.L3]

city: Cambridge

first: Jun

middle: I

last: Park

address: 455 Main St

institute: Whitehead Institute

data_processing:
The read pairs were mapped to the canonical chromosomes of the Drosophila melanogaster genome (assembly BDGP6/dm6) using STAR 2.7.1a; default parameters, except '--alignIntronMax 25000'), indexed with all FlyBase genes (FB2020_06 Dmel Release 6.37) and the option '--sjdbOverhang 100'.
Gene counts were obtained using featureCounts; v 2.0.1, with '-M --fraction -p -s 2') and the same gene annotations.
Assembly: BDGP6/dm6
Supplementary files format and content: tab-delimited; raw gene counts

organism: Drosophila melanogaster

source_name: adult testes

growth_protocol: Flies were reared at 25C in Bloomington fly food M. Testes were dissected from 1-3-day old males.

extract_protocol:
Testes were dissected from 1-3-day old males and RNA extracted using Direct-zol RNA miniprep kit
rRNA-depleted RNA-seq libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems).

value: adult testes


title: CT_H3K27me3_BL13days.prox_185782

description: UA 13 dpa BL proxial region H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).

value: Connective tissue cells


title: WM35-2


title: adult testes modulo mutant, rep 3, lane 2 [Exp.3.L2]


title: CT_H3K4me3_BL13days.prox_185781

description: UA 13 dpa BL proxial region H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: WM793-3


title: CT_H3K4me1_BL13days.prox_185780

description: UA 13 dpa BL proxial region H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: female, iron sufficient, rep2

value: Sprague-Dawley

value: Hippocampus

value: female


title: WM35-1


title: CT_H3K27me3_BL13days.dist_185790

description: UA 13 dpa BL distal region H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_BL13days.prox_185779

description: UA 13 dpa BL proxial region IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: WM164-3

value: WM164-no treatment


title: WM164-2


title: adult testes modulo mutant, rep 2, lane 3 [Exp.2.L3]


title: adult testes modulo mutant, rep 2, lane 2 [Exp.2.L2]


title: CT_IgG_BL9days_185774

description: UA 9 dpa BL IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_BL9days_185775

description: UA 9 dpa BL H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K27me3_BL5days_185772

description: UA 5 dpa BL H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_BL9days_185776

description: UA 9 dpa BL H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes modulo mutant, rep 2, lane 1 [Exp.2.L1]


title: CT_H3K4me3_BL5days_185771

description: UA 5 dpa BL H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_BL5days_185769

description: UA 5 dpa BL IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: WM164-1


title: SKMel28-3

value: SKMel28-no treatment


title: adult testes modulo mutant, rep 1, lane 3 [Exp.1.L3]


title: SKMel28-2


title: adult testes modulo mutant, rep 1, lane 2 [Exp.1.L2]


title: CT_H3K27me3_BL9days_185777

description: UA 9 dpa BL H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes modulo mutant, rep 3, lane 1 [Exp.3.L1]


title: CT_H3K4me3_mUA_185766

description: mature UA H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: SKMel28-1


title: CT_H3K4me1_mUA_185765


title: adult testes modulo mutant, rep 1, lane 1 [Exp.1.L1]


title: CT_H3K27me3_BL13days.dist_185762


title: CT_IgG_mUA_185764

description: mature UA IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_BL13days.dist_185761

description: UA 13 dpa BL distal region H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_BL5days_185770

description: UA 5 dpa BL H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: 1205Lv-3

value: X1205Lv-no treatment


title: 1205Lv-2


title: 1205Lv-1


title: adult testes wt, rep 3, lane 2 [Ctrl.3.L2]


title: CT_IgG_BL13days.dist_185759

description: UA 13 dpa BL distal region IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes wt, rep 3, lane 1 [Ctrl.3.L1]


title: CT_H3K4me3_BL13days.prox_185756


title: CT_H3K4me1_BL13days.prox_185755

value: H3K4me1 (Abcam #ab8895)


title: CT_H3K27me3_BL13days.prox_185757

description: UA 13 dpa BL proxial region H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_BL13days.dist_185760

description: UA 13 dpa BL distal region H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: Hermes4B-3

source_name: Melanocytes

value: Hermes4B-no treatment


title: CT_IgG_BL13days.prox_185754

source_name: Connective tissue cells


title: CT_H3K27me3_mUA_185767

description: mature UA H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).

