title: APP-PS1_6172

source_name: Hippocampus

extract_protocol:
Hippocampal tissue from four WT pigs, four PS1 pigs and four APP/PS1 pigs were quickly removed after sacrificing the animals, dissected on ice and immediately submerged into liquid nitrogen and stored at -135oC. Tissues were homogenized in 1mL cold homogenization buffer (20mL Thioglycerol per millilitre of Homogenization solution) using a blender. Homogenates were left to settle on ice. Homogenates (200mL) were mixed with equal volume Lysis buffer and added to cartridges (Maxwell® 16 LEV simplyRNA Tissue Kit; Promega). DNAse I solution was added before samples were processed on Maxwell ® 16 Instrument. Eluted RNA was stored in -70oC.
Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Europe Genome Center. Total RNA was subjected to oligo dT based mRNA enrichment. 100 bp paired-end read sequencing was performed on BGIseq-500 with DNBseq technology. More than 20 million clean reads were obtained per sample.

value: Hippocampus


title: patient 14, tumor

status: Public on Feb 04 2024

type: SRA

city: Laval

first: Maya

last: Saleh

state: Qc

address: 531 Boulevard des Prairies

department: Armand Frappier Santé Biotechnologie

country: Canada

institute: INRS

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
matrices generated by CellRanger were then processed using Seurat, followed by filtering and doublet removal steps
Normalization was done using SCTransform and rPCA Integration was performed in Seurat
Assembly: GRCh38
Supplementary files format and content: Giraud_Chalopin_innate_HCC_processed_count_data_mat.tsv.gz, raw count matrix after sample integration (rows are genes, columns are barcodes
Supplementary files format and content: Giraud_Chalopin_innate_HCC_metadata.tsv.gz, meta information corresponding to barcodes in the count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: Hepatocellular Carcinoma

extract_protocol:
15.000 single CD45+ panTCRαβ- CD19- innate immunity cells were loaded into a chip to form Gel Bead-in-Emulsion in the Chromium Controller. Single-cell libraries were generated using the Single Cell 3' reagent Kit v3.1 (10X Genomics) as per the manufacturer’s protocol.
cDNA was amplified by 12 PCR cycles and 12 cycles were also performed for library preparation (single index PCR). Libraries were pooled and sequenced on a NovaSeq 6000.

tag: tissue

value: Hepatocellular Carcinoma

tag: cell type

value: innate immune cells


title: Participant 7: CD8+ TM- T-cells

city: Leiden

first: Linda

last: Voogd

state: South-Holland

address: Albinusdreef 2

department: Infectious Diseases

country: Netherlands

institute: Leiden University Medical Center

library_source: transcriptomic

data_processing:
Single-end reads of 50 bps. in length were aligned against he human reference genome Homo sapiens GRCh38.91
Analysis of reads was performed in Rstudo v1.2 using the DESeq2 package
DESeq2 parameters were log2 fold change treshold 1, read count >4 per gene, adjusted p-value cut off= 0.05 and the DESeq2 multifactor design formula=‘~donor + cell population’
Assembly: GRCh38.91
Supplementary files format and content: .xlsx files contain the raw read counts for each sample for the identified gene
Supplementary files format and content: FG_All_mapped_reads Corrected.xlsx file contains the corrected read counts (according to the size factor) for each gene in each sample

molecule: total RNA

source_name: CD8+ T-cell

extract_protocol:
RNA was extracted from lysed (QIAzol) sorted T-cells using an miRNeasy Mini Kit (Qiagen) and eluted into DNA Lobind Eppendorf Tubes
RNA was amplified to cDNA using the SMART-Seq version 4 Ultra Low Input RNA Kit for Sequencing (Takara Bio)

value: CD8+ T-cell

tag: hla-e genotype


title: KO77_T354M_Rep1

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

country: USA

institute: University of Wisconsin-Madison

description: -77KO expressing Gata2 T354M mutant replicate 1

data_processing:
Sequencing reads were aligned by STAR (version 2.5.2b) to mouse genome (mm10, chromosomes 1 to 19, X, Y, and M) with GENCODE comprehensive gene annotation (version M16) on the reference chromosomes only. Command line options for STAR followed ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh)
Gene expression levels were quantified by RSEM (version 1.3.0) with command line options following ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh).
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

organism: Mus musculus

source_name: Lin- hematopoietic progenitor cells

extract_protocol:
total RNA
standard NuGEN Ovation protocol

value: Lin- hematopoietic progenitor cells

tag: genotype

value: T354M rescue

tag: treatment

value: Cells were infected with MSCV vector coding GATA2 T354M mutant. Cells were cultured for 3 days and RNA was harvested.


title: APP-PS1_6171

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Reads were aligned to the porcine genome build Sscrofa11.1 (Ensemble release 92) using HISAT2 aligner (v2.1.0)
Transcript quantification was performed using htseq-count (v0.9.1)
Read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM)
Differentially expressed genes were determined from count tables using DEseq2 (v2.11.40.6)
Assembly: Sscrofa11.1 (Ensemble release 92)
Supplementary files format and content: tab-delimited file containing TPM values for each sample

organism: Sus scrofa


title: patient 13, tumor


title: Participant 6: CD8+ TM- T-cells


title: Participant 4: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: APP-PS1_6170


title: patient 12, tumor


title: Participant 5: CD8+ TM- T-cells


title: KO77_R307W_Rep4

description: -77KO expressing Gata2 R307W mutant replicate 4

value: R307W rescue

value: Cells were infected with MSCV vector coding GATA2 R307W mutant. Cells were cultured for 3 days and RNA was harvested.


title: APP-PS1_6027


title: MDSC-c4, CD36high CD163+ LOX1med, pool of 5 patients

data_processing:
Initial quality steps were done using fastp 0.23.2
Read mapping were performed using STAR 2.7.10a with human Gencode release 44 (Gencode v44 primary assembly, GRCh38)
ReadsPerGene.out.tab STAR output of all 9 samples were merged to obtain the raw count matrix, named raw_counts_RNASeq_matrix.txt
Raw counts were cpm transformed. Tab delimited table is named cpm_counts_RNAseq_matrix.tsv
Assembly: GRCh38
Supplementary files format and content: tab-delimited tsv file including raw counts of the 9 samples (6 innate cells, 3 THBS1 monocytes populations)
Supplementary files format and content: tab-delimited tsv file including cpm counts of the 9 samples (6 innate cells, 3 THBS1 monocytes populations)

source_name: liver

growth_protocol: Innate immunity cells from HCC#17, HCC#18, HCC#19, HCC#20, HCC#23 and HCC#24 were isolated using the same sorting strategy designed for scRNAseq experiments, i.e. CD45+ panTCRαβ- CD19-. THBS1 monocyte (c0, c3 and c4) populations were isolated according to the following sorting strategy: CD36high CD163- LOX1+ (c0),  CD36high CD163- LOX1- (c3) and CD36high CD163+ LOX1med (c4). Viability and single cells were verified under microscope and cells were immediately lysed in RNA extraction buffer and stored at -80°C. Sorted THBS1 monocytes cells were pooled from 5 HCC patients.

extract_protocol:
RNA were extracted using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were constructed using Low Input Library Prep Kit (TakaraBio) and sequenced on a NovaSeq 6000 with a run configuration of 2×150 bp.

value: liver

value: THBS1 monocyte sorted


title: KO77_R307W_Rep2

description: -77KO expressing Gata2 R307W mutant replicate 2


title: PS1_495


title: KO77_R307W_Rep3

description: -77KO expressing Gata2 R307W mutant replicate 3


title: Participant 4: CD8+ TM- T-cells


title: MDSC-c3, CD36high CD163- LOX1-, pool of 5 patients


title: PS1_540


title: Participant 3: CD8+ TM- T-cells


title: MDSC-c0, CD36high CD163- LOX1+, pool of 5 patients


title: PS1_538


title: Participant 2: CD8+ TM- T-cells


title: KO77_R307W_Rep1

description: -77KO expressing Gata2 R307W mutant replicate 1


title: OE-TabHLH489_5DPA_grain_rep3

city: Qingdao

first: Jinyang

last: Lyu

state: Shandong

address: BinHai road

department: School of Life Sciences

country: China

institute: Shandong University

data_processing:
The RNA-seq clean reads were mapped to the reference genome IWGSC Refseq v1.1 using Bowtie2
Htseq-count with default parameters was used to calculate the gene read counts
The gene read counts were normalized to TPM and calculated the gene expression level by Salmon.
Assembly: IWGSC_Refseq_v1.1
Supplementary files format and content: text file includes read counts of genes for each sample
Supplementary files format and content: text file includes TPM value of genes for each sample

organism: Triticum aestivum

source_name: Grain

growth_protocol: The plants were cultivated in a greenhouse under a 16-hour light (22 °C)/8-hour dark (16 °C) cycle, maintaining approximately 50% relative humidity.

extract_protocol:
Total RNA was extracted from grains using M5 HiPer Plant RNeasy Complex Mini Kit (Mei5bio). 1 μg total RNA was used for the construction of sequencing libraries.
The sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

value: Grain

value: TabHLH489 overexpression

tag: time

value: 5 days post anthesis


title: innateCHC24, innate from patient 24

value: innate immune sorted


title: PS1_508


title: innateCHC23, innate from patient 23


title: WT_852

value: WT


title: OE-TabHLH489_5DPA_grain_rep1


title: Participant 1: CD8+ TM- T-cells


title: innateCHC20, innate from patient 20


title: WT_317245


title: Rabbit ear hypertrophic sca with drug-loaded MNs treatment, rep2, scRNA-seq [MNs-2]

city: Wuhan

first: Zhuo-ran

last: Yang

state: Hubei

address: No. 1037 Luoyu Road, Hongshan District

department: Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering

institute: Huazhong University of Science and Technology (HUST)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oryctolagus cuniculus

source_name: Rabbit ear hypertrophic scar

extract_protocol:
The ventral epidermis and dermis of the rabbit ear scar tissues were saved and cut into small pieces to further disassociated into single cell suspension. Cell viability were detected by trypan blue staining. Single-cell gel beads-in-emulsion generation, barcoding, sample cleanup, cDNA amplification, and cDNA library construction were performed. Subsequently, cDNA library was sequenced and bioinformatic information was analyzed.
Library was performed according to the manufacturer's instructions (single cel 3' v2 protocol, 10x Genomics)

treatment_protocol: The treatment of drug-loaded MNs was applied on HS tissue once a week for 3 consecutive weeks.

