title: shRB-Rep2-H4K5Ac

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg38/GRCh38 genome assembly using Bowtie2 version 2.3.3.1 with the following configurations: bowtie2-align-s --wrapper basic-0 -k 2 -p 6
Peak calling was performed using MASC2 (v2.0.10) with pvalue cutoff = 1.0e-05.
bedGraph files were generated by MACS2 (v2.0.10)
BedGraph files were converted into BigWig files using UCSC's "wigToBigWig" command.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: bigWig files containing ChIP-seq reads pileup signals.

source_name: Prostate

growth_protocol: Cells were cultivated at 37°C and 5% CO2 in DMEM containing 10% fetal bovine serum (FBS) (Gibco) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
C4-2 cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with indicated antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: untreated

value: prostate cancer

tag: cell line

value: Acetyl Histone H4 (Lys5) (Millipore, 07-327)

value: shRB


title: shcon-Rep1-H4K5Ac

status: Public on Aug 30 2022

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: chip antibody

tag: genotype/variation

value: shcon


title: CD45- EpCAM+ IEC from Maf.flox mice (replicate 1)

city: Berlin

first: Christian

last: Neumann

address: Hindenburgdamm 30

country: Germany

institute: Charité-Universitätsmedizin Berlin

library_source: transcriptomic

data_processing:
Raw sequence reads were mapped to the mouse GRCm38/mm10 genome with Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and differential gene expression analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: counts, FPKM

molecule: total RNA

organism: Mus musculus

source_name: CD45- EpCAM+ IEC from Maf.flox mice

growth_protocol: IECs were FACS-sorted from the small intestine. IECs were defined as viable CD45- EpCAM+ cells.

extract_protocol:
Total RNA was purified with miRNeasy Micro Kit (Qiagen) from FACS-sorted IECs isolated from small intestine. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
mRNA 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 using either dUTP for directional library or dTTP for non-directional library.

tag: tissue

value: Small intestine

value: CD45- EpCAM+ IEC

tag: mouse background


title: SY5Y_RBM45KO-1-dmso_rep2

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

description: replicate 2, RBM45 KO clone 1 SH-SY5Y control (ribodepleted-RNA-seq)

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
alignment (HiSAT2 2.1.0) to UCSC genomes; hg19
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
read count measurements (Subread 1.6.3, featureCounts 1.6.5)
differential gene expression analysis (DESeq2 1.32.0, R 3.6.0)
differential exon usage analysis (DEXSeq 1.38.0, R 3.6.0)
annotation, de novo motif enrichment (homer 4.11.1, MEME 5.0.5)
downstream expression analyses (R 3.6.0, RStudio)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (.bw), read counts (.output), alignment (.bam)

growth_protocol: 1:1 Eagle's Minimum Essential Medium + Ham's F12 Nutrient Mix, 10% heat-inactivated FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO2, humidified

extract_protocol:
total RNA extraction performed using TRIzol, DNase-I treated, isolated by PCI extraction and EtOH precipitation
library generated using ribodepletion of total RNA (NEB #7870), followed by construction with NEBNext Ultra II non-directional RNA library prep kit (NEB #7770)

treatment_protocol: (1) no treatment, (2) control treatment with 0.1% DMSO in differentiation media (1x Neurobasal A, Penicillin/Streptamycin, 1x GlutaMax, 1x B27 supplement), (3) differentiation with 10 µM RA/0.1% DMSO in differentiation media

value: SK-N-SH neuroblastoma subline

tag: strain

tag: genotype

value: Cas9-guided RBM45 KO, isogenic clonal isolate #1

tag: treatment

value: control treatment, 0.1% DMSO for seven days


title: SY5Y_RBM45KO-1-gm_rep1

description: replicate 1, RBM45 KO clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)

value: no treatment, culture media only


title: CaMKK2KO

city: DURHAM

first: William

last: Tomaszewski

address: 303 Research Dr.

department: Immunology

institute: Duke University

data_processing:
The Cell Ranger pipeline (10X Genomics) was used to perform sample demultiplexing and to generate FASTQ files for the gene expression and hashtag libraries. FASTQ files were demultiplexed from the raw sequencing reads (bcl2fastq, v2.20), aligned to the mouse mm10 reference genome (cellranger, v4.0.0), and raw gene count matrices were generated using STAR (v2.7.5c) in Cellranger using default parameters.
The cell-hashing matrix is included in the processed files for each genotype. When constructing a single-cell object, the gene expression and cell-hashing assays should be stored in a list as "Gene Expression" and "Antibody Capture" respectively. Demultiplexing the biological replicates in each genotype can be easily achieved using the "HTODemux" Seurat function. There are only 4 features (rows) in the "Antibody Capture" assay (M1,M2,M3,M4), which correspond to the 4 biological replicates included in each genotype. The hashtag antibodies were provided by BioLegend and are in the following format ("Feature" = "BioLegend Cat#"): M1 = Totalseq B0301, M2 = Totalseq B0302, M3 = Totalseq B0303, and M4 = Totalseq B0304. Code to reproduce this, will be included in the methods section of the manuscript associated with this data.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes. *barcodes.tsv = Barcode sequences that correspond to column indices in matrix.mtx. *features.tsv = Gene IDs.

molecule: polyA RNA

source_name: Live CD45+ CaMKK2 KO glioma immune infiltrate

extract_protocol:
Immune tumor infiltrates were isolated using FACS sorting. Single-cell suspensions were loaded on the 10x Genomics Chromium controller, and mRNA converted to cDNA lirbaries. Single-cell libraries were sequenced on a Novaseq 6000 150PE S-Prime flowcell. Libraries were sequenced in single index mode with the following read lengths: 28x8x91
10x Chromium Single Cell 3' Kit using the v3.1 chemistry

treatment_protocol: tumor-bearing hemispheres were harvested on day 14 post tumor implantation. Tissue was transferred to a Dounce Tissue Homogenizer with 5 mLs of digestion cocktail containing 0.05 mg ml-1 LIberase DL (Roche), 0.05 mg ml-1 Liberase TL (Roche), 0.2 mg ml-1 DNase I (Roche) in HBSS with calcium and magnesium. A cell suspension was obtained after 5-10 strokes with the loose-fitting (A-size) pestle. The cell mixture was then incubated at 37 °C for 15 min in a water bath to obtain a single-cell suspension. The single-cell suspension was then passed through a 70-µm filter. After centrifugation, the cells were resuspended in 1x RBC Lysis Buffer (Thermo Fisher Scientific) for 3 minutes. Myelin was removed from the sample with Percoll centrifugation. Samples were centrifuged and mixed with 30% Percoll (Sigma Aldrich) and centrifuged at 500g for 20 min at 18 °C with no brake. The myelin layer and Percoll were then aspirated and the pellet was re-suspended in PBS before counting on an automated cell counter (Thermo Fisher Scientific). Samples were processed as described above, and after viability and extracellular staining, each biological replicate for each genotype was stained with four unique oligo-tagged TotalSeqB (Biolegend) antibodies. Samples were incubated for 30 minutes on ice. Samples were then sorted on a FACSAria II (BD Biosciences) and enriched for CD45+ Live cells.

tag: strain background

value: CaMKK2 KO

value: Total Infiltrating Leukocytes


title: SY5Y_RBM45KO-1-ra_rep1

description: replicate 1, RBM45 KO clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: shRB-Rep1-H4K5Ac


title: WT

source_name: Live CD45+ WT glioma immune infiltrate

value: CaMKK2 WT


title: SY5Y_RBM45KO-1-gm_rep2

description: replicate 2, RBM45 KO clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)


title: CD45- EpCAM+ IEC from Vil.Cre Maf.flox mice (replicate 2)

value: Vil.Cre Maf.flox


title: shRB-Rep2-BRD4


title: CaMKK2KO [HTO]


title: SY5Y_RBM45KO-2-dmso_rep1

description: replicate 1, RBM45 KO clone 2 SH-SY5Y control (ribodepleted-RNA-seq)

value: Cas9-guided RBM45 KO, isogenic clonal isolate #2


title: shcon-Rep2-H4K5Ac


title: shRB-Rep1-BRD4


title: SY5Y_RBM45KO-1-dmso_rep1

description: replicate 1, RBM45 KO clone 1 SH-SY5Y control (ribodepleted-RNA-seq)


title: shcon-Rep1-BRD4


title: WT [HTO]


title: SY5Y_control-2-ra_rep1

description: replicate 1, Cas9 Control clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: Cas9 Control, no gRNA, isogenic clonal isolate #2


title: HCT116 p53+/+ MANIO rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description:
HCT116 cell treated with MANIO replica N3
countsAnnotation.txt (column9)
N6_F

data_processing:
Raw sequence files were subjected to quality control analysis using FastQC (v 1.3). Transcript quantification was conducted with STAR (v2.5.3a), mapped to the human genome version GRCh38 and with reference annotation.
Read counts generated by STAR with HT-seq count option
Counts were analyzed by using DESeq2 package. An BH adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Genome_build: Ensembl human GRCh38
Supplementary_files_format_and_content: countsAnnotation.txt is Text file with the raw counts.

source_name: HCT116 cell

growth_protocol: HCT116 p53+/+ cells were maintained in RPMI medium supplemented with 10% FBS, antibiotics (100 units/mL penicillin plus 100 mg/mL streptomycin) and 2mM L-glutamine. Cells were seeded in 75 cm2 flasks at a density of 1.5×106 cells/well.

extract_protocol:
Cells were collected 24 hours after treatment and total RNA was extracted using the IllustraTM RNAspin Mini RNA Isolation Kit. RNA integrity was checked by the Agilent 2100 Bioanalyzer.
Sequencing libraries were produced following the TruSeq RNA Library kit v2 protocol by Illumina and starting from 1 µg of RNA. A total of eight samples, four treatment and four controls were sequenced using HiSeq 2500, obtaining ≈25M raw reads per sample.

treatment_protocol: Cells were treated with MANIO or DMSO solvent control in quadruplicate 24 hours later at ~60% confluence.

