title: Raji G4access KM Rep2

description: Treated with 100 uM KM05283 for 2hours

data_processing:
Raw sequencing reads were aligned using Bowtie2 to the human (Hg19), mouse (mm9), drosophila (dm6) and yeast (sacCer3) genomes. Sequence reads that aligned multiple times in the genomes with equal alignment scores, were discarded as well as the duplicate reads with identical coordinates (sequencing depth taken into account) to remove potential sequencing and alignment artifacts. Aligned reads were elongated in silico using the DNA fragment size inferred from paired-reads using an in-house developed R pipeline (PASHA) or using MACS2 which also allows peak calling for G4-ChIP and G4access. MACS2 was run with recommended settings (PMID: 18798982). Bedgraph generated by MACS2 were then converted to wig files (bin10) and scaled using PASHA which uses the sequencing depth. Wiggle files representing average enrichment score every 10bp were generated.
Genome_build: hg19, mm9, dm6, sacCer3
Supplementary_files_format_and_content: bed, wig

value: B lymphocyte; Burkitt's lymphoma

tag: experiment

value: No spike

value: 2 hours


title: 10A_M_1529

status: Public on Apr 14 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

tag: age

tag: Sex

value: male

tag: strain


title: Raji G4access KM Rep1

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

country: France

institute: IGMM

description: Treated with 100 uM KM05283 for 2hours

organism: Homo sapiens

source_name: Raji B cells

growth_protocol: Raji and K562 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamine (2 mg/ml) at 37°C and 5% CO2. Haacht cells were grown in DMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) at 37°C and 5% CO2. Hybrid ES cells were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% heat-inactivated fetal bovine serum), penicillin/streptomycin (100 units/mL) and (ESGRO mouse LIF Medium Supplement (1000 units/mL) at 37°C and 5% CO2. S2 cells were cultured in Schneider’s S2 Drosophila medium supplemented with 10% heat-inactivated fetal bovine serum, penicillin/streptomycin (100 units/mL) at 27°C. Yeast S288C (BY4741) haploid cells were grown in YPD (2% glucose) at 30°C.

extract_protocol:
For G4 access: Trypsinized Haacht cells, resuspended S2 cells and suspension of K562, Raji and mouse ESC cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Haacht cells were suspended in 5 mL of permeabilization buffer (150 mM of sucrose, 80 mM Kill, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) and homogenized using a Dounce (40 strokes). For MNase digestion, 5x10^6 cells per titration point were resuspended in 50 μL of prewarmed permeabilization buffer supplemented with 0.2% (v/v) NP40 and incubated 5 minutes at 37ºC. Digestion took place by adding a volume of 500 mL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) to each reaction. Either 3.1, 6.2, 12.5, 25 or 50U MNase (Merck, 10107921001) were added to the MNase reaction buffer and incubated at 37 ºC for 10 min. Digestion was stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. The digestions were incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Trish pH 8) and 1 mL of water. Before DNA purification, digestions were incubated with 5 mL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 8 mL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. To verify the performance of the digestion, 125 μL of each sample was cleaned-up using QI quick PCR Purification Kit (QIAGEN, 28106). Digestions were assessed by agarose gel and Bioanalyzer (Fig. 1c). The remaining digestions were purified by phenol-chloroform and ethanol precipitation for subsequent steps.
Yeast S288C were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Pellets from 100mL culture (OD: 0.5) were suspended in 600ul cell breaking buffer (20% glycerol, 100mM Tris pH 7.5), 600µl zirconia beads (0.5mm), 10µl of 100x protease inhibitors (Roche, 06538282001). Beads beating was performed in 1.5mL screw cap tubes in a Bullet Blender (Next advance) for 4 x 3min at a strength of 8 in a cold room. Cell suspensions were recovered by puncturing the bottom of tube (23 gauge syringes) and spined at 170 ruff for 3min into a 5mL Eppendorf tube. Everything was transferred into 1.5mL Eppendorf, then centrifuged for 5min at max speed and the top layers were discarded. Samples were suspended in 300ul of prewarmed NP buffer (50mM NaCl, 10mM Tris pH 7.4, 5mM MgCl2, 1mM CaCl2, 0.2% NP40 (v/v), 0.5mM spermidine (Sigma, S0266-1G), 0.007% B-Mercaptothion (Sigma, M3148-100ML). Digestion took place by adding a volume of 300µL prewarmed NP buffer supplemented with either 60u, 30u, 15u, 7.5u, 3.75, 1.9u, 1u of MNase (Merck 10107921001). Digestions were stopped on ice and by adding 150μL of stop buffer (5% SDS, 50mM EDTA). Before DNA purification, digestions were incubated with 5 µL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 10 µL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. Purification was done with two consecutive phenol and one chloroform steps followed by ethanol and linear acrylamide precipitation. Purified DNAs were once again incubated with 5µl RNaseq A (Thermofisher, EN0531) to get rid of persistent RNA contaminations.
The phenol-chloroform purified DNAs were subjected to size selection to remove fragments larger than 100 bp. For that, 1 µg of each digestion product was migrated in a 4-20% polyacrylamide Novant TBE gel (Thermofisher, EC6225BOX) at 100 V for 60 min. The gels were stained with Sober® Gold (Thermofisher, S11494) for 30 min. Fragments according to the size range of 0-100 bp were cut out from the gel and transferred to 0.5-mL Eppendorf tubes, previously punctured in the bottom with a 0.45 µm needle. These tubes were inserted into 1.5-mL tubes and centrifuged 10 min at 15.300 ruff to move the cotted gel through the hole, generating gel beads. To elute the DNA from the beads, 700 μL of water was added and the tubes were incubated overnight at 55 ºC in a thermomixer at 1500 rpm. DNA was purified by transferring the samples (DNA eluate and gel beads) to the top of a 0.22 µm spin filter (Agilent 5185-5990). Spin filters were centrifuged 2 min at 15.300 ruff to recover the DNA eluate. DNA was precipitated with isopropanol and linear acrylamide. Size-selection was verified by Bioanalyzer (Fig. 1c). To assess the optimal MNase titration point in terms of G-quadruplex (G4) forming sequence enrichment, the relative amount of targeted G4s was evaluated by qPCR (Extended Data Fig. 1a). The titration points showing a percentage of mononucleosomal fraction of 30% of the total DNA (excluding subnucleosomal fraction) as quantified using Bioanalyzer chips gave the best qPCR enrichment in targeted G4s after size selection. This observation was further confirmed when sequencing the corresponding libraries.
For Pol II ChIP-seq, fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter.
G4access and ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to standard protocol.

treatment_protocol: For the Pyrido statin experiments, cells were treated with 10 µM pyritization. For DMSO (0.1%), Triptolide (1 µM), KM05283 (100 µM), cells were treated for 2hours.

tag: cell type

tag: cell line

value: Raji

tag: spike-in reference organism

tag: spike-in cell line

tag: chip antibody

tag: treatment

tag: concentration

tag: duration


title: MCT-week3-2 [M_430_2]

city: 咸阳

first: yangfan

last: jia

state: 陕西

address: 中国陕西省杨凌区

country: China

institute: 西北农林科技大学

library_source: transcriptomic

data_processing:
Cleaned raw data were aligned to the rat reference genome (NCBI: GCA_000001895.4) using Hisat2 (v2.0.5). FeatureCounts (v2.0.3) was used to count the reads numbers mapped to each gene.
Genes showing an adjusted P value < 0.05 and |log2 (fold change) | > log2 (1.5) identified by the DESeq2 R package (1.32.0) were assigned as differential expressed genes. Data processing and visualization using Tidyverse R Package (1.3.1).
Assembly: GCA_000001895.4
Supplementary files format and content: counts

molecule: total RNA

organism: Rattus norvegicus

source_name: lung

growth_protocol: Male SD rats were treated with PBS buffer or monocrotaline for one to three weeks. Then the lung tissues were harvested for total RNA extraction and library preparation.

extract_protocol:
RNA was harvested using Trizol (TaKara).
RNA libraries for RNA-seq were prepared using the Next UltraTM Directional RNA Library Prep Kit for Illumina (NEB, MA, USA)following manufacturer's protocols.

tag: tissue

value: lung

value: SD

tag: genotype

value: WT

value: MCT (50mg/kg), 21days


title: Raji G4access DMSO Rep2

description: Treated with 0.1% DMSO for 2hours

value: DMSO

value: 0.1% DMSO


title: 10A_M_1528


title: P2

city: Chicago

first: Ruli

last: Gao

state: Illinois

address: 303 East Superior

department: Department of Biochemistry and molecular genetics

institute: Northwestern University

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequencing reads using Trim_Galore
Alignment to the reference genome was done using STAR
Read counts and gene expression values were calculated using RSEM
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file including count values for each Sample

source_name: ATC cell line

extract_protocol:
Whole-cell RNA extraction was performed according to the manufacturer’s instructions (Fisher TR 118–100ML)
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: anaplastic thyroid cancer

tag: tissue source

value: ATC cell line

value: anaplastic thyroid cancer tumor cell

value: untreated


title: Raji G4access DMSO Rep1

description: Treated with 0.1% DMSO for 2hours

tag: experiment


title: 10A_M_1527

tag: brain region


title: MCT-week3-1 [M_430_1]


title: 10A_M_1526

tag: age


title: P1


title: 10A_M_1530

tag: Sex


title: K562 G4access Rep2

source_name: K-562 cells

value: Erythroleukemic cell; Chronic myelogenous leukemia


title: 10A_M_1525

tag: strain


title: MCT-week3-3 [M_430_3]


title: PBS-week3-3 [C_430_3]

value: PBS, 21days


title: NORM20

description: 10X genomics 3'-scRNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger V3.0 mkfastq
cellranger V3.0 count
reads are mapped to hg20
UMI counts are summarized are gene expression levels
Genome_build: hg20
Supplementary_files_format_and_content: tab-delimited text files of UMI values for all samples
Supplementary_files_format_and_content: tab-delimited text file of cell annotation

source_name: Thyroid adjacent normal tissue

growth_protocol: Single cell suspensions are made from fresh tumors

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3 ' protocol (PN-1000075)
single cell 3' RNAseq

treatment_protocol: untreated

value: differentiated papillary thyroid cancer

value: fresh thyroid tissue

tag: sample type

value: surgical sample


title: NORM19

description: 10X genomics 3'-scRNAseq

value: thymic cancer


title: 10A_M_1523

value: male


title: 10A_M_1524


title: K562 G4access Rep1 2

tag: cell type

tag: cell line

value: No spike


title: NORM18

description: 10X genomics 3'-scRNAseq


title: ATC18

description: 10X genomics 3'-scRNAseq

source_name: Thyroid tumor tissue


title: PBS-week3-2 [C_430_2]

value: lung

value: SD


title: 10A_M_1522


title: PBS-week3-1 [C_430_1]

value: WT


title: ATC17

description: 10X genomics 3'-scRNAseq


title: 10A_M_1521


title: MCT-week2-2 [M_423_2]

value: MCT (50mg/kg), 14days


title: MCT-week2-3 [M_423_3]


title: K562 G4access Rep1 1

tag: spike-in reference organism

tag: spike-in cell line


title: ATC15

description: 10X genomics 3'-scRNAseq

tag: treatment


title: PBS-week3-4 [C_430_4]