value: Rabbit ear hypertrophic scar

tag: cell line

value: drug-loaded MNs treatment


title: Rabbit ear hypertrophic sca with drug-loaded MNs treatment, rep1, scRNA-seq [MNs-1]

description: 10x Genomics


title: Fielder_5DPA_grain_rep3


title: innateCHC19, innate from patient 19


title: WT_2E

value: Hippocampus


title: Fielder_5DPA_grain_rep2


title: innateCHC18, innate from patient 18


title: Rabbit ear hypertrophic scar without treatment, rep2, scRNA-seq [HS-2]

description: 10x Genomics


title: Fielder_5DPA_grain_rep1


title: WT_1E


title: Rabbit ear hypertrophic scar without treatment, rep1, scRNA-seq [HS-1]

description: 10x Genomics


title: OE-TabHLH489_5DPA_grain_rep2


title: M47_ZT22_Nac_S11

status: Public on Feb 03 2024

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

state: PA

address: 450 Technology Drive

institute: University of Pittsburgh

data_processing:
Quality control was performed by Fastqc
Perform trimming by trimmomatic, allign the sequence using Hisat2 with Ensembl reference and read count with Hiseq
Assembly: GRCh38
Supplementary files format and content: processed_Nac_CPMfiltered_log2DEseq2.csv; processed_DLS_CPMfiltered_log2DEseq2.csv; processed_DMS_CPMfiltered_log2DEseq2.csv

source_name: NAc

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent), respectively. Libraries were prepared using the Smartseq stranded total RNA ultra-low input sample preparation kits (Illumina).

value: NAc

tag: strain

tag: Sex

value: Male


title: M42_ZT14_Nac_S7

description: processed_Nac_CPMfiltered_log2DEseq2.csv


title: M44_ZT18_Nac_S9


title: M43_ZT14_Nac_S19


title: M45_ZT18_Nac_S21


title: M48_ZT22_Nac_S23


title: M37_ZT10_Nac_S5


title: M38_ZT10_Nac_S17


title: M40_ZT10_Nac_S26


title: M34_ZT6_Nac_S3


title: M31_ZT2_Nac_S1


title: F53_ZT6_Nac_S29

value: Female


title: F52_ZT6_Nac_S25


title: F47_ZT18_Nac_S22


title: F44_ZT14_Nac_S27


title: F51_ZT6_Nac_S16


title: Minipigno.557APP/PS1 so2709P5-No inhibition

source_name: Ear biopsy

extract_protocol:
Porcine fibroblasts were obtained from ear biopsies from WT, PS1 and APP/PS1 Göttingen minipigs and cultured in porcine fibroblast medium (Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma Aldrich), 10% FBS (Life Technologies), 1% P/S (P/S, 10,000 units/mL and 10,000μg/mL; Life Technologies), 1% Gln (2.92g/100mL) and 6.667ng/mL Fibroblast Growth Factor-basic (bFGF; Life Technologies)) in 5% CO2 in a humidified chamber at 37oC. Established fibroblasts were split in a 1:3 ratio every 3 days using 0.05% trypsin EDTA (Life Technologies). All fibroblasts used in this study were tested negative for mycoplasma (MYCOPLASMACHECK, Eurofins Genomics).
Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Europe Genome Center. Total RNA was subjected to oligo dT based mRNA enrichment. 50 bp single-end read sequencing was performed on BGIseq-500 with DNBseq technology. More than 20 million clean reads were obtained per sample.

value: Ear biopsy

value: Fibroblasts

value: Vehicle


title: F46_ZT18_Nac_S10


title: F41_ZT14_Nac_S8


title: F48_ZT18_Nac_S28


title: innateCHC17, innate from patient 17


title: F37_ZT10_Nac_S6


title: F42_ZT14_Nac_S20


title: F33_ZT2_Nac_S14


title: M35_ZT6_Nac_S15


title: M32_ZT2_Nac_S13


title: F36_ZT6_Nac_S4


title: F31_ZT2_Nac_S2


title: M9_ZT2_Nac_S8


title: M8_ZT2_Nac_S24


title: M7_ZT2_Nac_S13


title: M5_ZT22_Nac_S16


title: M4_ZT22_Nac_S6


title: M29_ZT18_Nac_S14


title: M3_ZT22_Nac_S22


title: M6_ZT2_Nac_S3


title: F49_ZT22_Nac_S12


title: M26_ZT18_Nac_S10


title: F50_ZT22_Nac_S24


title: M27_ZT18_Nac_S20


title: M28_ZT18_Nac_S4


title: M25_ZT14_Nac_S22


title: M24_ZT14_Nac_S12


title: M23_ZT14_Nac_S3


title: M22_ZT14_Nac_S19


title: M15_ZT6_Nac_S20


title: M21_ZT14_NAc_S8


title: M14_ZT6_Nac_S10


title: M2_ZT22_Nac_S11


title: M16_ZT10_Nac_S7


title: F38_ZT10_Nac_S18


title: M13_ZT6_Nac_S25


title: M12_ZT6_Nac_S15


title: M10_ZT2_Nac_S18


title: F9_ZT2_Nac_S9


title: F7_ZT2_Nac_S14


title: Hi-C_Cut14-3xsAID+5aIAA_rep2

city: Lyon

first: Léonard

last: Colin

address: 9, rue du Vercors

department: LBMC

country: France

institute: ENS de Lyon

description: Schizosaccharomyces pombe Sp972

library_source: genomic

data_processing:
For calChIPseq, an nf-core modified pipeline was used (https://www.biorxiv.org/content/10.1101/2022.03.18.484892v2) to generate normalized bigwig files
For Hi-C, raw reads were merged with the cat command and hicstuff version 3.1.2 was used to generate the 2D maps and the distance law plots by iterative mapping using bowtie2 with enzyme set as DpnII. Insulation scores were determined with cooltools.
Assembly: For Hi-C, the pombeASM294v2 genome was used but the mitochondrial chromosome was removed. For calChIPseq, chromosome II right arm was extended to include a partial telomeric sequence as described previously (https://www.biorxiv.org/content/10.1101/2022.03.18.484892v2)
Supplementary files format and content: Hi-C Matrices were converted to cooler format (.cool) with hicstuff for use in downstream analysis.
Supplementary files format and content: Bigwig files (.bigwig) for the Ips were bp normalized and corrected for calibration as described previously (https://www.biorxiv.org/content/10.1101/2022.03.18.484892v2) for downstream analysis.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Cells were grown in Pombe Minimal Glutamate media at 32°C and arrested in mitosis by a thiamine repressible system leading to APC inhibition (nmt41-slp1) at 32°C for a total of 3hours with 20uM thiamine.

extract_protocol:
Cells were fixed with 1% (ChIP) or 3% (Hi-C) formaldehyde 5mn at 32°C, 20mn at 19°C and quenched 5mn with 125mM glycine before being put on ice, washed with 1X PBS and frozen in liquid nitrogen. For ChIP, fixed cerevisae cells with Psm3-GFP tagged cohesin were added and cells were lysed with precellys, sonicated with S220 covaris, clarified twice by centrifugation and subjected to overnight immunoprecipitation before washes. DNA was eluted and purified with Qiagen Quiaquick columns. For Hi-C, cells were lysed with precellys, digested with DpnII overnight, filled in with dTTP, dGTP, dCTP and biotin-14-dATP for 45mn at 37°C, ligated for 4hr at 25°C and crosslinks were reversed overnight, and DNA was recovered with Phenol/Chloroform/IAA extraction and Amicon 30K column washes.
For ChIPseq, NEBNext UltraII DNA Library Prep Kit E7645 and adapters E6609 were used. For Hi-C, libraries were performed with separate reagents, removing biotin from unligated ends with Klenow DNA Polymerase I, sonicating with Covaris, repairing extremities, A-tailing libraries and ligated NextFlex Adapters (CAT NOVA 514102)
Libraries were sequenced with pairedend sequencing 150bp on a Novaseq6000

treatment_protocol: Degron-tagged strains were treated with 100nM 5-adamantyl-IAA for 1hr before the end of the arrest (Dhp1-3xsAID) or 30mn before the end of the arrest (Rpb1-3xsAID).

value: fission yeast

value: 20uM Thiamine for 3hrs at 32 C (from t=0 to t=3). At t=1, added 100nM 5aIAA in NaOH.


title: Hi-C_wild-type+5aIAA_rep1

description: Schizosaccharomyces pombe Sp972


title: M11_ZT6_Nac_S5


title: M1_ZT22_Nac_S1


title: INPUT_dhp1_OFF_rep1

description: Schizosaccharomyces pombe Sp972

value: 20uM Thiamine for 3hrs at 32 C (from t=0 to t=3). At t=2, added 100nM NaOH.


title: Hi-C_Cut14-3xsAID+5aIAA_rep1

description: Schizosaccharomyces pombe Sp972


title: F5_ZT22_Nac_S17


title: F3_ZT22_Nac_S23


title: INPUT_dhp1_ON_rep2

description: Schizosaccharomyces pombe Sp972

value: 20uM Thiamine for 3hrs at 32 C (from t=0 to t=3). At t=2, added 100nM 5aIAA in NaOH.


title: M17_ZT10_Nac_S17


title: F29_ZT18_Nac_S15


title: M18_ZT10_Nac_S1


title: F4_ZT22_Nac_S7


title: INPUT_dhp1_ON_rep1

description: Schizosaccharomyces pombe Sp972


title: IP_8WG16_dhp1_OFF_rep2

description: Schizosaccharomyces pombe Sp972


title: IP_8WG16_dhp1_OFF_rep1

description: Schizosaccharomyces pombe Sp972


title: IP_8WG16_dhp1_ON_rep1

description: Schizosaccharomyces pombe Sp972


title: F25_ZT14_Nac_S23


title: F24_ZT14_Nac_S13


title: F28_ZT18_Nac_S5


title: F27_ZT18_Nac_S21


title: F21_ZT14_Nac_S9


title: Hi-C_rpb1_ON_rep2

source_name: Schizosaccharomyces pombe

value: Schizosaccharomyces pombe

value: 20uM Thiamine for 3hrs at 32degreeC (from t=0 to t=3). At t=2,5, added 100nM NaOH.


title: F20_ZT10_Nac_S21


title: Hi-C_rpb1_OFF_rep2

value: 20uM Thiamine for 3hrs at 32degreeC (from t=0 to t=3). At t=2,5, added 100nM 5aIAA in NaOH.


