title: K27ac_HS_22RV1_H1KO

value: Heat shock at 42℃ for 60 min (HS)


title: Input_K27ac_NHS_22RV1_H1KO

status: Public on Sep 02 2025

type: SRA

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

library_source: genomic

data_processing:
basecalling: bcl2fastq v2.20.0
Adapter trimming: Trimmomatic v0.38
Align: Bowtie 1.1.2
Deduplication: Picard 1.118 MarkDuplicates
Peak calling: MACS2 2.1.1.20160309
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: 22RV1 and SM1 cells were grown at 37°C with 5% CO2 in a humidified atmosphere in RPMI 1640 supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Chromatin preparation and ChIP were performed with the SimpleChIP Plus Enzymatic Chromatin IP kit (Cell signaling Technology) following the manufacturer’s instructions.
ChIP-seq libraries were constructed with the TruSeq ChIP Library Preparation Kit (Illumina).

treatment_protocol: The HSF1 and DBC1 genes were knocked out from 22RV1 and SM1 cells using CRISPR/Cas9 gene editing technology. Cells were treated with or without heat shock at 42℃ for 60 min (HS or NHS).

tag: chip antibody

tag: cell line

tag: cell type

value: Castration-resistant prostate cancer cells

tag: treatment

value: Non-heat shock (NHS)


title: GM12878, Nuclei, 500K, biol rep 3

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description: Library name: GM12878 500K N3

library_source: transcriptomic

data_processing:
Quality Control & Trimming: Raw reads were quality-checked with FastQC. Adapters and low-quality bases were trimmed using fastp, removing the first 3 bases and reads shorter than 30 bp.
rRNA Filtering: Reads mapping to rRNA were filtered using rRNAdust
Mapping: Filtered reads were aligned to the hg38 genome using STAR, allowing only uniquely mapping reads.
Post-processing: BAM files were sorted, indexed, and converted to strand-specific CTSS bed files. Unmatched G additions were corrected on the 5′ end, and final BigWig files were generated.
QC Metrics: Alignment complexity was assessed with Preseq, and alignment statistics were computed using samtools stats and flagstat.
Assembly: hg38
Supplementary files format and content: CTSS BigWig files: strand-specific coverage tracks with counts representing the number of 5′ ends of CAGE tags per genomic position, split into plus and minus strands.

molecule: nuclear RNA

growth_protocol: K562 were cultured in Advanced RPMI 1640 including 1 mM sodium pyruvate and 11.1 mM D-Glucose; HepG2 in DMEM medium without sodium pyruvate and 25 mM D-Glucose; A549 in Ham's F-12 Nutrient Mix including 1 mM sodium pyrivate; 1 mM L-Glutamine and 10 mM D-Glucose; HCT116 in DMEM medium including 1 mM sodium pyruvate and 5,6 mM D-Glucose; GM12878 in RPMI 1640 medium without sodium pyruvate and 11,1 mM D-Glucose. 10% v/v FCS and 1% v/v Penicillin-Streptomycin were added to all media compositions and 1% v/v L-Glutamine specifically for K562. All 5 cell lines were reared in Corning T-25 or T-75 flasks and incubated at 37°C and 5% CO₂.

extract_protocol:
Nuclei extraction was performed by employing a combination of hypotonic lysis buffer (10 mM Tris-HCl, pH 7,4; 10 mM NaCl; 3 mM MgCl2; 1% m/v BSA; 1% v/v 0,1% Tween-20; 0,1% NP-40; 0,01% Digitonin) including RNase inhibitors (4 mU/µl SUPERaseIn; 4 mU/µl Protector RNaseInh) and application of sheer forces by running the suspension through a 24 G needle for 10 times. Total RNA of nuclei or whole cell samples was extracted using the PureLink RNA Mini Kit with on-column DNase digestion. RNA quality was verified using the RNA 6000 Pico reagents and chips for automated gel electrophoresis on a 2100 Bioanalyzer.
SLIC-CAGE libraries for all samples were generated as outlined in Cvetesic N et al., 2018 (doi: 10.1101/gr.235937.118), including the addition of carrier RNA, reverse transcription, oxidation and biotinylation of capped RNA species, removal of ssRNA overhangs and incompletely transcribed RNA, cap-trapping on Streptavidin beads, release of single-stranded cDNA, adapter ligation and second-strand synthesis, digestion of carriers, size selection and PCR amplification. Libraries were pooled and single-end sequenced on an Illumina NextSeq550 sequencer using High Output v2.5 kits for 75 cycles.

treatment_protocol: 4 replicates of each 1 M GM12878 cells were treated with 10 µM triptolide for 5 h and 3 control replcates with 1 M GM12878 cells were acquired by applying DMSO as vehicle to the cells.


title: GM12878, Nuclei, 5M, biol rep 2

description: Library name: GM12878 5M N2


title: K27ac_NHS_22RV1_H1KO

value: H3K27ac (Abcam, ab4729)


title: Input_HSF1_HS_22RV1_D1KO


title: WT_mESC_CTCF_Rep1

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

description: Library name: Sample_6

data_processing:
ChIP-seq
ChIP-seq rads were trimmed using trommomatic (v0.39). Low-quality bases (Phred score <3) were removed from the read ends, and a sliding window of 4 bases was used to trim when the average quality dropped below 15. Reads shorter than 36 bp after trimming were discarded.
ChIP-seq pair-end reads were aligned against mm10 based custom reference genomes that included the sequence of the corresponding enhancer at the insertion site (Gata6 +100kb), using Bowtie2(v2.5.4). Bowtie2 alignment was restricted to concordant alignments, allowing up to two valid alignments per read
batch effect correction was performed by applying quantile normalization separately for each antibody across the different genotypes and replicates
Assembly: mm10 based custom refence genomes
Supplementary files format and content: Bigwig; for each sample the bigwig files show the quantile normalized signal for biological replicate

organism: Mus musculus

source_name: Mouse ESCs (E14Tg2a)

growth_protocol: Mouse ESCs (E14Tg2a) were cultured on gelatin-coated plates at 37°C with 5% CO2 in the presence of Knock-out DMEM, supplemented with 15% FBS , 0.1 mM 2-mercaptoethanol, 1x Glutamax, 1× penicillin–streptomycin, 1× MEM non-essential amino acids and leukemia inhibitory factor (LIF).

extract_protocol:
Briefly, ~4 × 107 and ~1 × 107 cells were used for co-activators and histone marks, respectivel. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature (RT) and quenched with 0.125 M glycine for 10 min. Cells were consecutively incubated with three different lysis buffers (Buffer 1_ 50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100; Buffer 2_ 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; Buffer 3_ 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in order to isolate chromatin. Next, chromatin was sonicated for 8 minutes in Buffer 3 (20 s on, 30 s off, 25% amplitude) using an EpiShear probe sonicator (Active Motif).  The sonicated chromatin was mixed with 3 μg of H3K27ac antibody or 10 μg of Rad21 antibody and incubated overnight at 4°C. Next, 50-100 μl of Dynabeads (Thermo Fisher, 10-002-D) were aliquoted into a microtube for each ChIP reaction. The dynabeads were washed with 1 ml of cold blocking solution (0,5% BSA and 1x PBS). The antibody bound chromatin was added to the washed beads and incubated for four hours at 4ºC. Magnetic beads were washed five times with RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0,7% Na-Deoxycholate). The chromatin was eluted and incubated at 65 °C overnight to reverse the crosslinking. Next, samples were treated with 0,2 mg/ml Rnase A and 0,2 mg/ml proteinase K. DNA  purification was performed using Zymoclean Gel DNA Recovery kit (Zymo Research, D4008).
TruSeq DNA Sample prep Kit (Illumina) ; starting material 10ng

treatment_protocol: Differentiation towards Neural Progenitor cells was performed by growing mESC for six days in N2B27 medium, supplemented with FGF and XAV

value: Mouse ESCs (E14Tg2a)

value: mESC

tag: genotype

value: Wild type

value: Actif Motif 61311


title: GM12878, Nuclei, 1M, biol rep 3

description: Library name: GM12878 1M N3


title: Input_HSF1_HS_22RV1


title: GM12878, Nuclei, 5M, biol rep 1

description: Library name: GM12878 5M N1


title: Enh-CBS_mESC_Rad21_Rep1

description: Library name: Sample_8

value: Enh-CBS

value: Abcam ab154769


title: K27ac_NHS_22RV1


title: GM12878, Nuclei, 1M, biol rep 2

description: Library name: GM12878 1M N2


title: GM12878, Nuclei, 1M, biol rep 1

description: Library name: GM12878 1M N1


title: GM12878, Nuclei, 10M, biol rep 2

description: Library name: GM12878 10M N2


title: GM12878, Nuclei, 500K, biol rep 1

description: Library name: GM12878 500K N1


title: GM12878, Cellular, 1M, biol rep 3

description: Library name: GM12878 1M C3

molecule: total RNA


title: WT_mESC_Rad21_Rep1

description: Library name: Sample_5


title: GM12878, Nuclei, 500K, biol rep 2

description: Library name: GM12878 500K N2


title: GM12878, Cellular, 1M, biol rep 2

description: Library name: GM12878 1M C2


title: Input_HSF1_NHS_22RV1_H1KO


title: WT_mESC_H3K4me1_Rep1

description: Library name: Sample_2

value: Actif Motif 39297


title: GM12878, Cellular, 1M, biol rep 1

description: Library name: GM12878 1M C1


title: WT_mESC_Total_RNA_PolII_Rep1

description: Library name: Sample_4

value: Actif Motif 39097


title: WT_mESC_H3K27Ac_Rep1

description: Library name: Sample_1

value: Actif Motif 39133


title: GM12878, Cellular, 500K, biol rep 3

description: Library name: GM12878 500K C3


title: WT_mESC_p300_Rep1

description: Library name: Sample_3

value: Actif Motif 61401


title: K526, Nuclei, 10M cells, biol rep 2

description: Library name: K562 10M N2


title: Adar1-KO_rep3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Library name: Sample6

library_source: transcriptomic single cell

data_processing:
Mapping was performed using CellRanger v7.2.0 with default parameters on the mouse reference transcriptome refdata-gex-mm10-2020 (GENCODE vM23/Ensembl 98; prebuilt Cell Ranger reference package) from 10X genomics. By default, CellRanger only annotates barcodes with more than 500 UMI counts as cells. Cellbender v3 (remove-background function) was employed to remove background signal (i.e. counts originating from ambient RNA molecules and random barcode swapping) before proceeding to downstream analyses. The resulting count matrices were imported into R (v 4.3.1) and subsequently analyzed using the Seurat (v 5.0.1) package. Count matrices were filtered to only keep cells with < 20% mitochondrial reads and 200-4000 detected genes (threshold defined as 4 times the mean median absolute deviation of the number of detected genes per cell). Gene counts were normalized using the NormalizeData function with default parameters. Principal Component Analysis (PCA) was performed with the RunPCA function. An elbow plot was generated using the ElbowPlot function to determine the optimal number of principal components (PCs) to be used for clustering. Cell clustering was performed based on the 15 top PCs using the shared nearest neighbor modularity optimization-based algorithm implemented in the FindNeighbors and FindClusters functions, the latter executed with a resolution of 0.5. UMAP dimensionality reduction was then computed based on the top 15 PCs. Differential expression analysis between all clusters was performed using the FindAllMarkers function with the following parameters: only.pos = T, min.pct = 0.5, logfc.threshold = 0.5. Only differentially expressed genes between the cluster of interest and all other clusters with an adjusted p-value < 0.05 were used for overrepresentation analyses (ORA). ORA was performed using DAVID on gene ontology (GO) Biological Process, Cellular Component and Molecular function; and KEGG gene sets. Pathways with an FDR < 0.05 were considered overrepresented. Pathway module scores were computed using the AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Filtered count matrices in HDF5 format.