title: 10A_M_1520


title: Sample 11_CD4+Tcells, CD4NIK,d2,biol rep 3

city: Hamburg

first: Ning

last: Song

state: Hamburg

address: Martinistrasse 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic package
Trimmed sequence reads were mapped to mm10 using Kallisto
Read count extraction and normalization were performed using Deseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include estimated counts for each Sample

source_name: kidney

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney

tag: strain background

value: NIK knockout

value: IRI


title: NORM21

description: 10X genomics 3'-scRNAseq


title: 10A_M_1519


title: K562 Input G4access Rep1

tag: chip antibody

tag: concentration

tag: duration


title: K562 G4access Rep1 3


title: MCT-week2-4 [M_423_4]

tag: tissue

tag: genotype


title: MCT-week2-1 [M_423_1]


title: PBS-week2-4 [C_423_4]

value: PBS, 14days


title: Sample 8_CD4+Tcells, CD4IKK1,d2,biol rep 5

value: IKK1 knockout


title: ATC14

description: 10X genomics 3'-scRNAseq

tag: disease state

value: anaplastic thyroid cancer

tag: tissue source

value: untreated


title: PBS-week2-3 [C_423_3]


title: 10A_M_1518

tag: brain region

tag: age


title: Sample 6_CD4+Tcells, CD4IKK1,d2,biol rep 3


title: PBS-week2-2 [C_423_2]

tag: strain

tag: Sex


title: ATC13

description: 10X genomics 3'-scRNAseq

tag: sample type


title: PBS-week2-1 [C_423_1]


title: Sample 9_CD4+Tcells, CD4NIK,d2,biol rep 1

tag: cell type


title: ATC11

description: 10X genomics 3'-scRNAseq


title: 10A_M_1517


title: 10A_M_1515


title: MCT-week1-4 [M_416_4]

value: MCT (50mg/kg), 7days


title: ATC09

description: 10X genomics 3'-scRNAseq

value: fresh thyroid tissue


title: Sample 4_CD4+Tcells, CD4IKK1,d2,biol rep 1


title: MCT-week1-3 [M_416_3]


title: 10A_M_1513


title: ATC08

description: 10X genomics 3'-scRNAseq

treatment_protocol: treated, 3 month of Atezolizumab/vermuafenib/cobimetinib

value: surgical sample


title: Sample 7_CD4+Tcells, CD4IKK1,d2,biol rep 4


title: 10A_M_1514


title: Sample 3_CD4+Tcells, CD4creControl,d2,biol rep 3


title: ATC10

description: 10X genomics 3'-scRNAseq


title: 10A_M_1512


title: ATC12

description: 10X genomics 3'-scRNAseq


title: MCT-week1-2 [M_416_2]


title: Sample 2_CD4+Tcells, CD4creControl,d2,biol rep 2


title: NORM07

description: 10X genomics 3'-scRNAseq

value: differentiated papillary thyroid cancer


title: Sample 5_CD4+Tcells, CD4IKK1,d2,biol rep 2


title: PTC07

description: 10X genomics 3'-scRNAseq


title: Sample 1_CD4+Tcells, CD4creControl,d2,biol rep 1


title: PTC06

description: 10X genomics 3'-scRNAseq


title: PTC05

description: 10X genomics 3'-scRNAseq


title: MCT-week1-1 [M_416_1]

value: male


title: PBS-week1-4 [C_416_4]

value: PBS, 7days


title: 10A_M_1510


title: PBS-week1-3 [C_416_3]

value: lung


title: PBS-week1-2 [C_416_2]

value: SD


title: Caspase1 knockout mice, Retina, Hypoxia, 3 day (post OIR), rep2

city: Detroit

first: Nikhlesh

middle: Kumar

last: Singh

state: Michigan

address: 6135 Woodward Avenue, #3414 IBio, #3414 IBio

institute: Wayne State University School of Medicine

data_processing:
STAR 2.7.5a alignment
htseq-count 0.6.1 tabulation
edgeR
Assembly: mm10
Supplementary files format and content: count data

source_name: Retina

extract_protocol:
RNA was extracted using TRIZOL
Lexogen QuantSeq 3'mRNAseq Library Prep FWD

treatment_protocol: C57BL/6 and Caspase1 KO mice were exposed to normoxia or oxygen-induced retinopathy and the eyes were enucleated and retinas isolated post 3 day OIR (hypoxia).

value: Retina

value: Caspase1 knockout

value: Hypoxia

value: Oxygen-induced retinopathy


title: Caspase1 knockout mice, Retina, Hypoxia, 3 day (post OIR), rep3


title: NORM03

description: 10X genomics 3'-scRNAseq

value: treated, 5 month of Dabrafenib/Trametinib


title: PTC04

description: 10X genomics 3'-scRNAseq


title: SH6253, Trim28-KO_WGBS_rep2, female

city: Grand Rapids

first: Tao

last: Yang

state: MI

address: 333 Bostwick Ave NE

department: Department of Cell Biology

institute: Van Andel Institute

data_processing:
Adaptor sequences and low-quality reads were trimmed from WGBS sequences using Trim Galore (v0.6).
Trimmed reads were aligned to the reference index that was generated using BISulfite-seq CUI Toolkit, BISCUIT, (0.3.16; github) based on mm10 reference genome (“index” and ‘align” modules in BISCUIT).
SAMBLASTER v0.1.24 was used to mark duplicates, and Samtools v1.9 was used to sort and index resulting bam files.
“pileup” and “vcf2bed” modules from BISCUIT were used to create VCF and bed files which contained methylation and SNP information.
R package dmrseq v1.10.1 was used to identify differentially methylated regions (DMR) with default setting. CpGs with zero reads in every sample were filtered out prior to DMR analysis.
Assembly: mm10
Supplementary files format and content: bigwig of CpG regions with dense of methylation level (beta value)

source_name: E17.5  rib caritilage

extract_protocol:
Genomic DNA was isolated from rib cartilage cells of E17.5 mouse embryos, using Quick-DNA Miniprep Plus kit (Zymo Research; Irvine, CA) according to the manufacturer’s protocol.
5 μg of DNA from each sample was sent to Fulgent Genetics (Temple City, CA). Fulgent performed the library prep using standard illuminal protocols.The library was sequenced as 150 bp paired end reads on an Illumina HiSeq2500 platform to obtain 30x coverage.

value: Rib caritilage cells

value: KO


title: SH6251, Trim28-KO_WGBS_rep1, male


title: SH6252, WT _WGBS_rep2, female

value: WT


title: Caspase1 knockout mice, Retina, Hypoxia, 3 day (post OIR), rep1


title: Caspase1 knockout mice, Retina, Normoxia, rep3

value: Normoxia

value: control


title: PBS-week1-1 [C_416_1]


title: PTC03

description: 10X genomics 3'-scRNAseq

value: fresh thyroid tissue


title: 10A_M_1511


title: Caspase1 knockout mice, Retina, Normoxia, rep2


title: SH6250, WT_WGBS_rep1, male


title: Palbp3

city: Suwon

first: Dong Hyun

last: Lee

address: 206, World cup-ro

country: South Korea

institute: ajou university

data_processing:
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2.
The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software.
Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-firststrand was applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cuffquant in Cufflinks ver 2.2.1[4] with
the strand-specific library option, --library-type=fr-firststrand and other default options was used. The gene annotation of the
reference genome hg38 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression
Assembly: values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit.
Supplementary files format and content: xlsx file
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: 1μM Palbociclib treated MCF7 for 4day

extract_protocol:
RNA was harvested using NucleoSpin RNA, Mini kit (MN). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacturer's protocols.

value: breast cancer

tag: cell line

value: cancer cell

value: 1uM Palbociclib treated for 4day


title: Palbo2


title: scRNA_Trim28 KO

description: growthplate

library_source: transcriptomic single cell

data_processing:
Base calling was done by Illumina RTA3, and output was demultiplexed and converted to FastQ format with Cell Ranger (10×Genomics, v3.1.0)
FASTQ files were aligned to mm10 reference genome using cell ranger count pipeline v4.0.0 with the default settings
The unique molecular identified (UMI) count matrixes were analyzed with Seurat R package v4.0.3
Assembly: mm10

source_name: E17.5  Hindlimb caritlage

extract_protocol:
Single cells were isolated from the E17.5 WT and Trim28 KO mouse hindlimb cartilage
Libraries were generated and sequenced by the Van Andel Institute Genomics Core. Cells were processed with 10× Chromium Next GEM Single Cell 3ʹ GEM kit (10×Genomics, v.3.1) according to the manufacturer’s instruction to target 6,000 cells per group. 28×98, paired end sequencing was performed on an Illumina NovaSeq 6000 sequencer using an SP reagent kit (v1.5) (Illumina Inc., San Diego, CA, USA).

value: Hindlimb caritilage cells


title: Caspase1 knockout mice, Retina, Normoxia, rep1


title: Palbo1


title: scRNA_WT

description: growthplate


title: PTC02

description: 10X genomics 3'-scRNAseq

value: differentiated papillary thyroid cancer

value: surgical sample

value: untreated


title: PTC01

description: 10X genomics 3'-scRNAseq


title: Sample 10_CD4+Tcells, CD4NIK,d2,biol rep 2

value: kidney

value: NIK knockout

value: IRI


title: Cis3

source_name: 5μM Cisplatin treated MCF7 for 4day

value: 5uM Cisplatin treated for 4day


title: C57BL/6 mice, Retina, Hypoxia, 3 day (post OIR), rep2

value: Retina

value: Hypoxia

value: Oxygen-induced retinopathy


title: PC3_RNAseq_dTAM_rep3

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

data_processing:
Fastaq files were aligned to the hg38 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
for RNA SEQ, reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; 50) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount 51 with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Genome_build: hg38

source_name: PC3 + H/F-mBAZ2A dTAM + sh hBAZ2A + GFP

growth_protocol: The PC3 cell line was purchased from the American Type Culture Collection. PC3 cells were cultured in RPMI 1640 medium and Ham's F12 medium (1:1; Gibco) containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). 2.5x106 cells were seeded in 150 mm tissue culture dishes (TPP®) and cultured for 2 to 3 days. All cells were regularly tested for mycoplasma contamination.