title: F6_ZT2_Nac_S4


title: Input_rpb1_OFF


title: Input_rpb1_ON


title: F19_ZT10_Nac_S11


title: Hi-C_rpb1_ON_rep1


title: INPUT_dhp1_OFF_rep2

description: Schizosaccharomyces pombe Sp972


title: F12_ZT6_Nac_S16


title: IP_Cnd2GFP_rpb1_ON


title: F18_ZT10_Nac_S2


title: Hi-C_rpb1_OFF_rep1


title: Hi-C_wild-type+5aIAA_rep2

description: Schizosaccharomyces pombe Sp972


title: F17_ZT10_Nac_S18


title: F11_ZT6_Nac_S6


title: IP_8WG16_dhp1_ON_rep2

description: Schizosaccharomyces pombe Sp972


title: Hi-C_dhp1_ON_rep2

value: 20uM Thiamine for 3hrs at 32degreeC (from t=0 to t=3). At t=2, added 100nM NaOH.


title: IP_Cnd2GFP_rpb1_OFF


title: M9_ZT2_DMS_S5

description: processed_DMS_CPMfiltered_log2DEseq2.csv

source_name: DMS

value: DMS


title: IP_Rpb1_rpb1_ON


title: F10_ZT2_Nac_S19


title: IP_Rpb1_rpb1_OFF


title: M8_ZT2_DMS_S25


title: Hi-C_dhp1_OFF_rep1

value: 20uM Thiamine for 3hrs at 32degreeC (from t=0 to t=3). At t=2, added 100nM 5aIAA in NaOH.


title: M7_ZT2_DMS_S1


title: M6_ZT2_DMS_S5


title: F1_ZT22_Nac_S2


title: M5_ZT22_DMS_S25


title: Input_Cnd2GFP_dInputp1_OFF_rep2

tag: antibody


title: Hi-C_dhp1_ON_rep1


title: M47_ZT22_DMS_S21


title: Input_Cnd2GFP_dInputp1_OFF_rep1


title: M45_ZT18_DMS_S25


title: Input_Cnd2GFP_dInputp1_ON_rep1


title: M44_ZT18_DMS_S17


title: IP_Cnd2GFP_dhp1_ON_rep2

value: GFP-tagged kleisin Cnd2 (A111-22 antibody)


title: M42_ZT14_DMS_S22


title: M40_ZT10_DMS_S20


title: Input_Cnd2GFP_dInputp1_ON_rep2


title: Hi-C_dhp1_OFF_rep2


title: IP_Cnd2GFP_dhp1_OFF_rep1


title: M4_ZT22_DMS_S1


title: M38_ZT10_DMS_S9


title: M34_ZT6_DMS_S28


title: M37_ZT10_DMS_S13


title: M31_ZT2_DMS_S25


title: M3_ZT22_DMS_S21


title: M29_ZT18_DMS_S21


title: IP_Cnd2GFP_dhp1_OFF_rep2


title: M27_ZT18_DMS_S17


title: WGBS TTF-PGCLC rep1

city: San Antonio

first: Yu-Huey

last: Lin

state: Texas

address: One UTSA Circle,

department: The Department of Neuroscience, Developmental and Regenerative Biology

institute: The University of Texas at San Antonio

data_processing:
WGBS data were processed using the comprehensive wg-blimp v10.0.0 software pipeline. In brief, all reads were trimmed with Trim Galore v0.6.5 to remove adaptors and the first four bases. Reads were mapped onto the mouse reference genome GRCm39 using bwa-meth and PCR duplicates were removed with the Picard toolkit. The analysis of differentially methylated regions (DMRs) was performed using metilene and BSmooth algorithms. Hierarchical clustering was performed using the clusterSamples function and PCA was performed using the PCASamples function from methylKit v1.22.0 using the percent methylation matrix as an input
Assembly: GRCm39
Supplementary files format and content: bedGraph

source_name: Primordial germ cell like cells

extract_protocol:
Cells were lysed in cell lysis buffer with Proteinase K solution and then genomic DNA was extracted from cells using the phenol:chloroform extraction method. Genomic DNA was then purified using Zymo Genomic DNA Clean & Concentrator kit according to the manufacturer’s instructions.
About 50ng of genomic DNA from each sample was subjected to bisulfite conversion. Preparation of the WGBS libraries was done using the Zymo Pico Methyl-Seq Library Prep Kit according to the manufacturer’s instructions.

value: Primordial germ cell like cells


title: WGBS TTF-PGCLC rep3


title: WGBS SSC-PGCLC rep1


title: M26_ZT18_DMS_S21

value: Male


title: WGBS PGC-PGCLC rep3


title: WGBS SSC-PGCLC rep3


title: WGBS SSC-PGCLC rep2


title: WGBS TTF-PGCLC rep2


title: M23_ZT14_DMS_S9


title: WGBS MEF-PGCLC rep3


title: WGBS MEF-PGCLC rep2


title: IP_Cnd2GFP_dhp1_ON_rep1


title: WGBS MEF-PGCLC rep1


title: WGBS PGC rep3

source_name: Primordial germ cells

value: Primordial germ cells


title: M21_ZT14_DMS_S17


title: M22_ZT14_DMS_S13


title: M2_ZT22_DMS_S25


title: WGBS PGC rep2


title: M18_ZT10_DMS_S5


title: WGBS PGC-PGCLC rep2


title: WGBS PGC-PGCLC rep1


title: WGBS PGC rep1


title: M28_ZT18_DMS_S13


title: WGBS TTF rep4

source_name: Tail tip fibroblasts

value: Tail tip fibroblasts


title: M17_ZT10_DMS_S9


title: M25_ZT14_DMS_S13


title: M24_ZT14_DMS_S17


title: WGBS TTF rep3


title: M13_ZT6_DMS_S1


title: WGBS MEF rep2

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts


title: WGBS TTF rep1


title: M16_ZT10_DMS_S13


title: M15_ZT6_DMS_S5


title: M14_ZT6_DMS_S9


title: WGBS MEF rep3


title: M12_ZT6_DMS_S5


title: WGBS TTF rep2


title: WGBS MEF rep1


title: M10_ZT2_DMS_S1


title: RNA-seq SSC-PGCLC rep2

data_processing:
All reads from the QuantSeq sequencing datasets were processed with cutadapt v1.18 to remove adaptors and poly-A sequences. Reads of 30-bp or longer were mapped to the GRCm39 version of the mouse reference genome using Rsubread v2.10.1.. All RNA-seq datasets were processed using the R software (version 4.1.1) packages edgeR v3.38.1 and DESeq2 v1.36 with default settings to detect differential gene expression levels, including <5% for false discovery rate and p <0.05. Data from biological replicates was averaged and differentially expressed genes were defined as those with a ≥1.5-fold difference in expression levels between the control ESC line and each set of iPSC lines produced in this study. Hierarchical clustering was performed using the hclust function and principal component analysis (PCA) was performed using the autoplot and prcomp function without scaling.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Cells were lysed in TRI reagent and total RNA was extracted using a Zymo Direct-zol RNA Miniprep kit. Total RNA was then incubated with RQ1 DNase to remove contaminating genomic DNA and was then re-purified using Zymo RNA Clean & Concentrator-5 kit according to the manufacturers instructions.
About 50 ng of total RNA from each sample was used for synthesis and amplification of cDNA. cDNA synthesis was performed by the UTSA Genomics Core using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD from Illumina (LEXOGEN).


title: M11_ZT6_DMS_S9


title: F8_ZT2_DMS_S2

value: Female


title: M1_ZT22_DMS_S1


title: RNA-seq SSC-PGCLC rep1


title: F9_ZT2_DMS_S26


title: F6_ZT2_DMS_S6


title: RNA-seq PGC-PGCLC rep2


title: F5_ZT22_DMS_S26


title: F52_ZT6_DMS_S17


title: RNA-seq PGC-PGCLC rep1


title: F51_ZT6_DMS_S6


title: RNA-seq PGC-PGCLC rep3


title: RNA-seq TTF-PGCLC rep2


title: RNA-seq SSC-PGCLC rep3


title: F46_ZT18_DMS_S22


title: F49_ZT22_DMS_S22


title: F45_ZT18_DMS_S14


title: RNA-seq TTF-PGCLC rep1


title: RNA-seq MEF-PGCLC rep3


title: WGBS SSC rep1

source_name: spermatogonial stem cells

value: spermatogonial stem cells


title: F47_ZT18_DMS_S18


title: RNA-seq MEF-PGCLC rep1


title: F48_ZT18_DMS_S26


title: WGBS SSC rep2


title: WGBS iPSC SCd5

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: F44_ZT14_DMS_S14


title: F41_ZT14_DMS_S14


title: F40_ZT10_DMS_S10


title: RNA-seq PGC rep2


title: RNA-seq PGC rep3


title: F43_ZT14_DMS_S18


title: F39_ZT10_DMS_S14


title: RNA-seq PGC rep1


title: RNA-seq TTF-PGCLC rep3


title: F42_ZT14_DMS_S10


title: F38_ZT10_DMS_S6


title: WGBS iPSC SCd2


title: F4_ZT22_DMS_S2


title: WGBS iPSC PG4a5


title: RNA-seq MEF-PGCLC rep2


title: F31_ZT2_DMS_S2


title: RNA-seq TTF rep3


title: F37_ZT10_DMS_S10


title: RNA-seq TTF rep2


title: WGBS iPSC SCa3


title: F28_ZT18_DMS_S22


title: RNA-seq TTF rep4


title: WGBS iPSC PG4a8


title: F33_ZT2_DMS_S26


title: WGBS iPSC TF15


title: WGBS iPSC TF16


title: RNA-seq MEF rep3


title: F29_ZT18_DMS_S18


title: F18_ZT10_DMS_S14


title: F3_ZT22_DMS_S22


title: WGBS iPSC PG2a2


title: RNA-seq TTF rep1


title: F14_ZT6_DMS_S2


title: RNA-seq MEF rep2


title: F2_ZT22_Nac_S12

value: NAc


title: F15_ZT6_DMS_S10


title: WGBS iPSC MF591


title: RNA-seq iPSC SCd5


title: RNA-seq iPSC SCd2


title: F10_ZT2_DMS_S6


title: F2_ZT22_DMS_S26


title: WGBS iPSC TF14


title: M7_ZT2_DLS_S3

description: processed_DLS_CPMfiltered_log2DEseq2.csv

source_name: DLS

value: DLS


title: F25_ZT14_DMS_S18


title: M6_ZT2_DLS_S7


title: F11_ZT6_DMS_S10


title: M47_ZT22_DLS_S23


title: WGBS iPSC MF56


title: F12_ZT6_DMS_S6


title: M50_ZT22_DLS_S23


title: M45_ZT18_DLS_S19


title: RNA-seq iPSC PG2a2


title: WGBS ESC rep3

source_name: embryonic stem cells

value: embryonic stem cells


title: RNA-seq iPSC PG4a8


title: M43_ZT14_DLS_S23


title: WGBS iPSC MF59


title: F1_ZT22_DMS_S2


title: RNA-seq iPSC TF16


title: RNA-seq iPSC SCa3


title: M49_ZT22_DLS_S27


title: M42_ZT14_DLS_S15


title: scleroderma skin derived fibroblast, control, Donor5

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt

source_name: scleroderma skin derived fibroblast

growth_protocol: SSc fibroblast were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from treated and untreated fibroblasts using quick-RNA MiniPrep Kit from (Zymo research).
RNA libraries for RNA-seq were prepared using Ilumina paltform via poly A enrichment method following manufacturer's protocols.