value: H3K27me3 (Active Motif #39155)


title: CT_H3K27me3_BL9days_185753

description: UA 9 dpa BL IgG H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes wt, rep 2, lane 3 [Ctrl.2.L3]


title: adult testes wt, rep 2, lane 2 [Ctrl.2.L2]


title: Hermes4B-2


title: CT_H3K4me1_BL9days_185750

description: UA 9 dpa BL IgG H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_BL9days_185751

description: UA 9 dpa BL IgG H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_BL9days_185749

description: UA 9 dpa BL IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes wt, rep 2, lane 1 [Ctrl.2.L1]


title: Hermes4B-1


title: CT_H3K27me3_BL5days_185747

description: UA 5 dpa BL H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: adult testes wt, rep 3, lane 3 [Ctrl.3.L3]


title: Hermes3A-3

value: Hermes3A-no treatment


title: CT_H3K4me3_BL5days_185746


title: adult testes wt, rep 1, lane 3 [Ctrl.1.L3]


title: CT_H3K4me1_BL5days_185745


title: adult testes wt, rep 1, lane 2 [Ctrl.1.L2]


title: CT_H3K27me3_mUA_185742


title: Hermes2-3

value: Hermes2-no treatment


title: adult testes wt, rep 1, lane 1 [Ctrl.1.L1]


title: Hermes3A-1


title: CT_IgG_mUA_185739


title: Hermes2-2


title: CT_H3K4me3_mUA_185741

value: H3K4me3 (Abcam #ab8580)


title: CT_H3K4me3_mHand_177601

description: mature Hand H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_mLA_177600

description: mature LA H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: Hermes2-1

value: skin


title: CT_H3K4me3_mUA_177599


title: Hermes1-BRAF-3


title: CT_H3K4me1_mUA_182553

description: mature UA H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_mHand_182555

description: mature Hand H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_mHand_164158

description: mature Hand IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_IgG_mUA_164156

description: mature UA IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: Hermes1-BRAF-2


title: CT_IgG_mLA_164157

description: mature LA IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K27me3_mHand_163658

description: mature Hand H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: Hermes1-BRAF-1


title: Hermes3A-2


title: OVCAR8-NC1

city: Guangzhou

first: Peng

last: Deng

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: OVCAR8 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and protien/histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: OVCAR8 cells were plated into 6-well plate 20 h before transfection with indicated siRNA.

value: high grade serous ovarian cancer (HGSOC)

value: siNC


title: CT_IgG_BL5days_185744

description: UA 5 dpa BL IgG control. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me1_mUA_185740


title: Hermes1-pLGH-3

value: pLenti-GFP-Hygromicin


title: CT_H3K4me3_mHand_163657

value: Connective tissue cells


title: OVCAR8-TEAD4

value: TEAD4 (Santacruz, sc-101184)


title: Hermes1-pLGH-2


title: OVCAR8-Input


title: Hermes1-pLGH-1


title: CT_H3K27me3_mLA_163654

description: mature LA H3K27me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: CT_H3K4me3_mLA_163653


title: OVCAR8-H3K27ac

value: H3K27ac (Abcam, ab4729)


title: OVCAR8-H3K27ac-Input


title: CT_H3K27me3_mUA_163650


title: OVCAR8-RAD21

value: RAD21 (Abcam, ab992)


title: CT_H3K4me3_mUA_163649

description: mature UA H3K4me3. It was prepared with CUT&Tag (Tanaka lab version protocol).


title: Sample 8_LMP_TAp63

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Count data were calculated with hiseq-count.
An acronym for tag count comparison (TCC) package in R software was used to normalize count data.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files

source_name: Th17 cell

growth_protocol: Human Th17 cells  were cultured with dynabeads human T-activator CD3/CD28, IL-1b, IL-23, anti-IL4 mAb, and anti-IFN-g mAb

extract_protocol:
total RNA were purified by ReliaPrep RNA cell miniprep system (Promega)
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent).

treatment_protocol: after 48 hors, cells were infected with retroviruses

value: Th17 cell

tag: genotype/variation

value: infected with retrovirus of LMP-hTAp63KD1-IRES-Thy1.1 on day2

value: infected Thy1.1+ cells are sorted on day9 and restimulated with PMA+ionomycin for 6hr on day18


title: OVCAR8-RAD21-Input


title: CT_IgG_mUA_163647


title: Sample 7_LMP

value: infected with retrovirus of LMP-non-silencing-IRES-Thy1.1 on day2


title: Sample 6_pMX_TAp63

value: infected with retrovirus of pMXs-humanTAp63a-IRES-NGFR on day2

value: infected NGFR+ cells are sorted on day9 and restimulated with PMA+ionomycin for 6hr on day18


title: CT_H3K4me1_mLA_163652

description: mature LA H3K4me1. It was prepared with CUT&Tag (Tanaka lab version protocol).