extract_protocol:
Total RNA from three independent dishes of PC3 cells transfected with plasmids enabling overexpression of BAZ2A-WT or BAZ2A-dTAM were purified with TRIzol reagent (Life Technologies). In order to remove DNA contaminants, the samples were treated with 1U DNaseI (Thermo Scientific) for 1h at 37°C and the RNA samples were re-purified using TRIzol. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the NovaSeq 6000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

treatment_protocol: Transfection with the indicated plasmids

value: PC3 cells (prostate cancer bone metastasis)

value: transfection with plasmid containing H/F-mBAZ2A dTAM, sh hBAZ2A and GFP reporter


title: Cis2


title: PC3_RNAseq_dTAM_rep2


title: C57BL/6 mice, Retina, Hypoxia, 3 day (post OIR), rep3

value: WT


title: Rib cartilage_Trim28 KO_rep2

data_processing:
The raw reads were mapped to the Mus musculus genome (mm10), and the read counts on transcripts/gene exons were estimated by Subjunc v1.6.4 and featureCounts v1.6.4.
The estimated read counts were used as the input for differential gene expression analysis using edgeR v3.32.138.
The Benjamini-Hochberg adjusted p-values (i.e., false discovery rate, FDR) were taken to determine differentially expressed genes (DEGs).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from Rib cartilage cells of E17.5 mouse embryos were harvest using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rib caritilage cells

value: KO


title: Rib cartilage_WT_rep2


title: Rib cartilage_Trim28 KO_rep1


title: Cis1

value: breast cancer

value: cancer cell


title: C57BL/6 mice, Retina, Hypoxia, 3 day (post OIR), rep1


title: PC3_RNAseq_dTAM_rep1


title: Doxo3

source_name: 100nM Doxo treated MCF7 for 4day

value: 100nM Doxo treated for 4day


title: Rib cartilage_WT_rep1


title: C57BL/6 mice, Retina, Normoxia, rep3

value: Normoxia

value: control


title: C57BL/6 mice, Retina, Normoxia, rep2


title: H3K9me3_Trim28-KO rep2

data_processing:
Reads were mapped to the mm10 reference genome by bowtie2 v2.3.5 and samtools v1.2
Peaks were called using MASC2 peak caller
Raw peak regions were merged using bedtools v2.29.2 (mergeBed -d 300)
Reads falling into raw peak regions were counted for individual samples using bedtools
Read counts were normalized as count-per-million (CPM) based on relative log expression normalization (RLE) methods implemented in edgeR v3.18.1. p-values were adjusted for comparison using the false discovery rate (FDR)
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Nuclei were isolated from 1×10^6 freshly prepared cells and followed by standard Cut&Run protocol
Libraries were constructed using Ultra II DNA Library Prep Kit (NEB; Ipswich, MA) according to the manufacturer’s protocol and sequenced as 150 bp paired-end sequencing runs on an Illumina Hiseq2500 platform to obtain around 40 million reads.
Cut&Run-seq

tag: gender

value: Male

tag: antibody

value: Anti-H3K9me3 (Abcam, #8898)


title: Doxo2

tag: treatment


title: PC3_RNAseq_WT_rep2

source_name: PC3 + H/F-mBAZ2A WT + sh hBAZ2A + GFP

value: transfection with plasmid containing H/F-mBAZ2A WT, sh hBAZ2A and GFP reporter


title: C57BL/6 mice, Retina, Normoxia, rep1


title: PC3_RNAseq_WT_rep1


title: Doxo1


title: H3K9me3_WT rep2


title: Control3

source_name: Control MCF7

value: Control


title: H3K9me3_Trim28-KO rep1

value: Female


title: mESC

city: Madison

first: Sushmita

last: Roy

state: Wisconsin

address: 330 N Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin-Madison

library_source: genomic single cell

data_processing:
FASTQ files were processed using the cellranger-atac pipeline available from 10X Genomics. Reads were aligned to the mm10 genome
Assembly: mm10
Supplementary files format and content: tab separated values files which include chromosomal coordinates, number of read pairs for each location, and associated barcode

source_name: mouse embryonic stem cells

growth_protocol: All cells were cultured in ESC media (Knockout DMEM plus 15% FBS, Pen/Strep, NEAA, L-glutamine, 2-mercaptoethanol, and leukemia inhibitory factor. Reprogramming cells also had doxycycline supplemented in culture media

extract_protocol:
Cells were dissociated from culture dish to create a single-cell suspension; nuclei isolation and transposition were performed on single-cell suspension samples
Performed droplet encapsulation on individual nuclei using the 10X Genomics Chromium System to generate sequencing library (steps performed according to 10X Genomics scATAC-seq instructions)

treatment_protocol: Reprogramming cells were treated with doxycycline (2ug/ml) and were plated on irradiated human foreskin fibroblasts. Media was replaced with fresh doxycline on days 2, 4, 6, 8, and 10 of reprogramming

value: mouse embryonic stem cells

tag: time


title: Crushed optic nerves, replicate 3 from awake animals

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

data_processing:
[basecalling and demultiplex]  The raw base call (.bcl) files were converted to demultiplexed fastq files with Bcl2fastq v2.19.1
[Trimming]  For all fastq files, the adapters and low-quality reads ending with quality score<20 were trimmed using Cutadapt (v1.8.1). Reads with length<20 after trimming were also discarded
[alignment]  The trimmed reads mapping to squirrel rRNA and tRNA reference were further removed. Remaining reads were aligned to the squirrel genome (Ensembl spetri2)[1] using Tophat2 (v2.1.1)
[featurecount]  For quantification of gene expression, only the unique alignments to exon regions were counted using featureCounts program (v1.6.0)
Genome_build: Ensembl spetri2
Supplementary_files_format_and_content: gene counts

organism: Ictidomys tridecemlineatus

source_name: Crushed optic nerves

extract_protocol:
Enucleated eyes were dissected to form posterior segment eye cups, which were then fixed in 4% paraformaldehyde in phosphate buffered saline(PBS) for 2–4 h at 4°C. Eyecups were either processed for vibratome sectioning (100um-thick sections, VT1000; Leica) or dissected to form retinal flat mounts. Flat-mounted retinas or retinal sections were blocked overnight in blocking buffer containing 6% normal donkey serum and 0.5% TritonX-100 in PBS at room temperature.
GS retinas and optic nerve tissue were collected and lysed in TRIzol (Thermo Fisher, Waltham, MA), total RNA was isolated and purified with miRNeasy kit (Qiagen, Hilden, Germany). TruSeq Stranded mRNA Library Prep Kit was used to generate the sequencing libraries (Illumina, San Diego, CA) following the manufacturer’s instructions.

tag: Stage

value: awake animals

value: Crushed optic nerves


title: MEF FBS Day 12

source_name: mouse embryonic fibroblast tissue

value: mouse embryonic fibroblasts

value: doxycycline-induced reprogramming

value: day 12


title: Input DNA_WT

extract_protocol:
Nuclei were isolated from 1×10^6 fxied cells and followed by standrad CHIP protocol
Libraries were constructed usingTruSeq ChIP Library Preparation kit (Illumina; San Diego, CA) according to the manufacturer’s instructions and sequenced as 150 bp paired-end sequencing runs on an Illumina Hiseq2500 platform to obtain around 40 million reads.

value: Rib caritilage cells

value: WT


title: Crushed optic nerves, replicate 2 from awake animals


title: Control1

value: breast cancer

value: cancer cell


title: MEF FBS Day 9

value: day 9


title: H3K9me3_WT rep1


title: Crushed optic nerves, replicate 1 from awake animals


title: Control2


title: H3K27ac_ Trim28-KO rep2

value: KO

value: Anti-H3K27ac (Active Motif; Carlsbad, CA)


title: PC3_RNAseq_WT_rep3

value: PC3 cells (prostate cancer bone metastasis)


title: H3K27ac_Trim28-KO rep1


title: Crushed optic nerves, replicate 2 from hibernators

value: hibernators


title: MEF FBS Day 3

value: day 3


title: H3K27ac_WT rep1

value: Female


title: Crushed optic nerves, replicate 1 from hibernators


title: MEF FBS Day 6

value: day 6


title: MEF


title: H3K27ac_WT rep2

value: Male


title: Crushed optic nerves, replicate 3 from hibernators

value: Crushed optic nerves


title: A2-1, spatial RNA-seq

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

data_processing:
Space Ranger (v 1.3.1)
Spatial transcriptome (ST) sequencing data were aligned to the E. voltai reference genome using the STAR method implemented in Space Ranger (v 1.3.1) to obtain a spot-barcode expression matrix (10X).
The ST data were normalized and scaled via “SCTransform” algorithm before spots clustering.
Assembly: E. voltai reference genome (PRJNA946944)
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial transcriptomics

organism: Electrophorus voltai

source_name: the main electric organ

extract_protocol:
The muscle tissues from the main EO were collected and frozen in an isopentane bath in liquid nitrogen. The treated tissues were then embedded in Optimal Cutting Compound (OCT) media and kept frozen. The embedded tissue blocks were cryosectioned in a cryostat to generate three 10-μm-thick sections. Sections were then placed on Visium Spatial Tissue Optimization Slide and Visium Spatial Slide, respectively, within the capture area. H&E staining and microscope brightfield imaging for sections were subsequently processed.
After section permeabilization, the spatial transcriptomics libraries were constructed following the manufacturer’s protocol (10X Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit).

value: the main electric organ

value: muscle cells


title: A2-3, spatial RNA-seq


title: A2-2, spatial RNA-seq


title: 10A_M_1516

source_name: C57BL/6J Male P56 Mouse Brain

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

value: male


title: npc1020_Post

status: Public on Apr 13 2023

type: RNA

city: Singapore

first: Narayanan

middle: Gopalakrishna

last: Iyer

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Centre Singapore

scan_protocol: PanCancer IO 360 Gene Expression Panel on Nanostring nCounter MAX Analysis System

data_processing: Raw expression data was normalized and analyzed using nSolver Advanced Analysis feature in nSolver analysis software (v4.0; NanoString Technologies, Inc.)

source_name: nasopharynx, on combination nivolumab and ipilimumab treatment

extract_protocol: RNA was extracted from frozen tissue biopsies using All Prep RNA and DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to manufacturer’s protocol. RNA was stored at -80°C until use.

treatment_protocol: Patients were treated with intravenous nivolumab 3 mg/kg every 2 weeks and ipilimumab 1 mg/kg every 6 weeks.  One cycle of treatment was 6 weeks.

value: M

tag: ethnic group

value: Malay

tag: smoking status

value: Non-smoker

tag: staging (who)

tag: staging (ajcc)

tag: metastasis?

value: Yes

tag: best overall response

value: PD

tag: baseline ebv dna (copies/ml)


title: npc1021_Pre

source_name: nasopharynx, pre combination nivolumab and ipilimumab treatment

tag: age

value: Chinese

value: Ex-smoker

value: No

value: SD


title: npc1014_Pre

source_name: lymph node met, pre combination nivolumab and ipilimumab treatment

tag: Sex

value: F

value: PR


title: npc1023_Pre


title: npc1033_Post

value: Others


title: npc1018_Pre


title: npc1019_Pre


title: npc1029_Post


title: npc1033_Pre


title: npc1028_Post


title: npc1019_Post


title: npc1014_Post

source_name: lymph node met, on combination nivolumab and ipilimumab treatment


title: npc1032_Post


title: npc1020_Pre


title: npc1013_Pre


title: npc1029_Pre


title: npc1013_Post


title: npc1040_Post


title: npc1018_Post


title: npc1016_Pre


title: npc1032_Pre


title: npc1021_Post


title: npc1040_Pre


title: npc1028_Pre


title: npc1012_Pre


title: npc1012_Post


title: npc1008_Post


title: npc1008_Pre


title: npc1010_Pre


title: npc1010_Post


title: Mouse brain spatial transcriptomics, E12, S. pneumoniae + ampicillin challenge, replicate 2

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description:
JCC350_V10F06-004-B1_2114500_e12-Tx
10x Genomics Visium

data_processing:
Sections were imaged on a Nikon Eclipse Ni-E scope.
Slide fiducials and tissue coverage areas were manually annotated using Loupe Browser (10X Genomics).
Data were analyzed using SpaceRanger (v1.2.1; 10X Genomics) using the corresponding mm10 reference, with the reverse read trimmed to 90 bp.
Assembly: mm10
Supplementary files format and content: H&E stained section images are included as processed data files in the .tif format.
Supplementary files format and content: Slide fiducials and tissue coverage manual annotations are included as processed data files in the .json format.
Supplementary files format and content: Filtered outputs from CellRanger (filtered_feature_bc_matrix) are included as processed data files in the .h5 format.