treatment_protocol: SSc fibroblasts were serum-starved for 12 h (1% Fetal bovine serum) followed by  LiCl treatment for 24 h.

value: scleroderma skin derived fibroblast

value: Fibroblast

value: control


title: WGBS ESC rep2


title: M48_ZT22_DLS_S3


title: RNA-seq iPSC PG4a5


title: scleroderma skin derived fibroblast, LiCL, Donor5

value: LiCL


title: scleroderma skin derived fibroblast, LiCL, Donor4


title: M46_ZT18_DLS_S27


title: WGBS ESC rep1


title: M37_ZT10_DLS_S7


title: scleroderma skin derived fibroblast, control, Donor3


title: M44_ZT18_DLS_S23


title: RNA-seq iPSC MF56


title: scleroderma skin derived fibroblast, LiCL, Donor2


title: M41_ZT14_DLS_S19


title: scleroderma skin derived fibroblast, control, Donor2


title: RNA-seq iPSC TF15


title: M4_ZT22_DLS_S27


title: scleroderma skin derived fibroblast, control, Donor4


title: RNA-seq iPSC MF591


title: TAX_293T_HiC

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

data_processing:
Hi-C data were processed with hicpro (Nicolas Servant, Genome Biol., 2015) using nf-core/hic (v1.3.0), Nextflow (v21.10.6), Bowtie(v2.3.5.1), Python (v3.7.6), Samtools (v1.9)
the parameters were as follows: nextflow hic_1.3.0/main.nf -c hic_1.3.0/conf/psmn.config -profile psmn --input 'fastq/*{1,2}.fastq.gz' --digestion hindiii --genome GRCh37 --restriction_site A^AGCTT --ligation_site AAGCTAGCTT --save_reference --save_nonvalid_pairs --save_aligned_intermediates --save_interaction_bam --bin_size 1000000,500000,50000,10000 --hicpro_maps --max_cpus 32 --max_memory '20 GB' -resume
Assembly: hg19
Supplementary files format and content: A list of genomic intervals related to the specified resolution (BED format)
Supplementary files format and content: A matrix, stored as standard triplet sparse format (i.e. list format)

source_name: embryonic kidney

growth_protocol: HEK293T cells were cultured in DMEM + 4.5 g/L D-Glucose + Pyruvate + GlutaMAX™, supplemented with 10 % heat-inactivated FBS and 1 % Penicillin/Streptomycin

extract_protocol: In situ Hi-C experiments were conducted following the method described by Rao and colleagues with slight modifications (Rao et al., Cell. 2014). Briefly, HindIII enzyme was used to digest cells overnight at 37°C with 500U, followed by biotin filling and proximity ligation for 4 hours at 18°C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified and sheared to ~300 bp fragments using Covaris S220 sonicator. The biotin-containing fragments were then immobilized on MyOne Streptavidin T1 beads. The NEXTflex adaptors were ligated, and the fragments were PCR amplified for 8 cycles using the KAPA HiFi Library Amplification Kit. Double-size selection was performed using AMPure XP beads to isolate fragments between 300 and 800bp

treatment_protocol: Cells were transiently transfected with either pSG5M-Tax or empty vector using Jetprime (Polyplus Transfection) following manufacturer’s instructions, and cells were harvested 48h post-transfection.

value: embryonic kidney

value: 293T HEK

value: fibroblast

value: WT


title: RNA-seq ESC rep1


title: SEC31B_pr_CTL_siGL2_rep3

data_processing:
Computational analysis of 4C-seq data was performed for each replicate and viewpoint using the fourSig pipeline (Williams, R.L. Nucleic Acids Res, 2014) with the following parameters: window.size=5, iterations=1000, fdr=0.001, and fdr.prob=0.01. For each viewpoint, triplicate outputs were normalized to each other using multiBamsummary and Bamcompare from deepTools.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

extract_protocol: not provided


title: CTL_293T_HiC


title: M38_ZT10_DLS_S15

value: Male


title: RNA-seq iPSC MF59


title: M40_ZT10_DLS_S11


title: RNA-seq iPSC TF14


title: SEC31B_pr_TAX_siGL2_rep3


title: UUO-G398

city: JiNan

first: Liu

middle: Xiao

last: Han

address: Baotu Spring Street

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using Seqtk.
The sample was mapped using Hisat2（version:2.0.4)
The quantification of transcripts expressed for each sequenced samples was performed using Stringtie（version:1.3.0）
Differentially expressed genes were identified using edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mus renal cortex

extract_protocol:
RNA was harvested using MJzol animal RNA Extraction Kit (MagBeads). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Aristolochic acid nephropathy (AAN) was induced by a one-time intraperitoneal injection of aristolochic acid (5 mg/kg body weight, A5512, Sigma-Aldrich) in PBS.  The sham mice were administered the same amount of PBS. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.
A midline abdominal incision was made andbilateral renal pedicles were clipped for 32 min at 37.5 °C (bilateral IRI, BIRI). Sham operations were performed with exposure of both kidneys but without induction of ischemia. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.
The unilateral ureteral obstruction (UUO) model  was generated by ligation of the left ureter.Sham operations were performed with exposure of both kidneys but without ligation of  ureter. After 7 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.

value: Mus renal cortex

tag: model

value: unilateral ureter obstruction (UUO)

value: Ligation of the left ureter. After 7 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: M36_ZT6_DLS_S18


title: SEC31B_pr_TAX_siGL2_rep2


title: M35_ZT6_DLS_S7


title: RNA-seq ESC rep3


title: Uterine cancer tissue, UT_T2

city: Thuwal

first: Jing

last: Kai

address: King Abdullah University of Science and Techonology

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

data_processing:
Raw image data file from high-throughput sequencingwas transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
The filtering process of raw reads data  is as follows: (1) Remove reads containing adapters. (Trimmomatic, v0.32) (2) Remove reads containing N > 10% (N represents the base cannot be determined).  (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
The filtering process of raw reads data  is as follows: (1) Remove reads containing adapters. (Trimmomatic, v0.32) (2) Remove reads containing N > 10% (N represents the base cannot be determined).  (3) Remove reads containing low quality (Qscore<= 5) base.
The resulting RNA-seq reads passed quality control were processed following the TCGA mRNA Analysis Pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#rna-seq-alignment-workflow) to generate the gene expression matrix with the value of transcripts per million (TPM). Briefly, the alignment was performed using a two-pass method with STAR to generate the  primary counting data, which includes a gene ID, unstranded, and stranded counts data.
Unstranded raw counts for all samples were extracted and combined to generate final raw_counts.txt
Assembly: GENCODE v36
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Uterine endometrioid adenocarcinoma

extract_protocol:
RNA from tissue specimens was extracted from fresh frozen tissues that were removed during surgery. Total RNA was extracted using a RNeasy mini kit (Qiagen, Germany), and was assessed using Bioanalyzer (Agilent, US), Nanodrop (Wilmington, DE) to ensure high quality and purity (RNA integrity number >7, OD260/280>1.8).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA).

value: Uterine endometrioid adenocarcinoma

tag: age

tag: gender

value: Female

tag: tumor grade

value: AJCC pTNM:pT2 Nx


title: RFX2_18_TAX_siGL2_rep3


title: UUO-G376


title: Healthy uterine tissue, UT_N1

institute: King Abdullah University of Science and Techonology

source_name: Uterine tissue, within normal limits

value: Uterine tissue, within normal limits

value: Not applicable


title: SEC31B_pr_TAX_siGL2_rep1


title: M34_ZT6_DLS_S11

value: DLS


title: scleroderma skin derived fibroblast, LiCL, Donor1

value: scleroderma skin derived fibroblast

value: Fibroblast


title: RNA-seq ESC rep2

value: embryonic stem cells


title: UUO-G329


title: RFX2_18_TAX_siGL2_rep1

value: embryonic kidney


title: scleroderma skin derived fibroblast, LiCL, Donor3

value: LiCL


title: M33_ZT2_DLS_S27


title: Sham for UUO-G374

value: Sham operations were performed with exposure of both kidneys but without ligation of  ureter.


title: Healthy liver tissue, LIV_N2

source_name: Liver tissue, within normal limits

value: Liver tissue, within normal limits


title: SEC31B_pr_CTL_siGL2_rep2

value: 293T HEK

value: fibroblast

value: WT


title: Liver cancer tissue, LIV_T3

source_name: Carcinoma of liver, hepatocellular

value: Carcinoma of liver, hepatocellular

value: Male

value: AJCC G1:Well differentiated


title: M32_ZT2_DLS_S3


title: RFX2_18_CTL_siGL2_rep1


title: SEC31B_pr_CTL_siGL2_rep1


title: UUO-G386

value: Mus renal cortex

value: unilateral ureter obstruction (UUO)

value: Ligation of the left ureter. After 7 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: M31_ZT2_DLS_S7

value: DLS


title: Liver cancer tissue, LIV_T2

value: AJCC G3:Poorly differentiated


title: CCNL1_pr_TAX_siGL2_rep3


title: Uterine cancer tissue, UT_T1

source_name: Serous carcinoma of the uterus, leiomyomata

value: Female

value: AJCC pTNM:pT1a N0


title: M17_ZT10_DLS_S11


title: Liver cancer tissue, LIV_T1


title: M29_ZT18_DLS_S15


title: CCNL1_pr_TAX_siGL2_rep2

value: embryonic kidney


title: RFX2_18_TAX_siGL2_rep2


title: Healthy liver tissue, LIV_N3

value: Not applicable


title: M27_ZT18_DLS_S19


title: M16_ZT10_DLS_S15


title: scleroderma skin derived fibroblast, control, Donor1

value: scleroderma skin derived fibroblast

value: Fibroblast

value: control


title: CCNL1_pr_TAX_siGL2_rep1

value: 293T HEK

value: fibroblast


title: M15_ZT6_DLS_S3


title: Renal cell carcinoma tissue, KI_T3

source_name: Carcinoma of kidney, renal cell, metastatic

value: Not reported


title: M26_ZT18_DLS_S23

value: Male


title: RFX2_18_CTL_siGL2_rep3

value: WT


title: Sham for UUO-G332

value: Mus renal cortex

value: Sham operations were performed with exposure of both kidneys but without ligation of  ureter.