value: human colon cancer cell

value: MANIO


title: SY5Y_control-2-ra_rep2

description: replicate 2, Cas9 Control clone 2 SH-SY5Y differentiated (ribodepleted-RNA-seq)


title: shcon-Rep2-BRD4

value: prostate cancer


title: HCT116 p53+/+ MANIO rep4

description:
HCT116 cell treated with MANIO replica N4
countsAnnotation.txt (column11)
N8_H


title: HCT116 p53+/+ MANIO rep2

description:
HCT116 cell treated with MANIO replica N2
countsAnnotation.txt (column7)
N4_D


title: HCT116 p53+/+ DMSO rep2

description:
HCT116 cell treated with DMSO replica N2
countsAnnotation.txt (column6)
N3_C

value: DMSO


title: mHiPPoE2_KORescue-2_rep2

description: replicate 2, KO Rescue clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
alignment (HiSAT2 2.1.0) to UCSC genomes; mm10
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
read count measurements (Subread 1.6.3, featureCounts 1.6.5)
differential gene expression analysis (DESeq2 1.32.0, R 3.6.0)
differential exon usage analysis (DEXSeq 1.38.0, R 3.6.0)
annotation, de novo motif enrichment (homer 4.11.1, MEME 5.0.5)
downstream expression analyses (R 3.6.0, RStudio)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (.bw), read counts (.output), alignment (.bam)

growth_protocol: Dulbecco's Modified Essential Medium, 10% FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO2, humidified

treatment_protocol: no treatment

value: transformed mouse hippocampal neuron cell

tag: library

value: ribo-depleted RNA-seq

value: Cas9-guided RBM45 KO +F-HA-tagged RBM45_mut[delta]gRNA, isogenic clonal isolate #2


title: HCT116 p53+/+ MANIO rep1

description:
HCT116 cell treated with MANIO replica N1
countsAnnotation.txt (column5)
N2_B


title: mHiPPoE2_KORescue-1_rep2

description: replicate 2, KO Rescue clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)

value: Cas9-guided RBM45 KO +F-HA-tagged RBM45_mut[delta]gRNA, isogenic clonal isolate #1


title: HCT116 p53+/+ DMSO rep3

description:
HCT116 cell treated with DMSO replica N3
countsAnnotation.txt (column8)
N5_E


title: HCT116 p53+/+ DMSO rep4

description:
HCT116 cell treated with DMSO replica N4
countsAnnotation.txt (column10)
N7_G


title: HCT116 p53+/+ DMSO rep1

description:
HCT116 cell treated with DMSO replica N1
countsAnnotation.txt (column4)
N1_A


title: SY5Y_control-2-gm_rep1

description: replicate 1, Cas9 Control clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)

value: SK-N-SH neuroblastoma subline


title: mHiPPoE2_KORescue-1_rep1

description: replicate 1, KO Rescue clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)


title: Chiifu-37-1

city: Gwangju,Korea

first: Jeong-Il

last: Kim

address: Chonnam National University, Gwangju 61186, Korea

department: Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University

country: South Korea

institute: Chonnam national university

description: replicate 1

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. rapa reference genome was obtained from Ensembl and were used using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using HTseq-count and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Assembly: B. rapa reference genome was obtained from Ensembl
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa

source_name: Whole plant

growth_protocol: 2 weeks old B. rapa plants were grown in 1/2MS only media prior to heat treatment.

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions. Libraries were then sequenced on NovaSeq 6000 system (Labgenomics Inc., South Korea).

treatment_protocol: 22; 2weeks old (non-heat treated), 37; 37°C heat treatment for 1 h

tag: cultivar

value: Chiifu

tag: flowering

value: early


title: Chiifu-22-3

description: replicate 3


title: SY5Y_control-1-ra_rep2

description: replicate 2, Cas9 Control clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: Cas9 Control, no gRNA, isogenic clonal isolate #1


title: mHiPPoE2_RBM45KO-2_rep1

description: replicate 1, RBM45 KO clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)


title: mHiPPoE2_RBM45KO-2_rep2

description: replicate 2, RBM45 KO clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)


title: Chiifu-22-2

description: replicate 2


title: Chiifu-37-3

description: replicate 3


title: mHiPPoE2_RBM45KO-1_rep2

description: replicate 2, RBM45 KO clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)

value: Cas9-guided RBM45 KO, isogenic clonal isolate #1


title: SY5Y_control-1-ra_rep1

description: replicate 1, Cas9 Control clone 1 SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: Chiifu-22-1

description: replicate 1


title: mHiPPoE2_RBM45KO-1_rep1

description: replicate 1, RBM45 KO clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)


title: mHiPPoE2_control-2_rep2

description: replicate 2, Cas9 Control clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)


title: gi-37-3

description: replicate 3

value: late


title: mHiPPoE2_KORescue-2_rep1

description: replicate 1, KO Rescue clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)


title: SY5Y_control-2-dmso_rep2

description: replicate 2, Cas9 Control clone 2 SH-SY5Y control (ribodepleted-RNA-seq)

value: control treatment, 0.1% DMSO for seven days


title: SY5Y_control-1-dmso_rep2

description: replicate 2, Cas9 Control clone 1 SH-SY5Y control (ribodepleted-RNA-seq)


title: CLIP_mHiPPoE-2_rep2_CLIP

description: replicate 2, CLIP RNA

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
demultiplexing (Python 2.7.11)
alignment (Novoalign 3.09.00) to mm10
paired sample peak-calling (MACS2 2.1.1.20160309)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, mm10)
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
Genome_build: UCSC mus musculus (mm10)
Supplementary_files_format_and_content: bigwig (.bw), peak files (.bed), alignment (.bam)

growth_protocol: Dulbecco's Modified Essential Medium, 10% FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO₂, humidified

extract_protocol:
CLIP RNA extraction performed according to iCLIP protocol (10.1016/j.ymeth.2013.10.011); size-matched input (SM input) RNA extraction performed in parallel as adapted from eCLIP protocol (10.1038/nmeth.3810)
libraries generated using iCLIP protocol with post-extraction input and CLIP RNA (10.1016/j.ymeth.2013.10.011)

treatment_protocol: cell lines transduced with lentivirus expressing FLAG-HA-tagged mouse RBM45 (mHiPPoE-2), expression confirmed by WB

value: WT

tag: antibody

value: CST HA-Tag (C29F4) Rabbit mAb (#3724)


title: mHiPPoE2_control-2_rep1

description: replicate 1, Cas9 Control clone 2 mHiPPoE-2 (ribodepleted-RNA-seq)

value: Cas9 Control, no gRNA, isogenic clonal isolate #2


title: SY5Y_control-1-gm_rep2

description: replicate 2, Cas9 Control clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)

value: no treatment, culture media only


title: SY5Y_control-2-gm_rep2

description: replicate 2, Cas9 Control clone 2 SH-SY5Y GM (ribodepleted-RNA-seq)


title: SY5Y_METTL3KO-ra_rep2

description: replicate 2, wild-type SH-SY5Y differentiated (ribodepleted-RNA-seq)

value: Cas9-guided METTL3 depletion, isogenic clonal isolate


title: SY5Y_METTL3KO-ra_rep1

description: replicate 1, wild-type SH-SY5Y differentiated (ribodepleted-RNA-seq)


title: SY5Y_control-1-dmso_rep1

description: replicate 1, Cas9 Control clone 1 SH-SY5Y control (ribodepleted-RNA-seq)


title: mHiPPoE2_control-1_rep1

description: replicate 1, Cas9 Control clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)

value: transformed mouse hippocampal neuron cell


title: SY5Y_control-2-dmso_rep1

description: replicate 1, Cas9 Control clone 2 SH-SY5Y control (ribodepleted-RNA-seq)


title: mHiPPoE2_wt_rep2

description: replicate 2, wild-type mHiPPoE-2 (ribodepleted-RNA-seq)

value: ribo-depleted RNA-seq

value: Wild-Type (WT)


title: CLIP_mHiPPoE-2_rep2_input

description: replicate 2, paired input RNA

value: no antibody


title: Chiifu-37-2

description: replicate 2


title: SY5Y_METTL3KO-dmso_rep2

description: replicate 2, wild-type SH-SY5Y control (ribodepleted-RNA-seq)

value: SK-N-SH neuroblastoma subline


title: gi-37-2

description: replicate 2

value: Chiifu


title: gi-22-2

description: replicate 2


title: mHiPPoE2_wt_rep1

description: replicate 1, wild-type mHiPPoE-2 (ribodepleted-RNA-seq)


title: gi-37-1

description: replicate 1


title: CLIP_mHiPPoE-2_rep1_CLIP

description: replicate 1, CLIP RNA


title: mHiPPoE2_control-1_rep2

description: replicate 2, Cas9 Control clone 1 mHiPPoE-2 (ribodepleted-RNA-seq)


title: SY5Y_control-1-gm_rep1

description: replicate 1, Cas9 Control clone 1 SH-SY5Y GM (ribodepleted-RNA-seq)


title: SY5Y_wt-ra_rep2


title: gi-22-3

description: replicate 3


title: CLIP_mHiPPoE-2_rep1_input

description: replicate 1, paired input RNA


title: gi-22-1

description: replicate 1


title: mHiPPoE2_METTL3KO_rep2

description: replicate 2, METTL3 KO mHiPPoE-2 (ribodepleted-RNA-seq)

value: Cas9-guided METTL3 KO, isogenic clonal isolate


title: mHiPPoE2_METTL3KO_rep1

description: replicate 1, METTL3 KO mHiPPoE-2 (ribodepleted-RNA-seq)


title: DART_mHiPPoE2-cyto-mut_rep2

description: replicate 2, cytoplasmic RNA control

data_processing:
adapter removal (Trimmomatic 0.38)
de-duplication (Python 2.7.11)
alignment (HiSAT2 2.1.0) to mm10
identify single-nucleotide m⁶A sites through C2U mutations (Bullseye, in review)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, mm10)
Genome_build: UCSC mus musculus (mm10)
Supplementary_files_format_and_content: matrix (.matrix), m⁶A site files (.bed), alignment (.bam)

extract_protocol:
TRIzol-extracted DNase-I treated RNA subject to in vitro DART treatment using 250 ng APOBEC-YTH or APOBEC-YTHmut, 50 ng of RNA in 50 µL 1x DART Buffer for 4 hr at 37˚C (10.1038/s41592-019-0570-0)
APOBEC1-YTH/YTHmut-treated RNA purified using QIAGEN RNeasy Micro Kit (QIAGEN #74004)
SMARTer Stranded Total RNA-Seq Kit pico v3 (Takara #634485)

treatment_protocol: 50 ng RNA with 250 ng APOBEC1-YTHmut in 1x DART Buffer with RNase inhibitor, 50 µL volume; incubated for 4 h at 37˚C with final RNA purification post-treatment (QIAGEN RNeasy Micro kit)

value: APOBEC1-YTHmut treated RNA


title: SY5Y_METTL3KO-dmso_rep1

description: replicate 1, wild-type SH-SY5Y control (ribodepleted-RNA-seq)


title: DART_mHiPPoE2-nuc-mut_rep1

description: replicate 1, nuclear RNA control


title: S9_rep2_RIP

city: Shenzhen

first: Chuanlin

last: Shi

address: Dapeng

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina CASAVA software was used for basecalling
For RNA-seq, we used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50 % in either one read
For RNA-seq, paired-end reads were mapped to the rice genome sequences using HISAT2
For RNA-seq, gene expression level quantification and differential expression analysis were conducted using Cufflinks
For small RNA-seq and RIP-seq, raw data (raw reads) of fastq format were firstly processed through in-house perlscripts
For small RNA-seq and RIP-seq,  reads were mapped to the Oryza sativa v7.0 genome sequences (MSU Rice Genome Annotation Project) using Bowtie
For small RNA-seq and RIP-seq, small RNA reads mapped to rRNAs were filtered and the remaining genome-mapped reads were normalized to reads per million reads (RPM). For small RNA annotation, rice noncoding RNA sequences were downloaded from the database RNAcentral, miRNA sequences were downloaded from miRBase (Release 22.1), repetitive genomic sequences were downloaded from the Oryza Repeat Database, and PHAS loci were from the previous study
For small RNA-seq and RIP-seq, the overall small RNA abundance for each PHAS locus was calculated by summing up the normalized abundance of small RNAs using featureCounts
Genome_build: Oryza sativa v7.0 genome sequences (MSU Rice Genome Annotation Project)
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include normalized abundance (FPKM) of all genes in wild-type and ago1d mutant anthers at developmental stages of S4-6, S7-8 and S9 grown under 28 °C and 22°C condition
Supplementary_files_format_and_content: small RNA-seq: tab-delimited text files include normalized abundance (RPM) of 21- and 24-PHAS loci in wild-type and ago1d mutant anthers at developmental stages of S4-6, S7-8 and S9 grown under 28 °C and 22°C condition
Supplementary_files_format_and_content: RIP-seq: tab-delimited text files include normalized abundance (RPM) of 21-nt and 24-nt phasiRNAs in input and RIP of AGO1d::AGO1d-FLAG transgenic plant anthers at developmental stages of S4-6, S7-8 and S9.