molecule: polyA RNA

source_name: Brain tumor

growth_protocol: CD45-negative and CD45-positive cells were sorted from tamoxifen and vehicle-treated NTv-a;hUBC-CreERT2;Adar1flox/flox tumors two weeks from treatment start and mixed in a 1:8 ratio.

extract_protocol:
Samples were then processed for single-cell sequencing using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index, 10x Genomics) and following the manufacturer’s instructions.
Libraries were quantified using a Qubit fluorometer (Thermo Fisher), quality-checked on a Fragment Analyzer (Agilent Technologies) and sequenced in a NovaSeq 6000 sequencer (Illumina; 10x paired-end sequencing: read 1 = 28 base pairs; read 2 = 90 base pairs) at the GTF of UNIL.

treatment_protocol: Upon tumor detection by MRI, mice were treated daily for 5 consecutive days with 100mg/kg tamoxifen (or vehicle, as a control) by intraperitoneal administration (i.e. 100μL of a 20mg/mL tamoxifen solution -dissolved in sunflower seed oil- for a 20g mouse).

tag: tissue

value: Brain tumor

tag: replicate

value: Tamoxifen


title: GM12878, Cellular, 250K, biol rep 3

description: Library name: GM12878 250K C3


title: GM12878, Cellular, 500K, biol rep 2

description: Library name: GM12878 500K C2


title: GM12878, Cellular, 250K, biol rep 2

description: Library name: GM12878 250K C2


title: Input_HSF1_NHS_22RV1_D1KO


title: GM12878, Cellular, 500K, biol rep 1

description: Library name: GM12878 500K C1


title: Input_HSF1_NHS_22RV1


title: GM12878, Cellular, 250K, biol rep 1

description: Library name: GM12878 250K C1


title: Input_HSF1_HS_22RV1_H1KO


title: K526, Nuclei, 2.5M cells, biol rep 1

description: Library name: K562 N4


title: K526, Nuclei, 10M cells, biol rep 1

description: Library name: K562 10M N1


title: K526, Nuclei, 2.5M cells, biol rep 3

description: Library name: K562 N6


title: Adar1-WT_rep3

description: Library name: Sample4

value: Vehicle


title: HSF1_HS_22RV1_H1KO

value: HSF1 (Enzo, ADI-SPA-901-F)

value: Heat shock at 42℃ for 60 min (HS)


title: K526, Nuclei, 2.5M cells, biol rep 2

description: Library name: K562 N5


title: Adar1-WT_rep2

description: Library name: Sample3


title: HSF1_HS_22RV1

value: Castration-resistant prostate cancer cells


title: Adar1-KO_rep2

description: Library name: Sample5


title: K526, Nuclei, 10M cells, biol rep 3

description: Library name: K562 10M N3


title: A549, Nuclei, 2.5M cells, biol rep 2

description: Library name: A549 N6


title: A549, Nuclei, 2.5M cells, biol rep 1

description: Library name: A549 N5


title: K526, Cellular, 2.5M cells, biol rep 1

description: Library name: K562 C1


title: K526, Cellular, 2.5M cells, biol rep 2

description: Library name: K562 C2


title: Adar1-KO_rep1

description: Library name: Sample1


title: HSF1_HS_22RV1_D1KO


title: K526, Cellular, 2.5M cells, biol rep 3

description: Library name: K562 C3


title: NHS_SM1_H1KO

data_processing:
Illumina bcl2fastq v2.20.0 software used for basecalling.
Sequenced RNA-seq reads were trimmed for adaptor sequence using Trimmomatic v0.38.
Paired end 101 bp reads generated from RNA-seq were mapped using HISAT2.1.0 to the Homo sapiens GRCh37 genome build and raw counts per quantified using HTSeq.
Fragments per kilobase of transcript per million mapped reads (FPKM) for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene.
Assembly: GRCh37
Supplementary files format and content: Matrix of gene expression measurements in FPKM

extract_protocol:
Total RNAs were purified using the RNeasy Plus Mini Kit (Qiagen).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Metastatic castration-resistant prostate cancer cells

value: Non-heat shock (NHS)


title: HSF1_NHS_22RV1_H1KO


title: HSF1_NHS_22RV1_D1KO


title: Adar1-WT_rep1

description: Library name: Sample2


title: A549, Cellular, 2.5M cells, biol rep 2

description: Library name: A549 C3


title: HSF1_NHS_22RV1


title: A549, Cellular, 2.5M cells, biol rep 1

description: Library name: A549 C1


title: HepG2, Nuclei 2.5M cells, biol rep 3

description: Library name: HepG2 N6


title: NHS_SM1_D1KO


title: HepG2, Cellular, 2.5M cells, biol rep 3

description: Library name: HepG2 C3


title: HepG2, Nuclei, 2.5M cells, biol rep 2

description: Library name: HepG2 N5


title: Irx3_cutnrun_Fasted_2

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

country: USA

institute: University of Utah

description:
Library name: B6_Irx3_CutNRun_Fasted_2
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet

data_processing:
CutNRun data aligned with bowtie.
Peaks called with Genrich.
Assembly: mm10
Supplementary files format and content: CutNRun: Genrich Peak calls, Bedgraph files.
Library strategy: CUT&Run

source_name: Hypothalamus

extract_protocol:
AmpureXP double sided cleanup, 0.1X TE Buffer elution.
Sequencing libraries were prepared from Cut and Run DNA samples (0.1 to 5 ng) using the New England Biolabs NEBNext Ultra II DNA Library Prep kit (cat#E7634L). PCR-amplified libraries (15 cycles) were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583) and the molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Libraries were normalized and pooled in preparation for Illumina sequencing.

treatment_protocol: Fasted for 72 hours with water, refed on normal chow.

value: Hypothalamus

value: WT

value: Fasted

tag: batch

tag: antibody

value: IRX3 Antibody:Santa Cruz IRX3 (G-6):sc-166877


title: Irx3_cutnrun_Fasted_3

description:
Library name: B6_Irx3_CutNRun_Fasted_3
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: HepG2, Cellular, 2.5M cells, biol rep 2

description: Library name: HepG2 C2


title: HepG2, Cellular, 2.5M cells, biol rep 1

description: Library name: HepG2 C1


title: HCT116, Cellular, 2.5M cells , biol rep 2

description: Library name: HCT116 C2


title: HepG2, Nuclei, 2.5M cells, biol rep 1

description: Library name: HepG2 N4


title: HCT116, Cellular, 2.5M cells , biol rep 1

description: Library name: HCT116 C1


title: HS_SM1


title: HS_22RV1_D1KO


title: NHS_SM1


title: Irx3_cutnrun_Fasted_1

description:
Library name: B6_Irx3_CutNRun_Fasted_1
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: Irx3_cutnrun_Fed_4

description:
Library name: B6_Irx3_CutNRun_Fed_4
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet

value: Fed


title: HS_22RV1_H1KO


title: Irx3_cutnrun_Fed_3

description:
Library name: B6_Irx3_CutNRun_Fed_3
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: Irx3_cutnrun_Fed_2

description:
Library name: B6_Irx3_CutNRun_Fed_2
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: MUTZ-3 DMSO 24hr rep2 [RNA-Seq]

city: Boston

first: Travis

last: Fleming

state: MA

address: 1 Blackfan St

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: 24hr MUTZ-3 DMSO RNA rep2

data_processing:
FASTQ files were demultiplexed with bcl2fastq and aligned to the hg38 reference genome using bowtie2 (version 2.5.2). Sam files were sorted, indexed and converted to bam files with Samtools (version 1.18). For data visualization in a genome browser, bam files were converted to bigwig files using the bamCoverage package from deepTools (version 3.5.4) normalizing by counts per million (CPM). Count tables for genes were also generated from bam files using the featureCounts package from Subread (version 2.0.6) and differential gene expression analysis was performed using DESeq2 (version 1.40.2). Results were visualized using ggplot2 (version 3.4.4).
Assembly: hg38
Supplementary files format and content: bigWig and tab-delimited text files which includes raw counts for each sample

growth_protocol: MUTZ-3 cells (DSMZ), HNT-34 cells (Creative Bioarray), and OCI-AML4 cells (DSMZ) were cultured at 37 °C in α-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned medium from 5637 cells (ATCC) and 1% penicillin/streptomycin. Confluency for all cells was maintained between 7 × 105 and 1.5 × 106 ml−1. UCSD-AML1 cells (a gift from Dr. Kimberly Stegmaier’s lab) were cultured at 37 °C in RPMI 1640 (Life Technologies) supplemented with 20% FBS, 1% penicillin/streptomycin and 10ng/mL GM-CSF (Peprotech). Confluency was maintained between 5 × 105 and 1.5 × 106 ml−1.

extract_protocol:
Total RNA was extracted using the RNeasy Micro kit (QIAGEN, 74004) from 10,000-50,000 cells sorted or harvested in 25 µl Buffer RLT Plus with 1% BME.
RNA libraries for RNA-seq were prepared using the SmartSeq2 protocol from the reverse transcription step using 10 ng of RNA. The whole transcriptome amplification step was set at ten cycles. Bulk RNA libraries were pooled at appropriate molar ratios to obtain at least 20 million reads per library. Libraries were subject to paired-end sequencing with 150 cycles.

treatment_protocol: Cells were treated with 500nM of dTAGV-1 or DMSO for 6-24 hours.

value: AML cell line

value: Control


title: MUTZ-3 DMSO 24hr rep3 [RNA-Seq]

description: Library name: 24hr MUTZ-3 DMSO RNA rep3


title: HS_22RV1


title: NHS_22RV1_D1KO


title: MUTZ-3 dTAGV-1 24hr rep3 [RNA-Seq]

description: Library name: 24hr MUTZ-3 dTAG RNA rep3

value: MECOM degradation


title: Irx3_cutnrun_NegCtrl

description:
Library name: B6_Irx3_CutNRun_NegCtrl
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: MUTZ-3 DMSO 6hr rep3 [RNA-Seq]

description: Library name: 6hr MUTZ-3 DMSO RNA rep3


title: MUTZ-3 DMSO 6hr rep2 [RNA-Seq]

description: Library name: 6hr MUTZ-3 DMSO RNA rep2


title: Irx3_cutnrun_Fed_1

description:
Library name: B6_Irx3_CutNRun_Fed_1
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: NHS_22RV1


title: MUTZ-3 dTAGV-1 24hr rep2 [RNA-Seq]

description: Library name: 24hr MUTZ-3 dTAG RNA rep2


title: Irx3_cutnrun_Refed12hr_4

description:
Library name: B6_Irx3_CutNRun_Refed12hr_4
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: NHS_22RV1_H1KO


title: MUTZ-3 dTAGV-1 6hr rep3 [RNA-Seq]

description: Library name: 6hr MUTZ-3 dTAG RNA rep3


title: MUTZ-3 dTAGV-1 6hr rep1 [RNA-Seq]

description: Library name: 6hr MUTZ-3 dTAG RNA rep1


title: MUTZ-3 dTAGV-1 24hr rep1 [RNA-Seq]

description: Library name: 24hr MUTZ-3 dTAG RNA rep1


title: Irx3_cutnrun_Refed12hr_3

description:
Library name: B6_Irx3_CutNRun_Refed12hr_3
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: H9 STB, CCR7 KO, biol rep4