value: H3K4me1 (Abcam #ab8895)


title: pancreas, Ad-M3C, day 10, r2

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

description: Day 10-2

library_source: transcriptomic single cell

data_processing:
Reads were stored in paired-end fastq format. Reads of one end of a fragment containing cell barcode/UMI information were subsequently extracted and added to the name of corresponding reads of the other end in fastq file containing molecular sequence. That barcode/UMI information was in fastq-R2 files. Next, the generated single-end fastq files were cleaned by Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter—length 30.
Then, FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied to check read quality followed by alignment on mm9 genome using STAR
UMI counts data from all cells were merged into one single matrix, which included the metadata information of each cell such as cell collection date, transdifferentiation time point, etc. Cells were selected for further analysis if they had at least 1,000 detected genes (with UMI count > 1). Genes were retained if they were detected in at least 10 cells. These rules resulted in a UMI count matrix with 2,641 valid cells and 15,143 detected genes.
Assembly: mm9
Supplementary files format and content: UMIcount_matrix.txt

source_name: pancreas

extract_protocol:
Adenovirus infected pancreas was perfused with 2 to 3 mL collagenase P (0.8 mg/mL) through the common bile duct and digested at 37 oC for 15 to 20 min. Digestion was stopped by adding 15 - 20 mL DMEM medium containing 10% FBS, 1% PenStrep and 1% HEPES (quenching buffer, QB). The suspension was filtered with 70 μm cell strainer. The filtrate was spun for 3 min at 300 g, 4 oC, resuspend the pellet with ice-cold DPBS to clear FBS twice dissociated the pellet into single cells using 1 mL TrypLE Express at 37 oC for 15 - 20 min, and mixed the solution up and down gently by P1000 pipette during the digestion process to improve the proportion of single cells. After digestion, the cell suspension was spun for 3 min at 300 g, 4 oC, resuspended with FACS buffer (DPBS with 0.5% BSA) and filtered with 40 μm strainer to obtain single cell suspension. The high viability single cells were labeled by Calcein Blue AM (1 mg/mL), which was added into cell suspension directly at the ratio of 1:2000. The single cells labeled by mCherry and Calcein Blue AM were sorted into cell lysis buffer in 96-well plates through Moflo Astrios 4 lasers flow cytometry. The collected samples were fast frozen at the mixture of dry ice and absolute ethanol.
scRNA-seq libraries were constructed according to the Smart-seq2 protocol except that oligo d(T) primers comprising 16-bp cell barcode sequence and 9-bp molecular barcode sequence were used to allow sample pooling and molecular counting. In addition, part of the TruSeq read2 sequence was used to replace the ISPCR sequence in the oligo d(T) primer thus to be compatible with Illumina sequence platform. Cells in lysis buffer were denatured, reverse transcribed in the presence of template switching oligos, and pre-amplified by adding both ISPCR and ISPCR-read2 primers with 24 PCR cycles. cDNA sequences of cells with different barcodes were then pooled together and purified using 0.8× AMPure XP beads (Catalog No. A63881, Beckman, Brea, CA). Homemade Tn5 enzyme was used to tagment cDNA. Final amplification was processed using P7-index primers (TruSeq) and P5-index primers (Nextera). Sequencing libraries were purified with 0.6× AMPure XP beads twice and with 1× AMPure XP beads once, and then sequenced on Illumina HiSeq X10 platform with default parameters.

value: pancreas

value: pancreatic cell

tag: age

value: 6-12 weeks old

tag: time point

value: day 10


title: pancreas, Ad-M3C, day 10, r5

description: Day 10-5

tag: tissue

tag: cell type


title: pancreas, Ad-M3C, day 10, r3

description: Day 10-3

tag: genotype

tag: treatment


title: pancreas, Ad-M3C, day 10, r4

description: Day 10-4


title: Sample 5_pMX

value: infected with retrovirus of pMXs-IRES-NGFR on day2


title: pancreas, Ad-M3C, day 10, r1

description: Day 10-1


title: pancreas, Ad-M3C, day 08, r5

description: Day 8-5

value: day 08


title: pancreas, Ad-M3C, day 08, r4

description: Day 8-4


title: week 4_patient.24

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Raw signal intensites were normalized using the RMA algorithm implemented with R 3.5.2 and Bioconductor oligo library.

label: biotin

source_name: skin

label_protocol: standard Affymetrix protocols

growth_protocol: not applicable

extract_protocol: standard Affymetrix protocols

treatment_protocol: subcutaneous injections of ixekizuma 80mg Q2W

tag: visitid

value: Ixekizumab 80mg Q2W

tag: pasi

tag: time

value: Gene expression data at week 4.

value: skin

tag: disease state

value: chronic plaque psoriasis


title: week 1_patient.49

value: Gene expression data at week 1.


title: week 1_patient.29


title: week 1_patient.3


title: SKNAS NB cell line

city: MEMPHIS

first: Richard

last: Chapple

state: Tennessee

address: 262 Danny Thomas Pl

institute: St Jude Children's Hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: SKNAS

extract_protocol:
Single cell suspensions of neuroblastoma cells were collected from NB cell lines cultured in standard conditions.  Pelleted cells are resuspended for sequencing with 10X Genomics kits.
Library was performed according to the manufacter’s instructions (10x Genomics). Single cell suspensions of neuroblastoma cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell line

value: SKNAS

value: neuroblastoma


title: SKNSH NB cell line

description: 10X Genomics

source_name: SKNSH

value: SKNSH


title: SKNFI NB cell line

description: 10X Genomics

source_name: SKNFI

value: SKNFI


title: baseline_patient.3

value: Gene expression data at baseline.