molecule: polyA RNA

source_name: embryonic brain

extract_protocol:
Whole heads from E12 embryos were used for analysis with a Visium spatial transcriptomics kit (10X Genomics, PN-1000184). Immediately after dissection, samples were frozen in isopentane chilled by liquid nitrogen, embedded in OCT (Sakura, 4583), and then stored at 280°C. Then, 10-mm sagittal sections were obtained beginning at the periphery to the midline according to 10X Genomics-suggested practices. Tissue permeabilization was optimized to 12 min. A single section was then obtained from each of four mice per condition, and two sections were placed on each Visium slide (i.e., one section from each condition).
Libraries were prepared according to manufacturer recommendations and sequenced on an Illumina NovaSeq platform with a sequencing configuration of 28-10-10-120 (R1-i7-i5-R2) at 200 million clusters per library.

tag: tissue

value: embryonic brain

tag: developmental stage

value: S. pneumoniae + ampicillin challenge

tag: slide

tag: slide area


title: Mouse brain spatial transcriptomics, E12, ampicillin control, replicate 4

description:
JCC350_V10F06-006-A1_2114507_e12
10x Genomics Visium

value: ampicillin control


title: Mouse brain spatial transcriptomics, E12, ampicillin control, replicate 1

description:
JCC350_V10F06-003-A1_2114495_e12
10x Genomics Visium


title: Mouse brain spatial transcriptomics, E12, ampicillin control, replicate 3

description:
JCC350_V10F06-005-A1_2114503_e12
10x Genomics Visium


title: Mouse brain spatial transcriptomics, E12, S. pneumoniae + ampicillin challenge, replicate 3

description:
JCC350_V10F06-005-B1_2114504_e12-Tx
10x Genomics Visium


title: Mouse brain spatial transcriptomics, E12, ampicillin control, replicate 2

description:
JCC350_V10F06-004-A1_2114499_e12
10x Genomics Visium


title: npc1007_Pre


title: SCAP KO Mouse T Cell 2 [SCAP-KO-2]

city: Shanghai

first: Haochen

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
We used Cutadapt (v1.15) software to filter the sequencing data to get high quality Clean Data for further analysis.
Reads were aligned to an assembly of Homo Sapiens (GRCh38) using STAR software (V2.7.10b) (https://github.com/alexdobin/STAR).
We used HTSeq (V0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene.
Assembly: hg38
Supplementary files format and content: Comma-separated values files include RAW count mapped to gene for each sample

source_name: T Cell

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
The sequencing libraries were generated and sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

tag: cell type

value: T Cell

tag: genotype

value: SCAP CKO


title: SCAP WT Mouse T Cell 2 [SCAP-WT-2]

value: WT

tag: treatment

value: SCAP WT


title: SCAP KO Mouse T Cell 1 [SCAP-KO-1]


title: SCAP KO Mouse T Cell 3 [SCAP-KO-3]


title: SCAP WT Mouse T Cell 3 [SCAP-WT-3]


title: SCAP WT Mouse T Cell 1 [SCAP-WT-1]


title: Mouse brain spatial transcriptomics, E12, S. pneumoniae + ampicillin challenge, replicate 1

description:
JCC350_V10F06-003-B1_2114496_e12-Tx
10x Genomics Visium


title: Mouse brain spatial transcriptomics, E12, S. pneumoniae + ampicillin challenge, replicate 4

description:
JCC350_V10F06-006-B1_2114508_e12-Tx
10x Genomics Visium


title: npc1005_Pre

source_name: liver met, pre combination nivolumab and ipilimumab treatment

value: Non-smoker


title: npc1001_Post

value: M

value: Yes


title: npc1002_Post

value: Chinese


title: npc1003_Pre

value: PD


title: npc1004_Pre

value: Smoker


title: npc1007_Post


title: npc1004_Post


title: npc1002_Pre

value: SD


title: npc1003_Post

value: F


title: Ethanol + ABT-888 INPUT [GAV012420_023]

first: Rajiv

middle: Pandit

last: Sharma

state: IL

address: 1601 W Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)

data_processing:
The resulting FASTQ files were checked for adapters and following QC, raw reads were aligned to the reference genome, mm10, in a splice-aware manner using the STAR aligner.
The expression level of the genes was quantified using FeatureCounts and Differential expression statistics (Log2 fold-change and p-value) were computed using edgeR on raw expression counts obtained from quantification. Prior to analysis, the counts were filtered to exclude any gene that either had less than a total of 500 counts across all samples or was detected in fewer than 3 samples.
The data were normalized using the trimmed mean of m-values (TMM) normalization. The normalized data were modeled across treatment status, i.e., Control, EtOH or EtOH+ABT-888, as well as by sample type, i.e., Input or TRAP (Pull-Down).
The terms of the model were tested using the likelihood ratio test, i.e., glmLRT function, within edgeR. Pairwise tests of the expression data were computed using the exactTest function within edgeR. In all cases, adjusted p-values were computed using false discovery rate (FDR) correction.
Assembly: mm10
Supplementary files format and content: Raw Counts Data text file

source_name: Prefrontal Cortex

extract_protocol:
PFC was  homogenized and subject to immunoprecipitation-driven RNA extraction according to the TRAP protocol as well as total-RNA extraction for the INPUTs. Briefly, PFC samples were homogenized in the appropriate buffer, centrifuged and supernatant (40 µL) was collected for total-RNA (INPUT), and the remaining supernatant (approximately 400 µL) was transferred to a separate tube and treated with anti-EGFP antibodies and Agarose Plus A/G beads overnight. After centrifugation, the supernatant was removed and the beads, containing ribosome-bound RNA (TRAP samples), were washed and eluted with QIAZOL (Qiagen # 79306). TRAP-RNA and total-RNA samples were extracted using the miRNeasy Mini Kit according to manufacturer’s instructions.
RNA integrity numbers (RIN)for eachRNA sampleweredetermined using an AgilentTapestationand samples were subjected to rRNA depletion and sequencing.
The RNAseq libraries were prepared for Illumina sequencing usinf CORALL Total RNA-seq Library Prep Kit with Unique Dual Indices. Final amplified libraries were purified, quantified and average fragment sizes confirmed to be 254 -323 and then subjected to test sequencing on MiniSeq instrument in order to check sequencing efficiencies. Sequencing was carried out on NovaSeq 6000 (Illumina), SP flowcell, 2x50 bp PE reads.

treatment_protocol: Adult mice were administered i.p. twice a day with normal saline (CTL) or ethanol (EtOH, to a final daily dose of 2 g/kg) for four consecutive days (two hours between the first and second injection of the day). ABT-888 (25 mg/kg) was co-administered with ethanol on the fourth day in a sub-group of mice that received ethanol in the previous three days (EtOH+ABT) (Vallerini et al., 2020). Two hours after the second injection on day 4, mice were sacrificed and PFC collected.

tag: animal id

value: Transgenic

value: Ethanol + ABT-888


title: Ethanol + ABT-888 INPUT [GAV012420_022]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Ethanol INPUT [GAV012420_020]

description: i.p Ethanol (2g/kg)

value: Ethanol


title: Ethanol INPUT [GAV012420_021]

description: i.p Ethanol (2g/kg)


title: Ethanol + ABT-888 INPUT [GAV012420_017]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Ethanol INPUT [GAV012420_016]

description: i.p Ethanol (2g/kg)


title: Ethanol + ABT-888 INPUT [GAV012420_014]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Control INPUT [GAV012420_015]

description: i.p Normal saline

value: Control


title: Control Pull-Down [GAV012420_007]

description: i.p Normal saline


title: Control Pull-Down [GAV012420_001]

description: i.p Normal saline


title: Ethanol Pull-Down [GAV012420_005]

description: i.p Ethanol (2g/kg)


title: Control INPUT [GAV012420_012]

description: i.p Normal saline


title: Ethanol Pull-down [GAV012420_009]

description: i.p Ethanol (2g/kg)


title: Control Pull-Down [GAV012420_004]

description: i.p Normal saline


title: Ethanol + ABT-888 Pull-down [GAV012420_010]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Ethanol Pull-Down [GAV012420_008]

description: i.p Ethanol (2g/kg)


title: Ethanol + ABT-888 Pull-Down [GAV012420_011]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Ethanol + ABT-888 Pull-Down [GAV012420_006]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: Control INPUT [GAV012420_019]

description: i.p Normal saline


title: G47Δ non-responder 3 (NR3)

city: Yakushiji

first: Kosuke

last: Inoue

state: Tochigi

department: Oral and maxillofacial surgery

country: Japan

institute: Jichi university

description: 4G bases per sample

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version 1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Tongue tumors

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

extract_protocol:
The tumors were extracted day 5 and RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat No. E7490) and NEBNext® Ultra II Directional RNA Library Prep Kit (Cat No. E7760) following manufacturer's protocols.

treatment_protocol: The tumors were inoculated with control (PBS) or G47Δ (1 × 106 pfu) in 20 μL of PBS containing 10% glycerol.

value: Tongue tumors

tag: cell line

value: SCCVII

value: squamous cell carcinoma

value: Wt

value: G47Δ inoculation


title: G47Δ non-responder 4 (NR4)

description: 4G bases per sample


title: G47Δ responder 5 (R5)

description: 4G bases per sample


title: G47Δ responder 1 (R1)

description: 4G bases per sample


title: G47Δ non-responder 5 (NR5)

description: 4G bases per sample


title: G47Δ responder 4 (R4)

description: 4G bases per sample


title: G47Δ non-responder 1 (NR1)

description: 4G bases per sample


title: G47Δ non-responder 2 (NR2)

description: 4G bases per sample


title: Mock 5 (M5)

description: 4G bases per sample

value: Control (PBS) inoculation


title: Mock 4 (M4)

description: 4G bases per sample


title: Ethanol INPUT [GAV012420_013]

description: i.p Ethanol (2g/kg)


title: Mock 3 (M3)

description: 4G bases per sample


title: G47Δ responder 3 (R3)

description: 4G bases per sample


title: G47Δ responder 2 (R2)

description: 4G bases per sample


title: Ethanol + ABT-888 Pull-Down [GAV012420_003]

description: i.p Ethanol (2g/kg)+ABT-888 (25mg/kg)


title: 4B-male-Bmal1-ZT12-misaligned_R1

city: Philadelphia

first: Antonijo

last: Mrčela

state: Pennsylvania

address: 3400 Civic Center Boulevard

department: Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

description: Eluted ChIP DNA from Male mouse at timepoint ZT12 of Bmal1 under the Misalignment protocol.

data_processing:
ChIP-seq was processed via the nf-core ChIP-seq pipeline v1.2.2 using the narrow peaks method.
In brief, BWA v0.7.17-r1188 aligned reads to the GRCm38 genome and MACS2 v2.2.7.1 performed peak calling and consensus peak merging.
The list of resulting differentially enriched genes were used for enrichment analysis using Enrichr (http://amp.pharm.mssm.edu/Enrichr/).
Assembly: GRCm38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (except for IgG libraries)

source_name: Liver

growth_protocol: Age-matched (8-16 weeks old) C57bl6 mice were used for all experiments and were kept under specific pathogen-free conditions. Mice were kept under 12:12 light:dark conditions with environmental enrichment (nestlet, shepherd shacks). All mice were housed with ad libitum access to food and water. Mice were fed standard chow diet until the beginning of week 1 of the control/misalignment paradigm, after which they were switched to a high-fat (42% calories from fat) diet (Envigo, Teklad TD.88137).