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 4480 Clayton Ave

institute: Washington University in St. Louis

data_processing:
Raw reads of RNA-seq libraries were processed using the RNA-seq pipeline (https://github.com/Zhang-lab/RNA-seq_QC_analysis) which consists of data processing, quality control, integrative analysis, and data visualization.
Assembly: human genome hg38 with STAR version 2.5.4b (Dobin et al., 2013). Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (version 1.4.6) (Liao et al., 2013), with hg38 gene annotation ENCODE V27 (Harrow et al., 2012).
Supplementary files format and content: TXT format, readcount table

extract_protocol:
Total RNA was isolated using NucleoSPIN RNA Mini Kit (Macherey-Nagel, 740955) and followed the manufacturer's instruction
cDNA library was constructed using the SMARTer cDNA kit (Clontech, 634933) and sequenced on an Illumina NovaSeq S4 2X150 platform

value: CCR7 KO H9

value: Syncytiotrophoblast (STB)

value: mutant


title: Irx3_cutnrun_Refed12hr_2

description:
Library name: B6_Irx3_CutNRun_Refed12hr_2
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: MUTZ-3 dTAGV-1 6hr H3K27ac ChIP

description: Library name: 6hr MUTZ-3 H3K27ac ChIP dTAG

data_processing:
FASTQ files were demultiplexed with bcl2fastq and aligned to the hg38 reference genome using bowtie2 (version 2.5.2). Sam files were sorted, indexed and converted to bam files with Samtools (version 1.18). For data visualization in a genome browser, bam files were converted to bigwig files using the bamCoverage package from deepTools (version 3.5.4) normalizing by counts per million (CPM). Peak calling was performed using MACS2 (version 2.2.9.1). NarrowPeak files from DMSO and dTAGV-1-treated cells were then merged and converted to SAF format to generate a consensus peak set for each cell line. This consensus peak file and corresponding bam files were then processed using the featureCounts package from Subread (version 2.0.6) to generate a count table for ChIP peaks.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: MUTZ-3 cells (DSMZ) were cultured at 37 °C in α-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned medium from 5637 cells (ATCC) and 1% penicillin/streptomycin. Confluency for all cells was maintained between 7 × 105 and 1.5 × 106 ml−1.

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed on chromatin from 1×106 CD34+ MUTZ-3-dTAG cells after treatment with 500nM dTAGV-1 or DMSO for 6 hours. Cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies, 28906), quenched with 0.125 M glycine and frozen at −80 °C and stored until further processing. ChIP reaction was performed with iDeal ChIP-seq kit for TFs (Diagenode, C01010055) with modifications of the manual detailed below. Lysed samples were sonicated using the E220 sonicator (Covaris, 500239) in microTUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris, 520045) with settings for 200-bp DNA shearing. Sheared chromatin was immunoprecipitated with 2.5 μg HA antibody (CST, HA-Tag (C29F4) Rabbit mAb #3724), 2.5 μg H3K27ac antibody (Diagenode, C15410196) or 2.5 μg IgG antibody (Diagenode, C15410206, RRID AB_2722554). Eluted and decross-linked DNA was purified with MicroChIP DiaPure columns (Diagenode, C03040001) and eluted in 30 μl of nuclease-free water.
ChIP and input libraries for sequencing were prepared with ThruPLEX DNA-Seq kit (Takara, R400674) and DNA Single Index kit, 12S Set A (Takara, R400695). Size selection steps were performed with Magbio Genomics HighPrep PCR beads (Fisher Scientific, 50-165-6582). The libraries were sequenced using the Illumina NextSeq 550 platform and the 150-bp paired-end configuration to obtain at least 20 million reads per sample.

treatment_protocol: Cells were treated with 500nM of dTAGV-1 or DMSO for 6 hours.

value: H3K27ac (Diagenode #C15410196)


title: MUTZ-3 6hr input

description: Library name: 6hr MUTZ-3 input


title: MUTZ-3 DMSO 24hr rep1 [RNA-Seq]

description: Library name: 24hr MUTZ-3 DMSO RNA rep1


title: MUTZ-3 DMSO 6hr H3K27ac ChIP

description: Library name: 6hr MUTZ-3 H3K27ac ChIP DMSO


title: H9 STB, CCR7 KO, biol rep3


title: MUTZ-3 DMSO 6hr rep1 [RNA-Seq]

description: Library name: 6hr MUTZ-3 DMSO RNA rep1


title: MUTZ-3 dTAGV-1 6hr MECOM-HA ChIP

description: Library name: 6hr MUTZ-3 MECOM-HA ChIP dTAG


title: H9 STB, CCR7 KO, biol rep2


title: MUTZ-3 DMSO 6hr MECOM-HA ChIP

description: Library name: 6hr MUTZ-3 MECOM-HA ChIP DMSO


title: MUTZ-3 DMSO 24hr rep3

description: Library name: 24hr MUTZ-3 DMSO ATAC rep3

data_processing:
FASTQ files were demultiplexed with bcl2fastq and aligned to the hg38 reference genome using bowtie2 (version 2.5.2). Sam files were sorted, indexed and converted to bam files with Samtools (version 1.18). For data visualization in a genome browser, bam files were converted to bigwig files using the bamCoverage package from deepTools (version 3.5.4) normalizing by counts per million (CPM). Peak calling was performed using MACS2 (version 2.2.9.1) with the flags --shift -100 and --extsize 200 to generate narrowPeak files. NarrowPeak files from DMSO and dTAGV-1-treated cells were then merged and converted to SAF format to generate a consensus peak set for each cell line. This consensus peak file and corresponding bam files were then processed using the featureCounts package from Subread (version 2.0.6) to generate a count table for ATAC peaks. Differential peak accessibility analysis was performed using DESeq2 (version 1.40.2). Results were visualized using ggplot2 (version 3.4.4).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Accessible chromatin was assessed using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) as previously described with the Omni-ATAC protocol. Cells were treated with 500nM dTAGV-1 or DMSO for 6 hours and then 50,000 live cells were sorted into PBS with 2% BSA. Cells were washed twice in 150μL and 50μL 1xPBS, resuspended in 50μL ATAC-seq lysis buffer, incubated for 10 min on ice and centrifuged at 400g for 10 min at 4 °C.
The pellet was incubated in the transposase reaction mix (25μL 2×TD buffer (Illumina), 2.5μL transposase (Illumina Cat# FC-121-1030) and 22.5μL nuclease-free water) for 30min at 37 °C with gentle agitation. After DNA purification with the Zymo DNA Clean and Concentrator Kit (Zymo, Cat# D4033) libraries were amplified with NEBNext High-Fidelity PCR Master Mix (NEB, Cat# M0541S) using custom Nextera primers. Libraries for sequencing were size selected with Agencourt AMPure XP beads (Beckman Coulter, Cat# A63880). DNA concentration was measured with an Invitrogen Qubit fluorometer (Life Technologies) and Agilent Fragment Analyzer. Libraries were subject to paired-end sequencing with 150 cycles.


title: H9 STB, CCR7 KO, biol rep1


title: MUTZ-3 DMSO 24hr rep2

description: Library name: 24hr MUTZ-3 DMSO ATAC rep2


title: Irx3_cutnrun_PosCtrl

description:
Library name: B6_Irx3_CutNRun_PosCtrl
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: MUTZ-3 dTAGV-1 6hr rep2 [RNA-Seq]

description: Library name: 6hr MUTZ-3 dTAG RNA rep2


title: Irx3_cutnrun_Fasted_4

description:
Library name: B6_Irx3_CutNRun_Fasted_4
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet


title: H9 STB, WT, biol rep4


title: MUTZ-3 dTAGV-1 6hr rep3

description: Library name: 6hr MUTZ-3 dTAG ATAC rep3


title: H9 STB, WT, biol rep3


title: MUTZ-3 dTAGV-1 6hr rep2

description: Library name: 6hr MUTZ-3 dTAG ATAC rep2


title: RNAseq_E1_545_E1_72_FD

description:
Library name: C57_RNAseq_FFR_E1_545_WT_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

data_processing:
RNA-seq Aligned with HISAT2, CutNRun Aligned with Bowtie2.
Gene expression counts with rSubread.
EdgeR differential expression analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq: EdgeR Output tab delimited, Counts matrices.

extract_protocol:
Qiagen RNeasy kit.
The Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Fasted for 72 hours with water.


title: H9 STB, WT, biol rep2


title: Anas platyrhynchos, retina, rep1

city: guagnzhou

first: Zhibin

last: Li

address: tianhe

country: China

institute: The Third Affiliated Hospital of Sun Yat-Sen University

description: Library name: AM3G1194

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics).
Assembly: F.catus_Fca126_mat1.0, Oreochromis_mossambicus_EIV1, ASM1899790v1, bMelUnd1.mat.Z, bGalGal1.mat.broiler.GRCg7b, ZJU1.0
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Anas platyrhynchos

source_name: Retina

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.

value: Retina

value: Retinal cells


title: RNAseq_E1_487_1_Fed

description:
Library name: C57_RNAseq_FFR_E1_487_1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: Ambystoma mexicanum, retina, rep1

city: guangzhou

address: tianhe road 600

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics) and Seurat.
Assembly: GRCh38.p14,MFA1912RKSv2,F.catus_Fca126_mat1.0,UU_Cfam_GSD_1.0,CU_Pguttatus_1,ASM1899790v1,HZGC01,Bangor_MerUng_6.1,serCan2020,bMelUnd1.mat.Z,ASM2559416v1,ASM1176430v1.1,mEriEur2.1,mRatBN7.2,bGalGal1.mat.broiler.GRCg7b,Oreochromis_mossambicus_EIV1,ZJU1.0,GRCm39,Sscrofa11.1,pvi1.1,CAS_Tse_1.0,Cavpor3.0,BCM_Maur_2.0,AmbMex60DD.
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Ambystoma mexicanum

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The human retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.The other 24 retina cells underwent library construction using DNBelab C4.


title: Rattus norvegicus, retina, rep1

organism: Rattus norvegicus


title: H9 STB, WT, biol rep1


title: H9 EVT, CCR7 KO, biol rep4

value: Extravillouls trophoblast (EVT)


title: IMR90, 6 weeks, rep3

city: Wuerzburg

first: Patrick

last: Lüningschrör

address: Versbacher Str. 5

department: Institute of Clinical Neurobiology

country: Germany

institute: University Hospital Wuerzburg

description: Library name: iPSC_IMR90_6w_3

data_processing:
Base calling with Illumina NextSeq 2000 RTA v4.12.2
FASTQ conversion with bcl-convert v4.3.6
Extraction of unique molecular identifier (UMI) sequences from the beginning of R2 reads using UMI-tools (Smith et al., 2017) v1.1.1 (parameters: extract --extract-method=regex --bc-pattern2=^(?P<umi_1>.{8})(?P<discard_1>.{6}).* for all read pairs)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 in paired-end mode (parameters: --nextseq-trim=20 -m 1 -a NNNNNNNNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=17 -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Alignment of trimmed reads to human genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters but including transcript annotations from RefSeq annotation version RS_2023_03 for GRCh38.p14
Deduplication of aligned reads with UMI-tools v1.1.1 (parameters: dedup --paired --random-seed 123456789 --multimapping-detection-method=NH)
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version RS_2023_03 for GRCh38.p14) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters:-p -B -C -s 2 -t exon -M -O --fraction)
Assembly: GCF_000001405.40/GRCh38.p14 primary assembly and mitochondrion
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: 3D Neuromuscular coculture

growth_protocol: Total RNA was isolated from two different lines of 3D Neuromuscular coculture at 1, 3 and 6 weeks.