title: pancreas, Ad-M3C, day 08, r3

description: Day 8-3


title: baseline_patient.50


title: week 1_patient.8


title: week 1_patient.50


title: TGW NB cell line

description: 10X Genomics

source_name: TGW

value: TGW


title: week 2_patient.21

value: Gene expression data at week 2.


title: pancreas, Ad-M3C, day 08, r2

description: Day 8-2

value: pancreas

value: pancreatic cell


title: NGP NB cell line

description: 10X Genomics

source_name: NGP

value: NGP


title: pancreas, Ad-M3C, day 08, r1

description: Day 8-1

value: 6-12 weeks old


title: KELLY NB cell line

description: 10X Genomics

source_name: KELLY

value: KELLY


title: MHHNB11 NB cell line

description: 10X Genomics


title: pancreas, Ad-M3C, day 06, r5

description: Day 6-5

value: day 06


title: IMR5 NB cell line

description: 10X Genomics


title: baseline_patient.39

value: Ixekizumab 80mg Q2W


title: baseline_patient.19

value: skin


title: week 1_patient.45

value: chronic plaque psoriasis


title: pancreas, Ad-M3C, day 06, r4

description: Day 6-4


title: pancreas, Ad-M3C, day 06, r3

description: Day 6-3


title: CHP212 NB cell line

description: 10X Genomics


title: baseline_patient.35


title: week 4_patient.47

value: Gene expression data at week 4.


title: CHP134 NB cell line

description: 10X Genomics


title: pancreas, Ad-M3C, day 06, r1

description: Day 6-1


title: pancreas, Ad-M3C, day 06, r2

description: Day 6-2


title: pancreas, Ad-M3C, day 04, r5

description: Day 4-5

value: day 04


title: BE2M17 NB cell line

description: 10X Genomics

value: neuroblastoma


title: pancreas, Ad-M3C, day 04, r4

description: Day 4-4


title: BE2C NB cell line

description: 10X Genomics


title: DD31_hichip

city: Boston

first: Salvador

last: Casani

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

data_processing:
HiChIP processing: Data were quality and adapter trimmed using seqPrep and mapped to the reference genome (hg38) using Bowtie2. Contact matrices were created with HiCPro. Chromatin loops were called with hichipper, using H3k27ac peaks and hg38 promoters as the predefined peak set to call anchors.
Bedpe contact pairs
Assembly: hg38
Supplementary files format and content: in table
Library strategy: HiChIP

source_name: Liposarcoma

extract_protocol:
Crosslinked chromatin was digested with MboI. Overhangs were filled in and marked with Biotin-dATP (ThermoFisher 19524016) and ends were ligated. Chromatin was then sheared on the Covaris E220 and ChIP was performed overnight for H3K27ac marked chromatin. Resulting DNA was purified using the Zymo clean and concentrate kit (DCC-100), bound to Streptavidin M280 beads (Invitrogen 11205D), and tagmented.
Libraries were amplified using the Nextera DNA Library Prep kit (Illumina)

value: Liposarcoma

value: Dedifferentiated Liposarcoma

value: No treatment

tag: antibody


title: GIMEN NB cell line

description: 10X Genomics

source_name: GIMEN

value: GIMEN


title: week 4_patient.5


title: week 1_patient.33

value: Gene expression data at week 1.


title: week 1_patient.2


title: baseline_patient.27

value: Gene expression data at baseline.


title: DD20_hichip


title: week 1_patient.47


title: baseline_patient.54


title: baseline_patient.15


title: pancreas, Ad-M3C, day 04, r1

description: Day 4-1

value: pancreas

value: pancreatic cell


title: DD10_hichip


title: pancreas, Ad-M3C, day 02, r5

description: Day 2-5

value: 6-12 weeks old

value: day 02


title: pancreas, Ad-M3C, day 04, r3

description: Day 4-3


title: pancreas, Ad-M3C, day 04, r2

description: Day 4-2


title: pancreas, Ad-M3C, day 02, r4

description: Day 2-4


title: week 4_patient.12


title: KO U2OS nascent DNA sequencing replicate 1

city: Oxford

first: Dragana

last: Ahel

state: Oxfordshire

address: South Parks Rd

department: Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
ConsensusPeaks_s4_5_6_c3_noh
unique_peaks_s4_5_6_vs_s1_2_3_ucsc_formated

data_processing:
The unprocessed reads were checked using FastQC.
Then the reads were trimmed using Trimgalore and mapped to the human genome using bowtie2.
Duplicates reads (mostly PCR duplicates) were removed to improve peak calling using Picard tools
Following deduplication, peak calling was performed using MACS2 for each individual sample.
Peaks from replicate samples were then combined using MSPC to generate consensus peaks for each sample group.
Assembly: Consensus peaks were compared between different sample groups to exclude common peaks and generate lists of unique peaks using BEDtools.
Supplementary files format and content: BED
Library strategy: Nascent DNA-seq