extract_protocol:
Samples were processed using the SimpleChIP Plus Sonication Chromatin IP Kit #56383 (Cell Signaling Technology, Inc.) according to manufacturer's instructions. Briefly, finely chopped samples were cross-linked with 37% formaldehyde for 12.5 min at room temperature. Isolated chromatin was fragmented using the Diagenode Bioruptor (ON 30 sec, OFF 45 sec) for 35 mins. An equal amount of chromatin from each sample was immunoprecipitated with normal rabbit IgG (#2729P) or Bmal1(D2L7G) rabbit mAb (#14020S), both antibodies were purchased from Cell Signaling Technology.
Libraries were prepared using the ThruPLEX DNA-Seq Kit (Takara Bio USA). Indexing was performed using the SMARTer DNA HT Dual Index Kit (Takara Bio USA).

treatment_protocol: Mice were exsanguinated via intracardiac perfusion, after which liver sections were excised and snap-frozen liver samples were pooled from three to four mice (200-220 g) for tissue cross-linking and sample preparation.

value: Liver

value: Male

tag: time

tag: chip antibody

value: Misaligned


title: Mock 2 (M2)

description: 4G bases per sample


title: 2B-male-Bmal1-ZT12-control_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT12 of Bmal1 under the Control protocol.


title: 6A-female-IgG-ZT12-control_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT12 of IgG under the Control protocol.

value: Female

value: IgG


title: 5A-female-IgG-ZT0-control_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT0 of IgG under the Control protocol.


title: 8A-female-IgG-ZT12-misaligned_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT12 of IgG under the Misalignment protocol.


title: 8B-female-Bmal1-ZT12-misaligned_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT12 of Bmal1 under the Misalignment protocol.


title: 4A-male-IgG-ZT12-misaligned_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT12 of IgG under the Misalignment protocol.


title: 3A-male-IgG-ZT0-misaligned_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT0 of IgG under the Misalignment protocol.


title: 2A-male-IgG-ZT12-control_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT12 of IgG under the Control protocol.


title: 7B-female-Bmal1-ZT0-misaligned_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT0 of Bmal1 under the Misalignment protocol.


title: 6B-female-Bmal1-ZT12-control_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT12 of Bmal1 under the Control protocol.


title: 3B-male-Bmal1-ZT0-misaligned_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT0 of Bmal1 under the Misalignment protocol.


title: 1A-male-IgG-ZT0-control_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT0 of IgG under the Control protocol.


title: 10A_M_998

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

tag: brain region

value: male

tag: strain


title: Ethanol Pull-Down [GAV012420_002]

description: i.p Ethanol (2g/kg)


title: 10A_M_997


title: 10A_M_999


title: 5B-female-Bmal1-ZT0-control_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT0 of Bmal1 under the Control protocol.


title: 10A_M_996


title: 7A-female-IgG-ZT0-misaligned_R1

description: Eluted ChIP DNA from Female mouse at timepoint ZT0 of IgG under the Misalignment protocol.


title: Mock 1 (M1)

description: 4G bases per sample


title: 10A_M_992


title: 10A_M_994


title: 10A_M_99


title: 10A_M_990


title: 10A_M_993


title: 10A_M_991


title: 1B-male-Bmal1-ZT0-control_R1

description: Eluted ChIP DNA from Male mouse at timepoint ZT0 of Bmal1 under the Control protocol.


title: 10A_M_985


title: 10A_M_984


title: 10A_M_979


title: 10A_M_988


title: 10A_M_975


title: 10A_M_98


title: 10A_M_982


title: 10A_M_987


title: 10A_M_971


title: 10A_M_978


title: 10A_M_983


title: npc1001_Pre

value: M

tag: ethnic group

value: Chinese

tag: smoking status

value: Ex-smoker

tag: staging (who)

tag: staging (ajcc)

tag: metastasis?