extract_protocol:
RNA extraction using QIAzol Lysis Reagent and purification using the NucleoSpin RNA kit.
Library preparation was performed using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara) with UMIs according to manufacturer´s instructions. The quality of the dual-indexed libraries was checked using 5200 Fragment Analyzer and the average size was calculated at appx. 400 bp.

value: 3D Neuromuscular coculture

value: Motorneurons, myoblasts and fibroblasts

tag: time

value: 6 weeks


title: RNAseq_E1_436_KO_72_FD

description:
Library name: C57_RNAseq_FFR_E1_436_KO_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus


title: IMR90, 6 weeks, rep2

description: Library name: iPSC_IMR90_6w_2

value: WT


title: RNAseq_E1_437_KO_72_FD

description:
Library name: C57_RNAseq_FFR_E1_437_KO_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: MUTZ-3 DMSO 24hr rep1

description: Library name: 24hr MUTZ-3 DMSO ATAC rep1


title: Irx3_cutnrun_Refed12hr_1

description:
Library name: B6_Irx3_CutNRun_Refed12hr_1
Irx3 Cut Run of Adult B6 Mouse Hypothalamus varying diet

value: IRX3 Antibody:Santa Cruz IRX3 (G-6):sc-166877


title: H9 EVT, CCR7 KO, biol rep2


title: IMR90, 3 weeks, rep3

description: Library name: iPSC_IMR90_3w_3

value: 3 weeks


title: RNAseq_E1_450_KO_72_FD

description:
Library name: C57_RNAseq_FFR_E1_450_KO_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E1_442_KO_72_FD

description:
Library name: C57_RNAseq_FFR_E1_442_KO_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 EVT, CCR7 KO, biol rep3


title: IMR90, 3 weeks, rep1

description: Library name: iPSC_IMR90_3w_1


title: RNAseq_E1_448_WT_72_FD

description:
Library name: C57_RNAseq_FFR_E1_448_WT_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 EVT, CCR7 KO, biol rep1


title: IMR90, 1 week, rep3

description: Library name: iPSC_IMR90_1w_3

value: 1 week


title: IMR90, 1 week, rep2

description: Library name: iPSC_IMR90_1w_2


title: H9 EVT, WT, biol rep4


title: IMR90, 1 week, rep1

description: Library name: iPSC_IMR90_1w_1


title: MUTZ-3 dTAGV-1 6hr rep1

description: Library name: 6hr MUTZ-3 dTAG ATAC rep1

value: AML cell line

value: MECOM degradation


title: RNAseq_E1_532_E1_Fed

description:
Library name: C57_RNAseq_FFR_E1_532_E1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Fed


title: 34D6, 6 weeks, rep1

description: Library name: iPSC_34D6_6w_1


title: RNAseq_E1_554_E1_Fed

description:
Library name: C57_RNAseq_FFR_E1_554_E1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 34D6, 6 weeks, rep2

description: Library name: iPSC_34D6_6w_2


title: H9 EVT, WT, biol rep3


title: IMR90, 6 weeks, rep1

description: Library name: iPSC_IMR90_6w_1


title: RNAseq_E1_544_E1_Fed

description:
Library name: C57_RNAseq_FFR_E1_544_E1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 34D6, 3 weeks, rep2

description: Library name: iPSC_34D6_3w_2


title: H9 EVT, WT, biol rep2


title: IMR90, 3 weeks, rep2

description: Library name: iPSC_IMR90_3w_2


title: 34D6, 3 weeks, rep3

description: Library name: iPSC_34D6_3w_3


title: 34D6, 1 week, rep3

description: Library name: iPSC_34D6_1w_3


title: H9 EVT, WT, biol rep1


title: RNAseq_E1_488_1_Fed

description:
Library name: C57_RNAseq_FFR_E1_488_1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 34D6, 6 weeks, rep3

description: Library name: iPSC_34D6_6w_3


title: 34D6, 1 week, rep1

description: Library name: iPSC_34D6_1w_1


title: 34D6, 1 week, rep2

description: Library name: iPSC_34D6_1w_2


title: RNAseq_E1_522_1_Fed

description:
Library name: C57_RNAseq_FFR_E1_522_1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 hTSC, CCR7 KO, biol rep3

value: CCR7 KO H9

value: human trophoblast stem cell (hTSC)

value: mutant


title: H9 hTSC, CCR7 KO, biol rep4


title: RNAseq_E1_504_1_Fed

description:
Library name: C57_RNAseq_FFR_E1_504_1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 hTSC, CCR7 KO, biol rep2


title: RNAseq_E1_444_WT_72_FD

description:
Library name: C57_RNAseq_FFR_E1_444_WT_72_FD
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: 72 FD


title: SOA RUNX1 ChIP TGFb, ChIP DNA S2

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

description:
Library name: SOA RUNX1 ChIP T, ChIP DNA S2
The raw data are being made available for access in GEO

data_processing:
basecalls were performed using DRAGEN BCL convert 4.2.7
Trimmomatic sliding window of 4 bp, minimum 20 phred score trimming
ChIP-seq reads were aligned end-to-end to the GRC mm39 genome using bowtie2 version 2.5.2
Filtered to remove alignments under a quality score of 30
Peaks were called using MACS2 with the q-value cut off of 0.1
bedgraphs were converted to bigwigs using bedGraphToBigWig
Assembly: NCBI RefSeq GRCm39 primary assembly
Supplementary files format and content: bigWig (except for input samples)

source_name: Mouse large biliary epithelial cells (MLE)

extract_protocol:
ChIP and DNA purification performed using the Cell Signaling #9003 SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) kit
2S Plus DNA library kit from IDT. Sequencing with Nextseq 2000 XLEAP

value: TGFb


title: H9 hTSC, CCR7 KO, biol rep1


title: RNAseq_KO_E2_286_72hFasted

description:
Library name: C57_RNAseq_FFR_KO_E2_286_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: SOA RUNX1 ChIP, ChIP DNA S1

description:
Library name: SOA RUNX1 ChIP V, ChIP DNA S1
The raw data are being made available for access in GEO

value: Mouse large biliary epithelial cells (MLE)

value: vehicle


title: SOA IP TGFb, Input DNA S10

description:
Library name: SOA IP T, Input DNA S10
The raw data are being made available for access in GEO


title: SOA RUNX1 TGFb, ChIP DNA S4

description:
Library name: SOA RX1 T, ChIP DNA S4
The raw data are being made available for access in GEO


title: SOA IP, Input DNA S9

description:
Library name: SOA IP V, Input DNA S9
The raw data are being made available for access in GEO


title: H9 hTSC, WT, biol rep4


title: RNAseq_WT_E2_282_72hFasted

description:
Library name: C57_RNAseq_FFR_WT_E2_282_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 hTSC, WT, biol rep3


title: SOA RUNX1, ChIP DNA S7

description:
Library name: SOA RX1 V, ChIP DNA S7
The raw data are being made available for access in GEO


title: SOA IP TGFb, Input DNA S6

description:
Library name: SOA IP T, Input DNA S6
The raw data are being made available for access in GEO


title: RNAseq_E1_514_1_Fed

description:
Library name: C57_RNAseq_FFR_E1_514_1_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Mouse spinal cord dorsal astrocytes, P24, Incision, Male 2

city: Cincinnati

first: Mark

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

description: Library name: MB24

data_processing:
Illumina BaseSpace Sequence Hub RNA-Seq Alignment v2.0.2
Reads were aligned to mm10 mouse reference genome using STAR.Normalization and Differential Gene Expression analysis was performed with DESeq2.
Quantification of aligned reads was performed using Salmon.
Normalized gene expression and differential gene expression analysis was performed with DESeq2
Assembly: mm10
Supplementary files format and content: All_result.xlslx file contains results of DESeq2 differential gene analysis at each developmental time point, and across time. DESeq2 hypothesis testing results are merged with normalized expression data for all samples.
Supplementary files format and content: All_results.xlsx file contains results of Gene Ontology (GO) Term Enrichment Analysis for incision-dependent DEGs and age-dependent DEGs. GO Term Enrichment Analysis was performed using gProfiler.

source_name: Dorsal spinal cord astrocyte nuclei

extract_protocol:
GFP+ nuclei (astrocytes) were selectively isolated using FANS, and nuclear RNA was extracted using Single Cell RNA purification kit (Norgen #51800).
cDNA libraries were constructed using NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biosciences #E6420L)

treatment_protocol: Neonatal mouse pups underwent unilateral hindpaw incision at postnatal day (P)3, or were exposed to isoflurane only as a control. Pups are Aldh1l1-creERT2xSun1-GFP, in which astrocytes are tagged with the nuclear envelope protein Sun1 fused to eGFP (Sun1-GFP).

value: Dorsal spinal cord astrocyte nuclei

value: Astrocyte

value: Incision

tag: age


title: RNAseq_WT_E2_280_72hFasted

description:
Library name: C57_RNAseq_FFR_WT_E2_280_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus

value: WT


title: Mouse spinal cord dorsal astrocytes, P24, Incision, Male 1

description: Library name: MB23


title: SOA RUNX1 TGFb, ChIP DNA S8

description:
Library name: SOA RX1 T, ChIP DNA S8
The raw data are being made available for access in GEO


title: H9 hTSC, WT, biol rep2


title: SOA RUNX1, ChIP DNA S3

description:
Library name: SOA RX1 V, ChIP DNA S3
The raw data are being made available for access in GEO


title: Mouse spinal cord dorsal astrocytes, P24, Incision, Female 2

description: Library name: MB22


title: Mouse spinal cord dorsal astrocytes, P24, Incision, Female 1

description: Library name: MB21


title: Mouse spinal cord dorsal astrocytes, P24, Naïve, Male 2

description: Library name: MB20

value: Naïve


title: H9 hTSC, WT, biol rep1


title: 34D6, 3 weeks, rep1

description: Library name: iPSC_34D6_3w_1

value: 3D Neuromuscular coculture

value: Motorneurons, myoblasts and fibroblasts

value: 3 weeks


title: Mouse spinal cord dorsal astrocytes, P24, Naïve, Male 1

description: Library name: MB19


title: RNAseq_KO_E2_269_72hFasted

description:
Library name: C57_RNAseq_FFR_KO_E2_269_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: H9 naïve hESC, CCR7 KO, biol rep2

value: CCR7 KO H9

value: naive human embryonic stem cell


title: Mouse spinal cord dorsal astrocytes, P24, Naïve, Female 3

description: Library name: MB18


title: Mouse spinal cord dorsal astrocytes, P24, Naïve, Female 2

description: Library name: MB17


title: H9 naïve hESC, CCR7 KO, biol rep1

value: mutant


title: Mouse spinal cord dorsal astrocytes, P24, Naïve, Female 1

description: Library name: MB16


title: RNAseq_E2_200_KO_Fed

description:
Library name: C57_RNAseq_FFR_E2_200_KO_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Fed


title: RNAseq_KO_E2_261_72hFasted

description:
Library name: C57_RNAseq_FFR_KO_E2_261_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Mouse spinal cord dorsal astrocytes, P10, Incision, Male 2

description: Library name: MB15


title: Mouse spinal cord dorsal astrocytes, P10, Incision, Male 1

description: Library name: MB14


title: H9 naïve hESC, WT, biol rep2


title: Mouse spinal cord dorsal astrocytes, P10, Incision, Female 2

description: Library name: MB13


title: H9 naïve hESC, WT, biol rep1


title: RNAseq_E5_180_KO_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_180_KO_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E5_195_KO_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_195_KO_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Mouse spinal cord dorsal astrocytes, P10, Incision, Female 1

description: Library name: MB12


title: Mouse spinal cord dorsal astrocytes, P10, Naïve, Male1

description: Library name: MB11


title: Mouse spinal cord dorsal astrocytes, P10, Naïve, Female 2

description: Library name: MB10


title: Mouse spinal cord dorsal astrocytes, P10, Naïve, Female 1

description: Library name: MB9


title: Mouse spinal cord dorsal astrocytes, P4, Incision, Male 3

description: Library name: MB8


title: RNAseq_E5_172_KO_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_172_KO_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: HEK293-ACE2 cells , Diversity control Biol Rep  2

city: Camperdown

first: G.

