title: HGPS-MSCs (P7, Vehicle)-2

city: changchun

first: yingying

last: sun

state: jilin

address: 5268 Renmin Street

department: school of life science

institute: northeast normal university

data_processing:
Raw reads were verified using fastqc and individual results were integrated using multiqc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore with default parameter
Trimmed sequence reads were mapped to Grch38 or mm10 using STAR and read counts were generated using STAR with GeneCounts parameter as well
Differentially expressed genes were calculated using Deseq2
Assembly: Grch38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Excel file of Deseq2 result

source_name: HGPS-MSCs

growth_protocol: HGPS-MSCs were maintained in DMEM supplemented with 10% fetal bovine serun (FBS) and atibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara)
RNA libraries for RNA-seq were prepared using TruePrep® RNA Library Prep Kit for Illumina following manufacturer's protocols
Oligo-dT enrichment

treatment_protocol: HGPS-MSCs were treated with UMI-77 (1uM)

value: HGPS-MSCs

value: mesenchymal stem cells

tag: genotype

value: LMNA c.1824C>T

value: continuous passage (P7)


title: HGPS-MSCs (P7, UMI-77 treated)-1

status: Public on Aug 26 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

value: continuous passage (P7, UMI-77 treated)


title: 8W_CG,rep1

city: Chongqing

first: Yuhan

last: Wang

address: Xinqiao Central Street, Shapingba District

institute: Army Medical University (Third Military Medical University)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Fresh brain tissue was anatomized into gray and white matters under the dissecting microscope and then cut into small tissue masses and transferred into gentleMACSTM C tubes (Miltenyi Biotec, Germany) containing papain and deoxyribonuclease. The C tubes were installed to the gentleMACS Octo Dissociator with the gentleMACS Program 37C_ABDK_01 running for 30 minutes. The effect of enzymolysis was terminated using horse serum, and after brief centrifugation and discarding the supernatant the pellet was collected and resuspended. The cell strainer with a diameter 70 μm was applied to filter the resuspended pellet and obtain cell suspension. The myelin debris remaining in the cell suspension was removed using Percoll solution by mean of density gradient centrifugation, and the red blood cell was eliminated from the cell suspension via red blood cell lysis buffer. Single-cell pellet was resuspended in 80μL PB buffer and incubated with 20μL CD11b/c (Microglia) MicroBeads for 30 minutes in the refrigerator. MS column was chosen for cell sorting and rinsed with 500 μL PB buffer inadvance. The single‑cell suspension was applied onto the column in the magnetic field of the MiniMACS™ separator and the column was washed with 500 μL PB buffer threetimes. Finally, 1mL PB buffer was pipetted onto the column, and the magnetically labeled cells, principally consisted of microglia, were flush out immediately by firmly pushing the plunger into the column.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, Atailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

tag: tissue

value: brain

tag: tissue region

value: gray matter

value: Microglia

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: condition

value: chronic cerebral hypoperfusion

tag: time


title: BC2118 RPMI H3K4me3

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: H3K4me3 ChIP-seq

library_source: genomic

data_processing:
ChIP-sequencing data were aligned to human genome hg38 with BWA. Samtools was used to filter reads with a quality score lower than 20. PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’ enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in all samples. DESeq2 package in R was used to identify significant changes in detected peaks among treatments. Samples derived from one donor were paired. Significant dynamics in peaks was defined by FC < 0.5 or FC > 2 and an FDR > 0.10.
Assembly: hg38
Supplementary files format and content: bigwig files

molecule: genomic DNA

source_name: monocytes from healthy donor

growth_protocol: PBMCs were isolated by Ficoll-Paque density gradient centrifugation (Lymphoprep, StemCell Technologies, Inc.). PBMCs were washed twice with PBS and were resuspended in RPMI 1640 culture medium supplemented with 1 mM pyruvate, 2 mM glutamax, and penicillin/streptomycin (Thermo Fisher Scientific). Monocytes were isolated from PBMCs by negative MACS isolation using human Pan Monocyte Isolation Kit (Miltenyi Biotec)

extract_protocol:
Monocytes were resuspended in RPMI culture medium containing 1% formaldehyde (Sigma Aldrich) and incubated for 10 min at RT. Formaldehyde was quenched using 125 mM glycine, which was incubated for 5 min at RT. Monocytes were washed twice in cold PBS supplemented with protease inhibitor cocktail (Roche). Cell pellets were snap frozen in liquid nitrogen and stored at -70°C until further use. Cells and nuclei were lysed using Magna ChIP™ Cell Lysis buffer and Nuclear Lysis buffer (Merck Millipore) according to manufacturer’s instructions. Lysates were sonicated using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30 s on, 30 s off, at 4°C) in a density of 15*106 cells/mL and spun down. Sheared chromatin was collected and fragment sizes were determined by DNA purification using MinElute Reaction Cleanup Kit (Qiagen) followed by gel electrophoresis. Immunoprecipitation was performed using the Magna ChIP™ A Chromatin Immunoprecipitation Kit (Merck Millipore) according to manufacturer’s instructions. In short, sonicated lysates derived from 5*105 cells were incubated overnight with 1 μg H3K4me3 antibody or H3K27ac (Diagenode) and protein A magnetic beads at 4 °C on a rotating platform. Protein A beads-antibody/chromatin complexes were washed with buffers provided by the Magna ChIP kit for 5 min at 4 °C on a rotating platform. Chromatin was eluted by incubation in Elution buffer supplemented with proteinase K (Magna ChIP kit, Merck Millipore) for 2 h at 62 °C, shaking, followed by 10 min at 95 °C. DNA was purified and eluted in 25 uL milliQ.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s instructions, with the following modifications. For adaptor ligation of each sample, 2.5 mL of the NEXTflex adaptor stock (600 nM, Bioo Scientific) was used. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up to ensure proper adapter removal. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 42 bp on an Illumina NextSeq500.

treatment_protocol: Human PBMCs were trained as described previously. Briefly, PBMCs and monocytes were seeded into 96-well flat bottom plates in a density of 5*106 cells/mL. Cells were allowed to adhere for 1 h at 37 ºC, 5 % CO2 (v/v). Cells were washed twice with PBS and where indicated, cells were treated with CD40-TRAF6 signaling inhibitor (10 µM, Sigma) for 1 hr. Subsequently, cells were stimulated with the primary stimulus HKCA (10^5 cells/ml, Invivogen) or culture medium for 24 h at 37 ºC, 5 % CO2 (v/v), in presence or absence of CD40-TRAF6 signaling inhibitor. After 24 h, supernatant was collected, cells were washed three times with PBS and incubated in culture medium containing 10% FBS for 5 days at 37 ºC, 5 % CO2 (v/v).

value: untreated

value: monocytes

tag: disease state

value: healthy donor


title: 8W_CW,rep1

value: white matter


title: AKR-naive-2

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: anterior cingulate cortex (ACC) tissue

extract_protocol:
Total RNAs were obtained from anterior cingulate cortex (ACC) tissues using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). TruSeq RNA Sample Prep Kit v2 for Illumina kit was used for the construction of sequencing libraries, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anterior cingulate cortex

value: AKR/J mice

value: naïve


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample8

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: bulk tumor

growth_protocol: Prostate orthotopic survival surgeries were performed on male mice where 20µg of two PX330 CRISPR-Cas9 constructs, one with a guide against p53, and another with guides against Pten and Rb1, were injected into the anterior lobe in 50µL volume. The lobe was then electroporated with two pulses of electricity and mice were monitored weekly for tumor formation post-surgery. Tumors were harvested at endpoint for analysis and sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: bulk tumor

value: tumor cells


title: HGPS-MSCs (P7, Vehicle)-1

value: HGPS-MSCs

value: mesenchymal stem cells

value: LMNA c.1824C>T

value: continuous passage (P7)


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample7


title: HGPS-MSCs (P3)-2

value: continuous passage (P3)


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample6


title: AKR-naive-1


title: HGPS-MSCs (P7, UMI-77 treated)-2

value: continuous passage (P7, UMI-77 treated)


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample5


title: 4W_SG,rep1

value: brain

value: gray matter

value: Microglia

value: Sprague-Dawley

value: male

value: sham


title: s1L1

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

data_processing:
Base-calling: bcl2fastq v2.20.0.422
Trimming: skewer 0.1.123
Alignment: STAR 2.5.3a
Expression: RSEM 1.3.0
DE: edgeR v.3.16.5
Assembly: ENSEMBL_GRCm38.89_p5
Supplementary files format and content: comma-delimited text file include TPM values for each sample

source_name: Pancreas

extract_protocol:
Mouse neonate islets were digested from pancreata and purified by Histopaque centrifugation. The isolated islets were trypsinized and sorted through flow cytometer for mCherry+ cells (β cell). The RNA extraction was performed on sorted cells via TRIzol phenol-chloroform.
DNA libraries were generated using Takara’s SMART-Seq v4 Low Input RNA Kit for Sequencing (Takara, Mountain View, CA) for cDNA synthesis and the Illumina NexteraXT DNA Library Preparation (Illumina, San Diego, CA) kit for cDNA dual indexing. Full-length cDNA fragments were generated from 1 to 10 ng total RNA by SMART (Switching Mechanism at 5′ End of RNA Template) technology. cDNA fragments were fragmented and dual indexed in a single step using the Nextera kit’s simultaneous transposon and tagmentation step. Quality and quantity of completed libraries were assessed using Agilent DNA series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit ds DNA HS Kit (Invitrogen, Carlsbad, CA), respectively. Each library was standardized to 2 nM.