value: Yes

tag: best overall response

value: PR


title: 10A_M_977

tag: age

tag: Sex


title: 10A_M_974


title: 10A_M_973


title: 10A_M_970


title: 10A_M_972


title: 10A_M_981


title: 10A_M_97


title: 10A_M_963


title: 10A_M_962


title: 10A_M_958


title: 10A_M_966


title: 10A_M_96


title: 10A_M_969


title: 10A_M_968


title: 10A_M_964


title: 10A_M_961


title: 10A_M_953


title: 10A_M_955


title: 10A_M_950


title: 10A_M_947


title: 10A_M_948


title: 10A_M_951


title: 10A_M_956


title: 10A_M_952


title: 10A_M_954


title: 10A_M_95


title: 10A_M_945


title: 10A_M_943


title: 10A_M_942


title: 10A_M_941


title: 10A_M_940


title: 10A_M_939


title: 10A_M_938


title: 10A_M_937


title: 10A_M_933


title: 10A_M_934


title: 10A_M_925


title: 10A_M_93


title: 10A_M_935


title: 10A_M_936


title: 10A_M_931


title: 10A_M_932


title: 10A_M_923


title: 10A_M_944


title: 10A_M_919


title: 10A_M_916


title: 10A_M_930


title: 10A_M_928


title: 10A_M_927


title: 10A_M_929


title: 10A_M_913


title: 10A_M_920


title: 10A_M_92


title: 10A_M_924


title: 10A_M_918


title: 10A_M_921


title: 10A_M_915


title: 10A_M_912


title: 10A_M_905


title: 10A_M_908


title: 10A_M_907


title: 10A_M_901


title: 10A_M_896


title: 10A_M_9


title: 10A_M_903


title: 10A_M_897


title: 10A_M_90


title: 10A_M_917


title: 10A_M_891


title: 10A_M_911


title: 10A_M_893


title: 10A_M_894


title: 10A_M_91


title: 10A_M_888


title: 10A_M_885


title: 10A_M_914


title: 10A_M_886


title: 10A_M_889


title: 10A_M_892


title: 10A_M_909


title: 10A_M_910


title: 10A_M_887


title: 10A_M_882


title: 10A_M_880


title: 10A_M_884


title: 10A_M_895


title: 10A_M_88


title: 10A_M_879


title: 10A_M_877


title: 10A_M_870


title: 10A_M_875


title: 10A_M_869


title: 10A_M_890


title: 10A_M_868


title: 10A_M_872


title: 10A_M_873


title: 10A_M_871


title: 10A_M_864


title: 10A_M_902


title: 10A_M_87


title: 10A_M_867


title: 10A_M_863


title: 10A_M_862


title: 10A_M_859


title: 10A_M_86


title: 10A_M_861


title: 10A_M_856


title: 10A_M_855


title: 10A_M_854


title: 10A_M_852


title: 10A_M_853


title: 10A_M_851


title: 10A_M_85


title: 10A_M_878


title: 10A_M_849


title: 10A_M_865


title: 10A_M_842


title: 10A_M_841


title: 10A_M_846


title: 10A_M_84


title: 10A_M_848


title: 10A_M_844


title: 10A_M_839


title: 10A_M_835


title: 10A_M_834


title: 10A_M_836


title: 10A_M_837


title: 10A_M_832


title: 10A_M_827


title: 10A_M_833


title: 10A_M_830


title: 10A_M_831


title: 10A_M_83


title: 10A_M_838


title: 10A_M_824


title: 10A_M_828


title: 10A_M_826


title: 10A_M_823


title: 10A_M_821


title: 10A_M_820


title: 10A_M_845


title: 10A_M_819


title: 10A_M_829


title: 10A_M_825


title: 10A_M_82


title: 10A_M_817


title: 10A_M_815


title: 10A_M_816


title: 10A_M_814


title: 10A_M_818


title: 10A_M_810


title: 10A_M_809


title: 10A_M_808


title: 10A_M_802


title: 10A_M_807


title: 10A_M_801


title: 10A_M_799


title: 10A_M_80


title: 10A_M_806


title: 10A_M_798


title: 10A_M_800


title: 10A_M_795


title: 10A_M_797


title: 10A_M_792


title: 10A_M_793


title: 10A_M_803


title: 10A_M_789


title: 10A_M_787


title: 10A_M_8


title: 10A_M_782


title: 10A_M_780


title: 10A_M_781


title: 10A_M_79


title: 10A_M_78


title: 10A_M_778


title: 10A_M_775


title: 10A_M_772


title: 10A_M_791


title: 10A_M_771


title: 10A_M_774


title: 10A_M_770


title: 10A_M_779


title: 10A_M_768


title: 10A_M_764


title: 10A_M_763


title: 10A_M_761


title: 10A_M_762


title: 10A_M_759


title: 10A_M_758


title: 10A_M_756


title: 10A_M_76


title: 10A_M_769


title: 10A_M_755


title: 10A_M_754


title: 10A_M_766


title: 10A_M_760


title: 10A_M_75


title: 10A_M_750


title: 10A_M_765


title: 10A_M_747


title: 10A_M_748


title: 10A_M_753


title: 10A_M_746


title: 10A_M_744


title: 10A_M_783


title: 10A_M_749


title: 10A_M_742


title: 10A_M_743


title: 10A_M_739


title: 10A_M_745


title: 10A_M_738


title: 10A_M_740


title: 10A_M_741


title: 10A_M_737


title: 10A_M_734


title: 10A_M_733


title: 10A_M_74


title: 10A_M_736


title: 10A_M_735


title: 10A_M_732


title: 10A_M_721


title: 10A_M_731


title: 10A_M_730


title: 10A_M_726


title: 10A_M_73


title: 10A_M_729


title: 10A_M_718


title: 10A_M_727


title: 10A_M_719


title: 10A_M_724


title: 10A_M_717


title: 10A_M_757


title: 10A_M_716


title: 10A_M_723


title: 10A_M_722


title: 10A_M_72


title: 10A_M_715


title: 10A_M_706


title: 10A_M_709


title: 10A_M_71


title: 10A_M_714


title: 10A_M_705


title: 10A_M_707


title: 10A_M_704


title: 10A_M_701


title: 10A_M_70


title: 10A_M_7


title: 10A_M_697


title: 10A_M_696


title: 10A_M_694


title: 10A_M_692


title: 10A_M_69


title: 10A_M_728


title: 10A_M_711


title: 10A_M_688


title: 10A_M_712


title: 10A_M_689


title: 10A_M_699


title: 10A_M_684


title: 10A_M_687


title: 10A_M_686


title: 10A_M_681


title: 10A_M_680


title: 10A_M_683


title: 10A_M_68


title: 10A_M_674


title: 10A_M_676


title: 10A_M_677


title: 10A_M_670


title: 10A_M_673


title: 10A_M_669


title: 10A_M_678


title: 10A_M_67


title: 10A_M_668


title: 10A_M_667


title: 10A_M_682


title: 10A_M_666


title: 10A_M_66


title: 10A_M_663


title: 10A_M_659


title: 10A_M_658


title: 10A_M_661


title: 10A_M_651


title: 10A_M_656


title: 10A_M_650


title: 10A_M_655


title: 10A_M_65


title: 10A_M_646


title: 10A_M_647


title: 10A_M_648


title: 10A_M_644


title: 10A_M_640


title: 10A_M_639


title: 10A_M_660


title: 10A_M_654


title: 10A_M_64


title: 10A_M_637


title: 10A_M_633


title: 10A_M_642


title: 10A_M_630


title: 10A_M_625


title: 10A_M_627


title: 10A_M_628


title: 10A_M_652


title: 10A_M_645


title: 10A_M_638


title: 10A_M_626


title: 10A_M_624


title: 10A_M_622


title: 10A_M_636


title: 10A_M_623


title: 10A_M_620


title: 10A_M_621


title: 10A_M_618


title: 10A_M_619


title: 10A_M_635


title: 10A_M_634


title: 10A_M_617


title: 10A_M_616


title: 10A_M_63


title: 10A_M_608


title: 10A_M_614


title: 10A_M_605


title: 10A_M_610


title: 10A_M_603


title: 10A_M_611


title: 10A_M_61


title: 10A_M_602


title: 10A_M_604


title: 10A_M_600


title: 10A_M_6


title: 10A_M_598


title: 10A_M_601


title: 10A_M_596


title: 10A_M_599


title: 10A_M_594


title: 10A_M_595


title: 10A_M_593


title: 10A_M_592


title: 10A_M_588


title: 10A_M_589


title: 10A_M_590


title: 10A_M_586


title: 10A_M_587


title: 10A_M_583


title: 10A_M_585


title: 10A_M_581


title: 10A_M_579


title: 10A_M_580


title: 10A_M_578


title: 10A_M_58


title: 10A_M_582


title: 10A_M_607


title: 10A_M_576


title: 10A_M_575


title: 10A_M_577


title: 10A_M_570


title: 10A_M_57


title: 10A_M_572


title: 10A_M_571


title: 10A_M_584


title: 10A_M_566


title: 10A_M_567


title: 10A_M_563


title: 10A_M_564


title: 10A_M_561


title: 10A_M_557


title: 10A_M_559


title: 10A_M_560


title: 10A_M_558


title: 10A_M_554


title: 10A_M_556


title: 10A_M_555


title: 10A_M_552


title: 10A_M_547


title: 10A_M_550


title: 10A_M_546


title: 10A_M_548


title: 10A_M_543


title: 10A_M_536


title: 10A_M_544


title: 10A_M_54


title: 10A_M_535


title: 10A_M_531


title: 10A_M_534


title: 10A_M_528


title: 10A_M_553


title: 10A_M_551


title: 10A_M_53


title: 10A_M_55


title: 10A_M_524


title: 10A_M_522


title: 10A_M_523


title: 10A_M_530


title: 10A_M_545


title: 10A_M_520


title: 10A_M_526


title: 10A_M_541


title: 10A_M_52


title: 10A_M_519


title: 10A_M_518


title: 10A_M_537


title: 10A_M_708


title: 10A_M_514


title: 10A_M_512


title: 10A_M_515


title: 10A_M_511


title: 10A_M_513


title: 10A_M_521


title: 10A_M_510


title: 10A_M_508


title: 10A_M_506


title: 10A_M_505


title: 10A_M_504


title: 10A_M_503


title: 10A_M_5


title: 10A_M_499


title: 10A_M_497


title: 10A_M_496


title: 10A_M_50


title: 10A_M_501


title: 10A_M_494


title: 10A_M_500


title: 10A_M_51


title: 10A_M_491


title: 10A_M_49


title: 10A_M_502


title: 10A_M_488


title: 10A_M_490


title: 10A_M_507


title: 10A_M_492


title: 10A_M_493


title: 10A_M_483


title: 10A_M_485


title: 10A_M_484


title: 10A_M_482


title: 10A_M_489


title: 10A_M_480


title: 10A_M_495


title: 10A_M_479


title: 10A_M_476


title: 10A_M_475


title: 10A_M_477


title: 10A_M_474


title: 10A_M_487


title: 10A_M_47


title: 10A_M_469


title: 10A_M_470


title: 10A_M_473


title: 10A_M_472


title: 10A_M_466


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title: 10A_M_465


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title: 10A_M_461


title: 10A_M_460


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title: 10A_M_46


title: 10A_M_458


title: 10A_M_450


title: 10A_M_459


title: 10A_M_452


title: 10A_M_456


title: 10A_M_457


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title: 10A_M_446


title: 10A_M_447


title: 10A_M_445


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title: 10A_M_442


title: 10A_M_440


title: 10A_M_451


title: 10A_M_45


title: 10A_M_44


title: 10A_M_439


title: 10A_M_437


title: 10A_M_43


title: 10A_M_430


title: 10A_M_431


title: 10A_M_436


title: 10A_M_429


title: 10A_M_432


title: 10A_M_427


title: 10A_M_428


title: 10A_M_422


title: 10A_M_420


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title: 10A_M_434


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title: 10A_M_413


title: 10A_M_414


title: 10A_M_419


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title: 10A_M_411


title: 10A_M_410


title: 10A_M_435


title: 10A_M_41


title: 10A_M_409


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title: 10A_M_408


title: 10A_M_406


title: 10A_M_405


title: 10A_M_404


title: 10A_M_403


title: 10A_M_417


title: 10A_M_400


title: 10A_M_401


title: 10A_M_40


title: 10A_M_416


title: 10A_M_399


title: 10A_M_4


title: 10A_M_395


title: 10A_M_397


title: 10A_M_398


title: 10A_M_394


title: 10A_M_393


title: 10A_M_390


title: 10A_M_387


title: 10A_M_39


title: 10A_M_386


title: 10A_M_391


title: 10A_M_389


title: 10A_M_385


title: 10A_M_384


title: 10A_M_383


title: 10A_M_381


title: 10A_M_380


title: 10A_M_379


title: 10A_M_38


title: 10A_M_378


title: 10A_M_402


title: 10A_M_377


title: 10A_M_376


title: 10A_M_373


title: 10A_M_374


title: 10A_M_371


title: 10A_M_370


title: 10A_M_372


title: 10A_M_37


title: 10A_M_367


title: 10A_M_369


title: 10A_M_365


title: 10A_M_368


title: 10A_M_364


title: 10A_M_366


title: 10A_M_36


title: 10A_M_360


title: 10A_M_359


title: 10A_M_357


title: 10A_M_358


title: 10A_M_362


title: 10A_M_352


title: 10A_M_356


title: 10A_M_353


title: 10A_M_351


title: 10A_M_348


title: 10A_M_350


title: 10A_M_349


title: 10A_M_35


title: 10A_M_343


title: 10A_M_344


title: 10A_M_363


title: 10A_M_34


title: 10A_M_340


title: 10A_M_337


title: 10A_M_339


title: 10A_M_338


title: 10A_M_341


title: 10A_M_335


title: 10A_M_332


title: 10A_M_333


title: 10A_M_342


title: 10A_M_330


title: 10A_M_336


title: 10A_M_334


title: 10A_M_329


title: 10A_M_355


title: 10A_M_346


title: 10A_M_328


title: 10A_M_325


title: 10A_M_327


title: 10A_M_33


title: 10A_M_324


title: 10A_M_345


title: 10A_M_323


title: 10A_M_322


title: 10A_M_321


title: 10A_M_320


title: 10A_M_319


title: 10A_M_32


title: 10A_M_318


title: 10A_M_313


title: 10A_M_331


title: 10A_M_314


title: 10A_M_312


title: 10A_M_306


title: 10A_M_308


title: 10A_M_31


title: 10A_M_311


title: 10A_M_304


title: 10A_M_30


title: 10A_M_301


title: 10A_M_310


title: 10A_M_302


title: 10A_M_307


title: 10A_M_3


title: 10A_M_303


title: 10A_M_298


title: 10A_M_299


title: 10A_M_290


title: 10A_M_293


title: 10A_M_295


title: 10A_M_294


title: 10A_M_292


title: 10A_M_288


title: 10A_M_29


title: 10A_M_309


title: 10A_M_286


title: 10A_M_284


title: 10A_M_283


title: 10A_M_282


title: 10A_M_278


title: 10A_M_279


title: 10A_M_281


title: 10A_M_297


title: 10A_M_276


title: 10A_M_275


title: 10A_M_274


title: 10A_M_269


title: 10A_M_271


title: 10A_M_270


title: 10A_M_296


title: 10A_M_267


title: 10A_M_27


title: 10A_M_268


title: 10A_M_287


title: 10A_M_266


title: 10A_M_260


title: 10A_M_265


title: 10A_M_285


title: 10A_M_259


title: 10A_M_26


title: 10A_M_258


title: 10A_M_263


title: 10A_M_256


title: 10A_M_257


title: 10A_M_255


title: 10A_M_254


title: 10A_M_277


title: 10A_M_272


title: 10A_M_253


title: 10A_M_252


title: 10A_M_251


title: 10A_M_248


title: 10A_M_247


title: 10A_M_25


title: 10A_M_250


title: 10A_M_245


title: 10A_M_243


title: 10A_M_242


title: 10A_M_244


title: 10A_M_240


title: 10A_M_24


title: 10A_M_241


title: 10A_M_238


title: 10A_M_236


title: 10A_M_234


title: 10A_M_237


title: 10A_M_235


title: 10A_M_239


title: 10A_M_23


title: 10A_M_226


title: 10A_M_230


title: 10A_M_229


title: 10A_M_231


title: 10A_M_228


title: 10A_M_224


title: 10A_M_232


title: 10A_M_227


title: 10A_M_246


title: 10A_M_222


title: 10A_M_22


title: 10A_M_223


title: 10A_M_219


title: 10A_M_220


title: 10A_M_218


title: 10A_M_217


title: 10A_M_215


title: 10A_M_216


title: 10A_M_214


title: 10A_M_213


title: 10A_M_211


title: 10A_M_210


title: 10A_M_204


title: 10A_M_207


title: 10A_M_203


title: 10A_M_202


title: 10A_M_201


title: 10A_M_195


title: 10A_M_199


title: 10A_M_196


title: 10A_M_200


title: 10A_M_2


title: 10A_M_198


title: 10A_M_192


title: 10A_M_191


title: 10A_M_194


title: 10A_M_193


title: 10A_M_188


title: 10A_M_186


title: 10A_M_184


title: 10A_M_208


title: 10A_M_183


title: 10A_M_182


title: 10A_M_209


title: 10A_M_18


title: 10A_M_174


title: 10A_M_175


title: 10A_M_178


title: 10A_M_177


title: 10A_M_187


title: 10A_M_176


title: 10A_M_190


title: 10A_M_19


title: 10A_M_189


title: 10A_M_168


title: 10A_M_170


title: 10A_M_167


title: 10A_M_17


title: 10A_M_185


title: 10A_M_162


title: 10A_M_163


title: 10A_M_164


title: 10A_M_161


title: 10A_M_165


title: 10A_M_16


title: 10A_M_180


title: 10A_M_166


title: 10A_M_158


title: 10A_M_156


title: 10A_M_155


title: 10A_M_154


title: 10A_M_153


title: 10A_M_152


title: 10A_M_151


title: 10A_M_1509


title: 10A_M_179


title: 10A_M_1505


title: 10A_M_1506


title: 10A_M_1504


title: 10A_M_1503


title: 10A_M_1502


title: 10A_M_150


title: 10A_M_1500


title: 10A_M_1499


title: 10A_M_159


title: 10A_M_1495


title: 10A_M_1497


title: 10A_M_1498


title: 10A_M_1496


title: 10A_M_157


title: 10A_M_1491


title: 10A_M_1494


title: 10A_M_149


title: 10A_M_1489


title: 10A_M_1492


title: 10A_M_1488


title: 10A_M_1487


title: 10A_M_1486


title: 10A_M_1508


title: 10A_M_1485


title: 10A_M_1483


title: 10A_M_1482


title: 10A_M_1480


title: 10A_M_1484


title: 10A_M_1501


title: 10A_M_1477


title: 10A_M_1479


title: 10A_M_148


title: 10A_M_1473


title: 10A_M_1472


title: 10A_M_1476


title: 10A_M_1469


title: 10A_M_1465


title: 10A_M_147


title: 10A_M_1478


title: 10A_M_1464


title: 10A_M_1462


title: 10A_M_1460


title: 10A_M_1470


title: 10A_M_1461


title: 10A_M_1457


title: 10A_M_1456


title: 10A_M_1458


title: 10A_M_1459


title: 10A_M_1454


title: 10A_M_1455


title: 10A_M_1450


title: 10A_M_1453


title: 10A_M_1449


title: 10A_M_1475


title: 10A_M_1448


title: 10A_M_1447


title: Rat,  MI3-1,MI3-2,  Day 28

city: Tianjin

first: Wenqi

last: Tao

address: 190 Jieyuan Road, Hongqiao District, Tianjin?