middle: Greg

last: Neely

state: NSW

address: Charles Perkins Centre, D17.

country: Australia

institute: University of Sydney

data_processing:
Sequenced reads were trimmed and aligned to reference sgRNA library (Weissman) using MAGeCK v0.5.9 to produce raw read counts
Supplementary files format and content: Weissman library (please see Addgene 1000000091)
Supplementary files format and content: Each txt file contains raw read counts for corresponding sample as determined by MAGeCK v0.5.9

source_name: Diversity control cells

growth_protocol: HEK293T-CRISPRa cells grown in DMEM supplemented with 10% HyClone FBS and 1% Penicillin-Streptomycin

extract_protocol:
Genomic DNA was extracted from cells using ISOLATE II Genomic DNA Kit (Bioline, BIO-52067). 25 ug genomic DNA was used as input for unsorted diversity control samples and 5 ug for sorted samples. PCR was assembled with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, M0541L), 0.4 uM P5 index primer mix and 0.4uM P7 indexing primer. PCR cycling conditions and primers were adapted from Sanson et al., 2018. Briefly, reactions were held at 95°C for 1 min, followed by 28 cycles of 94°C for 30 s, 53°C for 30 s and 72°C for 30 s, followed by a final 72°C extension step for 10 min. Amplicons were gel extracted and purified using the ISOLATE II PCR & Gel Kit (Bioline, BIO-52060) and the quality and concentration of DNA assessed via 2100 BioAnalyzer Instrument (Agilent Technologies, G2939BA). Next generation sequencing was performed on Illumina Novoseq 6000.
NA

treatment_protocol: Transduced HEK293T-CRISPRa cells were selected on puromycin, then incubated with SARS-CoV-2 virus for 72 hours at a lethal dose of 90%

tag: infection

value: Control


title: Mouse spinal cord dorsal astrocytes, P4, Incision, Male 2

description: Library name: MB7


title: HEK293-ACE2 cells , Diversity control Biol Rep  1


title: Mouse spinal cord dorsal astrocytes, P4, Incision, Male 1

description: Library name: MB6


title: Mouse spinal cord dorsal astrocytes, P4, Incision, Female 1

description: Library name: MB5


title: RNAseq_WT_E2_279_72hFasted

description:
Library name: C57_RNAseq_FFR_WT_E2_279_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E5_223_WT_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_223_WT_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: HEK293-ACE2 cells, Selected Biol Rep  2

source_name: Surviving SARS-CoV-2 cells


title: Mouse spinal cord dorsal astrocytes, P4, Naïve, Male 1

description: Library name: MB3


title: RNAseq_E5_216_WT_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_216_WT_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: HEK293-ACE2 cells, Selected Biol Rep  1


title: Mouse spinal cord dorsal astrocytes, P4, Naïve, Female 2

description: Library name: MB2


title: Mouse spinal cord dorsal astrocytes, P4, Naïve, Female 1

description: Library name: MB1


title: Homo sapiens, retina, rep1

value: Retina


title: Mouse spinal cord dorsal astrocytes, P4, Naïve, Male 2

description: Library name: MB4


title: RNAseq_E5_173_KO_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_173_KO_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: 170207O_26_Vil_9o

city: Beijing

first: Zehua

last: Zeng

state: State...

address: 49 Huayuan North Road, Haidian District, Beijing

department: Department of Obstetrics and Gynecology

institute: Peking University Third Hospital

description:
RNA-seq of Homo sapiens: Villi
h5 for counts and loom for velocyto

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 7.0
Quality control filtering was applied to remove any cells where fewer than 500 reads or 250 genes or greater than 15% mitochondrial reads.
We used velocyto to compute the clipped and unclipped matrices for the bam files generated by cellranger, and for each sample a loom file was generated
Assembly: GRCh38
Supplementary files format and content: h5
Supplementary files format and content: loom

source_name: Placental villi

extract_protocol:
Villous tissues at gestational weeks 6–10 were thoroughly washed with cold PBS, trimmed into fragments and enzymatically digested for 10 min at 37 °C. Decidual tissues at gestational weeks 6–10 were thoroughly washed with cold PBS, trimmed into fragments and enzymatically digested for 30 min at 37 °C with 1 mg/ml type IV collagenase (Gibco) and 20 U/ml DNase I (Sigma) in RPMI 1640 medium (Thermo Fisher Scientific) with vigorous shaking with The cell suspension was centrifuged at 300 g for 10 min at 4°C. The cell pellet was resuspended in PBS-bovine serum albumin (BSA) (1× PBS and 0.04% BSA). Cell viability was assessed using Trypan blue (Bio-Rad) exclusion method on a TC20 automated cell counter (Bio-Rad). All the samples were processed on both Drop-seq and 10x platforms as the sample yielded enough cells. vigorous shaking. The cell suspensions were filtered through a 70-μm cell straine. The flow-through was centrifuged and resuspended in red blood cell lysis buffer (Invitrogen). with an enzyme cocktail containing 0.125% trypsin (Sigma), 1 mg/ml type IV collagenase (Gibco) and 20 U/ml DNase I (Sigma) in Dulbecco’s modified eagle medium (DMEM, HyClone) with vigorous shaking. The cell suspensions were filtered through a 70-μm cell straine. The flow-through was centrifuged and resuspended in red blood cell lysis buffer (Invitrogen).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: Placental villi

tag: gastation

tag: individuality

value: pregnant 15


title: RNAseq_E2_WT_180_WT_Fed

description:
Library name: C57_RNAseq_FFR_E2_WT_180_WT_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 170207O_26_Dec_9o

description:
RNA-seq of Homo sapiens: Decidua
h5 for counts and loom for velocyto

source_name: Decidua

value: Decidua


title: RNAseq_E2_WT_188_WT_Fed

description:
Library name: C57_RNAseq_FFR_E2_WT_188_WT_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E5_199_WT_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_199_WT_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Old Rat Heart Rep2

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

country: United Kingdom

institute: University of Liverpool

description: Rats were euthanised by a Schedule one procedure and the cardiac left ventricle dissected and snap frozen in RNALater.

data_processing:
These are raw data with adapters removed.
raw FASTQ
Salmon was used to quantify trqnscripte
Assembly: mRatBN7.2 NCBI
Supplementary files format and content: comma-deliminated text file includes TPM values for each biological replicate

organism: Rattus rattus

source_name: heart left ventricle

extract_protocol:
RNA extraction was performed using the RNeasy Fibrous Tissues kit (Qiagen, UK) as per manufacturer’s instructions. Approx. 30mg of tissue was lysed and homogenised using an ultra turrax (IKA Homogeniser, Sigma, UK) in buffer RLT before proteinase K digestion steps, total RNA bound followed by several washing steps and DNase digestion and total RNA eluted. Total RNA integrity was confirmed using the Bioanalyzer (Agilent Technologies, USA). Ribosomal RNA (rRNA) was depleted from RNA samples by using the Ribo-Zero™ rRNA Removal Kit (Epicentre, USA) in accordance with the instructions of the manufacturer.
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, so they are paired-end reads but the orientation of the RNA strand is preserved in the first strand
Illumina Hiseq 4000 and NovaSeq series sequencer  2x150

treatment_protocol: Natural Ageing Aging

tag: strain

value: Wistar-Kyoto

tag: age (months)

tag: Sex

value: male

value: wild type genotype

value: heart left ventricle

tag: individual

tag: material type

value: organism part

tag: developmental stage

value: old adult


title: Young Rat Heart Rep3

tag: cell type

value: young adult


title: Old Rat Heart Rep3

tag: genotype


title: Young Rat Heart Rep2

tag: tissue


title: 170207N_25_Vil_8o

value: pregnant 14


title: RNAseq_E2_WT_181_WT_Fed

description:
Library name: C57_RNAseq_FFR_E2_WT_181_WT_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus

value: WT

tag: treatment


title: Young Rat Heart Rep1


title: Anas platyrhynchos, retina, rep1


title: 170207N_25_Dec_8o


title: 170207M_21_ViL_7O

value: pregnant 13


title: Pantherophis guttatus, retina, rep1

organism: Pantherophis guttatus


title: RNAseq_E2_KO_190_KO_Fed

description:
Library name: C57_RNAseq_FFR_E2_KO_190_KO_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Fed

tag: batch


title: RNAseq_E2_KO_189_KO_Fed

description:
Library name: C57_RNAseq_FFR_E2_KO_189_KO_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Felis catus, retina, rep1

organism: Felis catus

value: Retina


title: RNAseq_E2_195_WT_Fed

description:
Library name: C57_RNAseq_FFR_E2_195_WT_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 170207M_21_Dec_7O


title: NAX, cells, pEDs, 3

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Library name: pEDs3

data_processing:
NovaSeq PE150 protocol was followed by the company Novogene
Assembly: hg38
Supplementary files format and content: gene_count

source_name: Normal axillary fibroblasts

extract_protocol:
Cells were washed with PBS x2 then lysis buffer from RNAeasy kits was added to well, mised with pipetting, and collected. RNA was further extracted as per RNAeasy kit protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis

value: Normal axillary fibroblasts

value: pEDs


title: NAX, cells, pEDs, 4

description: Library name: pEDs4


title: 170207L_20vil_9m

value: Placental villi

value: pregnant 12


title: RNAseq_E2_204_KO_Fed

description:
Library name: C57_RNAseq_FFR_E2_204_KO_Fed
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: NAX, cells, pEDs, 2

description: Library name: pEDs2


title: NAX, cells, GSI, 3

description: Library name: GSI3

value: DAPT


title: 170207L_20Dec_9m

value: Decidua


title: 170207L_19vil_6o

value: pregnant 11


title: NAX, cells, GSI, 2

description: Library name: GSI2


title: NAX, cells, pEDs, 1

description: Library name: pEDs1


title: Old Rat Heart Rep1

value: Wistar-Kyoto

value: male

value: wild type genotype

value: heart left ventricle

value: organism part


title: RNAseq_E4_WT_216_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_WT_216_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus

value: WT


title: NAX, cells, GSI, 1

description: Library name: GSI1


title: keratinocyte, cells, siNCSTN, 6

description: Library name: kN6

source_name: neonatal foreskin keratinocyte

value: neonatal foreskin keratinocyte

value: siNCSTN


title: Cavia porcellus, retina, rep1

organism: Cavia porcellus

value: Retina


title: keratinocyte, cells, siNCSTN, 5

description: Library name: kN5


title: RNAseq_E4_WT_221_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_WT_221_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: keratinocyte, cells, siNCSTN, 4