source_name: Bone

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
Genomic DNA was prepared using DNeasy Blood & Tissue Kit (Qiagen), according to the manufacturer’s instructions.
Purified DNA was sonicated to obtain fragments of average size of 200-300 bp. DNA was then concentrated using SPRIselect beads (Beckman Coulter) and eluted in TE buffer. 1 mg of DNA was used with NEBNext Ultra DNA Library Prep Kit (New England Biolabs) and NEBNext Multiplex Oligos for Illumina kit for adaptor ligation, as instructed by the manufacturer’s protocol. DNA was then purified using SPRIselect beads, and eluted in water. BrdU labelled E. coli genomic DNA was processed in the same way for library preparation, and used as a spike control for BrdU immunoprecipitation. DNA was denatured at 95°C for 5 min and quickly cooled on ice. It was then incubated anti-BrdU antibody (BD347580) for 2 h in IP buffer (PBS, 0.0625% Triton X-100), after which Protein G Dynabeads were added for further 2 h incubation. Beads were pelleted and washed in IP and TE buffers using a magnetic rack, after which immunoprecipitated DNA was eluted by incubating beads in elution buffer (TE, 1% SDS) for 15 min at 65 °C. DNA was then purified using SPRIselect beads, and amplified for 15 cycles with Illumina indexing primers using NEBNext Ultra II kit and NEBNext Multiplex Oligos for Illumina kit. Amplified libraries were cleaned using SPRIselect beads and used for sequencing on NovaSeq 6000 platform.

treatment_protocol: We pulsed the cells with 100 mM BrdU for 2 h and collected them for isolation of genomic DNA. All samples were prepared in triplicates.

value: Bone

value: Osteosarcoma

value: BrdU-labelled


title: KO U2OS nascent DNA sequencing replicate 3


title: KO U2OS nascent DNA sequencing replicate 2


title: baseline_patient.17

value: Ixekizumab 80mg Q2W

value: skin

value: chronic plaque psoriasis


title: pancreas, Ad-M3C, day 02, r3

description: Day 2-3


title: pancreas, Ad-M3C, day 02, r2

description: Day 2-2


title: WT U2OS nascent DNA sequencing replicate 3

description:
ConsensusPeaks_s1_2_3_c3_noh
unique_peaks_s1_2_3_vs_s4_5_6_ucsc_formated

value: WT


title: pancreas, Ad-M3C, day 02, r1

description: Day 2-1


title: WT U2OS nascent DNA sequencing replicate 2


title: baseline_patient.5


title: week 1_patient.38


title: week 2_patient.29

value: Gene expression data at week 2.


title: week 2_patient.40


title: WT U2OS nascent DNA sequencing replicate 1


title: pancreas, Ad-M3C, day 01, r7

description: Day 1-7

value: day 01


title: pancreas, Ad-M3C, day 01, r6

description: Day 1-6


title: pancreas, Ad-M3C, day 01, r8

description: Day 1-8


title: KO U2OS CENP-B input

data_processing:
The unprocessed reads were first run through FastQC to check the quality of the sequencing.
Then the reads were trimmed using Trimgalore and mapped to the human genome using bowtie2.
The mapped reads are then used to call enrichment peaks using MACS2.
Once called, the peaks are filtered according to the stringent threshold (using the -log10 of the FDR p-value of 2.8e-28).
Peaks common to all 3 replicates in each group are obtained by merging peaks between samples using MSPC.
Assembly: GRCh38/hg38
Supplementary files format and content: BedGraph; coverage per chromosome