organism: Oryza sativa

source_name: spikelets

growth_protocol: Rice plants were grown in paddy fields in Shanghai. For temperature treatment, rice plants grown in the paddy field in Shanghai were transferred to growth chambers when the anther development reached stage 3, corresponding to 0.5 cm inflorescences. Temperature treatment was carried out at an average temperature of 22 °C and 28°C for lower and normal control temperature treatments under 75% relative humidity with 12 h light/12 h dark until anthesis. After temperature treatment, rice plants were transferred to the paddy field for grain filling

extract_protocol:
All samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen)
All of the RNA-seq, small RNA-seq and AGO1d-FLAG RIP-seq libraries were prepared for sequencing using standard Illumina protocols
RNA-seq, small RNA-seq and AGO1d-FLAG RIP-seq

value: untreated

value: AGO1d::AGO1d-FLAG transgenic plants

tag: rip antybody

value: anti-FLAG antibody (Cat. M185-3L, MBL, Japan)


title: S9_rep3_input

treatment_protocol: For temperature treatment, rice plants grown in the paddy field in Shanghai were transferred to growth chambers when the anther development reached stage 3, corresponding to 0.5 cm inflorescences. Temperature treatment was carried out at an average temperature of 22 °C and 28°C for lower and normal control temperature treatments under 75% relative humidity with 12 h light/12 h dark until anthesis


title: S9_rep2_input


title: DART_mHiPPoE2-nuc-DART_rep2

description: replicate 2, nuclear RNA DART

treatment_protocol: 50 ng RNA with 250 ng APOBEC1-YTH in 1x DART Buffer with RNase inhibitor, 50 µL volume; incubated for 4 h at 37˚C with final RNA purification post-treatment (QIAGEN RNeasy Micro kit)

value: APOBEC1-YTH treated RNA


title: S9_rep1_RIP


title: SY5Y_wt-gm_rep1

description: replicate 1, wild-type SH-SY5Y GM (ribodepleted-RNA-seq)


title: SY5Y_METTL3KO-gm_rep1


title: SY5Y_METTL3KO-gm_rep2

description: replicate 2, wild-type SH-SY5Y GM (ribodepleted-RNA-seq)


title: DART_mHiPPoE2-nuc-DART_rep1

description: replicate 1, nuclear RNA DART


title: DART_mHiPPoE2-cyto-mut_rep1

description: replicate 1, cytoplasmic RNA control


title: S8_rep3_RIP


title: DART_HEK293T-cyto-mut_rep1

description: replicate 1, cytoplasmic RNA control

data_processing:
adapter removal (Trimmomatic 0.38)
de-duplication (Python 2.7.11)
alignment (HiSAT2 2.1.0) to mm10
identify single-nucleotide m⁶A sites through C2U mutations (Bullseye, in review)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, hg19)
Genome_build: UCSC homo sapiens (hg19)
Supplementary_files_format_and_content: matrix (.matrix), m⁶A site files (.bed), alignment (.bam)

value: transformed human embryonic kidney cell


title: S8_rep3_input


title: SY5Y_wt-ra_rep1

value: differentiation, 10 µM RA in 0.1% DMSO for seven days


title: DART_mHiPPoE2-cyto-DART_rep2

description: replicate 2, cytoplasmic RNA DART


title: DART_HEK293T-cyto-DART_rep2

description: replicate 2, cytoplasmic RNA DART


title: DART_mHiPPoE2-cyto-DART_rep1

description: replicate 1, cytoplasmic RNA DART


title: S9_rep3_RIP


title: S8_rep2_RIP


title: DART_mHiPPoE2-CA-DART_rep2

description: replicate 2, CA-RNA DART


title: SY5Y_wt-dmso_rep2

value: control treatment, 0.1% DMSO for seven days


title: DART_mHiPPoE2-nuc-mut_rep2

description: replicate 2, nuclear RNA control


title: SY5Y_wt-dmso_rep1


title: S9_rep1_input


title: DART_HEK293T-nuc-mut_rep2

description: replicate 2, nuclear RNA control


title: S8_rep2_input


title: DART_HEK293T-cyto-mut_rep2

description: replicate 2, cytoplasmic RNA control


title: SY5Y_wt-gm_rep2

value: no treatment, culture media only


title: WMI41_MI

first: Wiebke

last: Winkler

address: Robert-Rössle-Straße 10

institute: Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association

data_processing:
Basecall using bcl2fastq version 2.20.0.422
Sequenced reads were trimmed for adaptor sequence and mapped to GRCm38 whole genome using salmon version 1.3.0 with parameters “quant --validateMappings -l A -p 8”
Read counts were assigned to genes by the Bioconductor package tximport version 1.20.0. Gene with counts less than 1 over all experiments, and Ig, TR & Jchain were discarded before normalisation
Normalisation & differential expression were carried out using Bioconductor package DESeq2 version 1.32.0, with the genotype nested in the cohort as experimental design.
Genome_build: GRCm38 with GENCODE m23 annotations
Supplementary_files_format_and_content: Tab-delimited text files (salmon output) containing TPM and read counts for transcripts

source_name: bone marrow CD138+TACI+ plasma cells

extract_protocol:
2,000 plasma cells were FACS-sorted into 75µL RLT buffer (QIAGEN, supplemented with BME) and frozen at -80°C. RNA was harvested using the RNeasy Micro kit (QIAGEN). Then cDNA was synthesized and amplified following the low-input RNA-Seq protocol from Rosales, Liang, Engel et al. (2019). cDNA was synthesized using SuperScriptII reverse transcriptase (Invitrogen), an Oligo-dT30VN and a TSO (template switching oligo); then cDNA was amplified using the KAPA HiFi polymerase (Roche) and the Oligo ISPCR as described.
cDNA libraries were constructed using the Nextera XT DNA library preparation kit (Illumunia) with Tagmentation (Tn5 DNA insertion method) to incorporate sequencing indices (Nextera XT index kit, Illumina). Finally AMPure beads (Beckman Coulter) were employed to purify the library.

tag: cohort

value: MMSET (M) cohort

value: bone marrow plasma cells


title: DART_mHiPPoE2-CA-mut_rep2

description: replicate 2, CA-RNA control

value: transformed mouse hippocampal neuron cell


title: WMI40_MI


title: DART_mHiPPoE2-CA-mut_rep1

description: replicate 1, CA-RNA control


title: S8_rep1_RIP


title: DART_mHiPPoE2-CA-DART_rep1

description: replicate 1, CA-RNA DART


title: WMI32_MI


title: DART_HEK293T-nuc-mut_rep1

description: replicate 1, nuclear RNA control


title: S8_rep1_input


title: S6_rep3_input


title: WMI17_MI


title: DART_HEK293T-CA-mut_rep2

description: replicate 2, CA-RNA control


title: WMI10_MI


title: DART_HEK293T-CA-mut_rep1

description: replicate 1, CA-RNA control


title: WMI34_I


title: DART_HEK293T-cyto-DART_rep1

description: replicate 1, cytoplasmic RNA DART


title: DART_HEK293T-CA-DART_rep1

description: replicate 1, CA-RNA DART


title: DART_HEK293T-nuc-DART_rep1

description: replicate 1, nuclear RNA DART


title: S6_rep3_RIP


title: WMI19_I


title: S6_rep2_input


title: S6_rep2_RIP


title: S6_rep1_RIP


title: WMI12_I


title: wt_s9_NT_sRNAseq_rep1

source_name: anthers

value: 28 C treatment

value: wild-type


title: DART_HEK293T-nuc-DART_rep2

description: replicate 2, nuclear RNA DART


title: wt_s9_LT_sRNAseq_rep3

value: 22 C treatment


title: wt_s9_NT_sRNAseq_rep2


title: DART_HEK293T-CA-DART_rep2

description: replicate 2, CA-RNA DART


title: WMI25_MI


title: CLIP_HEK293T_rep2_input

description: replicate 2, paired input RNA

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
demultiplexing (Python 2.7.11)
alignment (Novoalign 3.09.00) to hg19
paired sample peak-calling (MACS2 2.1.1.20160309)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, hg19)
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
Genome_build: UCSC homo sapiens (hg19)
Supplementary_files_format_and_content: bigwig (.bw), peak files (.bed), alignment (.bam)

extract_protocol:
CLIP RNA extraction performed according to iCLIP protocol (10.1016/j.ymeth.2013.10.011), size-matched input (SM input) RNA extraction performed in parallel as adapted from eCLIP protocol (10.1038/nmeth.3810)
libraries generated using iCLIP protocol with post-extraction input and CLIP RNA (10.1016/j.ymeth.2013.10.011)

treatment_protocol: cell lines transduced with lentivirus expressing FLAG-HA-tagged human RBM45 (HEK293T), subject to 300 mJ/cm2 UV irradiation (254 nm) in PBS prior to collection of cell culture

value: WT

value: no antibody


title: CLIP_HEK293T_rep1_input

description: replicate 1, paired input RNA


title: CLIP_HEK293T_rep1_CLIP

description: replicate 1, CLIP RNA

value: CST HA-Tag (C29F4) Rabbit mAb (#3724)


title: wt_s9_LT_sRNAseq_rep2


title: S6_rep1_input

value: untreated


title: wt_s9_NT_sRNAseq_rep3


title: WMI27_I


title: wt_s9_LT_sRNAseq_rep1


title: CLIP_HEK293T_rep2_CLIP

description: replicate 2, CLIP RNA


title: WMI33_M


title: G3_DMSO treated_Vehicle control

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

data_processing:
Real-Time Analysis (RTA) software, Illumina used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with following parameters: LEADING:3 TRAILING:3 HEADCROP:10 MINLEN:50
Sequence reads were mapped to hg38 whole genome using STAR Aligner
Read counts were generated from aligned BAM files using FeatureCounts tool by mapping to GRCh38 genome assembly.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files include read count values

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were grown in a humidified chamber maintained at 37⁰C and 5% CO2. The cells were cultured in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated using an RNA extraction reagent prepared in-house.
Libraries were prepared using TruSeq RNA Kit. according to the manufacturer's instructions. Briefly, mRNA was fragmented and reverse transcribed using oligo-dT primers to synthesize cDNA. The double-stranded cDNAs were end-repaired, polyadenylated, and ligated with adapter sequences followed by size selection for approximately 250-450 bp using AMPure XP beads. Uracil-containing strands were degraded by treatment with USER Enzyme. Sequencing was performed using Illumina Novaseq 6000 Platform in paired-end reads format with the Phred score of 64.