value: Pancreas

value: Pancreatic Beta cell

value: Rosa26-lsl-H2B-mCherry/+; Ucn3-Cre/+; Robo1+/+; Robo2+/+

tag: age

value: neonate day 13


title: HGPS-MSCs (P3)-1


title: 4W_SW,rep1

value: white matter


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample4

value: bulk tumor

value: tumor cells


title: HepG2 NR2E3-depleted using shRNA targeting NR2E3 for FAIRE-seq analysis

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 36 bp
Cleaned reads were aligned to the UCSC hg38 genome using Bowtie version 2.4.5. Only uniquely mapping reads were retained. BAM files were sorted by samtools version 1.14.
We set width of peaks and minimum distance between peaks to 300bp.
The peaks located in alternative chromosomes were removed.
Assembly: hg38

growth_protocol: HepG2 cells:EMEM, 5% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For FAIRE-seq analysis, cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Branson S250 ultrasonicator (Nat Protoc 2012 7, 256–267).
The purified DNA was used for sequencing based on the protocol (Nat Protoc 2012, 7, 256-267). 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13-16 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Depletion of NR2E3 protein in HepG2 cells using lentiviral-particles expressing small hairpin RNA targeting NR2E3 (shNR2E3) or scrambled control (shCT).

value: Liver cancer cells

value: NR2E3 depleted


title: NR2E3 KO Tumor_3

data_processing:
For RNA-seq analysis, single-end reads were aligned to the mm10 genome from UCSC using TopHat software.
For RNA-seq analysis, the read counts were next computed using FeatureCounts program.
Differential gene expression analyies was performed the DESeq. 2 method. For FAIRE-seq, cleaned reads were aligned to the UCSC hg38 genome using Bowtie version 2.4.5. Only uniquely mapping reads were retained. BAM files were sorted by samtools version 1.14.
Assembly: mm10
Supplementary files format and content: txt inclduing FPKM value in each gene

source_name: Liver

extract_protocol:
For RNA-seq analysis, miRvana RNA isolation kit (Cat# AM1560) was used to extract RNAs from mouse liver tumor tissues.
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit from Illumina.

value: Liver

value: Tumor

value: Male


title: 4W_CW,rep1

value: brain

value: chronic cerebral hypoperfusion


title: HepG2 scrambled shRNA control for FAIRE-seq analysis

value: Control


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample3


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample2


title: WT_Tumor_3


title: T046  (patient 7) tumour core

city: Xi’an

first: Lei

last: Zhang

address: No. 620, West Chang'an Avenue

institute: Shaanxi Normal University

data_processing:
The raw sequence reads were analyzed by Cell Ranger v.4.0.0/6.1.1 with default parameters.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with read counts for each sample

source_name: Brain

extract_protocol:
Depletion of leukocytes was performed using CD45 MicroBeads (130-045-801, Miltenyi Biotec) and then endothelial cell enrichment was performed using CD31 MicroBeads (130-091-935, Miltenyi Biotec). To enrich mural cells, CD45 negative selected cells were incubated with PDGFRβ-Biotin antibody (130-118-985, Miltenyi Biotec) and then PDGFRβ+ cells were isolated using Biotin MicroBeads (130-090-485, Miltenyi Biotec).
scRNAseq libraries were prepared using Chromium Single Cell 3' V3 Reagent Kit (10X Genomics) according to the manufacturer’s protocol.

value: adult

value: Glioblastoma tumor core


title: SNHG26_ASO_TNF rep3

type: RNA

city: Nanjing

first: Dongqing

last: Li

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

description: Gene expression data of Human primary keratinocytes transfected with SNHG26_ASO

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:  Array Type: Clariom_S_Human  Analysis Type: Expression (Gene)  Analysis Version: version 2  Summarization Method: Gene Level - SST-RMA  Pos vs Neg AUC Threshold: 0,7  Genome Version: hg38 (Homo sapiens)  Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv  Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings:  • Gene-Level Fold Change < -2 or > 2  • Gene-Level P-Value < 0,05  • Anova Method: ebayes  • A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.  • DABG < 0,05

label: biotin

source_name: primary keratinocyte transfected with  SNHG27_ASO oligoes, , followed by TNF treat 8 hours

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Human adult primary keratinocytes (C0055C; Thermo Fisher) were cultured in Epilife medium supplement with Human Keratinocyte Growth Supplement (HKGS, S0015, Thermo Fisher) and 1X Penicillin-Streptomycin.

extract_protocol: The total RNA was extracted by miRNeasy mini Kits (Qiagen) following the manufacture instruction.

treatment_protocol: When cells grow to 60% confluent, 10nM SNHG26-ASO or Ctrl-ASO was transfected for 24 hours followed by TNFa stimulation for another 3 hours.

value: Primary Keratinocytes

tag: gene silencing

value: SNHG26 ASO

tag: stimulation

value: TNF


title: NR2E3 KO Tumor_1


title: N046 ( (patient 7) tumor peripheral tissue

value: Glioblastoma tumor peripheral tissue


title: SNHG26_ASO_TNF rep2

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used


title: 4W_CG,rep1

value: gray matter

value: Microglia

value: Sprague-Dawley

value: male


title: WT_Tumor_1


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample1

value: bulk tumor

value: tumor cells


title: KO-CM3_1

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

country: Germany

institute: Medical Faculty of Mannheim Heidelberg University

data_processing:
FastqCleaner was used for trimming
bowtie2 was used for mapping
Gene annotation was performed with bioMaRt
Read counts were normalized to counts per million
Differential expression analysis was performed using Deseq2 from R. Differentially expressed Genes were selected with (0.75<FC>1.5 and FDR<0.05).
Assembly: mm10
Supplementary files format and content: Excel files from differentially expressed genes

source_name: Cardiomyocytes

extract_protocol:
Endothelial cells were isolated with CD146 magnetic beads, and RNA from Ecs were isolated with Macharey-Nagel RNA isolation kit, fibroblasts were isolated with Feeder removal beads. Cardiomyocyte isolation was performed after Langendorff perfussion.
BGI

value: Heart

value: Cardiomyocytes

value: Gadlor-KO

value: 2 weeks TAC


title: N043  (patient 4) tumor peripheral tissue

value: Lower grade glioma tumor peripheral tissue


title: KO-CM1_1


title: T038  (patient 5) tumour core

value: adult


title: T045  (patient 6) tumour core

value: Glioblastoma tumor core


title: microglia FA biol rep2

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

country: Italy

institute: University of Rome Tor Vergata

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted  in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts
Supplementary files format and content: tab-delimited text files including normalized counts

source_name: cerebellum

extract_protocol:
Total RNA was extracted using Direct-zolTM RNA MiniPrep (ZYMO RESEARCH). 125ng of total RNA was used for the construction of sequencing libraries.
NEGEDIA Digital mRNA-seq research  grade sequencing service (Next Generation  Diagnostic srl)
NEGEDIA Digital mRNA-seq

value: cerebellum

value: primary microglia


title: microglia FA biol rep3


title: microglia FA biol rep4


title: T043  (patient 4) tumour core

value: Lower grade glioma tumor core


title: N045  (patient 6) tumor peripheral tissue

value: Glioblastoma tumor peripheral tissue


title: WT-CM6_1

value: WT


title: microglia FA biol rep1


title: Ctrl_ASO_TNF rep2

source_name: primary keratinocyte transfected with  Ctrl_ASO oligoes, followed by TNF treat 8 hours

value: Primary Keratinocytes

value: control ASO

value: TNF


title: SNHG26_ASO rep1

source_name: primary keratinocyte transfected with  SNHG26_ASO oligoes

value: SNHG26 ASO


title: SNHG26_ASO rep3


title: T037  (patient 3) tumour core


title: SNHG26_ASO_TNF rep1


title: SNHG26_ASO rep2


title: WT_Tumor_2

value: Liver

value: Tumor

value: Male


title: WT-CM2_1

value: Heart

value: Cardiomyocytes


title: N037  (patient 3) tumor peripheral tissue

value: Lower grade glioma tumor peripheral tissue


title: Ctrl_ASO_TNF rep3


title: KO-241-FB_1

source_name: Primary FBs

value: Primary Cardiac fibroblasts

value: Gadlor-KO

value: 2 weeks TAC


title: microglia WT biol rep4

value: cerebellum

value: primary microglia


title: Ctrl_ASO rep3

source_name: primary keratinocyte transfected with  Ctrl_ASO oligoes


title: N038 ( (patient 5) tumor peripheral tissue

value: adult

value: Glioblastoma tumor peripheral tissue


title: KO-CM2_1


title: KO-242-FB_1


title: KO-240-FB_1


title: N036 (patient 2) tumor peripheral tissue


title: WT-CM1_1

value: WT


title: microglia WT biol rep2


title: microglia WT biol rep3


title: microglia WT biol rep1


title: N027 (patient 1) tumor peripheral tissue


title: c532_rna

city: London

first: Nazif

last: Alic

address: Gower St

country: United Kingdom

institute: UCL

data_processing:
Read quality assessed with FastQC, and trimming has been done using cutadapt
Aligned to D. melanogaster genome and counted with Salmon
Analysed with DESeq2

organism: Drosophila melanogaster

source_name: whole flies

extract_protocol:
CD Genomics carried out the protocol can be found here https://www.cd-genomics.com/ribosome-profiling.html
https://www.cd-genomics.com/ribosome-profiling.html

treatment_protocol: For ribo samples, To block translational elongation, cycloheximide was added to cell culture medium to a final  concentration of 100 μg/ml

value: whole flies

value: female


title: Ctrl_ASO rep1

value: Primary Keratinocytes

value: control ASO


title: WT-277-FB_1


title: primary progressive, line 4, scRNAseq

city: Cleveland

first: Benjamin

last: Clayton

state: OH

address: 2109 Adelbert Rd BRB739A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 10x Genomics

data_processing:
Demultiplexin,  barcode processing, and UMI counting was performed using 10x Genomics Cell Ranger v3.0.2.
Data analysis was performed with Seurat in R.
Assembly: GRCh38
Supplementary files format and content: filtered barcode, features, and matrix outputs from 10x Genomics Cell Ranger v3.0.2