extract_protocol:
Cells were cross-linked at room temperature for 10 min using 1% formaldehyde. Cross-linking reaction was quenched by the addition of 125 mM glycine for 5 min, after which cells were washed in PBS. Cells were then resuspended in the lysis buffer (50 mM Tris pH 7.5, 500 mM NaCl, 3mM CaCl2, 1 % Triton-X, 0.1% SDS, 0.1% Sodium Deoxycholate, Protease Inhibitors), and chromatin was digested by the micrococcal nuclease for 20-25 min at 37 °C. Reactions were stopped by the addition of 10mM EDTA and 20 mM EGTA, and then briefly sonicated. Samples were then cleared by centrifugation at 4 °C, and a fraction of the chromatin extract was saved for DNA purification (input). Chromatin extracts were diluted to 50 mM Tris pH 7.5, 250 mM NaCl, 1 % Triton-X, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors), and incubated with CENP-B antibody for 1 h. Protein G Dynabeads (Life Technologies) were washed and added to the samples, which were then incubated overnight at 4 °C. Following immunoprecipitation, beads were pelleted using a magnetic rack, and washed 3 times in 50 mM Tris pH 7.5, 250 mM NaCl, 2 mM EDTA, 1 % Triton-X, 0.1% SDS, 5 times in 50 mM Tris pH 7.5, 500 mM NaCl, 2 mM EDTA, 1 % Triton-X, 0.1% SDS, once in 10 mM Tris-HCl pH 7.5, 0.25 M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, and once in 10 mM Tris pH 7.5, 1 mM EDTA. Beads were then resuspended in 10 mM Tris pH 7.5, 1 mM EDTA, 1 % SDS and incubated at 65 °C for 15 min. Eluted DNA and input samples were treated with RNase A at 37 °C for 30 min, and with Proteinase K at 65 C overnight in a buffer containing 50 mM Tris HCl pH7.5, 300 mM NaCl and 1% SDS. DNA was then isolated using SPRIselect beads (Beckman Coulter) and used for construction of libraries.
Briefly, NEBNext Ultra DNA Library Prep Kit (New England Biolabs) was used for adaptor ligation. DNA was then purified using SPRIselect beads, and amplified for 15 cycles with Illumina indexing primers using NEBNext Ultra II kit and NEBNext Multiplex Oligos for Illumina kit as instructed by the manufacturer’s protocol. Amplified libraries were cleaned using SPRIselect beads and used for sequencing on NovaSeq platform.


title: pancreas, Ad-M3C, day 01, r4

description: Day 1-4


title: pancreas, Ad-M3C, day 01, r5

description: Day 1-5


title: pancreas, Ad-M3C, day 01, r3

description: Day 1-3


title: KO U2OS CENP-B ChIP replicate 3

description: coverage_consensus_filtered_KO_rep1_rep2_rep3_bg


title: KO U2OS CENP-B ChIP replicate 1


title: KO U2OS CENP-B ChIP replicate 2


title: WT U2OS CENP-B ChIP replicate 3

description: coverage_consensus_filtered_WT_rep1_rep2_rep3_bg


title: pancreas, Ad-M3C, day 01, r2

description: Day 1-2


title: pancreas, Ad-M3C, day 01, r1

description: Day 1-1


title: week 2_patient.3


title: WT U2OS CENP-B ChIP replicate 2


title: WT U2OS CENP-B ChIP replicate 1


title: baseline_patient.7


title: week 4_patient.3

value: Gene expression data at week 4.


title: pancreas, no treatment, day 0, r4

description: Day 0-4

value: no treatment

value: day 0


title: baseline_patient.43

value: Gene expression data at baseline.


title: baseline_patient.32


title: week 1_patient.54

value: Gene expression data at week 1.


title: WT U2OS CENP-B input


title: baseline_patient.20


title: week 4_patient.37


title: week 1_patient.57


title: LPS853_hichip_rep2

data_processing:
HiChIP processing: Data were quality and adapter trimmed using seqPrep and mapped to the reference genome (hg38) using Bowtie2. Contact matrices were created with HiCPro. Chromatin loops were called with hichipper, using H3k27ac peaks and hg38 promoters as the predefined peak set to call anchors.
Supplementary_files_format_and_content: Bedpe contact pairs
Assembly: hg38
Library strategy: HiChIP

value: Untreated


title: pancreas, no treatment, day 0, r3

description: Day 0-3

value: pancreas

value: pancreatic cell

value: 6-12 weeks old


title: LPS853_hichip_rep1


title: pancreas, no treatment, day 0, r1

description: Day 0-1


title: LPS141_hichip_rep2


title: pancreas, no treatment, day 0, r2

description: Day 0-2


title: Hepa1-6_15.5K_RIP_PEN_seq_rep5

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the mouse reference genome (mm10) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of mice (mm10) was downloaded from the UCSC Genome Browser site. Mouse gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for mouse snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: mm10

growth_protocol: Hepa1-6-FLAG-15.5K stable cells were cultured in DMEM (Gibico) with 10% fetal bovine serum (FBS, Gibico), 1% penicillin-streptomycin solution (Gibico) and 1μg/mL puromycine (MCE) at 37℃ at 5% CO2.

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G and the RNA fraction was extracted using RNAzol reagent.
For RIP-PEN-seq, RIP RNA was subjected to rRNA removal and further used to generate the library using the TruSeq Samll RNA sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Stable overexpression of 15.5K

value: anti-FLAG [Proteintech, cat# 66008-3-Ig]


title: LPS141_hichip_rep1


title: 0009, Acute MIS-C, CD4

city: New York

first: Donna

last: Farber

address: 701 West 168th Street, HHSC 1313

institute: Columbia University

description:
raw_counts.csv
MISC009.AC.CD4

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for each Sample
Supplementary files format and content: comma-delimited CSV file combined for all Samples

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from cells sorted in RLT lysis buffer (Qiagen) using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation.