treatment_protocol: 0.2 million MCF-7 cells were seeded in 35mm dishes. After 48 h, the cells were washed with DPBS and treated with 10 μM Karanjin. The control group was treated with 0.1% DMSO. After 24 hours of treatment the cells were harvested.

value: DMSO for 24 hours

value: Breast cancer cell line

value: Wild type


title: ago1d_s9_NT_sRNAseq_rep3

value: ago1d knockout


title: WMI26_M


title: G2_DMSO treated_Vehicle control


title: K2_Karanjin_10uM treated

value: 10 uM Karanjin  for 24 hours


title: WMI18_M


title: K1_Karanjin_10uM treated


title: G1_DMSO treated_Vehicle control


title: ago1d_s9_NT_sRNAseq_rep1


title: WDIZ3_DI

value: Ccnd1 (D) cohort


title: whole blood, 208_D28

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing raw Kallisto gene count from individual samples

source_name: whole blood

extract_protocol:
RNA recovered from Paxgene tubes using the Qiagen PAXgene Blood RNA isolation Kit
Libraries created using Illumina Stranded Total RNA Prep with Ribo-Zero Plus
Final sequencing libraries generated using the IDT-Ilmn RNA UD Indexes SetA, and QC performed prior to sequencing using the Bioanalyzer and DNA 1000 reagents

value: whole blood

tag: individual

tag: infection

tag: time

value: day 28


title: WMI09_C

value: MMSET (M) cohort

tag: cell type

value: bone marrow plasma cells


title: ago1d_s9_LT_sRNAseq_rep3


title: WMI24_C


title: ago1d_s9_LT_sRNAseq_rep2


title: WMI31_C


title: wt_s8_NT_sRNAseq_rep3

value: 28 C treatment


title: WMI11_M


title: ago1d_s9_LT_sRNAseq_rep1


title: K3_Karanjin_10uM treated

tag: cell line


title: WMI16_C


title: whole blood, 204_D0

tag: tissue

value: control

value: day 0


title: WDI22_DI


title: whole blood, 207_D8

value: day 8


title: wt_s8_NT_sRNAseq_rep2

value: wild-type


title: WDIZ1_DI


title: WDI31_DI


title: whole blood, 205_D14

value: day 14


title: ago1d_s9_NT_sRNAseq_rep2


title: WDI13_DI


title: wt_s8_NT_sRNAseq_rep1


title: whole blood, 208_H3


title: whole blood, 202_D10

value: day 10


title: wt_s8_LT_sRNAseq_rep2

value: 22 C treatment


title: whole blood, 207_D0


title: wt_s8_LT_sRNAseq_rep3


title: whole blood, 205_D10


title: WDI15_I


title: WDI33_I


title: WDI02_DI


title: WDI24_I


title: wt_s8_LT_sRNAseq_rep1


title: whole blood, 208_D10


title: WDI04_I


title: whole blood, 203_D28


title: ago1d_s8_NT_sRNAseq_rep3


title: whole blood, 202_D8


title: WDI32_D


title: ago1d_s8_NT_sRNAseq_rep1


title: whole blood, 206_D28


title: ago1d_s8_NT_sRNAseq_rep2


title: WDI23_D


title: whole blood, 205_D8


title: WDI14_D


title: whole blood, 203_D14


title: ago1d_s8_LT_sRNAseq_rep2


title: ago1d_s8_LT_sRNAseq_rep1


title: WDI07_D


title: whole blood, 202_D0


title: WDI30_C


title: wt_s6_NT_sRNAseq_rep3


title: wt_s6_NT_sRNAseq_rep2


title: whole blood, 209_D28


title: wt_s6_NT_sRNAseq_rep1


title: WDI16_C


title: WDI01_C


title: wt_s6_LT_sRNAseq_rep3


title: whole blood, 205_D0


title: whole blood, 206_D14


title: wt_s6_LT_sRNAseq_rep1


title: wt_s6_LT_sRNAseq_rep2


title: whole blood, 201_D28


title: Run 3

city: New York

first: Sana

last: Chintamen

institute: Columbia University Irving Medical Center

data_processing:
Cell ranger mfastq run with default parameters
Cell ranger counts run with default parameters
Processed counts matrices were filtered and integrated across runs using Seurat v 4.0.
Unsupervised hierarchical clustering performed using FindClusters on Seuratv4.0.
Genome_build: mm10
Supplementary_files_format_and_content: count matrices for each run (matrix.mtx files) with cell IDs (barcodes) and gene names (features)
Supplementary_files_format_and_content: Cluster ID file containing cell barcode (with run number following underscore) and cluster ID

source_name: Hippocampal myeloid cell

extract_protocol:
Brains were harvested following PBS perfusion. Hippocampi were then microdiseccted after which the tissue was homogenized and passed through magnetic columns for myelin removal and flow cytometer for enrichment of viable microglia
Library was prepared to manufacturer's (10x Genomics) instructions

treatment_protocol: Mice were injected with Tamoxifen 100mg/kg) for four consecutive days to induce recombination of floxed -tdTomato reporter gene in myeloid cells

value: Cx3cr1CreERT2/+  ; Rosa26tdTomato/+; NestinTK-eGFP/+

value: tdTomato+

value: Bilateral Hippocampi


title: whole blood, 203_D10


title: Run 2


title: ago1d_s8_LT_sRNAseq_rep3

value: ago1d knockout


title: Run 1


title: whole blood, 209_H3


title: ago1d_s6_NT_sRNAseq_rep3


title: 80ES

first: Christine

last: Becker

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.40

data_processing:
Quality trim to remove low quality reads and reads shorter than 45bps
Reads are mapped to ensembl_mm9_genome supplied with Mus_musculus.GRCm38.96.gtf junction file by STAR-2.6.1d
Duplicates were removed by Picard2.20.2 MarkDuplicates (https://broadinstitute.github.io/picard/)
Read counts for each gene were obtained by Subread/1.6.3 featureCounts (Liao et al ., 2014)
Gene annotations were obtained by biomaRt
Low-expressed genes were  filtered when counts were no more than 10 in at least 5 samples.
Raw counts were further normalized by edgeR TMM method
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files

source_name: Lung Tissue

growth_protocol: Pulmonary fibrosis was induced in C57Bl/6 mice by intrapulmonary delivery of bleomycin or recombinant adenovirus TGF-β (Ad-TGF-β). Bleomycin (1.5 U/kg) or saline administered by oropharyngeal instillation and Ad-TGF-β1 (VQAd CMV mTGF-β1-Viraquest), (2 x 109 pfu per mouse) or empty vector was administered via the intranasal route. In both animal models, treatment with drugs was started on day 10 and drugs were administered daily by oral gavage (saracatinib 20mg/kg; nintedanib 60mg/kg; pirfenidone 300mg/kg) until day 28. Mice were euthanized, and lungs were harvested on day 28 for fibrosis analysis. Mice of both sexes were studied and 15-20 mice per group were used. All animal procedures were approved by the Institutional Animal Care and Use Committees (IACUC) from National Jewish Health and Yale University.

extract_protocol:
Left lungs were used for RNA extraction via miRNeasy Mini Kit (Qiagen-217004) according to the manufacturer's instructions. The purity of the RNA was verified using a NanoDrop at 260 nm, and the quality of the RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)
Libraries were prepared using KAPA Stranded mRNA-Seq Kit. mRNA was enriched by ribosomal RNA depletion.
Library quality was checked using Agilent TapeStation analyzer and sequencing was performed with NovaSeq (2X100, 25 M reads per sample).

treatment_protocol: Mouse lungs were isolated from bleomycin and TGF-β mice models (8 conditions: 5 replicates each of bleomycin + vehicle, bleomycin + saracatinib, saline + vehicle, saline + saracatinib, TGF-β + vehicle, TGF-β + saracatinib, empty vector + vehicle, empty vector + saracatinib).

tag: inhibitor

value: saracatinib

tag: stimulation

value: Empty vector

tag: timepoint

value: 18 days after treatments


title: ago1d_s6_NT_sRNAseq_rep2

tag: treatment

tag: genotype


title: 8TV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.39

value: vehicle

value: Adenovirus TGF-beta

tag: strain


title: whole blood, 206_D10

value: whole blood


title: whole blood, 208_D0

value: control


title: WDI21_C

value: Ccnd1 (D) cohort

value: bone marrow plasma cells


title: ago1d_s6_LT_sRNAseq_rep3


title: 79ES

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.38


title: ago1d_s6_NT_sRNAseq_rep1

value: 28 C treatment


title: 77ES

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.37


title: whole blood, 208_D8

value: day 8


title: whole blood, 203_D8


title: 76ES

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.36


title: 75ES

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.35


title: ago1d_s6_LT_sRNAseq_rep1


title: whole blood, 201_D14

value: day 14


title: whole blood, 209_D10

value: day 10


title: wt_s9_NT_RNAseq_rep2

value: wild-type


title: wt_s9_NT_RNAseq_rep3


title: wt_s9_NT_RNAseq_rep1


title: 65EV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.32


title: 7TV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.34


title: whole blood, 207_D28

value: day 28


title: whole blood, 206_D8


title: 66EV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.33


title: whole blood, 204_H3


title: wt_s9_LT_RNAseq_rep3

value: 22 C treatment


title: whole blood, 203_D0

value: day 0


title: 63EV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.30


title: wt_s9_LT_RNAseq_rep2


title: whole blood, 204_D28


title: ago1d_s6_LT_sRNAseq_rep2

value: ago1d knockout


title: whole blood, 201_D10


title: whole blood, 209_D8


title: wt_s9_LT_RNAseq_rep1


title: 62EV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.29

value: Empty vector


title: ago1d_s9_NT_RNAseq_rep3


title: 4BV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.28

value: Bleomycin

value: 18 days after treatments


title: ago1d_s9_NT_RNAseq_rep2


title: whole blood, 207_D14


title: 46BS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.27

value: saracatinib


title: normal tissue(adjacent normal skin tissues)

city: Nanchang

first: Dewu

last: Liu

address: 17 Yongwai Street

institute: Institute of Burn Injury, The First Affiliated Hospital of Nanchang University

description:
miRNA
CK

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt.
The clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2.
The small RNA expression level is calculated by counting absolute numbers of molecules using counts per million (CPM).
Differential expression analysis was performed using the PossionDis, FDR≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference.
Assembly: miRBase
Supplementary files format and content: tab-delimited text files include councounts per million (CPM) values for each Sample

source_name: adjacent normal skin tissues

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions
Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments.