description: Library name: kN4


title: 170207K_16_Vil_6y

value: pregnant 10


title: RNAseq_E4_WT_202_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_WT_202_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 170207K_16_Dec_6y


title: keratinocyte, cells, siNCSTN, 2

description: Library name: kN2


title: keratinocyte, cells, siNCSTN, 1

description: Library name: kN1


title: RNAseq_E4_KO_199_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_KO_199_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: keratinocyte, cells, scRNA, 6

description: Library name: kC6

value: scRNA


title: keratinocyte, cells, scRNA, 5

description: Library name: kC5


title: RNAseq_E5_181_WT_72hr_fast

description:
Library name: C57_RNAseq_FFR_E5_181_WT_72hr_fast
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: NAX, cells, GSI, 4

description: Library name: GSI4

value: Normal axillary fibroblasts


title: RNAseq_E4_KO_197_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_KO_197_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: keratinocyte, cells, scRNA, 4

description: Library name: kC4


title: 170207J_15_Dec_7m

value: pregnant 9


title: RNAseq_E4_KO_198_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_KO_198_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 170207L_19Dec_6o

value: Decidua


title: keratinocyte, cells, scRNA, 3

description: Library name: kC3


title: RNAseq_E4_WT_196_HYP_72hFasted

description:
Library name: C57_RNAseq_FFR_E4_WT_196_HYP_72hFasted
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: fibroblast, cells, siNCSTN, 3

description: Library name: fN3

source_name: neonatal foreskin fibroblast

value: neonatal foreskin fibroblast


title: RNAseq_E5_KO4_HYP

description:
Library name: C57_RNAseq_FFR_E5_KO4_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Fed


title: keratinocyte, cells, scRNA, 1

description: Library name: kC1


title: fibroblast, cells, siNCSTN, 2

description: Library name: fN2


title: keratinocyte, cells, scRNA, 2

description: Library name: kC2


title: 170207I_14_Vil_8m

description:
RNA-seq of Homo sapiens: Villi
h5 for counts and loom for velocyto

value: Placental villi

value: pregnant 8


title: keratinocyte, cells, siNCSTN, 3

description: Library name: kN3


title: 170207H_13_Vil_6m

value: pregnant 7


title: RNAseq_E5_KO3_HYP

description:
Library name: C57_RNAseq_FFR_E5_KO3_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: fibroblast, cells, siNCSTN, 1

description: Library name: fN1


title: 170207H_13_Dec_6m

description:
RNA-seq of Homo sapiens: Decidua
h5 for counts and loom for velocyto


title: fibroblast, cells, scRNA, 2

description: Library name: fC2


title: 170207J_15_Vil_7m


title: 170207H_12_Vil_6m

value: pregnant 6


title: 170207H_12_Dec_6m


title: RNAseq_E5_WT4_HYP

description:
Library name: C57_RNAseq_FFR_E5_WT4_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus


title: 170207I_14_Dec_8m


title: Kasumi-1_ShUSP5_rep1

city: Shanghai

first: Zhi-xin

state: Shanghai

address: No. 507 Zhengmin Road, Yangpu District

department: Department of Thoracic Surgery, Shanghai Pulmonary Hospital

institute: Tongji University

description:
Library name: Kasumi-1_ShUSP5_Lib_1
Kasumi-1 cells transfected with shUSP5

data_processing:
The raw sequencing reads were aligned to the human genome (GRCh38) using the STAR aligner. Differential gene expression was performed using DESeq2.
Differentially expressed genes were filtered based on |Fold Change| > 1.5 and p value < 0.05.
Pathway analysis was conducted using DAVID with Gene Ontology (GO) and KEGG pathway enrichment analyses.
The processed data files were in tab-delimited format: gene_count_matrix, gene_fpkm_matrix, gene_tpm_matrix.
Assembly: Human genome GRCh38 was used as the reference genome.
Supplementary files format and content: The processed data files include raw counts for each sample in gene_count_matrix, FPKM values in gene_fpkm_matrix, and TPM values in gene_tpm_matrix.

source_name: bone marrow

growth_protocol: Kasumi-1 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) at 37°C and 5% CO₂.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina) following the manufacturer's protocol.

treatment_protocol: Transfected with ShAE, ShUSP5, or ShNC vectors using Lipofectamine 3000, following the manufacturer's protocol.

value: bone marrow

tag: cell line

value: acute myeloid leukemia cell

value: shUSP5 (USP5 knockdown)

value: transfected with shUSP5


title: Kasumi-1_ShAE_rep3

description:
Library name: Kasumi-1_ShAE_Lib_3
Kasumi-1 cells transfected with shAE

value: shAE (AE knockdown)

value: transfected with shAE


title: Kasumi-1_ShAE_rep2

description:
Library name: Kasumi-1_ShAE_Lib_2
Kasumi-1 cells transfected with shAE


title: 170207G_7_vil_7m

value: pregnant 5


title: fibroblast, cells, scRNA, 3

description: Library name: fC3

value: scRNA


title: Kasumi-1_ShUSP5_rep2

description:
Library name: Kasumi-1_ShUSP5_Lib_2
Kasumi-1 cells transfected with shUSP5


title: 170207G_7_Dec_7m


title: 170207F_6VIL_8M

value: pregnant 4


title: RNAseq_E5_KO2_HYP

description:
Library name: C57_RNAseq_FFR_E5_KO2_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: Kasumi-1_ShNC_rep2

description:
Library name: Kasumi-1_ShNC_Lib_2
Kasumi-1 cells transfected with shNC

value: shNC (control)

value: transfected with shNC


title: RNAseq_E5_WT3_HYP

description:
Library name: C57_RNAseq_FFR_E5_WT3_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: WT

value: Fed


title: Kasumi-1_ShAE_rep1

description:
Library name: Kasumi-1_ShAE_Lib_1
Kasumi-1 cells transfected with shAE


title: Kasumi-1_ShNC_rep3

description:
Library name: Kasumi-1_ShNC_Lib_3
Kasumi-1 cells transfected with shNC


title: HCC95-KO-PTPRZ1,rep3(WGS)

city: Xi'an

first: Yihui

last: Zhang

state: Shanxi

address: No.229 Taibai North Road

institute: Northwest University

description: Library name: HCC95-KO-PTPRZ1,rep3

data_processing:
Sequence read quality was assessed using FastQC (version 0.11.9), adapters were trimmed using trim_galore (version 0.6.10). Reads passing Illumina’s chastity filter were mapped to the human reference genome (hg38) using BWA (version 0.7.17). The Genome Analysis Toolkit (GATK, version 4.2.6.1) was used to call variants with the default parameters of GATK Best Practices. The resulting variant call format (VCF) files were filtered to retain variants with DP > 9 and AF > 0.1 using bcftools (version 1.21). The variant was discarded if the candidate mutation had not previously been observed in the dbSNP database. Indels were considered “near” low complexity regions if any position within 10 bp or at least one third of positions within 50 bp were masked by repetitive intervals. Subsequently, sites where each DNA-edited cell line showed either a heterozygous SNP or an indel call that was not observed in the unedited cell line were considered as mutations if at least 30% of reads in the edited cell line contained the mutation, no allelic content derived from the mutation was present in the unedited line.
Assembly: hg38
Supplementary files format and content: variants with the default parameters of GATK Best Practices.

source_name: lung

extract_protocol:
Genomic DNA was extracted from isogenic HCC95-NC and HCC95-KO-PTPRZ1 cell lines using the TIANamp Genomic DNA Kit (TIANGEN) , with quality verified by Quibt4 and electrophoresis. Genomic DNA were sonicated to generate chromatin fragment on a Covaris M220 Focused-ultrasonicator (Insert, microTUBE 130 µL; Temperature, 7°C; Peak Incident Power, 50W; Duty Factor, 20%; Treatment Time, 65s). Libraries were prepared from 4 μg fragmented DNA (~350 bp) with the Illumina TruSeq DNA PCR-Free Kit and sequenced on NovaSeq X Plus (PE150, 30× coverage).
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the WGS library using the NEBNext Ultra II DNA Library Prep Kit for Illumi-na (NEB, E7645).

value: lung

value: human lung epithelial cells


title: RNAseq_E5_WT1_HYP

description:
Library name: C57_RNAseq_FFR_E5_WT1_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus


title: 170207F_6DEC_8M

value: Decidua


title: RNAseq_E5_WT2_HYP

description:
Library name: C57_RNAseq_FFR_E5_WT2_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E4_WT_4_HY

description:
Library name: C57_RNAseq_FFR_E4_WT_4_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: HCC95-KO-PTPRZ1,rep1(WGS)

description: Library name: HCC95-KO-PTPRZ1,rep1


title: fibroblast, cells, scRNA, 1

description: Library name: fC1

value: neonatal foreskin fibroblast


title: HCC95-KO-PTPRZ1,rep2(WGS)

description: Library name: HCC95-KO-PTPRZ1,rep2


title: 170207E_5_vil_100

value: Placental villi

value: pregnant 3


title: Kasumi-1_ShUSP5_rep3

description:
Library name: Kasumi-1_ShUSP5_Lib_3
Kasumi-1 cells transfected with shUSP5

value: bone marrow

value: acute myeloid leukemia cell

value: shUSP5 (USP5 knockdown)

value: transfected with shUSP5


title: RNAseq_E5_KO1_HYP

description:
Library name: C57_RNAseq_FFR_E5_KO1_HYP
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_E4_WT_3_HY

description:
Library name: C57_RNAseq_FFR_E4_WT_3_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: HCC95,rep2(input)

description: Library name: HCC95,rep2


title: HCC95,rep1(input)

description: Library name: HCC95,rep1


title: 170207E_5_Dec_100

description:
RNA-seq of Homo sapiens: Decidua
h5 for counts and loom for velocyto


title: RNAseq_E4_WT_2_HY

description:
Library name: C57_RNAseq_FFR_E4_WT_2_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: Mesocricetus auratus, retina, rep1

organism: Mesocricetus auratus

value: Retina


title: Kasumi-1_ShNC_rep1

description:
Library name: Kasumi-1_ShNC_Lib_1
Kasumi-1 cells transfected with shNC


title: RNAseq_E4_WT_1_HY

description:
Library name: C57_RNAseq_FFR_E4_WT_1_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: 170207E_4_Dec_8y

value: pregnant 2


title: mock14DISE42_4

city: Taipei

first: Wei-Yi

last: Lin

state: Taipei City

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Agronomy

country: Taiwan

institute: National Taiwan University

description: Library name: mock14DISE42_4

data_processing:
R program
Sequence reads were trimmed for adaptor sequence/low-quality sequence and poor-quality bases elimination using Trimmomatic v0.38 with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Trimmed sequence reads were mapped to Setaria_italica_v2.0 using by the HISAT2 software (v2.1.0).
Read count extraction and normalization were performed using FeatureCounts (v2.0.0)  and DESeq2 (v1.26.0), respectively. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR.
Assembly: Setaria_italica_v2.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Setaria italica

source_name: roots

growth_protocol: Surface-sterilized foxtail millet seeds germinated and grew  in a growth chamber with a 12 h light (28 °C)/ 12 h dark (22 °C) cycle. Two weeks old seedings were transplanted to cones. Half of plants were inoculated with Claroideoglomus etunicatum and the rest were kept as mock.