source_name: iPSC-derived culture

extract_protocol:
Day 85 cultures from 16 lines were detached enzymatically in parallel using papain (Worthington; LK003153) and were filtered through 40µm Flowmi Cell Strainers (Scienceware; H13680-0040) to obtain a single cell suspension. The ran on a 10x Chromium Controller followed by RNA extraction in GEMs according to manufacturer's instructions (10x Genomics Single Cell 3' v3)
Library was prepared according to manufacturer's instructions (10x Genomics Single Cell 3' v3)

value: iPSC-derived culture

value: astrocyte, oligodendrocyte, OPC, neuron


title: Ctrl_ASO_TNF rep1

value: TNF


title: WT-260-FB_1

value: Heart


title: Single Cell KO_Skin

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

description:
Snhg26 KO mice single cell seq
KoSkin1_filtered_feature_bc_matrix.zip

data_processing:
ChIP-seq and CHIRP-seq: Raw sequencing data were quality assessed using Trimmomatic v0.36 by trimming reads of low qualities and with a length less than 20 nucleotides. Clean reads were mapped to GRCh38 human reference genome using Bowtie2 followed by removing PCR duplicates using Picard (v2.20.4) tools. The mapped reads were converted into bigwig format for IGV viewer using deepTools bamCoverage function. Peaks were called using MACS2 (v2.2.6) with the default parameter. Peaks from two biological replicates were merged and filtered using Bedtools.
scRNA-seq: Raw single cell sequencing data were processed using the standard 10X Cell Ranger (v5.0.1) analysis workflow, including demultiplexing, aligning to the GRCm39 (mm39) mouse reference genome, barcode counting and unique molecular identifier (UMI) quantification.
Assembly: GRCh38 for human;GRCm39 for mouse
Supplementary files format and content: Excel file contains the peaks of CHIP-seq.
Supplementary files format and content: tar files contain the raw count data of mouse scRNA-seq.
Supplementary files format and content: Excel file contains the peaks of CHIRP-seq.

source_name: Back skin

growth_protocol: Human adult primary keratinocytes (C0055C; Thermo Fisher) were cultured in Epilife medium supplement with Human Keratinocyte Growth Supplement (HKGS, S0015, Thermo Fisher) and 1X Penicillin-Streptomycin. Snhg26-Ko mice and WT mice were breed in specific pathogen-free conditions in Comparative Medicine Biomedicum (KMB) animal facility in Karolinska Institutet. All the mouse experiments were approved by committee on animal experimentation of Swedish Board of Agriculture (Jordbruksverket).

extract_protocol: Mice skin and wound cells were purified by using Whole Skin Dissociation Kit (Miltenyi Biotec). Single cell cDNA library was prepared according the manufacture demonstration (10x genomic)

value: Skin

tag: gender

value: Male

value: 8 weeks

value: Snhg26 KO

tag: chip antibody


title: Single Cell KO_Wound

description:
Snhg26 KO mice single cell seq
KoWound1_filtered_feature_bc_matrix.zip

value: Wound


title: KO-133-EC_1

source_name: Primary ECs

value: Primary Endothelial Cells

value: Gadlor-KO

value: 2 weeks TAC


title: primary progressive, line 3, scRNAseq

description: 10x Genomics


title: c533_rna


title: Single Cell WT_Wound

description:
WT mice single cell seq
WtWound1_filtered_feature_bc_matrix.zip

value: WT


title: Single Cell WT_Skin

description:
WT mice single cell seq
WtSkin1_filtered_feature_bc_matrix.zip


title: WT-283-FB_1

value: Primary Cardiac fibroblasts


title: wt3_rna

value: whole flies

value: White Dahomey

value: female


title: U2AF1-S34F infected, replicate 3

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

data_processing:
FastQC 0.11.5 was used to check data quality, and skewer 0.2.2 was used to trim off the adapter sequence remove poor quality reads, and all reads were trimmed to 140 basepairs for rmats
2 pass mapping with STAR 2.7.5a was performed. All the data was mapped as one to the Mus_musculus GRCm39 genome. Splice sites from this  were incorperated into a new mouse genome for the second pass individual STAR mapping for splicing analysis and counts
Counts from the 2nd STAR mapping were input into EdgeR 3.32.1 for differential gene expression. Stringtie 2.1.4 was used to make GTF files from the bam files and merged  for use in rmats .4.1.0 for differential splicing analysis.
Assembly: Mus_musculus GRCm39
Supplementary files format and content: countts table output by STAR. Genes by Sample number,

source_name: bone marrow neutrophils

growth_protocol: Mice carrying transgenes expressing either U2AF1-WT or U2AF1-S34F were injected I.P. with 9-tert-Butyl Doxycycline HCl daily for four days to induce the transgenes.

extract_protocol:
RNA was harvested using RNAeasy mini kits (Qiagen)
RNA libraries for RNA-seq were prepared using a Takara Bio Smart-Seq v4 Ultra-low input RNA kit in conjunction with an Illumina Nextera XT DNA library prep kit.
RNA-seq on the NovaSeq 6000 on a S4 flowcell with 2x150 bp sequencing chemistry.

treatment_protocol:
24 hours later, mice were either injected I.P. with 10e8 CFU of E. coli H9049 or were left uninfected. Mice were humanely euthanized 4 hours later.
Bone marrow neutrophils were isolated using the Miltenyi mouse neutrophil isolation kit.

value: bone marrow neutrophils

value: E. coli infection for 4 hrs


title: primary progressive, line 2, scRNAseq

description: 10x Genomics

value: iPSC-derived culture

value: astrocyte, oligodendrocyte, OPC, neuron


title: NR2E3 KO Tumor_2

value: Liver

value: Tumor


title: wt2_rna


title: KO-131-EC_1

value: Heart


title: c531_rna


title: U2AF1-S34F infected, replicate 1


title: Ctrl_ASO rep2

value: Primary Keratinocytes

value: control ASO


title: wt1_rna


title: AKR-naive-3

source_name: anterior cingulate cortex (ACC) tissue

value: anterior cingulate cortex

value: AKR/J mice

value: naïve


title: KO-105-EC_1

value: Primary Endothelial Cells

value: Gadlor-KO

value: 2 weeks TAC


title: secondary progressive, line 4, scRNAseq

description: 10x Genomics


title: WT-35-EC_1

value: WT


title: U2AF1-S34F infected, replicate 2


title: secondary progressive, line 3, scRNAseq

description: 10x Genomics


title: U2AF1-WT infected, replicate 4


title: KO-108-EC_1


title: T027 (patient 1) tumour core

value: adult

value: Lower grade glioma tumor core


title: c532_ribo

value: whole flies

value: female


title: c533_ribo


title: primary progressive, line 1, scRNAseq

description: 10x Genomics

value: iPSC-derived culture

value: astrocyte, oligodendrocyte, OPC, neuron


title: U2AF1-WT infected, replicate 1

value: bone marrow neutrophils

value: E. coli infection for 4 hrs


title: WT-34-EC_1

value: Heart


title: wt3_ribo

value: White Dahomey


title: U2AF1-WT infected, replicate 2


title: secondary progressive, line 2, scRNAseq

description: 10x Genomics


title: WT-31-EC_1


title: U2AF1-WT infected, replicate 3


title: WT-32-EC_1


title: relapsing remitting, line 3, scRNAseq

description: 10x Genomics


title: CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_5]

first: William

last: Grey

address: 1 Midland Road

institute: Francis Crick Institute

description:
Cks2KO_LSK_5
Haematopoietic cells

data_processing:
Read adapter removal and trimming done with Trimmomatic/0.36.
Read alignment done with STAR/2.5.2a.
Gene counting done with RSEM/1.2.31.
Differential gene expression done with DESeq2 1.20.0.
Assembly: Mouse Ensembl GRCm38 - release 89.
Supplementary files format and content: normalised_data.txt: Tab-delimited text file containing log2 normalised expression values (columns = samples; rows = genes).

source_name: Bone Marrow

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
Total RNA (KAPA Hyper prep with Riboerase).

value: Bone Marrow

value: LSK cells

value: 8 weeks


title: U2AF1-S34F uninfected, replicate 3


title: U2AF1-S34F uninfected, replicate 4


title: relapsing remitting, line 2, scRNAseq

description: 10x Genomics


title: relapsing remitting, line 4, scRNAseq

description: 10x Genomics


title: wt1_ribo


title: c531_ribo


title: CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_3]

description:
Cks2KO_LSK_3
Haematopoietic cells


title: secondary progressive, line 1, scRNAseq

description: 10x Genomics


title: U2AF1-S34F uninfected, replicate 1


title: healthy control, line 4, scRNAseq

description: 10x Genomics


title: CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_4]

description:
Cks2KO_LSK_4
Haematopoietic cells


title: wt2_ribo


title: U2AF1-S34F uninfected, replicate 2


title: relapsing remitting, line 1, scRNAseq

description: 10x Genomics


title: U2AF1-WT uninfected, replicate 3


title: CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_2]

description:
Cks2KO_LSK_2
Haematopoietic cells


title: CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_1]

description:
Cks2KO_LSK_1
Haematopoietic cells


title: U2AF1-WT uninfected, replicate 4


title: healthy control, line 3, scRNAseq

description: 10x Genomics


title: U2AF1-WT uninfected, replicate 2


title: CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_5]

description:
Cks1KO_LSK_5
Haematopoietic cells


title: U2AF1-WT uninfected, replicate 1


title: CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_3]