title: Healthy liver tissue, LIV_N1

value: Liver tissue, within normal limits


title: M25_ZT14_DLS_S11

value: DLS


title: Renal cell carcinoma tissue, KI_T1

value: Carcinoma of kidney, renal cell, metastatic


title: RFX2_18_CTL_siGL2_rep2


title: Sham for BIRI-G667

value: bilateral ischemia/reperfusion injury (BIRI)

value: Sham operations were performed with exposure of both kidneys but without induction of ischemia.


title: BIRI-G833

value: A midline abdominal incision was made andbilateral renal pedicles were clipped for 32 min at 37.5 °C. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: M10_ZT2_DLS_S27


title: M24_ZT14_DLS_S15


title: Sham for UUO-G331

value: unilateral ureter obstruction (UUO)


title: CCNL1_pr_CTL_siGL2_rep1

value: embryonic kidney


title: NBT_S288CdU_Chard_R9

city: Vancouver

first: Abdul Muntakim

last: Rafi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

description: filtered_test_data_with_MAUDE_expression.txt.gz

library_source: other

data_processing:
For the random promoter library, the paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints.
N80 promoters were aligned to themselves using Bowtie2 to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster. The NBT libraries were aligned to the promoter sequences we ordered using Bowtie2.
For N80 library, mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP). For NBT library, expression level for each promoter (as in the processed files) was calculated using MAUDE (de Boer and Ray et al. 2018. BMC Bioinformatics), using the read abundance in each sorting bin as input, and estimating the initial abundance of each sequence as the average relative abundance of that sequence across all bins.
Assembly: R64
Supplementary files format and content: compressed text files containing promoter sequences and their corresponding expression levels
Library strategy: promoter seq

molecule: other

organism: Saccharomyces cerevisiae

source_name: Promoter library

growth_protocol: The random promoter library in E. coli theoretically contained about 74 million random promoters and was transformed into S288c (delta URA3) yeast yielding 200 million transformants, which were selected in SD-Ura media. 1 L of chardonnay grape must (filtered) was inoculated with the pool to an initiate OD600 of 0.05 and grown at room temperature without continual shaking, with the culture diluted as needed with fresh chardonnay grape must to maintain OD below 0.4, for a total growth time of 48 hours and having undergone >5 generations. Prior to each OD, the culture was gently agitated to decarbonate it, waiting for the resulting foam to die down before agitating again, and continuing until no more bubbles were released. Yeast were then sorted and sequencing libraries prepared, with sequencing libraries pooled and sequenced on an Illumina NextSeq. The same procedure was performed with the designed promoter library.

extract_protocol:
Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins, done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center.

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

tag: media

value: Chardonnay grape must

tag: libraryid

value: NBT/designed


title: M23_ZT14_DLS_S19


title: Sham for UUO-G328


title: AAN-G388

value: aristolochic acid nephropathy (AAN)

value: a one-time intraperitoneal injection of aristolochic acid (5 mg/kg body weight) in PBS. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: BIRI-G855


title: BIRI-G887


title: Renal cell carcinoma tissue, KI_T4

source_name: Carcinoma of kidney, renal cell, clear cell

value: Fuhrman G3:Nuclei very irregular


title: Renal cell carcinoma tissue, KI_T5

source_name: Carcinoma of kidney, renal cell, chromophobe

value: Female

value: Fuhrman G2:Nuclei slightly irregular


title: F7_ZT2_DLS_S4


title: CCNL1_pr_CTL_siGL2_rep3

value: 293T HEK

value: fibroblast

value: WT


title: Sham for BIRI-J745

value: Mus renal cortex


title: M14_ZT6_DLS_S7

value: DLS

value: Male


title: F6_ZT2_DLS_S29


title: NBT_S288CdU_Chard_R6


title: NBT_S288CdU_Chard_R5


title: Healthy kidney tissue, KI_N3

source_name: Kidney tissue, within normal limits

value: Kidney tissue, within normal limits

value: Not applicable


title: Sham for BIRI-J744

value: bilateral ischemia/reperfusion injury (BIRI)

value: Sham operations were performed with exposure of both kidneys but without induction of ischemia.


title: M13_ZT6_DLS_S11


title: CCNL1_pr_CTL_siGL2_rep2

value: embryonic kidney


title: Renal cell carcinoma tissue, KI_T2

source_name: Carcinoma of kidney, renal cell, papillary


title: AAN-G391


title: Healthy kidney tissue, KI_N2


title: NBT_S288CdU_Chard_R4

value: Chardonnay grape must

value: NBT/designed


title: NBT_S288CdU_Chard_R8


title: M1_ZT22_DLS_S3


title: Healthy colorectal tissue, COAD_N3

source_name: Colorectal tissue, within normal limits

value: Colorectal tissue, within normal limits


title: F50_ZT22_DLS_S24

source_name: DLS


title: Healthy colorectal tissue, COAD_N2


title: NBT_S288CdU_Chard_R7


title: AAN-G379

value: aristolochic acid nephropathy (AAN)

value: a one-time intraperitoneal injection of aristolochic acid (5 mg/kg body weight) in PBS. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: F49_ZT22_DLS_S28

value: Female


title: Healthy kidney tissue, KI_N1


title: NBT_S288CdU_Chard_R19


title: AAN-G357


title: F48_ZT18_DLS_S28


title: NBT_S288CdU_Chard_R18


title: Sham for AAN-G399

value: The normal mice were administered the same amount of PBS as control mice.


title: F9_ZT2_DLS_S28


title: Colorectal cancer tissue, COAD_T5

source_name: Adenocarcinoma of rectum

value: Adenocarcinoma of rectum

value: AJCC G2:Moderately differentiated


title: Healthy colorectal tissue, COAD_N5


title: NBT_S288CdU_Chard_R3


title: Sham for AAN-G384

value: Mus renal cortex

value: WT


title: F5_ZT22_DLS_S4

value: DLS


title: F51_ZT6_DLS_S19


title: Colorectal cancer tissue, COAD_T3

source_name: Adenocarcinoma of colon

value: Adenocarcinoma of colon

value: Male


title: Sham for AAN-G361


title: NBT_S288CdU_Chard_R2


title: Healthy colorectal tissue, COAD_N4

value: Not applicable


title: Sham for AAN-G353


title: NBT_S288CdU_Chard_R14


title: NBT_S288CdU_Chard_R13


title: F43_ZT14_DLS_S16


title: Healthy breast tissue, BRCA_N2

source_name: Breast tissue, within normal limits

value: Breast tissue, within normal limits


title: F47_ZT18_DLS_S20


title: F42_ZT14_DLS_S20


title: Colorectal cancer tissue, COAD_T4


title: NBT_S288CdU_Chard_R17


title: NBT_S288CdU_Chard_R16


title: F45_ZT18_DLS_S16


title: 1137

city: Austin

first: Steven

last: Vokes

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

description: 2-400K cells from posterior forelimbs from Gli3-null embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

data_processing:
Base calling was done using Illumina bcl2fastq version 2.20.0
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.3.5).
Peak calling was done using MACS2

source_name: anterior mouse forelimb

extract_protocol:
2-400K cells from anterior, posterior or whole forelimbs from wild-type embryos incubated with anti-SMARCC1 or anti-Rabbit IGG antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC. Samples were library prepped and run on a BioAnalyzer to assess quality prior to sequencing.
Libraries prepared using the NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S), PCR amplified for 14 cycles and cleaned up using SparQ PureMag beads (QuantaBio 95196-060) at a ratio of 0.8x beads.
NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S)

value: anterior mouse forelimb

value: Gli3Xt-J ; Gli3-/-

value: Anterior forelimb pair (~2-400K cells)

tag: Stage


title: 1133

description: 2-400K cells from posterior forelimbs from Gli3-heterozygous embryos incubated with anti-Rabbit IGG antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

tag: tissue

value: Gli3Xt-J ; Gli3+/-


title: Healthy colorectal tissue, COAD_N1

value: Colorectal tissue, within normal limits


title: 1138

tag: cell type


title: 1126


title: F44_ZT14_DLS_S24


title: 1136

description: 2-400K cells from anterior forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

value: Gli3Xt-J ; Gli3+/+


title: Colorectal cancer tissue, COAD_T2


title: NBT_S288CdU_Chard_R15

value: Chardonnay grape must

value: NBT/designed


title: 1131


title: Breast Cancer tissue, BRCA_T20

source_name: Adenocarcinoma of breast, ductal

value: Adenocarcinoma of breast, ductal

value: Female

value: Nottingham G3:8-9 points High combined grade (unfavorable)


title: NBT_S288CdU_Chard_R10


title: F46_ZT18_DLS_S24


title: Healthy breast tissue, BRCA_N1


title: 1143


title: Breast Cancer tissue, BRCA_T19

source_name: Carcinoma in situ of breast, ductal

value: Carcinoma in situ of breast, ductal

value: Nottingham G2:6-7 points Intermediate combined grade (moderately favorable)


title: F41_ZT14_DLS_S12

value: DLS


title: 1139


title: Breast Cancer tissue, BRCA_T21

source_name: Adenocarcinoma of breast, lobular

value: Adenocarcinoma of breast, lobular

value: Not reported


title: NBT_S288CdU_Chard_R11


title: Breast Cancer tissue, BRCA_T17

value: SBR  GRADE 3


title: 1127

value: anterior mouse forelimb


title: F37_ZT10_DLS_S8


title: F40_ZT10_DLS_S21


title: Colorectal cancer tissue, COAD_T1

value: Adenocarcinoma of colon

value: AJCC G1:Well differentiated


title: mock/HP1β strain, ATAC-Seq rep2

city: Saitama

first: Taiki

last: Shimizu

country: Japan

institute: RIKEN

data_processing:
The adaptor sequences in ChIP-seq reads were trimmed using FASTP (0.23.2)
Trimmed reads were aligned to the sacCer3 genome using Bowtie2 (2.4.2)
Duplicated reads were removed using picard (2.18.2)
bigWig files were generated using deeptools (3.3.2)
Assembly: sacCer3
Supplementary files format and content: bigWig

growth_protocol: Cells grown on YPD plate at 30°C for 2 days were shaked in YPD medium at 30°C for 3 hours (final OD600=1).