tag: disease state

value: adjacent normal skin tissues

tag: age

value: 45–58 years


title: 42BS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.26


title: ago1d_s9_NT_RNAseq_rep1


title: 64EV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.31

value: vehicle


title: ago1d_s9_LT_RNAseq_rep3


title: whole blood, 204_D10

value: whole blood


title: ago1d_s9_LT_RNAseq_rep2


title: ChIP-Seq_U2OS_RUVBL2_rep2

city: Beijing

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

institute: Peking University

description:
Pol II degron 6h
Illumina Prep Kit libraries

data_processing:
In order to improve the mapping ratio, paired-end sequencing reads were removed low-quality reads and adaptors with Cutadapt V1.18 (TELP libraries: -a CCCCCCCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 15,15; Illumina Prep Kit libraries: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGA -q 15,15)  (Martin, 2011), and then the filtered reads were mapped to the mm10 or hg19 genome with bowtie2 (for TELP libraries, the parameter --very-sensitive-local was used; for Illumina Prep Kit libraries the default parameter was used.) (Langmead and Salzberg, 2012);
in order to improve the accuracy of mapping, duplicate, discordantly and multi-mapping reads were removed with Sambamba V 0.6.8 (Tarasov et al., 2015). To compare the Ruvbl1 and Ruvbl2, all the bam files were down sampled to get the same numbers of reads with Picard V2.17.0 (Broad_Institute, 2019). In order to visualize the data, the final unique bam files were converted into bigwig files and visualized with Integrative Genomics Viewer (IGV)(Robinson et al., 2011).
For Pol II ChIP-Seq data, because the two samples in time points of mock, auxin 12 h and the three samples in time points of dox, auxin 0.5 h, and auxin 1 h were not performed in the same batch. In order to compare the data between each time point, the data at each time point was down sampled to equal reads with Picard V2.17.0 (Broad_Institute, 2019), and the two-time points of mock and dox were performed quantile normalization with DANPOS2 V2.2.2 (Chen et al., 2013).
Then the samples of auxin 0.5 h and auxin 1 h were scaled according to the dox sample’ quantile normalization scaling factor of each bin, the sample of auxin 12 h was scaled according to the Mock sample’ quantile normalization scaling factor of each bin.
For INO80, P400, CTCF, SMC1 ChIP-Seq, to compare in different time points, the reads were also down sampled to equal with Picard V2.17.0 (Broad_Institute, 2019).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: bigwig file contain the genome-wide binding profile of each protein

source_name: U2OS cells

growth_protocol: For Ruvbl2 degron cells ChIP-seq, Ruvbl2-mAID tagged mESC (V6.5) cell lines were cultured in 0.2 % gelatin coated 15 cm plates with irradiated mouse embryonic fibroblasts (MEF) in DMEM-KO (Gibco, 10829018) containing 15% FBS, 1000 U/ml mouse leukemia inhibiting factor (mLIF), 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1× nonessential amino acids, and 1× penicillin/ streptomycin at 37 °C with 5% CO2, as described previously (Jiang et al., 2020). All the mESCs were harvested for the follow-up experiments after two passages of MEF feeders. For human cells and cancer cells Ruvbl2 ChIP-Seq, GM12878 (human lymphoblastoid cells, Female) cells were cultured in RPMI 1640 media (Gibco, 11879020) with 2 mM L-glutamine supplemented 15% FBS, 1 mM sodium pyruvate (Gibco, 11360070) and 1× penicillin/ streptomycin; K562 cells (Human chronic myeloid leukemia cells) were cultured in RPMI 1640 media with 2 mM L-glutamine supplemented 15% FBS, 1 mM sodium pyruvate (Gibco,11360070), 1x nonessential amino acids (Milipore, TMS-001-C), 0.1 mM β-mercaptoethanol (Sigma, M3148), and 1× penicillin/ streptomycin; MCF-7 (human breast cancer cells) were cultured in Minimum Essential Medium (MEM, Gibco, A4192201) containing 15% FBS and 1× penicillin/ streptomycin; HCT116 cells (Human colon carcinoma cells) were cultured in DMEM (Gibco, C11995500BT) supplemented 10% fetal bovine serum and 1× penicillin/ streptomycin; U2OS cells (human osteosarcoma cells) were cultured in DMEM supplemented 10% FBS and 1 penicillin/ streptomycin; Hela cells (human cervical carcinoma cells) were cultured in DMEM supplemented 15% FBS and 1× penicillin/ streptomycin; HepG2 cells (human hepatoblastoma cell) were maintained in DMEM supplemented 10% FBS with 1× penicillin/ streptomycin.

extract_protocol:
the crosslinked cells were digested using MNase (200 U/ 20 million cells in 1 ml sonication buffer, for 15 min at 37 °C), then dissociated in Bioruptor Sonication Device (high energy for 30s on and 60s off, work on 20 cycles). Lysates were centrifuged twice at 1,2000 rpm for 10 min at 4 °C, 20 μl supernatant were sampled as input, the rest supernatant were transferred into 2 new DNase free tube (500 μl/ tube) , then 1 μl GFP abs (Abcam, no. ab290), and equal isotype IgG control (Millipore, no. 12-370, 12-371), or 1 μg of RPB1 abs (Abcam, No. ab817), INO80 abs (Proteintech, no.18810-1-AP), p400 abs (Bethyl, no. A300-541A), Smc1a abs (Bethyl, no. A300-055A), and 2 μl CTCF abs (ABclonal, no. A1133) or 5 μl RUVBL2 abs (ABclonal, no. A1905) were added for each ChIP reaction, respectively, and incubated overnight at 4 °C with low speed rotation, the antibody enriched DNA was extracted by Tris saturated equilibrium phenol (25:24:1) (pH8.0).
The RUVBL1/2, Pol II (RPB1), CTCF and SMC1 ChIPed DNA were delivered to library preparation through TELP method (Peng et al., 2015), and mESCs INO80 and P400 ChIPed DNA and human and cancer cells RUVBL2 ChIPed DNA were subjected for library construction using the NEBNext Ultra II DNA library prep kit according to the manufacturer-supplied protocol, the 200~400 bps length amplified DNA were recovered and analyzed with Qubit assays and Fragment Analyzer, and finally subject to HiSeq Xten PE150 sequencing (Novogene, Beijing).

treatment_protocol: after two passages For Ruvbl2 degron cells, 2 μg/ml Doxycycline (Dox) were added into the medium for 24 h to induce the OsTir1 expression, and then 500 μM auxin (3-indole acetic acid) were appended for the 0.5h, 1h and 12h to induce the RUVBL2 degradation. Then cells were harvested and crosslinked using 1% formaldehyde for 10 min at room temperature, finally, cells were subjected for ChIP.

tag: antibody

value: embryonic stem cells

tag: agent

value: Pol II degron 6h

tag: time point


title: ChIP-Seq_U2OS_RUVBL2_rep1


title: whole blood, 201_D8

tag: individual

value: day 8


title: whole blood, 202_D28

tag: infection


title: 41BS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.25


title: ago1d_s9_LT_RNAseq_rep1


title: 37BS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.24


title: 2BV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.23


title: whole blood, 209_D0

value: control

tag: time


title: wound tissue(diabetic chronic wounds)

description:
miRNA
Case

source_name: diabetic chronic wounds

value: diabetic chronic wounds


title: 28BS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.22


title: whole blood, 207_D10

value: day 10


title: ChIP-Seq_U2OS_Input

tag: cell type


title: 25TS

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.21

value: Adenovirus TGF-beta


title: wt_s8_NT_RNAseq_rep2

value: 28 C treatment

value: wild-type


title: whole blood, 206_D0

value: day 0


title: ChIP-Seq_MCF7_RUVBL2_rep1

description:
WT untreated MCF7
Illumina Prep Kit libraries

source_name: MCF7 cells

tag: cell line

value: WT


title: wt_s8_NT_RNAseq_rep1


title: ChIP-Seq_MCF7_RUVBL2_rep2


title: whole blood, 205_D28

tag: tissue

value: day 28


title: 24TS

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.20

tag: inhibitor

value: saracatinib

value: 18 days after treatments


title: ChIP-Seq_MCF7_Input


title: wt_s8_NT_RNAseq_rep3


title: 23TS

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.19

tag: stimulation


title: 21BV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.18

value: Bleomycin

tag: timepoint


title: whole blood, 204_D8


title: wt_s8_LT_RNAseq_rep3

tag: treatment

value: 22 C treatment


title: wt_s8_LT_RNAseq_rep1

tag: genotype


title: ChIP-Seq_K562_RUVBL2_rep2

description:
WT untreated K562
Illumina Prep Kit libraries

source_name: K562 cells


title: MS7_29

description:
Normal Donor
raw_data.txt
ipf_voom_normalized.txt

data_processing:
FastQ files were trimmed with TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Quality control was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) before and after quality trim
Reads were aligned with STAR aligner (version 2.6.1d, using the default settings) to the HG38 human genome and ENSEMBL94 annotation GTF file
Summarization with featureCounts of the Subread package (feature Counts release 1.6.3 and picard version 2.18.21)
Samples were normalized using voom (limma package)
Genome_build: HG38
Supplementary_files_format_and_content: tab delimited text files

source_name: Normal Human Lung Fibroblast

growth_protocol: Experiments were performed using primary normal human lung fibroblasts (NHLF). Cells were serum-starved overnight and then incubated with inhibitors (saracatinib: (0.3 μM), nintedanib: (1 μM), pirfenidone: (20 μg/ml) or vehicle (DMSO)) for 60 min followed by stimulation with human recombinant TGF-β (2 ng/ml) or vehicle control for 24 hours in the continued presence of the inhibitors.

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (Qiagen-217004) according to the manufacturer's instructions. The purity of the RNA was verified using a NanoDrop at 260 nm, and the quality of the RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)
Libraries were prepared using KAPA Stranded mRNA-Seq Kit. mRNA was enriched by ribosomal RNA depletion.
Library quality was checked using Agilent TapeStation analyzer and sequencing was performed with NovaSeq (2X100, 25 M reads per sample).

treatment_protocol: NHLFs were treated with drugs or vehicle controls with and without TGF-β (10 conditions: 3 replicates each of vehicle A + media; vehicle A + TGF-β; saracatinib + TGF-β; nintedanib + TGF-β; pirfenidone + TGF-β; saracatinib + vehicle B; nintedanib+ vehicle B; pirfenidone + vehicle B; vehicle A + vehicle B; media + vehicle B).