description:
Cks1KO_LSK_3
Haematopoietic cells


title: Size-matched input for FTO iCLIP

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the cDNA sequence, were initially trimmed to 49 nt from the 3'-end, and duplicates were discarded. Reads were de-multiplexed, and the random positions, barcodes, and any 3'-bases matching Illumina adaptors were removed. Remaining reads longer than 25 nt were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using TopHat with default settings. To prevent false assignment of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis. Note that this record contains demultiplexed but un-trimmed reads.
CLIP Tool Kit (CTK) was used to identify RNA-binding sites at single-nucleotide resolution.We  called CITS peaks on individual iCLIP replicates as well as SMI samples. CITS with FDR ≤ 0.01 were considered as significant. The identified iCLIP CITS were further normalized using SMI CITS by utilizing underlying reads from each dataset and performing a differential analysis (iCLIP/SMI). Remaining peaks from individual replicates were merged for downstream analysis.   miCLIP-seq data were processed similarly to the iCLIP-seq data (except for the SMI step), and putative anti-m6A mediated CITS were identified (FDR ≤ 0.01).
To generate meta-gene plots, the entire length of each gene (divided into 3 parts: 5’UTR, CDS, 3’UTR) plus 1kb upstream and downstream was allocated into 100 bins on the x-axis, the number of bins in each part is proportional to the median length of that part in all protein-coding genes. The Y-axis denotes coverage enrichment ratio over input/bin/gene, the shaded bands around each line represent 1xSE. All calculations and visualizations were performed with the R package 'GenomicPlot' (URL: https://github.com/shuye2009/GenomicPlot), the smoothing was done using R function "smooth.spline" in the stats package with the parameter df=20.
Assembly: hg19
Supplementary files format and content: BED files containing merged crosslink-induced termination site (CITS) locations from multiple replicates.
Supplementary files format and content: PDF files contains a meta-gene plot showing the mean normalized FTO iCLIP read density in different parts of the gene upon either ZBTB48 knockdown or control non-targeting knockdown. Figure was generated directly from aligned reads.

growth_protocol: Cell cultures were maintained in Dulbecco's modified Eagle's medium (DMEM) (Wisent Bioproducts catalogue number 319-005-CL) supplemented with 10% FBS (Wisent Bioproducts catalogue number 080-705), sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Lysates were treated with Turbo DNase (Thermo Fisher Scientiﬁc) and RNase I (Thermo Fisher Scientiﬁc) diluted 1/250 in PBS for 5 minutes at 37°C to digest genomic DNA and partially digest RNA to short fragments of an optimal size range. RNA-protein complexes were puriﬁed using 100 mL of protein G Dynabeads (Thermo Fisher Scientiﬁc) and 10ug antibody, with 2% (20ul) of the total lysate retained for use as a size-matched input (SMI) control. SMI samples were processed as previously described (Van Nostrand et al., 2016). Following stringent high salt washes, the immunoprecipitated RNA was 3′ end dephosphorylated and ligated to a pre-adenylated adaptor at the 3′ end, as described previously. After extensive additional washes and buffer exchange, the immunoprecipitated RNA was 5′ end-labeled using ATP [γ-32P]. The puriﬁed protein-RNA complexes and SMI control samples were separated with SDS-PAGE and transferred to nitrocellulose membrane. Protein was digested using proteinase K, the RNA was puriﬁed using phenol/chloroform. miCLIP procedure was performed as decribed. Total RNA was extracted from HEK293 cells using TRIzol as per manufacturer's protocol. RNA was treated with DNase I to eliminate any contaminating genomic DNA. We used 12 μg of total RNA for miCLIP-seq. 2 μL of RNA Fragmentation Reagents was added to the RNA suspended in 20 μL of sterile water. The mixture was incubated in a heat block at 75°C for exactly 12 minutes. 2.2 μL of stop solution was added to stop the reaction. The fragmented RNA was incubated with 10 μg of m6A antibody for 2 hours at 4°C. RNA-antibody complexes were UV crosslinked twice with 0.15 J/cm2 at 254 nm in a Stratalinker 1800.  Protein G Dynabeads (100 μL) were added, and the samples were rotated for 2 hours at 4°C. Remaining steps, including dephosphorylation, adapter ligation, SDS-PAGE, and RNA-extraction are similar to the iCLIP procecure.
Purified RNA was reverse transcribed into cDNA. The cDNA was size selected by resolving samples on a 6% TBE-Urea gel, circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR ampliﬁed using AccuPrime SuperMix I (Thermo Fisher Scientiﬁc). The ﬁnal PCR libraries were puriﬁed by agarose gel electrophoresis using gel extraction columns (QIAGEN). The eluted DNA from the low, middle, and high fractions was pooled together and submitted for sequencing.

treatment_protocol: HEK293 cells were crosslinked (150mJ/cm2) at 254 nm with a Stratalinker 1800.

value: human embryonic kidney cells (HEK293)

value: FTO ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-FLAG containing FTO.

value: FLAG-FTO was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to crosslinking.

tag: protocol

value: iCLIP-seq

tag: clip antibody

value: none (input)

tag: barcoded reverse_transcription_primer


title: CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_4]

description:
Cks1KO_LSK_4
Haematopoietic cells

tag: cell type

tag: genotype


title: wt3_drosophila

data_processing:
Read quality assessed with FastQC, and trimming has been done using cutadapt
Aligned to D. melanogaster genome and counted with Salmon
Analysed with DESeq2
Supplementary files format and content: containing read counts for genes analysed in corresponding samples

source_name: Midgut

extract_protocol:
Trizol
Glasgow Polyomics

treatment_protocol: size selection of RNAs less than 200 nucleotides in length using mirVANA RNA isolation kit AND demethylated using rtStar™ tRF&tiRNA Pretreatment Kit

tag: tissue

value: Midgut


title: RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 2

data_processing:
RNAseq reads were trimmed using Cutadapt with the following parameters : -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 --quality-cutoff=20
Reads were aligned to human genome GRCh38 using STAR (version 2.7.6.a).
For differential analysis, gene-level read counts were quantified using RSEM (version 1.3.3) and normalized by variance-stabilizing transformation using DESeq2 76. Adjusted p-value ≤ 0.05 and log2fold change +/- 1 were used to determine significantly regulated genes.
Assembly: hg38
Supplementary files format and content: *genes.results files are tab-delimited output of RSEM gene-level quantification, containing gene ID, transcript IDs, length, effective length, expected count, TPM and FPKM.
Supplementary files format and content: siZBTB48_ZBTB48_vs_siNT_DESeq2_results_table.tab is a tab-delimited output from DESeq2 analysis and contains base mean, log2-fold change, test statistic, raw and adjusted p-values from the comparison of siZBTB48 with control knockdown.

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit.
Poly-A selected, rRNA-depleted libraries were generated from 1 μg of input RNA using the TruSeq Illumina library preparation kit (Epicenter) as per the manufacturer’s recommendations. The quantified pool was hybridized at a final concentration of 2.21 pM

tag: cell line

tag: treatment

value: knockdown of non-targeting control


title: wt2_drosophila

tag: Sex

value: female


title: WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_5]

description:
WT_LSK_5
Haematopoietic cells

value: WT


title: CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_1]

description:
Cks1KO_LSK_1
Haematopoietic cells


title: RNA-seq of HEK293 cells upon knockdown of ZBTB48, replicate 2

value: knockdown of ZBTB48


title: WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_4]

description:
WT_LSK_4
Haematopoietic cells


title: RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 1


title: healthy control, line 2, scRNAseq

description: 10x Genomics

value: iPSC-derived culture

value: astrocyte, oligodendrocyte, OPC, neuron


title: wt1_drosophila


title: WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_3]

description:
WT_LSK_3
Haematopoietic cells


title: c532_drosophila


title: c533_drosophila


title: healthy control, line 1, scRNAseq

description: 10x Genomics


title: Empty VLP,scRNAseq

city: Shanghai

first: Sikai

last: Ling

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

data_processing:
Base-calling software, version, parameters: DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.
Data filtering steps: NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (default parameter)
Read alignment software, version, parameters: STARsolo (version 2.7.10a) along with mouse genome mm10 (ensembl annotation version 100). Seurat package (version: 4.1.1, https://satijalab.org/seurat/)  utilizing graph-based cluster method (resolution = 0.8). FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Additional processing software (e.g., peak-calling, abundance measurement),version,parameters;etc: Monocle2 (http://cole-trapnell-lab.github.io/monocle-release) using DDR-Tree and default parameter. Significant mean and Cell Communication significance (p-value<0.05) was calculated based on the interaction and the normalized cell matrix achieved by Seurat Normalization. Single-cell regulatory network inference and clustering (pySCENIC, v0.9.5) (Aibar et al., 2017) workflow, using the 20-thousand motifs database for RcisTarget and GRNboost. QuSAGE (2.16.1) analysis. FindMarkers with wilcox rank sum test algorithm was used under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10 (ensembl annotation version 100)
Supplementary files format and content: barcodes.tsv.gz: Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. matrix.mtx.gz: Significant mean and Cell Communication significance (p-value<0.05) was calculated based on the interaction and the normalized cell matrix achieved by Seurat Normalization.

source_name: Retina

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 20 U/mL Papain and 30 U/mL DNase I for 10 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific).

value: Retina

tag: strain

value: 8 week

value: wild type


title: WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_2]

description:
WT_LSK_2
Haematopoietic cells

value: Bone Marrow

value: LSK cells


title: Autoimmune hepatitis patient PBMC

city: Fukushima

first: Kazumichi

last: Abe

state: Fukushima

address: 1 Hikarigaoka

country: Japan

institute: Fukushima Medical University

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq2 (ver2.20)
Sequence data was processed using Cell Ranger 5.0.0
Assembly: GRCh38

source_name: human peripheral blood mononuclear cell (from 4 persons)

extract_protocol:
Peripheral blood was drawn from each patient and volunteer into a tube containing EDTA-2Na and centrifuged to separate PBMCs and frozen. All samples were thawed on same day and immediately processed 10x Genomics Gene Expression 3' Chromium V 2.0 per manufacturer's instructions. A single cell suspension was obtained by filtering with a 40 μm cell strainer.
Library preparation were performed with the Single Cell 3' Library & Gel Bead Kit v3.1 according to the 10X Genomics' standard protocol.