value: peripheral blood

tag: condition

value: Acute MIS-C

value: PBMC (primary)

tag: cell type (sorted)

tag: individual


title: week 1_patient.20

value: Ixekizumab 80mg Q2W

value: skin

value: chronic plaque psoriasis


title: baseline_patient.33


title: Hepa1-6_15.5K_RIP_PEN_seq_rep4


title: 0004, MIS-C-R, CD4

description:
raw_counts.csv
MISC004.FU.CD4

value: MIS-C-R


title: week 1_patient.15


title: Hepa1-6_15.5K_RIP_PEN_seq_rep3


title: 0017, Acute MIS-C, CD4

description:
raw_counts.csv
COV17.AC.CD4


title: 0033, Acute MIS-C, CD4

description:
raw_counts.csv
COV033.AC.CD4


title: week 4_patient.32

value: Gene expression data at week 4.


title: 0013, MIS-C-R, CD4

description:
raw_counts.csv
COV13.FU.CD4


title: baseline_patient.49


title: week 2_patient.8

value: Gene expression data at week 2.


title: week 1_patient.4


title: Cisplatin, biological replicate 6, scRNAseq

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Neuroblastoma tumor

extract_protocol:
Single cell suspensions of neuroblastoma cells were generated according to the manufacturer's instructions (Worthington Papain Dissociation System, CAS: 9035-81-1).  Breifly, minced neuroblastoma tissue is dissociated by incubation with activated papain at 37oC followed by trituration.  Papain dissociation is then halted with ovomucoid.  A single step discontinuous density gradient separates intact cells from cell membranes, and then the pelleted cells are resuspended for sequencing with 10X Genomics kits.
Library was performed according to the manufacter’s instructions (10x Genomics). Single cell suspensions of neuroblastoma cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Neuroblastoma tumor

value: adrenal neuroblastoma

value: Dbh-iCre;LSL-MYCN

value: Cisplatin - 2mg/kg


title: pancreas, no treatment, day 0, r5

description: Day 0-5

value: pancreas

value: pancreatic cell

tag: strain

value: no treatment

value: day 0


title: Hepa1-6_15.5K_RIP_PEN_seq_rep2

value: Stable overexpression of 15.5K

value: anti-FLAG [Proteintech, cat# 66008-3-Ig]


title: Cisplatin, biological replicate 5, scRNAseq

description: 10X Genomics


title: Vehicle, biological replicate 5, scRNAseq

description: 10X Genomics

value: Vehicle


title: 0009, MIS-C-R, CD4

description:
raw_counts.csv
COV009.FU.CD4

value: peripheral blood

value: PBMC (primary)


title: 0018, Acute MIS-C, CD4

description:
raw_counts.csv
C0V018.AC.CD4

value: Acute MIS-C


title: 9630, MIS-C-R, CD4

description:
raw_counts.csv
X9630.FU.CD4

value: MIS-C-R


title: Vehicle, biological replicate 3, scRNAseq

description: 10X Genomics


title: baseline_patient.37

value: Ixekizumab 80mg Q2W

value: Gene expression data at baseline.

value: skin

value: chronic plaque psoriasis


title: 9630, Acute MIS-C, CD4

description:
raw_counts.csv
X9630.AC.CD4


title: Cisplatin, biological replicate 4, scRNAseq

description: 10X Genomics

value: Neuroblastoma tumor

value: adrenal neuroblastoma

value: Dbh-iCre;LSL-MYCN


title: baseline_patient.8


title: baseline_patient.47


title: week 4_patient.54

value: Gene expression data at week 4.