extract_protocol:
Cell wall was digedsted using zymolyase, and the genomic DNA was digested using Tn5 transposes (illumina).
ATAC-seq libraries were prepared with Nextera index kit (illumina)


title: F4_ZT22_DLS_S24


title: NBT_S288CdU_Chard_R12


title: SUV39H1/HP1β strain, ATAC-Seq rep2


title: Breast Cancer tissue, BRCA_T15


title: F35_ZT6_DLS_S12


title: Breast Cancer tissue, BRCA_T18


title: SUV39H1/mock strain, ATAC-Seq rep2


title: N80_Chard_R8


title: N80_Chard_R9


title: F34_ZT6_DLS_S4


title: mock/mock strain, ATAC-Seq rep2

value: mock/mock


title: N80_Chard_R7


title: F38_ZT10_DLS_S16


title: SUV39H1/mock strain, ATAC-Seq rep1


title: Breast Cancer tissue, BRCA_T16

value: SBR  GRADE 2


title: F33_ZT2_DLS_S4


title: N80_Chard_R6


title: Breast Cancer tissue, BRCA_T13


title: Breast Cancer tissue, BRCA_T12


title: N80_Chard_R2


title: F31_ZT2_DLS_S8


title: F36_ZT6_DLS_S8


title: F39_ZT10_DLS_S12


title: SUV39H1/HP1β strain, ATAC-Seq rep1


title: Breast Cancer tissue, BRCA_T14

value: NSABP Grade:Nuclear 2 of 3 & Histologic 3 of 3


title: N80_Chard_R18

value: Chardonnay grape must


title: F29_ZT18_DLS_S20


title: mock/HP1β strain, ATAC-Seq rep1


title: N80_Chard_R4


title: mock/mock strain, ATAC-Seq rep1


title: F28_ZT18_DLS_S24


title: N80_Chard_R5


title: N80_Chard_R16


title: N80_Chard_R3


title: N80_Chard_R15


title: Breast Cancer tissue, BRCA_T7


title: WT strain, ATAC-Seq rep2

value: WT


title: SUV39H1/mock strain, rep1, input

data_processing:
The adaptor sequences in ChIP-seq reads were trimmed using FASTP (0.19.5)
Trimmed reads were aligned to the sacCer3 genome using Bowtie2 (2.4.2)
Duplicated reads were removed using picard (2.18.2)
bigWig files were generated using deeptools (3.3.2)
Assembly: sacCer3
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching, cell wall was digested using zymolyase. Cells  were lysed, and chromatin was sonicated by Picoruptor (Diagenode) .
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit complemented with xGen™ Stubby Adapter and UDI Primers (IDT).


title: WT strain, ATAC-Seq rep1


title: Breast Cancer tissue, BRCA_T11

value: Adenocarcinoma of breast, ductal


title: F21_ZT14_DLS_S20

value: Female


title: N80_Chard_R14


title: N80_Chard_R19


title: F3_ZT22_DLS_S28


title: Breast Cancer tissue, BRCA_T10

value: NSABP Grade:Nuclear 3 of 3 & Histologic 3 of 3


title: N80_Chard_R13


title: Breast Cancer tissue, BRCA_T9

source_name: Adenocarcinoma of breast, ductal, recurrent


title: F2_ZT22_DLS_S4


title: SUV39H1/HP1β strain, rep2, input


title: N80_Chard_R17


title: SUV39H1/HP1β strain, rep1, input


title: N80_Chard_R12


title: Breast Cancer tissue, BRCA_T5

value: Adenocarcinoma of breast, ductal, recurrent

value: Nottingham G3:8-9 points High combined grade (unfavorable)


title: Breast Cancer tissue, BRCA_T8


title: mock/HP1β strain, rep2, input


title: N80_Chard_R11


title: SUV39H1/HP1β strain, rep1, H3K9me3


title: mock/HP1β strain, rep1, input


title: F13_ZT6_DLS_S8

value: DLS


title: F20_ZT10_DLS_S12


title: SUV39H1/HP1β strain, rep2, H3K9me3


title: SUV39H1/mock strain, rep2, input


title: Breast Cancer tissue, BRCA_T6


title: F25_ZT14_DLS_S16


title: F19_ZT10_DLS_S16


title: Breast Cancer tissue, BRCA_T1


title: Meningioma tissue, LGG_T6

source_name: Meningioma, benign

value: Meningioma, benign

value: WHO Grade I


title: E9-SRG3-2G

description: 150-200K cells from pooled forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

source_name: whole mouse forelimb

extract_protocol:
2-400K cells from anterior, posterior or whole forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC. Samples were library prepped and run on a BioAnalyzer to assess quality prior to sequencing.
Libraries prepared using the NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S), PCR amplified for 14 cycles and cleaned up using SparQ PureMag beads (QuantaBio 95196-060) at a ratio of 0.8x beads.
NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S)

value: whole mouse forelimb

value: Swiss-webster

value: Forelimb pair (~150-200K cells)


title: SUV39H1/HP1β strain, rep2, HP1β

value: HP1{beta} (MBL, BMP002)


title: S52, Contol, 24 hours treamant with DMSO [YT_7]

city: Edmonton

first: Yasser

last: Tabana

state: AB

address: 87 Avenue and 114 Street

department: Pharmacy

institute: University of Alberta

data_processing:
Kallisto v 0.46.0
Sequence reads were not trimmed
Sequence reads were mapped to GRCh38 using Kallisto pseudo‐alignment (parameters- 100 permutations, bias correction, default parameters)
Read count extraction and normalization were performed using Kallisto
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes count data for each sample

source_name: PBMC

extract_protocol:
RNA was isolated from PBMCs using the RNeasy Mini Kit (Qiagen). The quality and quantity of RNA were tested using a NanoDrop ND-1000 spectrophotometer,  using the TruSeq RNA Library Prep Kit v2 (Illumina).
100 ng of total RNA was used to make RNAseq libraries using the TruSeq RNA Library Prep Kit v2 (Illumina). Oligo dTs conjugated to paramagnetic beads were used to pull down polyadenylated mRNAs through sequential EtOH washes that eliminated non‐polyadenylated transcripts, and the recovered mRNA was fragmented chemically to be used for the first- and second-strand cDNA synthesis. cDNAs were blunted, A‐tailed and 12 cycles of PCR were used to incorporate Illumina adapters containing multiplexing barcodes. Sequencing was performed on a HiSeq 2500 instrument using a paired-end 150-cycle protocol with demultiplexing carried out in the instrument.

value: PBMC

value: DMSO


title: Meningioma tissue, LGG_T5


title: Breast Cancer tissue, BRCA_T2


title: Meningioma tissue, LGG_T4

source_name: Meningioma, atypical

value: Meningioma, atypical

value: WHO Grade II


title: SUV39H1/HP1β strain, rep2, H3K9me2


title: N80_Chard_R10

source_name: Promoter library

value: Chardonnay grape must


title: F11_ZT6_DLS_S12


title: C72, treated, 24 hours treamant with Compound B [YT_12]

value: WT

value: Compound B


title: SRG3-P-50-3

description: 2-400K cells from pooled posterior forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

source_name: posterior mouse forelimb

value: posterior mouse forelimb

value: Posterior forelimb pair (~2-400K cells)


title: SUV39H1/mock strain, rep2, H3K9me2


title: Brain cancer tissue, LGG_T3

source_name: Oligodendroglioma, anaplastic

value: Oligodendroglioma, anaplastic

value: Female

value: WHO Grade III


title: C62, treated, 24 hours treamant with Compound B [YT_11]


title: Breast Cancer tissue, BRCA_T4

value: Adenocarcinoma of breast, ductal

value: Nottingham G3:8-9 points High combined grade (unfavorable)


title: SRG3-P-50

value: Swiss-webster


title: Brain cancer tissue, LGG_T2

source_name: Oligoastrocytoma, anaplastic

value: Oligoastrocytoma, anaplastic

value: Male


title: S72, Contol, 24 hours treamant with DMSO [YT_9]

value: PBMC


title: SUV39H1/HP1β strain, rep1, H3K9me2


title: Brain cancer tissue, GBM_T1

source_name: Glioblastoma multiforme

value: Glioblastoma multiforme

value: WHO Grade IV


title: S62, Contol, 24 hours treamant with DMSO [YT_8]

value: DMSO


title: C52, treated, 24 hours treamant with Compound B [YT_10]


title: Breast Cancer tissue, BRCA_T3

value: Nottingham G2:6-7 points Intermediate combined grade (moderately favorable)


title: SRG3-P-50-2


title: SUV39H1/HP1β strain, rep1, HP1β

value: HP1{beta} (MBL, BMP002)


title: Brain cancer tissue, LGG_T1


title: C71, treated, 12 hours treamant with Compound B [YT_6]

value: WT

value: Compound B


title: mock/HP1β strain, rep2, H3K9me2


title: SRG3-A-50-3

description: 2-400K cells from pooled anterior forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.

value: anterior mouse forelimb

value: Anterior forelimb pair (~2-400K cells)


title: mock/HP1β strain, rep1, H3K9me2


title: SUV39H1/mock strain, rep1, H3K9me2


title: E9-SRG3-1A

value: whole mouse forelimb

value: Forelimb pair (~150-200K cells)


title: SRG3-A-50


title: WT strain, RNA-Seq rep2

data_processing:
The adaptor sequences in RNA-seq reads were trimmed using FASTP (0.20.1)
The number of trimmed reads were counted using sailfish (0.10.1)
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample

extract_protocol:
RNA was extracted using phenol/chlorophorm. Genomic DNA in the extracted DNA was removed by Dnase treatment.
RNA libraries for RNA-seq were prepared using KAPA RNA hyperprep Kit.


title: mock/HP1β strain, rep1, HP1β


title: SRG3-A-50-2


title: ATAC-Seq KWe20

description: 50k cells from anterior forelimbs from individually genotyped embryos treated with Transposase for 1H at 37degC.

extract_protocol:
50K cells from anterior forelimbs from individually genotyped embryos treated with Transposase for 1H at 37degC. Samples were library prepped and run on a BioAnalyzer to assess quality prior to sequencing.
ATAC
NEB high fidelity 2x master mix and ATAC primers

value: Anterior forelimb pair (50K cells)


title: WT1

city: Shanghai

first: Yijie

last: Tao

state: 上海

address: 800 Xiangyin Road

institute: Naval Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count, FPKM values for each Sample

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: hepatocellular carcinoma cells


title: S51, Contol, 12 hours treamant with DMSO [YT_1]


title: C51, treated,12 hours treamant with Compound B [YT_4]


title: mock/HP1β strain, rep2, HP1β


title: KO SCRN1

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: SCRN1 KO


title: ATAC-Seq KWe19


title: RNA-Seq KWe284

description: Forelimb pairs from individually genotyped embryos were were flash-frozen, prepped in 500ul Trizol for RNA and Dnase treated. 580ng total RNA; RIN number of 10

data_processing:
Sequenced reads were aligned to the mm10 mouse genome using Salmon (version 1.9.0).
Transcripts per million (TPM) were obtained usinng  R package tximeta (version 1.16.0).