value: Media

value: Vehicle B

value: 24 Hours


title: ChIP-Seq_K562_RUVBL2_rep1


title: ago1d_s8_NT_RNAseq_rep2

value: ago1d knockout


title: ago1d_s8_NT_RNAseq_rep3


title: 21TS

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.17

tag: strain


title: wt_s8_LT_RNAseq_rep2


title: MS7_27

value: Vehicle A


title: whole blood, 201_D0

value: whole blood

value: control


title: whole blood, 202_D14

value: day 14


title: MS7_30


title: 19TS

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.16

value: Adenovirus TGF-beta


title: ChIP-Seq_HepG2_RUVBL2_rep2

description:
WT untreated HepG2
Illumina Prep Kit libraries

source_name: HepG2 cells


title: MS7_26


title: 16BV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.15

value: vehicle


title: 118SS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.12

value: saline


title: ChIP-Seq_Hela_RUVBL2_rep1

description:
WT untreated Hela
Illumina Prep Kit libraries

source_name: Hela cells

value: Hela

value: WT


title: ChIP-Seq_HepG2_RUVBL2_rep1


title: MS7_28


title: ago1d_s8_LT_RNAseq_rep1


title: ChIP-Seq_Hela_Input


title: 121SS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.14

value: saracatinib


title: ChIP-Seq_HepG2_Input


title: 12TV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.13

value: 18 days after treatments


title: wt_s6_NT_RNAseq_rep3

value: 28 C treatment

value: wild-type


title: ChIP-Seq_Hela_RUVBL2_rep2


title: ago1d_s8_LT_RNAseq_rep3

value: 22 C treatment


title: ChIP-Seq_HCT116_RUVBL2_rep2

description:
WT untreated HCT116
Illumina Prep Kit libraries

source_name: HCT116 cells


title: ago1d_s8_LT_RNAseq_rep2


title: wt_s6_NT_RNAseq_rep2


title: 113SS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.9


title: wt_s6_NT_RNAseq_rep1


title: ChIP-Seq_K562_Input


title: 117SS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.11


title: MS7_24

value: Pirfenidone

value: Vehicle B


title: 114SS

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.10


title: ago1d_s8_NT_RNAseq_rep1

value: ago1d knockout


title: MS7_23

value: 24 Hours


title: 10BV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.7

value: Bleomycin


title: ChIP-Seq_GM12878_RUVBL2_rep2

description:
WT untreated GM12878
Illumina Prep Kit libraries

source_name: GM12878 cells


title: ChIP-Seq_HCT116_RUVBL2_rep1


title: MS7_22


title: MS7_25

value: Vehicle A


title: 11TV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.8


title: wt_s6_LT_RNAseq_rep2


title: ChIP-Seq_HCT116_Input


title: MS7_20

value: Nintedanib


title: ChIP-Seq_GM12878_RUVBL2_rep1


title: 102SV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.3


title: MS7_17

description:
Normal Donor
raw_data.txt
ipf_voom_normalized.txt

value: Saracatanib


title: MS7_21


title: MS7_19


title: 109SV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.6

value: vehicle


title: ago1d_s6_NT_RNAseq_rep1


title: wt_s6_LT_RNAseq_rep3


title: ago1d_s6_LT_RNAseq_rep3


title: MS7_18


title: PI_rabbit_ad_female

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
After merging replicates, coverage tracks _10.bedGraph) were obtained using deepTools (Ramírez et al. 2014) bamCoverage function with bin width 10 bp and RPKM normalization.
Peak calling was performed only for male_MSL2 and M1_wt_male_MSL2 samples using MACS version 2 against preimmune control (PI_rabbit_ad_male) (Zhang et al. 2008) in paired-end mode (option format=BAMPE).
Peaks with p value less than 1x10-2 were passed to the IDR pipeline to access reproducibility of chip-seq replicates (https://sites.google.com/site/anshulkundaje/projects/idr).
Optimal set of reproduced peaks (IDR p value < 0.05) was chosen for each sample and passed to further analysis.
Genome_build: dm6
Supplementary_files_format_and_content: Processed data was obtained by MACS2 and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions (only for male_MSL2 and M1_wt_male_MSL2 samples)  and coverage (bedGraph) (for all samples except PI_rabbit_ad_male_R1_001)

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Lines of Drosophila melanogaster were grown in population cages at 25 degrees. For chromatin preparation adult 3-day old flies were chosen.

extract_protocol:
For immunoprecipitation chromatin was pre-cleared with Protein A Dynabeads (Thermo Fisher), blocked with 0.5% BSA. Samples containing 20 µg of DNA equivalent in 0,5 mL of nuclear lysis buffer were incubated overnight, at 4°C on a rotary shaker, with rabbit antibodies against MSL1 (1:300), MSL2 (1:200), MSL3 (1:200), or with nonspecific IgG purified from rabbit preimmune sera (control). Chromatin–antibody complexes were collected using blocked Protein A Dynabeads (Thermo Fisher) at 4°C over 5 h. After three rounds of washing with nuclei lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), treated with RNase A for 30 min and proteinase K overnight, incubated at 65 °C for 6 hours and extracted  with ChIP DNA Clean&Concentrator (Zymo Research).
The ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep kit, as described in the manufacturer’s instructions. In short, eluted DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using NEB primers for 15-16 cycles using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). Diluted libraries were clustered on a pair-read flowcell and sequenced using a NovaSeq 6000 system (Illumina, United States).

treatment_protocol: Samples of 500 mg each of adult flies were ground in a mortar in liquid nitrogen and resuspended in 10 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Complete Protease Inhibitor Cocktail V. The suspension was then homogenized subsequently in a Potter (10 strokes) and a Dounce (tight pestle, 15 strokes) homogenizers and filtered through 70 µm MACS SmartStrainers (Miltenyi Biotec, United States). The homogenate was cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10 mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 0.1% SDS, 0.5 mM PMSF, Calbiochem Complete Protease Inhibitor Cocktail V). The suspension was incubated for 30 min at 4°C  and then sonicated with Covaris ME220 (50x15 s with 30 s intervals at 6°C, peak power 75.0, duty % factor 25, cycles/burst 1000), and 50 µL aliquots were used to test the extent of sonication and to measure DNA concentration. Chromatin was then transferred to 1.5 ml-eppendorf tubes and centrifuged at 14000 rpm for 10 min at 4 °C. Finally, supernatants were pooled, aliquoted and frozen in liquid nitrogen.

tag: Sex

value: female

tag: protein

value: Preimmune control

tag: antibody source

value: rabbit

value: Oregon-R

value: wt


title: ago1d_s6_NT_RNAseq_rep3

value: 28 C treatment


title: MS7_15

value: TGFb


title: ChIP-Seq_GM12878_Input

tag: antibody

value: WT

tag: agent


title: 105SV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.4

value: saline

value: 18 days after treatments


title: M1_wt_male_MSL3

value: male


title: ago1d_s6_NT_RNAseq_rep2

value: ago1d knockout


title: ago1d_s6_LT_RNAseq_rep2

value: 22 C treatment


title: wt_s6_LT_RNAseq_rep1

value: wild-type


title: PI_rabbit_ad_male


title: MS7_14

value: Pirfenidone

value: 24 Hours


title: female_MSL3


title: MS7_16

value: Saracatanib

value: Vehicle B


title: male_MSL3


title: 101SV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.2

value: vehicle


title: 106SV

description:
ipfm.bleo.counts.raw.txt
ipfm.bleo.counts.TMMnormalized.txt
ipfm.5


title: 10TV

description:
ipfm.tgfb.counts.raw.txt
ipfm.tgfb.counts.TMMnormalized.txt
ipfm.1

value: Adenovirus TGF-beta


title: ago1d_s6_LT_RNAseq_rep1


title: Resident (E11_2), HTO

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
The sequencing data was processed using CellRanger software.
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: DN T cells derived from different LNs

extract_protocol:
Mice were sacrificed and lymph nodes were isolated. Single cell suspnesion was created. Single cell suspensions were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII.
Single cells were sorted using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 or v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
Chromium single cell 3´v2 and v3 (10XGenomics)

value: LN

value: wild type

value: B/6 mice were untreated. For identification of source tissue, cells from different lymph nodes were marked with unique hashtags before pooling.


title: M1_d41_85_M2_MSL3

value: female

value: rabbit

value: Oregon-R


title: RNA_L2C_DMSO rep1

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

data_processing:
For the raw sequencing reads of total RNA-seq, the three leading nucleotides of read2 generated from TSO were removed. Then the adaptors were removed with Trimmomatic (v0.39) if present. The cleaned reads were mapped to GRCm38 reference genome using STAR (v2.7.8a) (Dobin et al, 2013). RSEM (v1.3.1) (Li & Dewey, 2011) was employed to quantify the genes expression levels with the transcriptome alignments generated by STAR as input. For differentially expression analysis, R package DESeq2 (v1.32.0) (Love et al, 2014) was utilized with raw counts from RSEM as input. The significantly changed genes were identified with adjusted p-value cutoff 0.05, fold change cutoff 2 and mean FPKM cutoff 1.
Assembly: mm10
Supplementary files format and content: txt files contain gene-level reads counts of RNA-seq

source_name: late 2-cell

growth_protocol: All animal experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. Collection of oocytes and in vitro fertilized embryos were described previously (Chen et al., 2021; Chen & Zhang, 2019). For allelic H3K27ac CUT&RUN profiling experiments, oocytes were collected from 6- to 8-week-old B6D2F1/J female mice (Jax 100006) and sperm were collected from 8- to 10-week-old PWK/PhJ male mice (Jax 003715). For CBP/p300 and HDACs inhibition experiments, both oocytes and sperm were retrieved from 6- to 8-week-old B6D2F1/J mice. The time when capacitated sperm were added to cumulus oocyte complexes in Human Tubal Fluid (HTF, Millipore) was considered as 0 hour post in vitro fertilization (0hpi). Embryos were cultured in potassium simplex optimized medium (KSOM, Milliplore) at 37°C under 5% CO2 with air.

extract_protocol: The total RNA-seq libraries were generated using the SMART-Seq Stranded Kit (Takara) following the manufacturer protocol.

treatment_protocol: To transiently inhibit CBP/p300, embryos were cultured in KSOM containing 10μM A-485 (Tocris) between 4 and 20hpi. For transient inhibition of HDACs, embryos were cultured in KSOM containing 50nM TSA (Sigma) between 0-20 or 8-28hpi. Embryos were washed at least six times when they were transferred between different culture conditions.

value: B6D2F1/J (female) X B6D2F1/J  (male)

value: late 2-cell

value: WT

value: treated with DMSO


title: M1_d1_15_M2_MSL3


title: RNA_L2C_A485 rep1

value: treated with A485


title: M1_wt_M2_MSL3


title: MS7_9

value: TGFb


title: MS7_10

value: Nintedanib

value: 24 Hours


title: M1_wt_male_MSL2

value: male


title: Cirulating (E10_2), HTO


title: RNA_L2C_DMSO rep2


title: MS7_8

value: Saracatanib


title: RNA_zygote_DMSO rep2

source_name: zygote

value: zygote


title: M1_wt_M2_MSL2


title: Cirulating (E10_2)

description: CD62L positive ITCs (multiplexed)

value: LN


title: MS7_11


title: Resident (E11_2)

description: CD62L negative, CD44 positive ITCs (multiplexed)

value: wild type


title: MS7_13

value: Pirfenidone


title: CXCR6, Itgb7 T cells in LN 4h pi (A2_2)

source_name: CXCR6 and Itgb7 positive T cells from poplitelial LN

value: B/6 mice were infected for 4h with 10e8 CFU in the foot pad with S aureus.