value: Autoimmune hepatitis

value: PBMC


title: RNA-seq of HEK293 cells upon knockdown of ZBTB48, replicate 1

value: human embryonic kidney cells (HEK293)


title: OA exposure, pH8.45R3

type: genomic

city: Fuzhou

first: Zhenyue

last: Lin

address: Minjiang university

institute: Minjiang university

hyb_protocol: The mixtures were hybridised to the GeoChip5 microarray.

scan_protocol: Scanned on a NimbleGen MS200 array system (Roche).

data_processing: The ImaGene version 6.0 (Biodiscovery, El Segundo, CA) was then used to determine the intensity of each spot, and identify poor-quality spots

organism: Galaxea fascicularis

source_name: Coral tissue

label_protocol: The experimental procedures were described elsewhere (Lu et al. 2012) in detail. Briefly, DNA for all samples was labeled with Cy5, purified and resuspended in 10 μl hybridization solution.

growth_protocol: Healthy G. fascicularis colonies were collected from the reef in South China Sea by Third Institute of Oceanography (TIO), State Oceanic Administration and placed in an aquarium (Minjiang University) containing approximately 400 L of artificial seawater prepared with Red Sea Salt (Hertzlia, Israel). The aquarium was equipped with K7-Pro 2 LED lamps under SPS/LPS mode (Noopsyche, Columbia, SC) and the seawater temperature was maintained at 25 °C.

extract_protocol: After the 10-day experimental period, 1 coral microcolony was randomly harvested from each replicate treatment tank (n=3 per treatment) for DNA extraction using a DNA Purification kit (Tiangen Biotech, Beijing).

treatment_protocol: A short-term OA experiment, G. fascicularis exposed to three pH scenarios including 8.45, 8.15 and 7.85 over a 10-day period, were conducted to examine the changes of the coral-associated bacterial community diversity. For detail methods of the OA experimental setup were characterized in a previous study. Briefly, seawater pH was manipulated via direct bubbling with CO2-enriched air or N2 to create three target conditions: acidified pH (7.85, DIC  2176 µmol kg-1), ambient pH (8.15, 2030 µmol kg-1), and alkalinized pH (8.45, 1833 µmol kg-1).

tag: stress

value: Coral tissue


title: c531_drosophila


title: PBS,scRNAseq


title: OA exposure, pH8.45R2


title: RIDE,scRNAseq


title: OA exposure, pH8.45R1


title: healthy control PBMC

tag: disease state

value: healthy control


title: OA exposure, pH8.15R1


title: OA exposure, pH8.15R3


title: OA exposure, pH7.85R3


title: WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_1]

description:
WT_LSK_1
Haematopoietic cells

tag: age

value: 8 weeks


title: OA exposure, pH7.85R1


title: OA exposure, pH7.85R2


title: ID12167912, Abaumannii, GuaBi, 1h

status: Public on Aug 25 2024

city: South San Francisco

first: Yutian

last: Peng

state: CA

address: 340 Point San Bruno

institute: Genentech Inc.

description:
ID12167912
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt

data_processing:
Ribosomal RNA contamination was removed from the fastq sequence files and reads were filtered for quality, keeping only reads where at least 70% of the cycles had Q scores Ñ23.
Single-end 50 bp reads were aligned to the E. coli K12 MG1655 and A. baumannii ATCC19606 genome using GSNAP version 2013-11-01 with the following parameters: -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap.
Uniquely mapped reads were used to obtain read counts and RPKMs per gene.
Assembly: ASM73714v1 (Abaumannii) and ASM584v2 (Ecoli K-12)
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample, column metadata (samples), and row metadata (genes)

organism: Acinetobacter baumannii

source_name: bacterial cell

extract_protocol:
RNA was extracted using RNeasy spin columns (Qiagen) according to the manufacturer’s protocol.
RNA-seq library generation was continued using the Truseq RNA Library Prep Kit v2 (Illumina) starting at the “Elute, Prime, Fragment” step and was completed according to the manufacturer’s protocol.

value: bacterial cell

value: GuaBi

tag: timepoint


title: OA exposure, pH8.15R2


title: ID12167906, Abaumannii, No Drug, 0h

description:
ID12167906
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt

value: No Drug


title: ID12167914, Abaumannii, GuaBi, 1h

description:
ID12167914
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167917, Abaumannii, Cipro, 1h

description:
ID12167917
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt

value: Cipro


title: ID12167907, Abaumannii, No Drug, 0h

description:
ID12167907
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167910, Abaumannii, No Drug, 1h

description:
ID12167910
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167911, Abaumannii, No Drug, 1h

description:
ID12167911
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167909, Abaumannii, No Drug, 1h

description:
ID12167909
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167916, Abaumannii, Cipro, 1h

description:
ID12167916
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167913, Abaumannii, GuaBi, 1h

description:
ID12167913
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167908, Abaumannii, No Drug, 0h

description:
ID12167908
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: ID12167915, Abaumannii, Cipro, 1h

description:
ID12167915
Abaumannii_counts.txt
Abaumannii_metadata_samples.txt
Abaumannii_metadata_genes.txt


title: C57BL/6j mice, nineteen-month-old, control, rep2

city: wuhan

first: li

last: ma

state: --- Select One ---

address: 262 Jinlong Street, Jiangxia,

institute: Chinese Academy of Sciences Wuhan Institute of Virology

data_processing:
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
When align reads to reference. Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using  Hisat2.
featureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: GRCm38
Supplementary files format and content: comma-separated csv file includes raw counts for each Sample

source_name: lung

growth_protocol: The MAV strain was cultured and quantified in Vero E6 cells using standard plaque-forming units techniques. Vero E6 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) medium supplemented with 10% FBS and incubated at 37°C incubator with 5% CO2.

extract_protocol:
The total RNA was extracted using the phenol-chloroform method following the instructions of the manufacturer.
Samples meeting the quality standards underwent mRNA enrichment using a Dynabeads mRNA Purification Kit, followed by fragmentation, reverse transcription, and synthesis of double-stranded cDNA.

treatment_protocol: Anesthesia was induced in the mice through intraperitoneal administration of tribromoethanol at a dose of 250 mg/kg body weight. Mice in the infected groups were intranasally inoculated with 2 × 105 plaque-forming units of MAV in 30 μL of DMEM per mouse, whereas mice in the uninfected groups were administered 30 μL of DMEM per mouse.

value: lung

value: nineteen-month-old

value: WT

tag: infection

value: DMEM


title: C57BL/6j mice, nineteen-month-old, control, rep1


title: C57BL/6j mice, nineteen-month-old, infected, rep1

value: DMEM, mouse-adapted SARS-CoV-2


title: C57BL/6j mice, nineteen-month-old, control, rep3


title: C57BL/6j mice, three-week-old, infected, rep1

value: three-week-old


title: C57BL/6j mice, three-week-old, infected, rep4


title: C57BL/6j mice, three-week-old, control, rep1


title: C57BL/6j mice, three-week-old, infected, rep3


title: C57BL/6j mice, three-week-old, infected, rep2


title: C57BL/6j mice, three-week-old, control, rep2


title: C57BL/6j mice, three-week-old, control, rep3


title: KO-2

first: Jieying

last: Zhu

address: Hengren Road

institute: Shanghai University of Sport

data_processing:
Reference genome and gene model annotation files weredownloaded from genome website directly. Index of the referencegenome was built using Hisat2 (v2.0.5) and paired-end cleanreads were aligned to the reference genome using Hisat2(v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generateadatabase of splice junctions based on the gene model annotation file andthusa better mapping result than other non- splice mapping tools.
Reference genome and gene model annotation files weredownloaded from genome website directly. Index of the referencegenome was built using Hisat2 (v2.0.5) and paired-end cleanreads were aligned to the reference genome using Hisat2(v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generateadatabase of splice junctions based on the gene model annotation file andthusa better mapping result than other non- splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mappedto each gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequenceper Millions base pairs sequenced, considers the effect ofsequencing depth and gene length for the reads count at the same time, andiscurrently the most commonly used method for estimating gene expressionlevels.
(For edgeR without biological replicates) Prior to differentialgene expression analysis, for each sequenced library, the read counts wereadjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed usingthe edgeR R package (3.22.5). The P values were adjusted usingthe Benjamini & Hochberg method. padj<=0.05and |log2(foldchange)| >= 1 were set as the thresholdforsignificantly differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: iWAT

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly- T oligo- attachedmagnetic beads. Fragmentation was carried out using divalent cations underelevated temperature in First Strand Synthesis Reaction Buffer(5X). First strandcDNA was synthesized using random hexamer primer and M- MuLVReverseTranscriptase, then use RNaseH to degrade the RNA. Second strand cDNAsynthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends viaexonuclease/polymerase activities. After adenylation of 3’ endsof DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNAfragments of preferentially 370~420 bp in length, the library fragmentswere purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, andthe library was finally obtained.
In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initiallyquantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and theinsertsize of the library is detected by Agilent 2100 bioanalyzer. After insert sizemeets the expectation, qRT-PCR is used to accurately quantify theeffective concentration of the library (the effectiveconcentration of the library is higher than that of 1 . 5 nM) to ensure the qualityof the library.

treatment_protocol: Knockout of adipocyte-KLF10 in iWAT of mice

value: iWAT

value: male

value: HFD-fed


title: KO-4


title: KO-1


title: KO-3


title: C57BL/6j mice, nineteen-month-old, infected, rep2


title: C57BL/6j mice, nineteen-month-old, infected, rep3


title: WT-3

value: Wildtype


title: WT-4


title: WT-2


title: S2D_αCD8-2

city: Charlottesville

first: Harish

last: Narasimhan

state: Virginia

address: 345 Crispell Drive

institute: University of Virginia

description: Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing

data_processing:
The spatial transcriptome (ST, 10x Visium) data were preprocessed using the 10x Genomics pipeline (Space Ranger) v2.0.1 using the hg38/mm10 genome. Only high-quality spots with sufficient covered genes (>=2000) were retained for the downstream analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: Respective matrix files
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Library strategy: Spatial transcriptomics

source_name: Lungs

extract_protocol:
Formalin fixed paraffin embedded lung sections (5um) were mounted onto Visium slide
Spatial transcriptome sequecing libraries were prepared with 10X Genomics Visium spatial gene expression slides and reagent kit according to manufacturer's instructions.