institute: Tianjin Union Medical Center

data_processing:
Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. 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
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Assembly: 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
Supplementary files format and content: Differential expression analysis of two groups was performed using the DESeq2 R package. Genes with a P-value <0.05 and |log2FoldChange|>1 found by DESeq2 were assigned as differentially expressed. We use Jvenn library to figure out differentially expressed genes (DEGs) overlapping between each two groups.
Supplementary files format and content: DEGs classified by Gene Ontology (GO) enrichment analysis, Reactome pathway enrichment analysis, and Bayesian network plots for enrichment analysis were applied by the clusterProfiler R package, ReactomePA R package, and CBNplot R package.Enrichment analysis results were visualized using the ggplot2 package as well as the pheatmap package in R software.

source_name: heart

extract_protocol:
Three biologicalreplicates were used for each experimental group. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer“s recommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext 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, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.
In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: The RNA-seq dataset M-GSGC0338616 contains mRNA expression levels from the cardiac tissues of sham group, MI group and DAPA group .

tag: tissue

value: heart

value: SD Rat


title: Rat, DAP(1st)2-1, DAP(1st)2-2, Day 28

tag: genotype


title: 10A_M_1446

city: La Jolla


title: Rat, DAP(1st)1-1, DAP(1st)1-2, Day 28


title: Rat,  MI2-1,MI2-2,  Day 28


title: Rat,DAP(1st)3-1, DAP(1st)3-2, Day 28


title: 10A_M_1445


title: 10A_M_1467


title: 10A_M_1444


title: 10A_M_1443


title: Rat, Sham3-1,  Sham3-2,Day 28


title: Rat, Sham2-1, Sham2-2, Day 28


title: 10A_M_1441


title: Rat, MI1-1,MI1-2, Day 28


title: 10A_M_1452


title: Rat, Sham1-1, Sham1-2, Day 28


title: 10A_M_144


title: Zebrafish pectoral fin, 24 hpf, IgG, biol rep2

city: Aurora

first: Brittany

last: Truong

state: CO

department: Craniofacial Development

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
Paired-end reads were trimmed using Cutadapt and aligned to the zebrafish genome danRer11 using Bowtie2 version 2.4.5. Peaks were called using MACS2 version 2.2.7.1 using the default settings. bigWig files were creating using deepTools and were normalized using RPGC with exact scaling
Assembly: danRer11
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

organism: Danio rerio

source_name: FAC-sorted Mmu:Prx1-EGFP positive pectoral fin cells

extract_protocol:
Tg(Mmu:Prx1-EGFP) wildtype embryos were subjected to fluorescence activated cell sorting at 24 hpf. Sorted cells were bound to Concanavalin A beads and subjected to CUT&RUN
The library was prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer's instructions

value: Wildtype

tag: antibody

tag: developmental stage

value: 24 hpf


title: Zebrafish pectoral fin, 24 hpf, H3K27Ac, biol rep2

value: FAC-sorted Mmu:Prx1-EGFP positive pectoral fin cells


title: Zebrafish pectoral fin, 24 hpf, Prdm1, biol rep2


title: 10A_M_1439


title: 10A_M_1438


title: 10A_M_1436


title: Zebrafish pectoral fin, 24 hpf, H3K27Ac, biol rep1


title: Zebrafish pectoral fin, 24 hpf, IgG, biol rep1


title: 10A_M_1437


title: 10A_M_1435


title: Zebrafish pectoral fin, 48 hpf, NRD MT, biol rep2

data_processing:
Paired end reads were trimmed and mapped to the zebrafish genome danRer11 using STAR Aligner version 2.7.10b. Aligned counts per gene were calculated using featureCounts. Differential expression between wildtype and prdm1-/- was analyzed using DESeq5
Assembly: danRer11
Supplementary files format and content: tab delimited text file for all samples including raw counts and log fold change

extract_protocol:
Tg(Mmu:Prx1-EGFP) wildtype and Tg(Mmu:Prx1-EGFP);prdm1am805/m805 embryos were subjected to fluorescence activated cell sorting at 48 hpf. RNA from sorted cells was extracted using the RNAqueous Micro Total RNA Isolation Kit following the manufacturer's instructions for cultured cells.
The library was prepared using the NEBNext Ultra II Directional RNA Library Kit for Illumina following the manufacturer's instructions.

value: 48 hpf


title: Zebrafish pectoral fin, 48 hpf, WT, biol rep2

data_processing:
Paired end reads were trimmed and mapped to the zebrafish genome danRer11 using STAR Aligner version 2.7.10b. Aligned counts per gene were calculated using featureCounts. Differential expression between wildtype and prdm1-/- was analyzed using DESeq4
Assembly: danRer11
Supplementary files format and content: tab delimited text file for all samples including raw counts and log fold change


title: 10A_M_1433


title: 10A_M_1432


title: 10A_M_1440


title: Male misaligned at 20:00, replicate 3

data_processing:
Raw RNA-Seq reads were aligned to the reference genome using STAR version 2.6.0c with parameters --runMode alignReads; --runThreadN 4; --readFilesCommand zcat; --outSAMunmapped Within KeepPairs. Additionally, STAR was provided with the gene models (Ensembl v93) in GTF format during alignments.
The Pipeline Of RNA-seq Transformations (PORT) version 0.8.5c-beta (https://github.com/itmat/Normalization) was used to perform normalization and quantification of the aligned data.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing PORT-normalized and quantified read counts for each genomic feature in each sample

extract_protocol:
RNA was extracted using a Direct-zol-96 kit per the manufacturer's instructions (Zymo Research).
RIN values were assessed via the Agilent TapeStation. Library prep was completed using poly(A) selection with a TruSeq stranded mRNA kit (Illumina) to remove rRNA and samples were barcoded using unique dual indexing before the samples were again assessed on the TapeStation to check the length distribution of the libraries. Paired end sequencing (150bp) was conducted on a HiSeq 4000 (Illumina) to generate approximately 312 million read pairs.

treatment_protocol: Mice were exsanguinated via intracardiac perfusion, after which liver sections were excised and placed into RNA later (Invitrogen). Samples were stored at 4°C before being transferred to -80°C for storage.

tag: treatment

value: Whole liver

value: Wild type


title: Male misaligned at 20:00, replicate 2

value: Misaligned


title: Zebrafish pectoral fin, 48 hpf, NRD MT, biol rep1

data_processing:
Paired end reads were trimmed and mapped to the zebrafish genome danRer11 using STAR Aligner version 2.7.10b. Aligned counts per gene were calculated using featureCounts. Differential expression between wildtype and prdm1-/- was analyzed using DESeq3
Assembly: danRer11
Supplementary files format and content: tab delimited text file for all samples including raw counts and log fold change


title: Male misaligned at 20:00, replicate 1


title: Zebrafish pectoral fin, 48 hpf, WT, biol rep1

data_processing:
Paired end reads were trimmed and mapped to the zebrafish genome danRer11 using STAR Aligner version 2.7.10b. Aligned counts per gene were calculated using featureCounts. Differential expression between wildtype and prdm1-/- was analyzed using DESeq2
Assembly: danRer11
Supplementary files format and content: tab delimited text file for all samples including raw counts and log fold change