title: 7397, MIS-C-R, CD4

description:
raw_counts.csv
X7937.FU.CD4


title: 4580, MIS-C-R, CD4

description:
raw_counts.csv
X4580.FU.CD4


title: Vehicle, biological replicate 4, scRNAseq

description: 10X Genomics


title: Cisplatin, biological replicate 3, scRNAseq

description: 10X Genomics

value: Cisplatin - 2mg/kg


title: Cisplatin, biological replicate 1, scRNAseq

description: 10X Genomics


title: 4580, Acute MIS-C, CD4

description:
raw_counts.csv
X4580.AC.CD4


title: 0009, Acute MIS-C, CD8

description:
raw_counts.csv
MISC009.AC.CD8


title: Vehicle, biological replicate 2, scRNAseq

description: 10X Genomics

value: DMSO


title: 0004, MIS-C-R, CD8

description:
raw_counts.csv
MISC004.FU.CD8


title: 0080, MIS-C-R, CD4

description:
raw_counts.csv
X0080.FU.CD4


title: Cisplatin, biological replicate 2, scRNAseq

description: 10X Genomics


title: week 4_patient.38


title: 0013, MIS-C-R, CD8

description:
raw_counts.csv
COV13.FU.CD8


title: week 4_patient.57


title: 0009, MIS-C-R, CD8

description:
raw_counts.csv
COV009.FU.CD8


title: 0033, Acute MIS-C, CD8

description:
raw_counts.csv
COV033.AC.CD8


title: 0017, Acute MIS-C, CD8

description:
raw_counts.csv
COV17.AC.CD8


title: week 4_patient.20


title: Sublining_macrophages_mBSA_wt_1_1st

first: Irina

last: Udalova

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

description: PolyA RNA

data_processing:
Reads were aligned to the reference and quality checked. Resulting data were mapped to the mm10 genome using STAR v2.7.5b with the options: --runMode alignReads --outFilterMismatchNmax 2. Uniquely mapped read pairs were counted over annotated genes using featureCounts v.2.0.0 with the options: -T 18 -s 2 -Q 255. Differential expression was then analysed with DESeq2 v1.24.0 (Love et al., 2014). Variance stabilised counts for all DESeq2 DEGs, likelihood ratio test, and false discovery rate (FDR) <0.01 were used for dimensionality reduction and the heatmaps. GO analysis was performed using one-sided
Assembly: mm10 (GRCm38)
Supplementary files format and content: countdata_FC.csv

source_name: knee cell suspensions

extract_protocol:
Sorting of synovial macrophages was carried out from the knee cell suspensions stained as paper described. Lining macrophages were defined as CD45+, Linage- (NK1.1, CD3, CD19), CD11b+, F4/80+ and VSIG4+ cells, whereas sublining macrophages were CD45+, Lin-, CD11b+, F4/80+ and VSIG4-. Two hundred macrophages were sorted through 70-µm nozzle directly into 2.2 µl of lysis buffer (composition detailed below) using BD FACS Aria III.
Two hundred lining and sublining macrophages from 3 WT and 3 IRF5KO mice, isolated from PBS and mBSA injected knees, were sorted into PCR tubes containing 2.2 µl lysis buffer (0.8% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor (Clontech)).
Samples were transferred into 96-well skirted PCR plate, sealed with an adhesive PCR plate seal (Thermo Fisher), and transferred to Oxford Genomics Centre on dry ice to be sequenced. Briefly, the preparation of libraries was done using NEBNext® Ultra-low/single cell (Smarter-like) protocol (New England BioLabs).

tag: phenotype

value: wild-type

value: mBSA

tag: replicate

tag: round of sequencing


title: Sublining_macrophages_mBSA_wt_2_1st

description: PolyA RNA


title: Lining_macrophages_mBSA_wt_2_1st

description: PolyA RNA


title: Sublining_macrophages_PBS_wt_2_1st

description: PolyA RNA

value: PBS


title: week 4_patient.43

tag: tissue


title: baseline_patient.51


title: baseline_patient.46


title: week 4_patient.21


title: Lining_macrophages_PBS_wt_2_1st

description: PolyA RNA

tag: cell type


title: week 2_patient.41

value: Gene expression data at week 2.


title: 9630, MIS-C-R, CD8

description:
raw_counts.csv
X9630.FU.CD8

value: peripheral blood

value: PBMC (primary)


title: Lining_macrophages_PBS_wt_1_1st

description: PolyA RNA


title: week 2_patient.38


title: 0018, Acute MIS-C, CD8

description:
raw_counts.csv
C0V018.AC.CD8

value: Acute MIS-C


title: week 1_patient.55

value: Ixekizumab 80mg Q2W

value: Gene expression data at week 1.


title: week 1_patient.24

value: skin


title: week 1_patient.21

value: chronic plaque psoriasis


title: week 2_patient.14


title: 9630, Acute MIS-C, CD8

description:
raw_counts.csv
X9630.AC.CD8


title: Lining_macrophages_mBSA_wt_1_1st

description: PolyA RNA


title: Sublining_macrophages_mBSA_IRF5KO_6_1st

description: PolyA RNA


title: 7397, MIS-C-R, CD8

description:
raw_counts.csv
X7937.FU.CD8

value: MIS-C-R


title: 4580, Acute MIS-C, CD8

description:
raw_counts.csv
X4580.AC.CD8


title: Lining_macrophages_mBSA_IRF5KO_6_1st

description: PolyA RNA


title: Sublining_macrophages_PBS_wt_1_1st

description: PolyA RNA


title: week 2_patient.47


title: 0080, MIS-C-R, CD8

description:
raw_counts.csv
X0080.FU.CD8


title: Sublining_macrophages_PBS_IRF5KO_6_1st

description: PolyA RNA


title: week 2_patient.20


title: week 1_patient.5


title: week 1_patient.27


title: 4580, MIS-C-R, CD8

description:
raw_counts.csv
X4580.FU.CD8


title: Lining_macrophages_PBS_IRF5KO_6_1st

description: PolyA RNA


title: Sublining_macrophages_mBSA_IRF5KO_5_1st

description: PolyA RNA


title: Sublining_macrophages_PBS_IRF5KO_5_1st

description: PolyA RNA


title: Lining_macrophages_mBSA_IRF5KO_5_1st

description: PolyA RNA