value: Lungs


title: S1A_IgG1

value: Control IgG


title: 3F2 Gata6 sgRNA#2 replicate 2

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

data_processing:
Paired-end read alignment to mouse genome (mm10 version) was performed with STAR aligner (version 2.7.10) with default setting. Samtools were used for filtering and sorting aligned reads before annotation to “mm10.GRCm38.95.gtf” gene version with featureCounts (subread 2.0.6 version). Only protein-coding and long-non-coding RNA transcripts were used for annotation and downstream differential expression analysis was performed with R package DESeq where we set a log2 fold change of 1.5 and P-adjusted of <0.05 as a cut off for calling deferentially expressed genes.
Assembly: mm10 and mm10.GRCm38.95.gtf
Supplementary files format and content: raw counts for all samples are submitted in tab delimited format with official gene symbol and ensembl gene id

source_name: XEN

extract_protocol:
RNA-seq libraries were prepared and sequenced by Novogene Bioinformatics Technology Co. Ltd.
Sequencing libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s instructions. High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform.

value: XEN

value: SGRNA#2 GATA6


title: 3f2_ev1

data_processing:
Paired-end reads were aligned to mouse genome (mm10 version) with bowtie2 (version 2.3.4.1) and ‘–local –very-sensitive-local -I 10 -X 2000’ option active. Picard tools, Samtools and Bedtools were used for filtering duplicate reads (‘MarkDuplicate’ option), low quality reads (MAPQ<20), chrM and blacklisted regions and converting files into sam, bam, bed bigWig format. All filtered reads were corrected for Tn5 insertions per read – pair by shifting +4 bp or −5 bp from the positive and negative strands, respectively. All corrected – filtered reads were used to generate bigWig files after merging replicate experiments
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
ATAC-seq during reprogramming was carried out as previously described with minor modifications (Buenrostro, et al., 2015).
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541), a uniquely barcoded primer per sample, and a universal primer. Samples were first subjected to 5 cycles of initial amplification. To determine the suitable number of cycles required for the second round of PCR (to minimize PCR bias) the library was assessed by quantitative PCR. Briefly, a 5 μL aliquot of the initial amplification sample was used for 20 cycles of qPCR. Linear Rn versus cycle was plotted to determine cycle number corresponding to 1/3 of maximum fluorescent intensity. For each sample, the remaining 45 μL of initial tagmented PCR product was further amplified for 5 more cycles using Nextera primers. Samples were subject to a dual size selection (0.55x–1.5x) using SPRIselect beads (Beckman Coulter,B23317). Fragment distribution of libraries was assessed with an Agilent Bioanalyzer and finally, the ATAC libraries were sequenced on an an Illumina NovaSeq 6000 (PE-50, 20 million reads per sample).

value: Empty vector


title: 3f2_ev2


title: 3f2_sgrna1_gata4

value: SGRNA#1 GATA4


title: gata6_rep3_xen

data_processing:
Paired-end reads were aligned to mouse genome (mm10 version) with bowtie2 (version 2.3.4.1) and ‘–local –very-sensitive-local’ option active. Picard tools, Samtools and Bedtools were used for filtering duplicate reads (‘MarkDuplicate’ option), low quality reads (MAPQ<20), chrM and blacklisted regions and converting files into sam, bam, bed bedGraph format. All filtered reads were used to generate bedGraphs and SEACR (version 1.3) was used to generate peaks with ‘0.01 non strigent’ options active. Only common peaks among triplicates were considered valid for both Gata4 and Gata6 (peak_gata4.bed & peak_gata6.bed files)
Assembly: mm10
Supplementary files format and content: bed files (chr/start/end)
Library strategy: Cut&Run

extract_protocol:
CUT&RUN on Gata4 and Gata6 factors was performed on 500,000 3F2 cells as previously described with minor modifications (Skene et all., 2018).
CUT&RUN libraries were prepared using the Thruplex Library Prep kit (Takara) according to the manufacturer’s instructions. The number of cycles for library PCR amplification was determined by running 10% of each library sample in an Applied Biosystems qPCR machine with 0.25μl Eva Green dye (Biotium 31000) for 40 cycles and adding cycles to each sample as described (Buenrostro, et al., 2015). Libraries were size selected with 1.5x volume SPRI beads (Beckman Coulter B23317) and sequenced at the Weill Cornell Genomics Resources Core Facility on an Illumina NovaSeq 6000 (PE-50, 30 million reads per sample).


title: S2A_IgG2


title: WT-1


title: gata4_rep2_xen


title: 3f2_sgrna2_gata6


title: gata6_rep1_xen


title: 3f2_sgrna2_gata4

value: SGRNA#2 GATA4


title: 3F2 Gata6 sgRNA#2 replicate 1


title: S1D_αCD8-1


title: gata4_rep3_xen


title: Vacuolin-1-4C-2

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

data_processing:
Raw reads were first trimmed using Trimmomatic (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base pairs (fewer than 3) were trimmed, and a 4-bp   sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Only reads having at least 50-bp were kept.
The resulting reads were mapped to the mm10 genome using STAR (v.2.5.2b) with the following parameters: -outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout -outSAMattributes NH HI AS NM MD -outFilterMultimapNmax 20 -outFilterMismatchNmax 999 -quantMode TranscriptomeSAM GeneCounts.
Then the ‘Trimmed Mean of M values’ normalization (TMM) method from the R/Bioconductor package edgeR package (v3.24.0) was used to calculate the normalized expression
The R/Bioconductor edgeR package (v3.24.0)was used to detect the differentially expressed genes between the different samples using the generalized linear model-based method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Count for each Sample

source_name: 4-cell embryos

extract_protocol:
Cellular RNA was collected using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, cat. no. RC112).RNA of embryos was extracted by the PicoPure RNA Extraction Kit (Arcturus, cat. no. KIT0204).
For the RNA-seq library of mESCs, Total RNA was used as input material for the RNA sample preparations. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNase H to degrade the RNA. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. The library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA) for preferentially cDNA fragments. After PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. For the RNA-seq library of embryos, 10-15 4-cell stage embryos were pooled per sample. The total RNA of each sample was extracted by the PicoPure RNA Extraction Kit (Arcturus, cat. no. KIT0204). 200 ng total RNA was used for library generation using SMARTer Stranded Total RNA-Seq Kit v2 (Takara, cat. no. 634836).

value: 4-cell embryos

value: Vacuolin-1 treated


title: 3f2_sgrna1_gata6

value: SGRNA#1 GATA6


title: 3F2 Gata6 sgRNA#1 replicate 2


title: 3F2 Gata4 sgRNA#2 replicate 2


title: 3F2 Gata4 sgRNA#1 replicate 2


title: 3F2 Gata4 sgRNA#2 replicate 1


title: 3F2 Gata4 sgRNA#1 replicate 1


title: 3F2 Gata6 sgRNA#1 replicate 1


title: 3F2 empty vector replicate2


title: gata6_rep2_xen


title: RV1B d4, rep 2

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

description:
9578-JB-5
instrument model: Illumina NovaSeq X Plus

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.
The reads were trimmed using Cutadapt v2.3. The reads were evaluated with FastQC (v0.11.8) to determine quality of the data and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011)..
Alignment options followed ENCODE standards for RNA-seq. QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL 102) using STAR v2/7.8a and assigned count estimates to genes with RSEM v1/3.3
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all Samples.

extract_protocol:
Total RNA was prepared using Trizol extraction.  RNA was double purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
cDNA libraries for next generation sequencing were prepared with a xGen Broad-range RNA Library Prep with xGen Normalase UDI Primers.
Samples were subjected to 151 bp paired-end sequencing using a NovaSeq S4 or NaveSeq X Plus flow cell according to the Illumina NovaSeq manufacturer’s protocol.

treatment_protocol: Mice were treated intranasally with sham LLC-MK2 cell lysate, 100,000 TCID50 units HCoV-NL63, or 1,000,000 PFU RV-A1B. At 48h their lungs were harvested for RNA.

value: lung

value: RV1B d4


title: NL63 d4, rep 2

description:
9578-JB-2
instrument model: Illumina NovaSeq X Plus

value: NL63 d4


title: 3F2 empty vector replicate1


title: NL63 d4, rep 1

description:
9578-JB-1
instrument model: Illumina NovaSeq X Plus


title: RV1B d4, rep 1

description:
9578-JB-4
instrument model: Illumina NovaSeq X Plus


title: gata4_rep1_xen


title: NL63 d2, rep 2

value: NL63 d2


title: RV1B d4, rep 3

description:
9578-JB-6
instrument model: Illumina NovaSeq X Plus


title: NL63 d2, rep 1


title: RV1B d6 NL63 d2, rep 3

value: RV1B d6 NL63 d2


title: NL63 d4, rep 3

description:
9578-JB-3
instrument model: Illumina NovaSeq X Plus


title: Sham d2, rep 1

value: Sham d2


title: Sham d2, rep 2


title: RV1B d2, rep 2

value: RV1B d2


title: RV1B d2, rep 3


title: NL63 d2, rep 3


title: sham d2, rep 3


title: siFlcn-4C-2

value: WT

value: Flcn knockdown


title: 24doxrep3input

city: Madison

first: Elaine

last: Alarid

state: WI

address: 111 Highland Avenue

institute: University of Wisconsin Madison

data_processing:
Data was processed from NovaSeq 6000 with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Breast cancer

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium, supplemented with 10% VWR fetal bovine serum, 1% sodium pyruvate, and 1% penicillin streptomycin in 10% CO₂ at 37°C. Prior to treatment, cells were synchronized and stripped of any contaminates after being cultured for 3 days in phenol-red free DMEM, supplemented with 10% 6x charcoal stripped FBS, 1% sodium pyruvate, 1% Pen/Strep, and 2% L-glutamine.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes prior to quenching and cell lysis. Genomic material was sonicated using a 550 sonic dismembrator (Fisher Scientific)
Libraries were prepared using the NEBNext Ultra II DNA Library. Prep Kit for Illumina. 500 pg DNA was used as starting material for IP samples and inputs. Libraries were amplified using 14 cycles on the Thermocycler. Amplified libraries were size selected for 370 bp using AMPure XP beads from Beckman Coulter. Final libraries were validated using the Agilent High Sensitivity DNA kit.

treatment_protocol: Cells were treated with 1 μg/mL doxycycline hyclate and 10 nM 17β-estradiol for 24, 48, or 72 hours, changing the media every 24 hours.