source_name: mouse forelimb

extract_protocol:
Whole forelimb pairs/sample flash frozen,  RNA-extracted in 500ul of Trizol and Dnase treated. RNA was run on a BioAnalyzer to assess quality (all samples had RIN numbers > 7.5) and 100-200ng of RNA was taken into cDNA prep.
Libraries were prepped by the BGI team as follows: libraries were 3'adenylated, adaptor-ligated, UDG digested and PCR amplified. Libraries were then circularized and amplified to make DNA nanoball to be sequenced on DNBseq platform.
Proprietary BGI DNB-seq platform

value: mouse forelimb

value: Right- and left forelimb pair (~700K cells)


title: ATAC-Seq KWe23


title: C61, treated,12 hours treamant with Compound B [YT_5]

value: PBMC


title: Vector


title: SUV39H1/mock strain, RNA-Seq rep2


title: S61, Contol, 12 hours treamant with DMSO [YT_2]


title: ATAC-Seq KWe14


title: SUV39H1/HP1β strain, RNA-Seq rep2


title: SR1

value: sorafenib resistance

value: sorafenib


title: WT strain, RNA-Seq rep1


title: RNA-Seq KW283

description: Forelimb pairs from individually genotyped embryos were were flash-frozen, prepped in 500ul Trizol for RNA and Dnase treated. 340ng total RNA; RIN number of 10


title: HEM-Chip flow3

city: Seoul

first: Sungjin

last: Min

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Yonsei University

data_processing:
For data processing, base calling software bcl2fastq2 (Version 2.20) with ASCII Q-score (offset 33) were used.
Reads for each sample were mapped to the reference genome by Tophat(v2.0.13). The aligned results were added to Cuffdiff(v2.2.1) to report differentially expressed genes.
Differentially expressed genes were selected with the following parameters: fold change > 2, p value < 0.05, and FDR < 0.1.
Functional annotation for gene ontology enrichment analysis was conducted based on the DAVID program (https://david.ncifcrf.gov).
Assembly: Human hg19
Supplementary files format and content: The tab-delimited excel file contains the FPKM values for each sample.
Supplementary files format and content: The lists of differentially expressed genes and ontology data are also included in tab-delimited excel files.

source_name: hiPSC-cardiomyocytes, hiPSC-cardiac fibroblasts, HUVECs

growth_protocol: Fabricated human cardiac tissues were cultured in a mixture of RPMI/B27 medium and Endothelial Cell Growth Medium-2 (EGM-2) at a ratio of 1:1 for 14 days. Plate static groups were cultured in 24-well plate and chip flow groups were cultured in microfluidic chips with flow

extract_protocol:
RNA samples were extracted from human cardiac tissues using RNeasy Mini Kit (Qiagen).
The Novaseq 6000 platform was used for sequencing, and the Illumina Truseq stranded mRNA kit (Illumina, San Diego, CA, USA) was used to prepare the sequencing libraries.

treatment_protocol: For fabrication of human cardiac tissues, hiPSC-CMs, hiPSC-CFs, and HUVECs were mixed in a 2:1:1 ratio. Then, 2.0 × 105 mixed cells were encapsulated in 20 µl HEM hydrogel for HEM groups or seeded in 96-well U-bottom plate for No HEM groups.

value: fabricated with HEM hydrogel and cultured in microfluidic chip with flow

value: Day 14 after fabrication


title: mock/HP1β strain, RNA-Seq rep2


title: No HEM-Chip flow1

value: hiPSC-cardiomyocytes, hiPSC-cardiac fibroblasts, HUVECs

value: fabricated without HEM hydrogel and cultured in microfluidic chip with flow


title: S71, Contol, 12 hours treamant with DMSO [YT_3]

value: WT

value: DMSO


title: SUV39H1/HP1β strain, RNA-Seq rep1


title: RNA-Seq KWe281

description: Forelimb pairs from individually genotyped embryos were were flash-frozen, prepped in 500ul Trizol for RNA and Dnase treated. 330ng total RNA; RIN number of 10


title: ATAC-Seq KWe18

value: anterior mouse forelimb


title: HEM-Chip flow1


title: Mutant PFN1 M114 het iMG 1 [E2]

city: Worcester

first: Elaine

last: Lim

state: MA

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

data_processing:
FastQC
multiqc
STAR aligner (2.7.0a)
HTSeq
Assembly: hg38

source_name: iPSC-derived

extract_protocol:
Total RNA was isolated with Direct-zol RNA Microprep Kit (Zymo Research, R2060) according to the manufacturer’s instructions.
RNA library preparation and sequencing was conducted by Novogene Co., LTD (Beijing, China) with a read length of 150 base pairs.

value: iPSC-derived

value: Induced microglia

value: iMG

value: mutant (M114T het)


title: Mutant PFN1 M114 het iMG 3 [E8]


title: SUV39H1/mock strain, RNA-Seq rep1


title: Heart, TE1

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

data_processing:
The sequencing reads were mapped to the reference mouse genome GRCm39 by HISAT 2.2.1
Read counts per gene locus were obtained with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited txt file containing raw counts for each sample

source_name: heart

growth_protocol: All the mice were housed in specific pathogen-free facilities at Xiamen University, following the guidelines of the Animal Care and Use Committee (Permit No. XMULAC20200150)

extract_protocol:
RNAs were purified from the livers  by Trizol Reagent
A cDNA library was subsequently prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (NRM605-01, Vazyme, Nanjing, China)

treatment_protocol: C57BL/6J male mice (8 weeks old) were divided into the exercise group and the control group. The mice in the exercise group underwent a treadmill running exercise protocol for 5 days per week over a period of 4 weeks. In the first week, the mice were subjected to adaptive training with the following protocol: 6 m/min for 5 min, 9 m/min for 5 min, 12 m/min for 5 min, and 15 m/min for 5 min. Subsequently, for the next 3 weeks, the mice were forced to run at 6 m/min for 5 min and 12 m/min for 35 min. Meanwhile, the mice in the control group were housed in cages without exercise. From the 2nd week of the study, 1×10^5 B16F10 cells were intravenously injected into the mice through the tail vein to induce cancer cachexia

value: heart

value: male

value: B16F10 cells+Exercise


title: SUV39H1/HP1β strain, rep2

data_processing:
Trimmed reads were aligned to the sacCer3 genome using Bowtie2 (2.4.2)
The matrix was built using HiCExplorer (3.4.3)
Assembly: sacCer3
Supplementary files format and content: .h5
Library strategy: Micro-C XL

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching, cell wall was digested using zymolyase. Cells  were fixed with 3 mM disuccinimidyl glutarate for 45 min and quenched. The chromatin was digested using Mnase, and the DNA was labeled using biotin-dATP and biotin-dCTP. After ligation, biotinated DNA was purified using agarose gel electrophoresis followed by streptavidin beads purification.
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit complemented with xGen™ Stubby Adapter and UDI Primers (IDT).


title: HEM-Plate static2

value: fabricated with HEM hydrogel and cultured in static well plate


title: No HEM-Chip flow3


title: mock/mock strain, RNA-Seq rep1

value: mock/mock


title: RNA-Seq KWe279

description: Forelimb pairs from individually genotyped embryos were flash-frozen, prepped in 500ul Trizol for RNA and Dnase treated. 310ng total RNA; RIN number of 10

value: mouse forelimb

value: Right- and left forelimb pair (~700K cells)


title: HEM-Chip flow2

value: fabricated with HEM hydrogel and cultured in microfluidic chip with flow

value: Day 14 after fabrication


title: No HEM-Chip flow2

value: hiPSC-cardiomyocytes, hiPSC-cardiac fibroblasts, HUVECs

value: fabricated without HEM hydrogel and cultured in microfluidic chip with flow


title: Mutant PFN1 M114 het iMG 2 [E5]


title: mock/HP1β strain, RNA-Seq rep1


title: Heart, TE3

value: WT


title: WT PFN iMG 6 [E4]


title: Heart, TE2


title: rlmnl3_RF_rep2

city: Beijing

first: Guifang

last: Jia

address: college of chemistry and molecular engineering, Peking University

institute: Peking University

description: ribosome protected fragments

data_processing:
Library strategy: Ribo-seq
Basecalling performed using Illumina CASAVA-1.8
Sequenced reads were aligned to TAIR10 Arabidopsis thaliana genome using HISAT2
FPKM of input samples and ribosome protected fragments were calculated using Htseq with default parameters
Translation efficiency was defined as the ratio of ribosome-protected fragments and mRNA input FPKM
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each input sample or ribosome protected fragment for each ribosome footprinting sample

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: All plants were grown at 22°C under long-day conditions (16 h light/8 h dark, white fluorescent tubes, 150 to 200 μmol m-2 s-1). Seedlings were collected from 14-day-old plants grown on half-strength MS nutrient agar plates (PhytoTechnology Laboratories).

extract_protocol:
One 15-cm plate of 10-day-old Arabidopsis was prepared for each sample. 4 ml lysis buffer (10 mM Tris, pH 7.4, 150 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U/ml SUPERasin) was added to Arabidopsis powder and then kept on ice for 15 min with occasional pipetting and rotating. After centrifugation at 15000 x g for 10 min, the supernatant was collected. To the lysate, 8 µl DNase Turbo was added. The lysate was then split by the ratio of 1:4 (Portion I/Portion II). 4 µl Super RNasin was added to Portion I. 40 µl MNase buffer and 3 µl MNase (6,000 gel units, NEB) was added to Portion II. Both portions were kept at room temperature for 15 min, and then 8 µl SUPERasin was added to Portion II to stop the reaction. Portion I was saved and mixed with 1 ml TRIzol to purify input mRNA. Portion II was used for ribosome profiling.
The library was constructed by Tru-seq small RNA sample preparation kit (Illumina). The sequencing data obtained from ribosome profiling (portion II) were denoted as ribosome-protected fragments and that from RNA input (portion I) as mRNA input. Translation efficiency was defined as the ratio of ribosome-protected fragments and mRNA input, which reflected the relative occupancy of 80S ribosome per mRNA species.

value: seedlings

value: rlmnl3 T-DNA insertion mutant


title: mock/mock strain, RNA-Seq rep2


title: WT PFN iMG 7 [E7]

value: iPSC-derived

value: Induced microglia


title: Heart, T1

value: B16F10 cells


title: rlmnl3_RF_rep1

description: ribosome protected fragments


title: SUV39H1/HP1β strain, rep1


title: WT PFN iMG 5 [E1]

value: iMG


title: Heart, E3

value: heart

value: male

value: Exercise


title: No HEM-Plate static2

value: fabricated without HEM hydrogel and cultured in static well plate


title: HEM-Plate static1

value: fabricated with HEM hydrogel and cultured in static well plate


title: No HEM-Plate static1


title: Heart, T3


title: Heart, T2


title: Heart, E2


title: HEM-Plate static3


title: No HEM-Plate static3


title: Heart, E1


title: SUV39H1/mock strain, rep1


title: SUV39H1/mock strain, rep2


title: rlmnl3_input_rep2


title: Col-0_RF_rep1

description: ribosome protected fragments

value: wild-type


title: mock/HP1β strain, rep1


title: rlmnl3_input_rep1


title: T24 P146 1

city: 南京

first: li

last: meiqian

address: 学府路12号

institute: 南京大学

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Data filtering steps:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: T24_miR-146a-5p overexpression