title: Male misaligned at 16:00, replicate 2


title: Male misaligned at 16:00, replicate 3


title: 10A_M_1430


title: Male misaligned at 16:00, replicate 1


title: Zebrafish pectoral fin, 24 hpf, Prdm1, biol rep1


title: 10A_M_1427


title: 10A_M_1428


title: 10A_M_1423


title: 10A_M_1422


title: 10A_M_1426


title: 10A_M_1420


title: 10A_M_1421


title: Male misaligned at 12:00, replicate 3


title: Male misaligned at 12:00, replicate 1


title: Male misaligned at 12:00, replicate 2


title: Male misaligned at 08:00, replicate 3


title: 10A_M_1418


title: Male misaligned at 08:00, replicate 2


title: 10A_M_1419


title: Male misaligned at 08:00, replicate 1


title: 10A_M_1431


title: 10A_M_1416


title: 10A_M_1417


title: 10A_M_142


title: 10A_M_1414


title: 10A_M_1415


title: Male misaligned at 04:00, replicate 1


title: 10A_M_1413


title: Male misaligned at 00:00, replicate 3


title: 10A_M_1412


title: 10A_M_1410


title: Male misaligned at 00:00, replicate 1


title: Male misaligned at 00:00, replicate 2


title: 10A_M_1409


title: 10A_M_141


title: Male control at 20:00, replicate 3

value: Control


title: Male control at 20:00, replicate 2


title: Male control at 20:00, replicate 1


title: 10A_M_1406


title: Male control at 16:00, replicate 1


title: Male control at 16:00, replicate 2


title: 10A_M_1405


title: 10A_M_1407


title: Male misaligned at 04:00, replicate 3


title: 10A_M_1402


title: Male misaligned at 04:00, replicate 2


title: Male control at 12:00, replicate 2


title: 10A_M_1401


title: 10A_M_1404


title: Male control at 16:00, replicate 3


title: Male control at 12:00, replicate 1


title: Male control at 08:00, replicate 3


title: 10A_M_140


title: 10A_M_1408


title: Male control at 08:00, replicate 2


title: 10A_M_1398


title: 10A_M_14


title: Male control at 08:00, replicate 1


title: Male control at 04:00, replicate 3


title: 10A_M_1395


title: Male control at 04:00, replicate 2


title: 10A_M_1394


title: 10A_M_1393


title: Male control at 00:00, replicate 3


title: Male control at 04:00, replicate 1


title: Male control at 00:00, replicate 2


title: Male control at 12:00, replicate 3


title: 10A_M_1392


title: 10A_M_1390


title: Male control at 00:00, replicate 1


title: 10A_M_1388


title: 10A_M_139


title: 10A_M_1389


title: Female misaligned at 20:00, replicate 1


title: Female misaligned at 20:00, replicate 2


title: 10A_M_1391


title: Female misaligned at 20:00, replicate 3


title: Female misaligned at 16:00, replicate 3


title: Female misaligned at 16:00, replicate 2


title: 10A_M_173


title: Female misaligned at 16:00, replicate 1


title: 10A_M_1383


title: 10A_M_1385


title: Female misaligned at 12:00, replicate 2


title: Female misaligned at 12:00, replicate 3


title: 10A_M_1381


title: 10A_M_1380


title: Female misaligned at 08:00, replicate 3


title: 10A_M_138


title: 10A_M_1379


title: Female misaligned at 08:00, replicate 1


title: 10A_M_1396


title: 10A_M_1378


title: Female misaligned at 04:00, replicate 3


title: 10A_M_1376


title: Female misaligned at 04:00, replicate 1


title: 10A_M_1374


title: Female misaligned at 00:00, replicate 3


title: 10A_M_1373


title: Female misaligned at 00:00, replicate 2


title: 10A_M_1371


title: 10A_M_1386


title: 10A_M_1370


title: Female misaligned at 00:00, replicate 1


title: Female control at 20:00, replicate 3


title: Female misaligned at 12:00, replicate 1


title: Female misaligned at 08:00, replicate 2


title: 10A_M_1369


title: 10A_M_137


title: Female control at 20:00, replicate 1


title: 10A_M_1368


title: 10A_M_1367


title: Female control at 16:00, replicate 2


title: 10A_M_1366


title: Female control at 16:00, replicate 3


title: 10A_M_1365


title: Female control at 16:00, replicate 1


title: 10A_M_1375


title: Female misaligned at 04:00, replicate 2


title: 10A_M_1364


title: Female control at 12:00, replicate 2


title: Female control at 12:00, replicate 3


title: 10A_M_1363


title: 10A_M_1360


title: Female control at 12:00, replicate 1


title: Female control at 08:00, replicate 2


title: 10A_M_136


title: 10A_M_1359


title: Female control at 08:00, replicate 1


title: Female control at 04:00, replicate 3


title: 10A_M_1358


title: 10A_M_1357


title: Female control at 20:00, replicate 2


title: Female control at 04:00, replicate 2


title: Female control at 04:00, replicate 1


title: Female control at 00:00, replicate 3


title: Female control at 00:00, replicate 2


title: 10A_M_1356


title: 10A_M_1352


title: 10A_M_1354


title: 10A_M_1355


title: 10A_M_1351


title: 10A_M_1350


title: Vehicle_r3

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
Poli A and adapters sequences were cleaned using bbduk software
Nextpresso pipeline was used to carry out the analysis
Alignment performed using TopHat aligner
Gene count matrices were produced using htseqcount
Assembly: mm10 and hg19

organism:
Homo sapiens
Mus musculus

source_name: PDX

extract_protocol:
Total RNA was isolated from frozen tissues and cultured cells using TRItidyG (A4051 PanReac AppliChem) . Reverse transcription was performed using TaqMan Reverse Transcription Reagents (ThermoFisher Scientific, N8080234).
Libraries for sequencing were constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina protocol | Lexogen  and sequenced using the 75-bp  protocol on a NextSeq500 (Illumina, San Diego, CA, USA).

tag: xenotransplanted cells

value: ScaBER

tag: cell line origin

value: human bladder cancer

value: Hsd:Athymic Nude-Foxn1nu

value: 14 days vehicle (0.5% methylcellulose, 0.1% Tween80)


title: Vehicle_r4


title: 10A_M_135

tag: brain region

value: male


title: Vehicle_r2

tag: strain


title: 10A_M_1349


title: Vehicle_r1


title: 10A_M_1348


title: Nintedanib_r4

value: 14 days Nintedanib (40mg/kg)


title: Female control at 08:00, replicate 3


title: 10A_M_1345


title: 10A_M_1346


title: 10A_M_1344


title: Nintedanib_r1


title: Nintedanib_r2


title: 10A_M_1343


title: 10A_M_1342


title: Alpelisib_r4

value: 14 days Alpelisib (25mg/kg)


title: Nintedanib_r3


title: Alpelisib_r3


title: Female control at 00:00, replicate 1


title: primary muscle cells from FSHD patient

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

description: Prime-seq

data_processing:
The zUMIs pipeline (version 2.9.7, Parekh et al. 2018; https://doi.org/10.1093/gigascience/giy059.) was used to filter the raw data, with a Phred quality score threshold of 20 for 2 barcode bases and 3 UMI bases. The filtered data was mapped to the human genome (GRCh38 Ensembl v105) using STAR (version 2.7.3a, Dobin et al. 2013 ; https://doi.org/10.1093/bioinformatics/bts635) and the reads counted using RSubread (version 1.32.4, Liao et al.2019; https://doi.org/10.1093/nar/gkz114) by applying a downsampling to the sample with the lowest number of reads.
Assembly: GRCh38 Ensembl v105
Supplementary files format and content: tab-delimited text file for sample barcodes and gene names
Supplementary files format and content: list of count matrices as sparseMatrix (*.dgecounts.rds)

source_name: skeletal muscle

growth_protocol: Muscle cells were cultured in a humidified atmosphere at 37 °C with 5% O2 and 5% CO2. Primary muscle cells were maintained in proliferating media Ham’s F-10 medium (Nutrient Mixture F10 Ham, with L-glutamine and sodium bicarbonate, Sigma #N9608) supplemented with 20% FBS (FBS, Thermo Fisher Scientific #A4766801), and 1% penicillin/streptomycin (Pen/Strep, Thermo Fisher Scientific #15140122), 10 ng/ml bFGF (Tebu-bio #100-18B), and 1 μM dexamethasone (Sigma-Aldrich #D4902).

extract_protocol:
Total RNA was isolated employing the PureLink RNA Mini Kit (Thermo Fisher, 12183020) including digestion of remaining genomic DNA according to producer′s guidelines. RNA was quantified using the Qubit RNA High Sensitivity Assay kit (Thermo Fisher, Q32855).
Prime-seq was carried out essentially as previously described (Janjic et al. 2022 DOI: 10.1186/s13059-022-02660-8). A step-by-step protocol, including all materials, is available on protocols.io (https://doi.org/10.17504/protocols.io.s9veh66). Total RNA was isolated employing the PureLink RNA Mini Kit (Thermo Fisher, 12183020) including digestion of remaining genomic DNA according to producer′s guidelines. RNA was quantified using the Qubit RNA High Sensitivity Assay kit (Thermo Fisher, Q32855).  20 ng of RNA from each sample was incubated with the reverse transcription mix, consisting of 30 units Maxima H- enzyme (Thermo Fisher, EP0753), 1× Maxima H- Buffer (Thermo Fisher), 1 mM each dNTPs (Thermo Fisher), 1 μM template-switching oligo, and 1 μM barcoded oligo (dT) primers. The reaction was incubated at 42 °C for 90 min.  Following cDNA synthesis, the samples from the same patient (FSHD or healthy donor) were pooled, cleaned, and concentrated with AMPure XP beads (Beckman Coulter, A63881) at a 1:1 ratio and eluted in 17 μL of nuclease-free water. Residual primers were digested using Exonuclease I (Thermo Fisher, EN0581) at 37 °C for 20 min followed by a heat inactivation step at 80 °C for 10 min. The samples were cleaned using AMPure XP beads at a 1:1 ratio, and eluted in 20 μL of nuclease-free water.  Second-strand synthesis and pre-amplification were performed in a 50 μL reaction, consisting of 1× KAPA HiFi Ready Mix (Roche, 7958935001) and 0.6 μM SingV6 primer, with the following PCR setup: initial denaturation at 98 °C for 3 min, denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, elongation at 68 °C for 4 min, and a final elongation at 72 °C for 10 min. Denaturation, annealing, and elongation were repeated for 11 cycles.  The resulting DNA was cleaned using AMPure XP beads at a ratio of 1:0.8 of DNA to beads and eluted with 10 μL of nuclease-free water. The DNA quantity was assessed using Qubit DNA High Sensitivity Assay kit (Thermo Fisher, Q32854) and the quality was assessed using an Agilent TapeStation with a High-Sensitivity DNA 5000 screen tape (Agilent, 5067-5592).  Libraries were prepared with the NEBNext Ultra II FS Library Preparation Kit (NEB, E6177S) according to the manufacturer instructions with the exception of adapter sequence and reaction volumes. Fragmentation was performed on 2.5 μL of cDNA using Enzyme Mix and Reaction buffer in a 6 μL reaction. A custom prime-seq adapter (1.5 μM) was ligated using the Ligation Master Mix and Ligation Enhancer in a reaction volume of 12.7 μL. The samples were then double-size selected using AMPure XP beads with a high cutoff of 0.5 and a low cutoff of 0.7. The samples were then amplified using Q5 Master Mix (NEB, M0544L), 1 μL i7 Index primer and 1 μL i5 Index primer using the following PCR conditions: 98 °C for 30 s; 11–12 cycles of 98 °C for 10 s, 65 °C for 1 min 15 s, 65 °C for 5 min; and 65 °C for 4 min. Double-size selection was performed once more as before.The quantity and quality of the libraries were also assessed as before.

treatment_protocol: FSHD and healthy donor muscle cells were induced to differentiate 24h after seeding with differentiating media. To induce differentiation, myoblasts were plated at a confluence of 45,000 cells/cm2 and, 24h after seeding, growth medium was replaced by differentiation media composed by DMEM:F12 (1:1, Sigma-Aldrich #D9785) supplemented with 20% knockout serum replacement (KOSR, Thermo Fisher Scientific #10828028), 3.151 g/L glucose, 10 mM MEM non-essential amino acids (Thermo Fisher Scientific #11140050), 100 mM sodium pyruvate (Thermo Fisher Scientific #11360070). Differentiation was carried out for 96h changing the media every other day. 60h after induction, cells were treated for 36h with 20µM of OICR9429 (Sigma, #SML1209) or DMSO as control for a total 96h differentiation.

value: skeletal muscle

tag: cell type

value: primary cells

tag: disease state

value: FSHD donor


title: 10A_M_1339


title: 10A_M_1337


title: primary muscle cells from healthy donor

description: Prime-seq

value: healthy donor


title: Alpelisib_r2


title: 10A_M_1338


title: 10A_M_1336


title: Alpelisib_r1


title: BOTH_r4

value: 14 days [Alpelisib (25mg/kg); Nintedanib (40mg/kg)] combination


title: 10A_M_1334


title: 10A_M_1333


title: BOTH_r3


title: 10A_M_1332


title: 10A_M_1331


title: 10A_M_133


title: 10A_M_1329


title: GFP+ cells, rep5

first: Suqi

last: Deng

address: Huangpu Avenue, Tianhe District, Guangzhou, China

institute: Jinan University

data_processing:
HISAT2 v 2.0.4
Sequenced reads were mapped to the the reference genome using HISAT2 v 2.2.1.
Quantification of gene expression levels were vst-normalized count data processed by DESeq2.
Assembly: m39
Supplementary files format and content: tab-delimited text files include vst normalized count values for each Sample.

source_name: bone marrow

growth_protocol: MLL-AF9/GFP cells were thawed in PBS and tail-vein injected in CD45.1 recipient mice.

extract_protocol:
RNA was harvested using TRIzol reagent (Life Technologies, Carlsbad, USA). 0.6-3.37 ug of total RNA was used for the construction of sequencing libraries. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Mice developing AML (GFP% reached 2% in perpipheral blood by flow cytometry) were sacrificed to collect bone marrow cells. Leukaemia cells (GFP+) and bone marrow micro-environment myeloid cells (GFP-CD11b+) were sorted by flow cytometry(BD FACSArial III).

value: bone marrow

value: acute myeloid leukemia cells


title: GFP+ cells, rep2


title: GFP+ cells, rep4


title: BOTH_r1


title: 10A_M_1341


title: 10A_M_1325