extract_protocol:
RNA was harvested using using the method described by Wang and Vodkin (1994, Plant Mol Biol Report 12, 132-145). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

treatment_protocol: At 6 weeks post inoculation, water was withold for two weeks. Roots were harvested at 7 and 14 days after drought.

value: roots

tag: sample group

value: mock


title: mock14DTT8_4

description: Library name: mock14DTT8_4

value: Taitung 8


title: AMF14DTT8_4

description: Library name: AMF14DTT8_4

value: Claroideoglomus etunicatum inoculation


title: mock7DISE42_3

description: Library name: mock7DISE42_3


title: RNAseq_E4_KO_4_HY

description:
Library name: C57_RNAseq_FFR_E4_KO_4_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO

value: Fed


title: 170207D_2_Dec_7y

value: pregnant 1


title: 170207D_2_Vil_7y

description:
RNA-seq of Homo sapiens: Villi
h5 for counts and loom for velocyto


title: SOA IP, Input DNA S5

description:
Library name: SOA IP V, Input DNA S5
The raw data are being made available for access in GEO

value: Mouse large biliary epithelial cells (MLE)

tag: chip antibody

value: vehicle


title: AMF7DTT8_3

description: Library name: AMF7DTT8_3


title: HCC95,rep3(input)

description: Library name: HCC95,rep3

value: lung

value: human lung epithelial cells


title: mock7DTT8_4

description: Library name: mock7DTT8_4


title: RNAseq_E4_KO_1_HY

description:
Library name: C57_RNAseq_FFR_E4_KO_1_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus


title: RNAseq_E4_KO_2_HY

description:
Library name: C57_RNAseq_FFR_E4_KO_2_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: AMF14DISE42_2

description: Library name: AMF14DISE42_2


title: OCI-AML5, scramble gRNA, rep3

city: Nashville

first: Alexander

middle: J

last: Silver

state: Tennessee

address: 2220 Pierce Ave

institute: Vanderbilt University School of Medicine

data_processing:
PE150, 50M reads
Data processing by Illumina Dragen RNA Pipeline (v3.6.3)
Assembly: hg38
Supplementary files format and content: Salmon output for each sample in tab-delimited .sf format containing raw counts and TPM by Ensembl transcript ID (ENST)
Supplementary files format and content: DESeq2 results for K562 in tab-delimited file listing HUGO and Entrez gene identifiers
Supplementary files format and content: DESeq2 results for OCI-AML5 in tab-delimited file listing HUGO and Entrez gene identifiers
Supplementary files format and content: DREAM results for K562 and OCI-AML5 in tab-delimited file listing HUGO and Entrez gene identifiers

source_name: hematopoietic

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 300 ng of polyA-selected RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: hematopoietic

value: acute myeloid leukemia

value: control

value: scramble gRNA


title: OCI-AML5, ASXL1 gRNA, rep3

value: ASXL1 gRNA


title: AMF7DISE42_4

description: Library name: AMF7DISE42_4

value: roots


title: mock14DTT8_3

description: Library name: mock14DTT8_3

value: mock


title: AMF14DTT8_2

description: Library name: AMF14DTT8_2

value: Taitung 8


title: RNAseq_72hFasted_E3_WT_2

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_WT_2
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

source_name: Hypothalamus

value: WT


title: mock7DISE42_2

description: Library name: mock7DISE42_2


title: 170207E_4_vil_8y

value: Placental villi

value: pregnant 2


title: OCI-AML5, ASXL1 gRNA, rep2


title: AMF14DISE42_4

description: Library name: AMF14DISE42_4

value: Claroideoglomus etunicatum inoculation


title: AMF7DISE42_3

description: Library name: AMF7DISE42_3


title: RNAseq_72hFasted_E3_KO_1

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_KO_1
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: KO


title: RNAseq_E4_KO_3_HY

description:
Library name: C57_RNAseq_FFR_E4_KO_3_HY
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Fed


title: mock7DTT8_3

description: Library name: mock7DTT8_3


title: mock14DISE42_2

description: Library name: mock14DISE42_2


title: AMF7DTT8_2

description: Library name: AMF7DTT8_2


title: RNAseq_72hFasted_E3_WT_1

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_WT_1
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_Fed_E3_KO_3

description:
Library name: C57_RNAseq_FFR_Fed_E3_KO_3
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: OCI-AML5, ASXL1 gRNA, rep1


title: AMF14DISE42_1

description: Library name: AMF14DISE42_1


title: OCI-AML5, scramble gRNA, rep1


title: RNAseq_Fed_E3_WT_3

description:
Library name: C57_RNAseq_FFR_Fed_E3_WT_3
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: mock14DTT8_1

description: Library name: mock14DTT8_1


title: AMF14DTT8_1

description: Library name: AMF14DTT8_1


title: K562, ASXL1 gRNA, rep3

value: chronic myelomonocytic leukemia


title: mock7DISE42_1

description: Library name: mock7DISE42_1


title: AMF7DISE42_2

description: Library name: AMF7DISE42_2


title: mock7DTT8_1

description: Library name: mock7DTT8_1


title: OCI-AML5, scramble gRNA, rep2


title: K562, scramble gRNA, rep3


title: RNAseq_Fed_E3_KO_1

description:
Library name: C57_RNAseq_FFR_Fed_E3_KO_1
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: mock14DISE42_3

description: Library name: mock14DISE42_3


title: AMF7DTT8_1

description: Library name: AMF7DTT8_1


title: K562, ASXL1 gRNA, rep2


title: RNAseq_Fed_E3_KO_2

description:
Library name: C57_RNAseq_FFR_Fed_E3_KO_2
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: i3N: TDP-43 KD + XRN1 KD + UPF1 KD 1

first: Irika

middle: R.

last: Sinha

address: 720 Rutland Ave Room 567

institute: Johns Hopkins University

description: Library name: TXU_1

data_processing:
Nextflow nf-core RNAseq (v3.18.0-gb96a753) pipeline built with Nextflow (v24.10.5, build 5935) was used to process FASTQ files using default presets.
Metadata added to DESeq2 object post-hoc
Counts and metadata extracted from DESeq2 object
Assembly: GrCh38
Supplementary files format and content: Annotated DESeq2 object
Supplementary files format and content: comma-separated value files containing raw counts from nf-core/rnaseq output DESeq2 object
Supplementary files format and content: comma-separated value files containing metadata

source_name: adult skin (leg)

growth_protocol: Human i3N iPSCs were maintained in Essential 8 media (ThermoFisher #A1517001) on plates coated with Matrigel (Corning #354277) and differentiated into i3N on Day 14 post-induction as previously detailed. All cells were maintained at 37°C with 5% CO2

extract_protocol:
RNA was extracted from cells in trizol
Stranded mRNA Prep Kit (Illumina) was used to prepare libraries as per the manufacturer’s protocol

treatment_protocol: To achieve a stable knockdown of TDP-43, i3N-iPSCs with a constitutively expressed CRISPRi module were transduced with a lentivirus expressing an sgRNA targeting TDP-43. sgTDP43 i3Neurons at differentiation day 5 were transduced with lentivirus expressing shRNAs targeting XRN1, UPF1, and/or SMG6 at 3 MOI individually or at 3 MOI each in combination. The neurons were harvested on differentiation day 14.

value: adult skin (leg)

value: i3Neurons (from WTC-11 iPSC line)

value: iPSC-derived glutamatergic neurons

value: sgTARDBP


title: K562, scramble gRNA, rep2

value: hematopoietic

value: control


title: RNAseq_Fed_E3_WT_2

address: 20 South 2030 East

description:
Library name: C57_RNAseq_FFR_Fed_E3_WT_2
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: Hypothalamus


title: i3N: TDP-43 KD + SMG6 KD + UPF1 KD 2

description: Library name: TUS_2


title: i3N: TDP-43 KD + SMG6 KD + UPF1 KD 1

description: Library name: TUS_1


title: i3N: TDP-43 KD + XRN1 KD + SMG6 KD 2

description: Library name: TXS_2


title: i3N: TDP-43 KD + XRN1 KD + SMG6 KD 1

description: Library name: TXS_1


title: K562, ASXL1 gRNA, rep1

value: ASXL1 gRNA


title: RNAseq_72hFasted_E3_KO_3

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_KO_3
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: RNAseq_72hFasted_E3_KO_2

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_KO_2
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: i3N: TDP-43 KD + XRN1 KD 1

description: Library name: TX_1


title: i3N: TDP-43 KD + XRN1 KD + UPF1 KD 2

description: Library name: TXU_2


title: RNAseq_72hFasted_E3_WT_3

description:
Library name: C57_RNAseq_FFR_72hFasted_E3_WT_3
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet


title: K562, scramble gRNA, rep1

value: scramble gRNA


title: i3N: TDP-43 KD + XRN1 KD 2

description: Library name: TX_2


title: i3N: TDP-43 KD 1

description: Library name: TDPKD_1


title: Channa argus, retina, rep1

description: Library name: AM3G1175

organism: Channa argus

source_name: Retina

value: Retina

value: Retinal cells


title: Valine deprivation, rep3

city: Lausanne

first: Felix

last: Naef

address: EPFL SV IBI

institute: EPFL

description: Library name: Val_3

data_processing:
Paired-end RNA-seq reads were aligned to the Ensembl GRCm38 primary assembly using STAR, with the Ensembl GTF (GRCm38.100) to build the index
Gene-level counts were generated via STAR --quantMode GeneCounts option
Normalization was performed using edgeR
Assembly: GRCm38 primary assembly
Supplementary files format and content: Tab-delimited text file include raw counts (unique mapping) for all samples
Supplementary files format and content: Tab-delimited text file include log2 CPM for all samples

growth_protocol: NIH3T3 mouse fibroblast cells were cultured in DMEM (high glucose, pyruvate) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were washed with cold PBS containing cycloheximide and lysed in polysome lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl₂, 1% Triton X-100, 5 mM DTT, 100 µg/ml CHX, DNase, RNase inhibitor, protease/phosphatase inhibitors). Lysates were cleared by centrifugation and RNA was extracted via phenol-chloroform and ethanol precipitation.
NEBNext Ultra II Directional RNA Library Prep with PolyA selection

treatment_protocol: For amino acid starvation, cells were switched to custom DMEM/F-12 medium lacking specific branched-chain amino acids (leucine, isoleucine, valine) and supplemented with 10% dialyzed FBS for 6 hours. Different combinations of leucine, isoleucine, and valine were added back to create separate starvation conditions (single, double, or triple).