title: male_MSL2

value: rabbit

value: wt


title: MS7_7


title: RNA_L2C_A485 rep2

value: B6D2F1/J (female) X B6D2F1/J  (male)


title: MS7_6

value: Vehicle A


title: MNase-Seq_mESCs_Dox_rep1

description: Illumina Prep Kit libraries

data_processing:
In order to improve the mapping ratio of the data, the adaptors and low-quality reads (MAPQ ≤ 15) were removed from paired-end sequencing reads firstly, then the reads were mapped to the mouse genome mm10 with bowtie2 (default parameters) (Langmead and Salzberg, 2012).
In order to increase the accuracy of the reads mapping, the duplicate, discordant and multi-mapping reads are removed, and reads in the range of 160-190bp were selected as the classic nucleosome with alignmentSieve from the deepTools (Ramirez et al., 2014), and the midpoint of the fragment were defined as the position of the nucleosome.
In order to explore the changes of MNase at the genome-wide level, bamCoverage (--MNase) from deepTools (Ramirez et al., 2014) was used to obtain the MNase track. In order to get a smoother track, gsmooth function of scipy (python package) was used to smooth the track. And the final tracks were used for meta-analysis in different chromatin regions.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file contain the genome-wide profile of histone

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: The native cell MNase-Seq was performed with some modifications according to the protocol described previously (Schones et al., 2008). Briefly, Dox and auxin-treated RUVBL2 degron mESCs with ~80% confluency were harvested with trypsinization and washed twice with ice-cold 1× PBS (20 million cells/ 5–10 ml). Spin down the cells at 350 g for 5 min at 4 °C.

extract_protocol:
Wash the nuclei with 1 ml re-suspended buffer (0.3 M Sucrose, 15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 1 x proteinase inhibitor cocktail, 0.2 mM spermine, 1 mM spermidine), spin down the nuclei at 350 g for 5 min at 4 °C, and re-suspend the nuclei with 1 ml of the MNase digestion buffer (0.3 M Sucrose, 50 mM Tris pH 7.5, 4 mM MgCl2, 5 mM CaCl2, 1 x proteinase inhibitor cocktail, and 12.5 U MNase per 1 million cells), incubate at 37 °C for 15 min to digest the chromatin (~80% mono-nucleosomes).
Then add 40 μl 0.5 M EDTA (final conc. 20 mM) and 40 μl 0.5 M EGTA (final conc. 20mM) to inactivate MNase. Place the mixture on ice and mix thoroughly by pipette. Centrifuge at 350 g for 5 min at 4 °C, discard the supernatant and then add the Proteinase K (500 μg/mL) buffer to incubate at 65 °C for 2 h, then inactivate the proteinase at 80 °C for 20 min, and eliminate RNA with 10 μl RNase A (incubate for 30 min at 37 °C).
The chromatin DNA were extracted using an equal volume of Phenol/chloroform/ isoamyl alcohol (25:24:1). Load the purified DNA from each reaction onto a 1 % agarose gel for electrophoresis examination. The excised mononucleosome bands (about 150 bp size) were extracted and purified using gel extraction kit, and elute the mononucleosome DNA. The DNA was next constructed for the NGS library using the NEB library kit ( NEB.E7645) following the manufacture’s instruction. Each condition was performed with two technical duplicates and finally subject to HiSeq Xten PE150 sequencing (Novogene, Beijing) and analysis.

treatment_protocol: Resuspend the cell pellets in 1 ml of ice-cold lysis buffer (0.3 M Sucrose, 15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 0.5 mM DTT, 1×proteinase inhibitor cocktail, 0.2 mM spermine, 1 mM spermidine, 0.02% NP-40), and incubate for 5 min on ice. Pellet the nuclei (10–20 million) by spinning at 350 g for 5 min at 4 °C.

value: RUVBL2 degron mESCs

value: Dox


title: M1_d1_15_M2_MSL2

value: female

value: Oregon-R


title: CXCR6, CD44 LN cells (D7)

source_name: CXCR6 and CD44 positive skin draining LN cells

value: untreated


title: MNase-Seq_mESCs_Dox_rep2

description: Illumina Prep Kit libraries


title: RNA_zygote_A485 rep1

value: WT

value: treated with A485


title: M1_d41_85_M2_MSL2


title: MS7_12

value: Nintedanib

value: TGFb

value: 24 Hours


title: MNase-Seq_mESCs_Auxin_1h_rep1

description: Illumina Prep Kit libraries


title: MNase-Seq_mESCs_Auxin_1h_rep2

description: Illumina Prep Kit libraries


title: female_MSL1


title: RNA_zygote_A485 rep2

value: zygote


title: M1_wt_M2_MSL1


title: ATAC_early2C_A485_rep1

data_processing:
For CUT&RUN sequencing data, the raw paired-end reads were trimmed with Trimmomatic (v0.39) (Bolger et al, 2014) to remove adaptors and the trimmed reads with length at least 35bp were retained. The cleaned reads were mapped to GRCm38 reference genome using bowtie2 (v2.4.2) (Langmead & Salzberg, 2012) with parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 --soft-clipped-unmapped-tlen. PCR duplicates were removed with Picard MarkDuplicates (v2.23.4). The mapped reads were further filtered to retain proper paired reads with fragment length at least 140 and mapping quality at least 30. The signal tracks were generated by bamCoverage in deeptools (v3.5.1) (Ramirez et al, 2016) with 100bp bin size and normalized with FPKM.    Since the H3K27ac showed different broad or narrow patterns in different stages of early embryos, the FPKM values were not directly comparable among stages. To make the FPKM values comparable, we followed the scaling method used in the previous study of H3K4me3 (Dahl et al., 2016), which also showed broad and narrow patterns in different stages. We used the signals in ESCs as reference so the ESCs had a scale factor of 1. We ranked the gene promoters by their H3K27ac signals. Then for each stage, we chose the median signal of the top 3,000 promoters, dividing from the median signals of the top 3,000 promoters in ESCs to obtain the sale factor for that stage. The FPKM signals in each stage were multiplied by the scale factor to derive the scaled FPKM, which was used in all the downstream analysis.    For allelic analysis, we used SNPsplit (v0.5.0) (Krueger & Andrews, 2016) to assign the mapped reads to maternal or paternal allele based on the SNPs information between B6D2F1and PWK/PhJ. The SNPs were downloaded from the Mouse Genomes Project (https://www.sanger.ac.uk/data/mouse-genomes-project/). The SNPs that were identical between C57BL/6J and DBA/2J while different with PWK/PhJ were used.
For the raw sequencing reads of total RNA-seq, the three leading nucleotides of read2 generated from TSO were removed. Then the adaptors were removed with Trimmomatic (v0.39) if present. The cleaned reads were mapped to GRCm38 reference genome using STAR (v2.7.8a) (Dobin et al, 2013). RSEM (v1.3.1) (Li & Dewey, 2011) was employed to quantify the genes expression levels with the transcriptome alignments generated by STAR as input. For differentially expression analysis, R package DESeq2 (v1.32.0) (Love et al, 2014) was utilized with raw counts from RSEM as input. The significantly changed genes were identified with adjusted p-value cutoff 0.05, fold change cutoff 2 and mean FPKM cutoff 1.
For analyzing ATAC-seq sequencing data, we used the ENCODE ATAC-seq pipeline (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline). ATAC-seq peaks within 1kb upstream or downstream of any known TSS were treated as promoter peaks, while ATAC-seq peaks with distance greater than 2.5kb to TSS were treated as distal peaks.
Assembly: mm10
Supplementary files format and content: bigWig files contain scaled H3K27ac CUT&RUN FPKMs and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq; bed files contain ATAC-seq peaks

source_name: early 2-cell

extract_protocol: CUT&RUN libraries were generated based on the original protocol (Meers et al, 2019) with some modifications to optimize for low-input cell numbers. For each library, 10μl BioMag Plus Concanavalin A beads (Polysciences) were washed twice in 1ml Binding Buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in 5μl Binding Buffer. Then embryos were added in 45μl Wash Buffer (20mM HEPES-NaOH pH7.5, 150mM NaCl, 0.5mM Spermidine, 1X Roche Protease Inhibitor Cocktail), mixed with the 5μl Binding Buffer containing beads and rotated for 10min at room temperature. After removing the liquid by putting the tube on the magnet stand, the beads were resuspended in 80μl antibody Incubation Buffer (1X Wash Buffer with 0.02% Digitonin and 2mM EDTA) with 1:100 diluted H3K27ac antibody (Millipore, 07-360) and rotated at 4oC overnight. Then the beads were washed twice with 100μl Wash Buffer with 0.02% Digitonin and pulled off the liquid. The beads were resuspended in 100μl Wash Buffer with 0.02% Digitonin and 500ng/ml pA-MNase, then rotated for 3h at 4oC. After washing the beads twice with 200μl Wash Buffer with 0.02% Digitonin, the beads were resuspended in 200μl ice-cold Wash Buffer with 0.02% Digitonin and 4μl 100mM CaCl2 and incubated at 0oC for 30min. The reaction was stopped by adding 23μl 10X Stop Buffer (1,700mM NaCl, 100mM EDTA, 20mM EGTA, 0.02% Digitonin, 250µg/ml RNase A, 250µg/ml Glycogen). Then the tube was incubated at 37oC for 10min to release the cut fragments into supernatant. The tube was put on a magnet stand and the supernatant was transferred to a new 1.5ml LoBind tube (Eppendorf) while the beads were discarded. 2.5μl 10% SDS and 2.5μl Proteinase K (20mg/ml) were added to the supernatant and incubated at 55oC for 1h. Then 25ng carrier RNA (Qiagen, 1068337) was added to the supernatant. The supernatant was mixed with 200μl Phenol:Chloroform:Isoamyl Alcohol (Invitrogen, 15593031) by vortexing then transferred to a phase-lock tube (QuantaBio, 2302830) and centrifuged at 16,000g for 5min at room temperature. The supernatant was transferred to a new 1.5ml LoBind tube, added 26μl 3M Sodium Acetate, 1μl Glycogen (20mg/ml) and 750μl cold 100% Ethanol, mixed by vortexing and stored at -20oC overnight. Then the tube was centrifuged at 16,000g for 20min at 4oC and the supernatant was discarded. The precipitate DNA pellet was washed with 1ml cold 80% Ethanol then centrifuged at 16,000g for 5min at 4oC and the supernatant was discarded. Finally the precipitate DNA pellet was dissolved in 25μl ultrapure H2O. The library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) following the manufacturer protocol.

value: early 2-cell

value: B6D2F1/J (female) x B6D2F1/J  (male)


title: MS7_4


title: ChIP-Seq_mESCs_RUVBL2_rep2

description:
GFP tagged
TELP libraries

source_name: mouse embryonic stem cells

value: embryonic stem cells

value: GFP tagged


title: Control-30

city: shenzhen

first: Yueying

last: Xiang

state: Guangdong

address: 1098 Xueyuan Avenue, Nanshan District,Shenzhen 518000,China

department: Shenzhen University General Hospital health management center

institute: shenzhen university

data_processing:
The sequence signatures with adapter ligation, low quality, and containing the unknown base > 5 were removed to obtain clean sequences.
The clean sequences were aligned to the human reference genome (UCSC hg19) by Burrows-Wheeler Aligner, and the alignment results were saved in BAM format files.
Further advanced analysis for the final BAM files, single nucleotide polymorphisms (SNPs) are detected by GATK and Insertion and Deletions (InDels) are detected by SAMtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files.