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: 1 μg/mL Dox for 24 hours


title: cortex_P10_wt

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

data_processing:
Reads were aligned and counted using CellRanger 6.1.1 (10x Genomics) using standard parameters
Seurat version 4.1 was used to analyze data
Low-quality nuclei were filtered out of the dataset: percentage mitochondrial genes >3%, nCount >20000 UMI or <300 genes. Doublets were also removed using scdblFinder.
Assembly: mm10 3.0.0
Supplementary files format and content: Seurat rds object file containing 8030 nuclei
Supplementary files format and content: CellRanger filtered output: h5 file with features (rows) and nuclei (columns) &  CellRanger raw output: h5 file with features (rows) and nuclei (columns)

source_name: cortex (brain)

extract_protocol:
Nuclei from whole cortex were obtained from one mouse at age P10, anesthetized with isoflurane and sacrificed by decapitation. The dissected cortex tissue was immediately placed in a dry-ice-cold tube for immediate freezing until processing for nuclei isolation. Dissected frozen cortex was resuspended and mechanically homogenized using dounce homogeneizer to release nuclei following the Salty EZ 10 protocol (dx.doi.org/10.17504/protocols.io.bx64prgw). Nuclei were then resuspended in 500μL of resuspension buffer and 50k  nuclei were sorted (BD ARIA) based on DAPI intensity. Nuclei were finally centrifuged at 500xg for 5 minutes and diluted in resuspension buffer to a concentration of 1200 nuclei/μl before encapsulation in 10x Chromium. All steps were carried on ice or at 4°C.
Libraries were prepared according to 10x Genomics 3’ version 3.1 chemistry & Illumina protocols

value: cortex (brain)

value: cortical cells

value: wild type

tag: developmental stage

value: Postnatal day 10

value: Female


title: siFlcn-4C-1

value: 4-cell embryos


title: RV1B d6 NL63 d2, rep 1

value: lung


title: 24-doxrep3input

tag: chip antibody

value: vehicle


title: siGFP-4C-2

value: GFP knockdown


title: RV1Bd2, rep 1


title: RV1B d6 NL63 d2, rep 2

value: RV1B d6 NL63 d2


title: siGFP-4C-1


title: Vacuolin-1-E2C-3

source_name: early 2-cell embryos

value: early 2-cell embryos

value: Vacuolin-1 treated


title: 72doxrep4

value: GRHL2 (Millipore, #HPA004820)

value: 1 μg/mL Dox for 72 hours


title: Vacuolin-1-E2C-2

value: WT


title: Vacuolin-1-E2C-1


title: WT-E2C-3

value: Vehicle treated


title: 48doxrep4

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: 1 μg/mL Dox for 48 hours


title: Vacuolin-1-4C-1


title: WT-E2C-2


title: WT-E2C-1


title: FlcnKO_Vacuolin-1_i2C_2

value: embryonic stem cell

value: Flcn KO


title: 24-doxrep4


title: WT-4C-2


title: 24doxrep4

value: 1 μg/mL Dox for 24 hours


title: FlcnKO_DMSO_i2C_2


title: WT-4C-1

value: 4-cell embryos


title: sgSV40_DMSO_i2C_2


title: 72doxrep3


title: sgSV40_Vacuolin-1_i2C_2


title: FlcnKO_DMSO_i2C_1


title: 72-doxrep4


title: 72-doxrep3


title: Ku80 CUT&Tag 1

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

description: CUT&Tag

data_processing:
For CUT&Tag analysis, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify CUT&Tag peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
Assembly: ToxoDB-57_TgondiiME49 genome
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: tachyzoites

growth_protocol: Transgenic strains were inoculated in 75 cm2 cell culture flasks and washed after 4 h to remove non-invasive parasites. Transgenic strains (1 x 107) were harvested after 20 h of incubation.

extract_protocol:
For CUT&Tag Library construction, the library was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina (Novoprotein, Suzhou, China) according to the manufacturer's instructions. Briefly, fresh tachyzoites were bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-HA) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG) for 1 h at room temperature. The parasites were then resuspended with pAG-Transposome buffer and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by MgCl2 treatment and DNA extraction was performed using DNA extract beads (Novoprotein, Suzhou, China).
For CUT&Tag Library construction, Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations (NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina B box, Novoprotein, Suzhou, China).

treatment_protocol: Transgenic parasite strains cultured in Vero cells were treated with either 500 μM IAA or vehicle for 12h or 24 h.

value: tachyzoites

value: RH

value: co-culture with DMSO vehicle for 24 h


title: Ku80 CUT&Tag 2

description: CUT&Tag


title: sgFlcn_i2C-2

value: Flcn knock down


title: AP2XII 8 CUT&Tag 1

description: CUT&Tag

value: co-culture with 500 μM IAA for 24 h


title: 48doxrep3


title: AP2XII 8 CUT&Tag 2

description: CUT&Tag


title: sgFlcn_i2C-1


title: 48-doxrep4

value: vehicle


title: sgSV40_i2C_1


title: sgSV40_i2C_2


title: 48-doxrep3

value: GRHL2 (Millipore, #HPA004820)


title: RS2Z35 iCLIP2 Replicate 3

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

institute: Goethe University Frankfurt

description:
iCLIP2
RS2Z35-bound RNA

data_processing:
Quality control: FastQC (v0.11.9)
Barcode and adapter trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --sjdbGTFfile ITAG4.0_gene_models.gff --sjdbOverhang 76 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.10), bedtools (v2.29.2): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0 && $6=="+") || ($3>=$7 && $6=="-")) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.1.2) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --method unique --random-seed=100
BAM to BED shifting one base upstream: bedtools (v2.29.2): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.29.2): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v385)
Processed reads from all three replicates were merged into a single file for each strand and subjected to peak calling using PureCLIP (version1.0.4) with default paraments.
The resulting crosslink sites were used for identifying RBP binding sites using the R/ Bioconductor package BindingSiteFinder (version 1.7.9; PMID: 31751605). Prior to binding site definition, the crosslink sites obtained from the peak calling step were filtered to remove those with the lowest 5% PureCLIP scores. Subsequently, gene-wise filter was applied to discard sites with the lowest 10% PureCLIP score on each gene, ensuring a fair filtering approach for genes irrespective of gene expression levels.
Assembly: Tomato Genome version SL4.0
Supplementary files format and content: bigWig files containing the genomic coordinates and duplicate removed counts of uniquely mapped X-links for each replicate separated by strand.
Supplementary files format and content: BED files containing the genomic coordinates of identified binding sites.
Library strategy: iCLIP2

organism: Solanum lycopersicum

source_name: Leaf

extract_protocol:
Cells were lysed and RNA-Protein-complexes were immunoprecipitated with GFP-Trap magnetic agarose beads (GFP Nanobody-coupled beads) and subjected to on-bead RnaseI treatment.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer and a second adapter containing a barcode was ligated to the cDNAs. The cDNA was pre-amplified for 6 cycles using short Solexa P3 and P7 primers. After a size selection on beads a second PCR amplification was performed with the normal P3 and P7 primers to generate the final iCLIP2 libraries.

treatment_protocol: Excised leaves from 8-week-old transgenic tomato (Solanum Lycopersicum) plants overexpressing GFP-tagged RS2Z35 and GFP-RS2Z36, respectively, were subjected to 1 h 40°C in sealed petri dishes on wet tissue paper in a water bath. Leaves were subsequently irridiated with 254 nm UV light at 750 mJ/cm² to crosslink proteins to nucleic acids.

value: Leaf

value: Heat stress

value: UV-crosslinking

tag: barcode sequence

value: NNNNNGCTCATNNNN


title: Vacuolin-1_i2C_2

value: WT

value: Vacuolin-1 treated


title: 24doxrep3

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)


title: RS2Z35 iCLIP2 Replicate 1

description:
iCLIP2
RS2Z35-bound RNA

value: NNNNNCTGATCNNNN


title: hPSC-hepatocytes, TP53 and PTEN knockout, rep1

first: Yijia

last: Chi

state: 上海

address: No. 555 Zuchongzhi Road, Pudong New District, Shanghai, China

institute: Shanghai Institute of Material Medica

data_processing:
Sequencing reads from SMART-seq3 were processed using Umi-tools (version 1.1.4) to extract UMI-containing reads, which were subsequently aligned to the GRCh38 human reference genome (Gencode v43) using STAR (version 2.7.11a).
UMI reads were assigned to exon features using featureCounts (version 2.0.3). Normalization and differential expression analysis of counts were performed using the Deseq2 R package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: human pluripotent stem cells

growth_protocol: The H1 human embryonic stem cells were obtained from WiCell and grown in Pluripotency Growth Master 1 (PGM1) human pluripotent stem cell culture medium (Cellapy). Human pluripotent stem cell H1 were seeded at the density of 5 x 104 cells/cm2 in Matrigel-coated 48-well plates and cultured in complete PGM1 culture media for 1-2 days. To generate definitive endoderm, H1 were cultured in 1640 medium supplemented with 0.5 mg/ml albumin fraction V and 100 ng/ml Activin a for 1 day. On the following 2 days, 0.1% and 1% insulin-transferrin-selenium (ITS) was added to DAY1 medium. On the following steps, we sequentially differentiated definitive endoderm into posterior foregut, hepatic progenitors and hepatocytes stage according to the previous reports (Wang et al., Cell Res. 2020)

extract_protocol:
RNA-sequencing libraries were prepared based on the smart-seq3 and smart-seq3xpress methods, with direct lysed cells for library construction.
RNA-sequencing libraries were prepared based on the smart-seq3 and smart-seq3xpress method.