value: fibroblasts

tag: time

value: amino acid starvation


title: RNAseq_Fed_E3_WT_1

city: Salt Lake City

first: Chris

institute: University of Utah

description:
Library name: C57_RNAseq_FFR_Fed_E3_WT_1
RNA-seq of Adult B6 Mouse Hypothalamus varying Genotypes and diet

value: WT


title: i3N: guide RNA control 1

description: Library name: SgC_1

value: sgControl


title: i3N: XRN1 KD + UPF1 KD 2

description: Library name: CXU_2


title: CUT&Tag_control

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

country: France

institute: CNRS

description: Library name: WT-anti-MYC

data_processing:
CUT&Tag: Raw paired-end reads were trimmed using Trim Galore (v.0.6.7) with default parameters. Trimmed reads were aligned to the TAIR10 reference genome using Bowtie2 (v.2.4.2 in --very-sensitive-local mode, with insert size constraints (-I 10 -X 700), and with --no-mixed and --no-discordant options to restrict alignments to properly paired reads. Reads mapping to organellar genomes (chloroplast or mitochondria) were filtered out, and only uniquely mapping reads with a mapping quality ≥ 10 were retained. BAM files were then sorted and indexed and insert size distributions were computed using Picard’s CollectInsertSizeMetrics. For sample normalization, exogenous E. coli DNA carried by the pA-Tn5 transposase was used as a spike-in control. Clean reads were aligned to the E. coli genome using Bowtie2, and a scaling factor was computed for each sample as the ratio between the number of E. coli reads in the sample and the smallest E. coli read count observed among all samples. These scaling factors were used to normalize read coverage when generating signal tracks (bigWig format) using bamCoverage of deepTools (v.3.5.1), with a bin size of 5 bp. (v.2.2.7.1) using corresponding inputs as a background and --nomodel and –extsize 200 options, and peaks called in the anti-MYC or anti-FLAG WT controls were removed.
Assembly: TAIR10 (Araport11 annotation)
Supplementary files format and content: CUT&Tag: bigWig format files with normalized read densities calculated in 5 bp bins.
Library strategy: CUT&Tag

organism: Arabidopsis thaliana

source_name: immature flower buds

growth_protocol: Plants were grown on soil in long-day conditions (16h light, 8h dark) at 23°C with 60% relative humidity.

extract_protocol:
CUT&Tag : nuclei were purified from 0.15 g of immature flower buds, and 400,000 nuclei were used for each reaction.
CUT&Tag: Libraries were amplified with 18 PCR cycles and > 75 bp DNA fragments were cleaned through two rounds of purification using 1.3x, then 0.8x AMPure Beads (Beckman Coulter A63880). Librairies were pooled before sequencing.

value: immature flower buds

tag: antibody

value: Myc-Tag Ab, Cell Signaling Technology ref.2276


title: i3N: guide RNA control 2

description: Library name: SgC_2

value: adult skin (leg)


title: Valine deprivation, rep2

description: Library name: Val_2


title: CUT&Tag_NDX-MYC

description: Library name: NDX-MYC


title: i3N: XRN1 KD + UPF1 KD 1

description: Library name: CXU_1

value: i3Neurons (from WTC-11 iPSC line)


title: CUT&Tag_FLAG-NDX

description: Library name: FLAG-NDX

value: Anti-FLAG M2 Ab, Sigma F1804-1MG


title: i3N: SMG6 KD + UPF1 KD 2

description: Library name: CUS_2

value: iPSC-derived glutamatergic neurons


title: ChIP_MYC-Ab_mail2-MAIL2-MYC_rep2

data_processing:
For all libraries, reads were trimmed and filtered for quality and adapter contamination using Trim Galore (v.0.6.7, Babraham Institute) with default parameters
RNA-seq: Filtered reads were aligned to the Arabidopsis reference genome (TAIR10) genome using STAR (v.2.7.9a). Reads aligning equally well to more than one position in the reference genome were discarded, and probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were generated using deeptools (v.3.5.1) bamCoverage with the option normalizeUsing CPM and binSize 1. Subsequent read counting for each gene and TE was performed using featureCounts (v.2.0.3) using the Araport11 genome annotation. Annotated TEs overlapping strongly (> 80%) with an annotated TE gene were considered TE genes, and the TE annotation was discarded. Differential expression analysis was performed using DESeq2 (v.1.36.0) with absolute fold-change ≥ 4 and Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed. For DEseq2 analysis of amiR-mail2 hypomorphic lines, criteria of absolute fold change ≥2 and Benjamini-Hochberg adjusted p-value < 0.05 were retained.
ChIP-seq: filtered reads were aligned to the TAIR10 Arabidopsis reference genome using bowtie2 (v.2.4.2), allowing only uniquely mapped reads with perfect matches. PCR duplicates were discarded using MarkDuplicates from the Picard Tools suite. Sample tracks were generated using deeptools (v.3.5.1) bamCoverage with the option normalizeUsing RPGC and binSize 1. Peaks calling was performed using MACS2 (v.2.2.7.1) using corresponding inputs as a background and --nomodel and –extsize 200 options, and peaks called in the anti-MYC or anti-FLAG WT controls were removed.
Assembly: TAIR10 (Araport11 annotation)
Supplementary files format and content: RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins.
Supplementary files format and content: ChIP-seq: bigWig format files with normalized read densities (Reads Per Genomic Content) calculated in 1 bp bins.

source_name: 14-day-old seedlings

extract_protocol:
RNA-seq : total RNA was extracted from aerial tissues of 12-day-old plants using RNAzol RT (RN190, Molecular Research Center, Inc). ChIP-seq : nuclei from 14-day-old plants were purified and chromatin was mainly sheared to 200-400 bp fragments using a Bioruptor UCD-200 (Diagenode) or a Covaris S220 Focused-ultrasonicator. Input and immunoprecipited fractions were purified for library construction.
RNA-seq: libraries were generated from about one µg total RNA at Beijing Genomics Institute (Hong Kong). ChIP-seq: libraries were generated from input or ChIPed DNAs at Beijing Genomics Institute (Hong Kong).

value: 14-day-old seedlings


title: i3N: SMG6 KD + UPF1 KD 1

description: Library name: CUS_1


title: i3N: XRN1 KD + SMG6 KD 2

description: Library name: CXS_2


title: i3N: XRN1 KD + SMG6 KD 1

description: Library name: CXS_1


title: Leucine, Isoleucine, and Valine deprivation, rep3

description: Library name: Triple_3


title: i3N: TDP-43 KD 2

description: Library name: TDPKD_2

value: sgTARDBP


title: i3N: XRN1 KD 1

description: Library name: CX_1


title: i3N: XRN1 KD 2

description: Library name: CX_2


title: i3N: Control 2

description: Library name: CON_2

value: iPSC-derived  glutamatergic neurons

value: control


title: Leucine, Isoleucine, and Valine deprivation, rep1

description: Library name: Triple_1


title: Leucine, Isoleucine, and Valine deprivation, rep2

description: Library name: Triple_2


title: i3N: Control 1

description: Library name: CON_1


title: ChIP_H3K27me3-Ab_WT_s3

value: H3K27me3 Ab, Diagenode C15410069


title: MDA-MB-231 cells, shRBMS3-C3, biol rep 2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Library name: shRBMS3-C3_r2

data_processing:
Salmon was used to align the reads to the human transcriptome (gencode v28).
DESeq2 was used to perform differential analysis.
Assembly: hg38
Supplementary files format and content: text file with differential analysis results from DESeq2

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% FBS and antibiotics at 37C and 5% CO2.

extract_protocol:
RNA extraction was performed using Trizol Reagent (Invitrogen) and phenol-chloroform method.
Libraries were prepared from 5ng of input RNA using the SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara), including depletion of ribosomal cDNA. Purification of samples was performed using Select-a-Size MagBeads (Zymo). Samples were quantified and quality was assessed with TapeStation D1000 HS tape (Agilent).

value: Breast cancer cells

value: RBMS3 KD2


title: ChIP_Flowers_INPUT_mail1_rep1


title: Leucine deprivation, rep3

description: Library name: Leu_3

value: fibroblasts


title: Leucine deprivation, rep2

description: Library name: Leu_2

value: amino acid starvation


title: MDA-MB-231 cells, shRBMS3-B3, biol rep 1

description: Library name: shRBMS3-B3_r1

value: RBMS3 KD1


title: MDA-MB-231 cells, shCTRL, biol rep 2

description: Library name: shCTRL-2_r2

value: WT


title: Leucine deprivation, rep1

description: Library name: Leu_1


title: ChIP_Flowers_INPUT_WT_rep1

value: immature flower buds


title: MDA-MB-231 cells, shRBMS3-C3, biol rep 1

description: Library name: shRBMS3-C3_r1


title: ChIP_Flowers_H3K27me3-Ab_mail1_rep1


title: RNA seq of Mouse NoIR_3

city: Seoul

first: Yoon-Jin

address: Nowon GU

institute: Korea Institute of Radiological & Medical Sciences

description: Library name: NoIR_3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10(UCSC) whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: Lung


title: MDA-MB-231 cells, shCTRL, biol rep 1

description: Library name: shCTRL-2_r1


title: Valine deprivation, rep1

description: Library name: Val_1


title: RNA seq of Mouse NoIR_2

description: Library name: NoIR_2


title: ChIP_INPUT_mail2-MAIL2-MYC_rep2


title: ChIP_Flowers_H3K27me3-Ab_WT_rep1


title: ChIP_H3K27me3-Ab_amiR-mail2_s3


title: RNA seq of Mouse IR_14d_3

description: Library name: 14d_3


title: ChIP_INPUT_mail1_rep2


title: RNA seq of Mouse IR_14d_2

description: Library name: 14d_2


title: Isoleucine deprivation, rep1

description: Library name: Ile_1


title: Isoleucine deprivation, rep2

description: Library name: Ile_2


title: RNA seq of Mouse IR_14d_1

description: Library name: 14d_1


title: RNA seq of Mouse IR_11d_3

description: Library name: 11d_3


title: ChIP_INPUT_WT_rep2


title: RNA seq of Mouse IR_11d_2

description: Library name: 11d_2


title: MDA-MB-231 cells, shRBMS3-B3, biol rep 2

description: Library name: shRBMS3-B3_r2


title: RNA seq of Mouse IR_11d_1

description: Library name: 11d_1


title: ChIP_H3K27me3-Ab_ring1a-ring1b_rep2

value: ring1a-2 ring1b-3


title: Leucine and Isoleucine deprivation, rep2

description: Library name: Double_2


title: RNA seq of Mouse IR_8d_3

description: Library name: 8d_3


title: RNA seq of Mouse IR_8d_2

description: Library name: 8d_2


title: Leucine and Isoleucine deprivation, rep1

description: Library name: Double_1


title: RNA seq of Mouse IR_8d_1

description: Library name: 8d_1


title: ChIP_H3K27me3-Ab_mail1-ring1a-ring1b_rep2

value: mail1-1 ring1a-2 ring1b-3


title: ChIP_H3K27me3-Ab_ndx_rep2


title: Isoleucine deprivation, rep3

description: Library name: Ile_3


title: RNA seq of Mouse NoIR_1

description: Library name: NoIR_1


title: RNA SRF-FUS_2

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: Library name: SRF-FUS-seq bio rep 2

data_processing:
Basecalls performed using CASAVA version 1.8.2
For RNA-seq analysis,reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID.
Assembly: GRCh38/mm10
Supplementary files format and content: Bigwig for ChIPseq, RNAseq Genome Tracks. Bed file for ChIP Peaks

source_name: Cell Culture

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagents and Direct-zol RNA Miniprep Kits (Zymo Research, R2052) according to manufacturer’s protocol. For ChIP-seq, cells were fixed and crosslinked with 4% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
For RNA-seq, stranded mRNA-Seq libraries were generated using KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB (NEB, E6177S). 10 ng of DNA was used as starting material for Input samples and 1 ng for IP samples. Libraries were amplified using 12 cycles for Input samples and 15 cycles for IP samples on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

value: Cell Culture

value: Fibroblast-like cells from C3H mouse embryo

value: SRF-FUS retroviral transduction, SMC differentiation


title: Control, complete medium, rep3

description: Library name: Ctrl_3


title: ChIP_H3K27me3-Ab_mail1-ndx_rep2

value: 14-day-old seedlings

value: mail1-1 ndx-7


title: RNA SRF-FUS_3

description: Library name: SRF-FUS-seq bio rep 3


title: Control, complete medium, rep2

description: Library name: Ctrl_2