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human bladder cells

value: miR-146a-5p overexpression


title: WT strain, rep2


title: mock/HP1β strain, rep2


title: Col-0_input_rep2


title: T24 PCV 2

source_name: T24_scramble control

value: scramble control


title: T24 P146 2


title: Heart, C2

value: Saline


title: WT strain, rep1

value: WT


title: Col-0_RF_rep2

description: ribosome protected fragments

value: seedlings


title: Col-0_input_rep1


title: Heart, C1


title: T24 PCV 1


title: CM8

status: Public on Feb 02 2024

type: RNA

city: São Paulo

first: Isabella

middle: Harumi Yonehara

last: Noma

state: Please select

address: Av Prof. Lineu Prestes, 580 - Bloco15

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: DNA from total leucocytes were firstly bisulfite converted using the EZ DNA Methylation Kit (Zymo Research Corporation, Irvine, CA, USA), then 500ng were hybridized in the Infinium Human Methylation 450k (IHM450K) BeadChip (Illumina, Inc., San Diego, CA, USA)

scan_protocol: Images were obtained using the Iscan system.

data_processing: Champ package for Rstudio was used to process data.

label: Cy3 and Cy5

source_name: genomic DNA from whole peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from whole peripheral blood using the Promega (Madison, Wisconsin, EUA) automated system with magnetic beads following the manufacturer’s instructions

tag: vitamin c


title: CM7


title: CM4


title: CM5


title: CM2


title: CM3


title: B8 – tetO-LIN28B  no dox

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: MLL-AF9 AML with LIN28B not induced

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 101 top-level assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.
Assembly: Ensembl_R101
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: bone marrow

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: bone marrow

value: acute myeloid leukemia

value: MLL-AF9 virus/tetO_LIN28B

value: No doxycycline


title: B6 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: D2 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: A7 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: Heart, C3

tag: genotype


title: B4 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced

tag: treatment


title: F1 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: A4 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: B1 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: B7 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced

value: doxycycline chow


title: C2 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: A3 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: A1 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: C1 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: D3 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: B9 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: B5 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: A6 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: A5 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: B2 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: C3 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: CM1


title: E4 – control

description: AML cells driven by MLL-AF9 retrovirus

value: MLL-AF9 virus


title: E3 – control

description: AML cells driven by MLL-AF9 retrovirus


title: E1 – control

description: AML cells driven by MLL-AF9 retrovirus


title: A8 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: B3 – tetO-LIN28B  no dox

description: MLL-AF9 AML with LIN28B not induced


title: C2C13 myotubes, kaempferol [Kaempferol3]

first: Xiaoning

last: Ji

address: No.16, Nanxiao street, Dongzhimen, Dongcheng District, Beijing, 100700, China

institute: China Academy of Chinese Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: C2C13 myoblast line

growth_protocol: The C2C12 cells were grown in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: At 70%–80% confluence, cells were cultured in DMEM supplemented with 2% horse serum and 1% penicillin-streptomycin for 6 days to induce differentiation into myotubes. All cells were maintained at 37°C in a humidified atmosphere containing 5% CO2. Media were replaced every two days. After differentiation was completed, cells were seeded at 1 × 10^4 cells per well into black bottom 96-well plates (Corning, USA) overnight. Then cells were treated with  25μM kaempferol for 24 hours.

value: C2C13 myoblast line

value: Skeletal muscle cell

value: C2C13 myoblast dedifferentiation

value: 25μM kaempferol


title: A2 – tetO-LIN28B dox

description: MLL-AF9 AML with LIN28B induced


title: C2C13 myotubes, kaempferol [Kaempferol1]


title: C2C13 myotubes, kaempferol [Kaempferol2]


title: C2C12 myotubes, without kaempferol [Control2]

source_name: C2C12 myoblast line

value: C2C12 myoblast line

value: C2C12 myoblast dedifferentiation

value: control


title: C2C12 myotubes, without kaempferol [Control1]


title: P3 Dok6 mut mice 3# sciatic nerve

first: Yan

last: Guo

address: DongDan santiao 5th

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using NovoMagic platform
gene expression quantification, differential expression analysis, and functional enrichment analysis, using R language
Differential expression analysis of two conditions was performed using the DESeq2R package (version 1.38.3).
The clusterProfiler package (4.6.2) was utilized for conducting the GO, KEGG, and GSEA analyses.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: sciatic nerves

extract_protocol:
RNA was harvested using standard extraction methods then apply strict quality control to RNA samples. The quality control method is mainly through the Agilent 2100 bioanalyzer.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: sciatic nerves

value: primary  cells

value: nerve cell

value: Dok6 KO

value: neurodevelopment


title: P3 Control mice 3# sciatic nerve

value: WT


title: P3 Dok6 mut mice 2# sciatic nerve


title: P3 Control mice 2# sciatic nerve


title: C2C12 myotubes, without kaempferol [Control3]


title: P3 Control mice 1# sciatic nerve


title: P3 Dok6 mut mice 1# sciatic nerve


title: Female Heart anti-PD-1 T-Cells 1

city: Bar Harbor

first: Dave

last: Serreze

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
FastQC (v0.11.9) was applied to raw sequence data for all samples to evaluate various aspects of sequencing quality, e.g. over-abundance of adaptors and over-represented sequence.
Trimmomatic (v0.39) was used for raw RNA-seq reads to remove Illumina adapter sequences by cropping reads to 100bp.
The EMASE (v0.10.16) pipeline was applied to align reads passing initial QC to GRCm38 and gene expression for all mice was quantified using expected counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include expected counts for each sample

source_name: Heart

extract_protocol:
Hearts were perfused with 3-4 mL of HBSS prior to digest. Diaphragm and lower limb soleus muscles were pooled together for skeletal muscle samples. Tissue from two mice were pooled together for digestion. Digestion took place at 37C for 1 hr in HBSS supplemented with 300U/mL collagenase, 5U dispase, and 10μg/ ml DNaseI.  Every 15 minutes samples were triturated 10 times using a 10mL pipette. Following digestion, samples were passed through a 70μm nytex nylon mesh and flooded with calcium and magnesium free HBSS supplemented with 0.5% FBS and 2mM EDTA. Red blood cell lysis was performed using Gey’s buffer. PI- CD45.1+ CD11b- CD11c- B220- CD90.2+ TCRβ+ cells were sorted directly into FBS followed by two washes with Dulbecco’s PBS w/calcium & magnesium. Sorted cells were flash frozen in RLT Buffer supplemented with 2-Mercaptoethanol (10μl/mL) and stored at -800 C until RNA extraction. After thaw, samples were homogonized using a 20-gauge needle. RNA was isolated using the RNeasy Micro kit and the Rneasy Mini kit with the optional Dnase digest step. RNA concentration and quality were assessed using the RNA 6000 Pico Assay. Further pooling of extracted RNA was performed to bring skeletal muscle samples to the necessary minimum input for library preparation with each final sample containing RNA from 2-12 total starting mice. Each pooling performed for skeletal muscle samples was also used for corresponding heart samples.
KAPA mRNA HyperPrep Kit

value: Heart

value: Female

value: NOD.Cg-H2-K1d-em1Dvs H2-Ab1g7-em1Dvs H2-D1b-em5Dvs Tg(HLA-DQA1,HLA-DQB1)1Dv/Dvs


title: Female Skeletal Muscle anti-PD-1 T-Cells 3

source_name: Skeletal Muscle

value: Skeletal Muscle


title: E2 – control

description: AML cells driven by MLL-AF9 retrovirus

value: bone marrow

value: acute myeloid leukemia

value: MLL-AF9 virus

value: No doxycycline


title: Female Heart anti-PD-1 T-Cells 3


title: Female Skeletal Muscle anti-PD-1 T-Cells 5


title: Male Skeletal Muscle anti-PD-1 T-Cells 2

value: Male


title: Male Skeletal Muscle anti-PD-1 T-Cells 1


title: Female Heart anti-PD-1 T-Cells 4


title: Female Skeletal Muscle anti-PD-1 T-Cells 4


title: Male Heart anti-PD-1 T-Cells 1


title: Female Heart anti-PD-1 T-Cells 2


title: Female Skeletal Muscle anti-PD-1 T-Cells 2


title: Female Heart anti-PD-1 T-Cells 5


title: Male Heart anti-PD-1 T-Cells 2


title: slamseq_washout_dtag3

city: Boston

first: Stuart

last: Orkin

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Childrens Hospital

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)
Library strategy: SLAM-seq

growth_protocol: C2C12 cells were grown following the standard protocol (Doynova et al., 2017). C2C12 myoblasts were propagated at 37°C, 5% CO2 in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Omega Scientific) and antibiotics (penicillin 100 U/ml, streptomycin 100μg/ml, Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep (Zymo Research) according to the manufacturer’s instructions except including 0.1 mM DTT to all buffers. Thiol modification was performed by 10 mM iodoacetamide treatment followed by quenching with 20 mM DTT. RNA was purified by ethanol precipitation
RNA-seq libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq 6000 with paired-end 150bp reads

treatment_protocol: C2C12 cells were seeded the day before the labeling experiment that allows exponential growth (50%-80% confluency for experiment). 0.5 × 106 C2C12 cells per replicate was incubated with 500 nM dTAG47/DMSO for 4h. (For washout experiments, after 4hrs. treatment with dTAG/DMSO, cells were washed twice with 1X PBS and grown for 5 days before S4U labeling). S4U labeling was performed by adding S4U to a final concentration of 100μM for an additional hour.

value: myoblast

value: dTag-Matr3 depleted

value: dTAG47washout + S4U labling

tag: time

tag: replicate


title: slamseq_washout_dtag2

tag: cell line


title: slamseq_washout_dmso1

value: DMSOwashout + S4U labling


title: slamseq_washout_dtag1


title: slamseq_dtag43

value: dTAG47 + S4U labling


title: slamseq_dtag42


title: slamseq_dtag41


title: slamseq_dmso43

value: DMSO + S4U labling


title: slamseq_washout_dmso3


title: slamseq_dmso41


title: slamseq_dmso42