treatment_protocol: We conducted lentivirus-based gene modification on hPSC-derived hepatocytes at the hepatic progenitor stage

value: human pluripotent stem cells

value: TP53 and PTEN knockout

value: hepatocytes differentiation


title: hPSC-hepatocytes, TP53 and PTEN knockout, rep2


title: RS2Z35 iCLIP2 Replicate 2

description:
iCLIP2
RS2Z35-bound RNA

value: NNNNNAAGCTANNNN


title: 24-doxrep3


title: sgSV40_Vacuolin-1_i2C_1

value: embryonic stem cell


title: sgSV40_DMSO_i2C_1

value: Vehicle treated


title: hPSC-hepatocytes, PIK3CA overexpression, rep1

value: PIK3CA overexpression


title: FlcnKO_Vacuolin-1_i2C_1

value: Flcn KO


title: 48doxrep2

value: GRHL2 (Millipore, #HPA004820)

value: 1 μg/mL Dox for 48 hours


title: hPSC-hepatocytes, PIK3CA overexpression, rep2


title: RS2Z35 iCLIP2 no UV control

description:
iCLIP2
RS2Z35-bound RNA

value: Leaf

value: Heat stress

value: no UV

value: NNNNNTCAAGTNNNN


title: RS2Z36 iCLIP2 Replicate 3

description:
iCLIP2
RS2Z36-bound RNA

value: UV-crosslinking

value: NNNNNCACTGTNNNN


title: DMSO_i2C_1

value: WT


title: DMSO_i2C_2


title: RS2Z36 iCLIP2 Replicate 2

description:
iCLIP2
RS2Z36-bound RNA

value: NNNNNGCCTAANNNN


title: FlcnKD_i2CLC_Tfe3_2

data_processing:
The raw CUT&Tag reads were trimmed by trim-galore (v 0.6.7). The clean reads were mapped to mm10 genome by bowtie2 (v 2.3.5.1) with following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Samtools (v 1.9) was used to convert and sort the SAM files into BAM format.
SEACR (v 1.3) was used for peaks calling by selecting the top 1% regions of AUC.
Deeptools (v 3.5.1) was used to convert the bam file to the bigwig file via bamCoverage. ComputeMatrix was used to calculate the overall CUT&Tag signal, and plotProfile was used for signal distribution visualization.
Assembly: mm10
Supplementary files format and content: bed files include peaks region for each Sample
Library strategy: CUT&Tag

extract_protocol:
5×105 cells were washed once with PBS and resuspended in ice-cold NE1 buffer for 10 min. Cells were fixed in 0.1% formaldehyde and incubated for 2 min and 2.5 M glycine was used to stop cross-linking. Cells were incubated with activated ConA beads for 10 min. The bead-bound cells were resuspended in 100 µL antibody buffer containing appropriate primary antibody. Primary antibody incubation was performed on a rotator at 4 °C overnight. Secondary antibody was diluted in antibody buffer and incubation was performed on a rotator for 1 h. After washing by wash buffer, the cells were incubated with pA-Tn5 (~0.04 uM) on the rotator for 1 h. The cells were resuspended in Tagmentation buffer for 1 h. Tagmentation was stopped by adding 10µL of 0.5M EDTA, 3µL 10% SDS, and 5 µL 10 mg/ml Proteinase K and incubated at 56 °C for 30 min. The DNA was extracted by chloroform.
For library amplification, 21 µL DNA was mixed with 2 µL of a universal i5, 2 µL of a uniquely barcoded i7 primer, and 25 µL NEBNext HiFi 2× PCR Master mix. The library was amplified by following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 45 s; 14 cycles of 98 °C for 15 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 4 °C.

value: DOX


title: 48-doxrep2

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: vehicle


title: FlcnKD_i2CLC_Tfe3_1

value: embryonic stem cell


title: Vacuolin-1_i2C_1

value: Vacuolin-1 treated


title: hPSC-hepatocytes, ARID1A and AXIN1 knockout, rep1

value: human pluripotent stem cells

value: ARID1A and AXIN1 knockout

value: hepatocytes differentiation


title: 72doxrep2

value: GRHL2 (Millipore, #HPA004820)

value: 1 μg/mL Dox for 72 hours


title: RS2Z36 iCLIP2 Replicate 1

description:
iCLIP2
RS2Z36-bound RNA

value: Leaf

value: Heat stress

value: NNNNNACATCGNNNN


title: hPSC-hepatocytes, ARID1A and AXIN1 knockout, rep2


title: 72-doxrep2


title: RS2Z36 iCLIP2 no UV control

description:
iCLIP2
RS2Z36-bound RNA

value: no UV

value: NNNNNCGTGATNNNN


title: FlcnKD_mESC_Tfe3_2

value: Flcn KO


title: 3F6 XEN replicate2

data_processing:
Paired-end read alignment to mouse genome (mm10 version) was performed with STAR aligner (version 2.7.10) with default setting. Samtools were used for filtering and sorting aligned reads before annotation to “mm10.GRCm38.95.gtf” gene version with featureCounts (subread 2.0.6 version). Only protein-coding and long-non-coding RNA transcripts were used for annotation and downstream differential expression analysis was performed with R package DESeq where we set a log2 fold change of 1.5 and P-adjusted of <0.05 as a cut off for calling deferentially expressed genes.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10 and mm10.GRCm38.95.gtf
Supplementary files format and content: raw counts for all samples are submitted in tab delimited format with official gene symbol and ensembl gene id

source_name: XEN 3F6

value: XEN 3F6

value: extraembryonic endoderm stem cells


title: hPSC-hepatocytes, TP53 knockout, rep1

value: TP53 knockout


title: FlcnKD_mESC_Tfe3_1


title: hPSC-hepatocytes, APC and TP53 knockout, rep2

value: APC and TP53 knockout


title: 24doxrep2

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: 1 μg/mL Dox for 24 hours


title: 24-doxrep2

value: vehicle


title: hPSC-hepatocytes, TP53 knockout, rep2

value: human pluripotent stem cells

value: hepatocytes differentiation


title: Intestine_C24V1V2_Input_rep1

first: Mark

last: Meyer

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
Data was processed from NovaSeqX with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig files for display in the UCSC genome browser

source_name: intestine (duodenum)

growth_protocol: C57BL/6 mice aged 8-9 wk (The Jackson Laboratory, Bar Harbor, ME) were housed in high density ventilated caging in the Animal Research Facility of University of Wisconsin-Madison under 12-hour light/dark cycles at 72°F and 45% humidity. All mice used in this study were maintained on a standard rodent chow diet (5008, Lab Diet, St. Louis, MO). All experiments and tissue collections were performed in the procedure rooms in the Research Animal Facility of University of Wisconsin-Madison. All animal studies were reviewed and approved by the Research Animal Care and Use Committee of University of Wisconsin-Madison under protocol A005478.

extract_protocol:
The kidneys were isolated, rinsed with cold 1× phosphate-buffered saline, and subjected to a cross-linking reaction for 10 min with 1.5% formaldehyde. After the fixative was neutralized for 5 min with glycine (0.125mfinal concentration), the kidney tissue was homogenized briefly in phosphate-buffered saline using a loose fitting Dounce pestle, and the cells were collected via 70-μm nylon cell strainers (BD Falcon). Cells were then subjected to ChIP analysis.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, #E7645S) with the NEBNext Multiplex Oligos for Illumina (NEB, #E6440S) according to the manufacturer’s protocols. Libraries were submitted to Azenta/Genewiz and sequenced on a NovaSeq X. Paired-end, 150 bp sequencing with a target of 30+ million reads was performed.

treatment_protocol: Animals were subjected to intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), or vehicle (EtOH, PBS). Animals were sacrificed and tissues collected at 30 min (PTH) or 60 min (all other treatments) and subjected to ChIP followed by ChIP-seq.

value: intestine (duodenum)


title: Kidney_C24V1V2_Input_rep1

source_name: kidney

value: kidney


title: FlcnKD_mESC_Tfeb_2

value: embryonic stem cell


title: 3F6 iPS  replicate2

source_name: iPS 3F6

value: iPS 3F6

value: induced pluripotent cell


title: hPSC-hepatocytes, APC and TP53 knockout, rep1


title: Kidney_C24V1V2_pCREB_PTH30_rep3

value: 230 ng/g bw PTH (30 min)


title: FlcnKD_i2CLC_Tfeb_1

value: Flcn KO

value: DOX


title: hPSC-hepatocytes, PIK3CA and MYC overexpression, rep2

value: PIK3CA and MYC overexpression


title: Kidney_C24V1V2_pCREB_PTH30_rep2


title: FlcnKD_mESC_Tfeb_1


title: Kidney_C24V1V2_pCREB_PTH30_rep1


title: 3F4 XEN replicate1

source_name: XEN 3F4

value: XEN 3F4

value: extraembryonic endoderm stem cells


title: 3F4 iPS replicate2

source_name: IPS 3F4

value: IPS 3F4


title: hPSC-hepatocytes, PIK3CA and MYC overexpression, rep1


title: 3F6 XEN replicate1

value: XEN 3F6