source_name: Blood, control

extract_protocol:
Genomic DNA was extracted from all donors using Magbead Blood DNA Kit (CWBIOTech, CW2361S) according to the manufacturer’s methods.
Products were purified using Agencourt AMPure XP beads (Beckman, p/n A63880) after sequencing library were constructed, the mitochondrial genome were captured with AI-Mito-Cap Kit (iGeneTech, Beijing, China) and sequenced on Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) with 150 base paired‐end reads.

tag: diagnosis

value: Control

value: blood

tag: age


title: M1_d1_15_M2_MSL1

value: rabbit


title: male_MSL1

value: male

value: wt


title: RNA_zygote_DMSO rep1

value: B6D2F1/J (female) X B6D2F1/J  (male)

value: treated with DMSO


title: MNase-Seq_mESCs_Auxin_0.5h_rep2

description: Illumina Prep Kit libraries

value: RUVBL2 degron mESCs


title: ChIP-Seq_mESCs_RUVBL1_rep2

description:
GFP tagged
TELP libraries


title: MS7_3

value: Vehicle A

value: Media


title: ATAC_early2C_DMSO_rep1

value: WT


title: M1_wt_male_MSL1

value: Oregon-R


title: MNase-Seq_mESCs_Auxin_0.5h_rep1

description: Illumina Prep Kit libraries


title: Control-28


title: ATAC_early2C_A485_rep2

value: treated with A485


title: MS7_2

value: 24 Hours


title: ChIP-Seq_mESCs_RUVBL2_RUVBL1_Input

description:
GFP tagged
TELP libraries


title: Steadystate_LC

city: Southampton

first: James

middle: David

last: Davies

state: Hampshire

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Samples were de-multiplexed with bcl2fastq tool from Illumina
Reads were  aligned to human_hg19 reference genome using STAR

source_name: human skin primary steady state LCs

growth_protocol: Following digest with dispase overnight at +4C, Digested LC were extracted from epidermis by 90 minute Liberase TM digestion +37C and Migrated LC were extracted from 48 hour culture of epidermis sheets. LCs were enriched using FACS (CD1a+, CD207+, HLADR+)

extract_protocol: cDNA libraries were  tagmented and PCR-amplified (Nextera tagmentation kit, Illumina)

treatment_protocol: Highly purified (CD1a+, CD207+, HLA-DR+) single human LCs were co-encapsulated with genetically-encoded beads (Drop-seq). Monodisperse droplets at 1 nl in size were generated using the microfluidic devices fabricated in the Centre for Hybrid Biodevices, University of Southampton. Following encapsulation, approximately 800 digested steady state LC STAMPS (beads exposed to a single cell) and 200 migratory LC STAMPS were taken further for library prep. The resulting libraries were run on a shared NextSeq run (1.5x105 reads for maximal coverage) at the Wessex Investigational Sciences Hub laboratory, University of Southampton, to obtain single cell sequencing data.

value: Epidermis

value: Langerhans cells (LC)

tag: condition

value: Digested


title: MS7_1


title: M1_d41_85_M2_MSL1

value: female


title: MS7_5

value: TGFb


title: Control-27

value: Control

value: blood


title: ATAC_early2C_DMSO_rep2

tag: cell type

value: early 2-cell

value: B6D2F1/J (female) x B6D2F1/J  (male)


title: ATAC_late1C_DMSO_rep2

source_name: late 1-cell

value: late 1-cell

value: treated with DMSO


title: ATAC_late1C_A485_rep1


title: ChIP-Seq_mESCs_P400_Dox_rep2

description:
RUVBL2 untreated
Illumina Prep Kit libraries

value: embryonic stem cells

value: RUVBL2 untreated

tag: time point


title: ChIP-Seq_mESCs_RUVBL2_rep1

description:
GFP tagged
TELP libraries

value: GFP tagged


title: Control-29

tag: tissue

value: male


title: Migrated_LC

source_name: human skin primary migratory LCs

value: Migrated


title: Control-26


title: ChIP-Seq_mESCs_RUVBL1_rep1

description:
GFP tagged
TELP libraries


title: ChIP-Seq_mESCs_P400_Auxin_1h_rep1

description:
RUVBL2 degron 1h
Illumina Prep Kit libraries

value: RUVBL2 degron


title: RNA_late2C_DMSO_rep2

value: late 2-cell

value: WT


title: ChIP-Seq_mESCs_P400_Dox_rep1


title: Control-22


title: RNA_late2C_DMSO_rep1


title: ATAC_late1C_A485_rep2

value: treated with A485


title: Control-25

value: female


title: RNA_late2C_TSA_rep1

value: treated with TSA


title: ChIP-Seq_mESCs_P400_Auxin_0.5h_rep2

description:
RUVBL2 degron 0.5h
Illumina Prep Kit libraries


title: RNA_late2C_TSA_rep2


title: Control-21

value: Control


title: RNA_early2C_A485_rep2


title: ATAC_late1C_DMSO_rep1


title: Control-19

value: blood


title: ChIP-Seq_mESCs_P400_Auxin_1h_rep2


title: RNA_early2C_A485_rep1

value: early 2-cell


title: Control-24


title: Control-23


title: RNA_early2C_DMSO_rep2

value: B6D2F1/J (female) x B6D2F1/J  (male)


title: H3K27ac_morula

data_processing:
For CUT&RUN sequencing data, the raw paired-end reads were trimmed with Trimmomatic (v0.39) (Bolger et al, 2014) to remove adaptors and the trimmed reads with length at least 35bp were retained. The cleaned reads were mapped to GRCm38 reference genome using bowtie2 (v2.4.2) (Langmead & Salzberg, 2012) with parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 --soft-clipped-unmapped-tlen. PCR duplicates were removed with Picard MarkDuplicates (v2.23.4). The mapped reads were further filtered to retain proper paired reads with fragment length at least 140 and mapping quality at least 30. The signal tracks were generated by bamCoverage in deeptools (v3.5.1) (Ramirez et al, 2016) with 100bp bin size and normalized with FPKM.    Since the H3K27ac showed different broad or narrow patterns in different stages of early embryos, the FPKM values were not directly comparable among stages. To make the FPKM values comparable, we followed the scaling method used in the previous study of H3K4me3 (Dahl et al., 2016), which also showed broad and narrow patterns in different stages. We used the signals in ESCs as reference so the ESCs had a scale factor of 1. We ranked the gene promoters by their H3K27ac signals. Then for each stage, we chose the median signal of the top 3,000 promoters, dividing from the median signals of the top 3,000 promoters in ESCs to obtain the sale factor for that stage. The FPKM signals in each stage were multiplied by the scale factor to derive the scaled FPKM, which was used in all the downstream analysis.    For allelic analysis, we used SNPsplit (v0.5.0) (Krueger & Andrews, 2016) to assign the mapped reads to maternal or paternal allele based on the SNPs information between B6D2F1and PWK/PhJ. The SNPs were downloaded from the Mouse Genomes Project (https://www.sanger.ac.uk/data/mouse-genomes-project/). The SNPs that were identical between C57BL/6J and DBA/2J while different with PWK/PhJ were used.
For the raw sequencing reads of total RNA-seq, the three leading nucleotides of read2 generated from TSO were removed. Then the adaptors were removed with Trimmomatic (v0.39) if present. The cleaned reads were mapped to GRCm38 reference genome using STAR (v2.7.8a) (Dobin et al, 2013). RSEM (v1.3.1) (Li & Dewey, 2011) was employed to quantify the genes expression levels with the transcriptome alignments generated by STAR as input. For differentially expression analysis, R package DESeq2 (v1.32.0) (Love et al, 2014) was utilized with raw counts from RSEM as input. The significantly changed genes were identified with adjusted p-value cutoff 0.05, fold change cutoff 2 and mean FPKM cutoff 1.
For analyzing ATAC-seq sequencing data, we used the ENCODE ATAC-seq pipeline (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline). ATAC-seq peaks within 1kb upstream or downstream of any known TSS were treated as promoter peaks, while ATAC-seq peaks with distance greater than 2.5kb to TSS were treated as distal peaks.
Assembly: mm10
Supplementary files format and content: bigWig files contain scaled H3K27ac CUT&RUN FPKMs and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq; bed files contain ATAC-seq peaks
Library strategy: CUT&RUN

source_name: morula

value: morula

value: B6D2F1/J (female) x PWK/PhJ (male)

value: untreated


title: ChIP-Seq_mESCs_INO80_Auxin_1h_rep2

value: embryonic stem cells


title: RNA_early2C_DMSO_rep1

value: treated with DMSO


title: ChIP-Seq_mESCs_P400_Auxin_0.5h_rep1


title: Control-20


title: H3K27ac_late2C


title: ChIP-Seq_mESCs_INO80_Dox_rep1

value: RUVBL2 untreated


title: Control-18


title: H3K27ac_early2C


title: ChIP-Seq_mESCs_INO80_Auxin_1h_rep1


title: H3K27ac_zygote

value: zygote


title: Control-17


title: Control-14


title: Control-15


title: ChIP-Seq_mESCs_INO80_Auxin_0.5h_rep1

value: RUVBL2 degron


title: ChIP-Seq_mESCs_INO80_Dox_rep2


title: Control-12

value: male


title: P7 No7 Control heart

city: Cincinnati

first: Mei

last: Xin

state: OH

address: 3333 Burnet Avenue

department: EHCB

institute: Cincinnati Children's Hospital

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKM for every gene

source_name: Cardiac cells

extract_protocol:
RNA isolation was performed by QIAGEN RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: Cardiac cells

value: saline


title: H3K27ac_ESC_500_rep2

source_name: ESC

value: ESC

value: WT


title: P7 No3 beta-blocker treated heart

value: beta-blocker for 7 days


title: P7 No2 beta-blocker treated heart


title: H3K27ac_GV

source_name: GV oocyte

value: GV oocyte


title: H3K27ac_MII

source_name: MII oocyte

value: MII oocyte


title: ChIP-Seq_mESCs_Endogenous_RUVBL2_rep2

description:
WT untreated
TELP libraries


title: ChIP-Seq_mESCs_Endogenous_RUVBL2_rep1

description:
WT untreated
TELP libraries


title: ChIP-Seq_mESCs_anti-GFP_Control

description:
WT untreated mES
TELP libraries


title: Control-10

value: Control

value: blood


title: Walnut_19W_pellicle rep3

city: Alar

first: Qiang

last: Jin

email: jqzky@163.com, qiangjin@taru.edu.cn

address: Alar 843300, China

institute: College of Horticulture and Forestry，Tarim University

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to M. viride genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters. Differentially expressed genes (DEGs) were identified by DEseq2 package, and only transcripts with fold change ≥ 2 and FDR ≤ 0.01 were considered as DEGs.
Assembly: JrSerr_v1.0
Supplementary files format and content: tab-delimited text files include FPKM values and counts for each sample.

organism: Juglans regia

source_name: pellicle tissues

growth_protocol: Walnut plant materials were planted and collected in a field in Aksu city, Xingjiang Province.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies). Samples were then subjected to poly(A) purification using oligo-dT beads (Life Technologies) followed by rRNA removal using Ribo-Zero Kit (Epicenter) according to the manufacturer’s instructions. RNA integrity was measured using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
Library construction were done using TruSeq® Stranded mRNA Library Prep Kit following the manufacturer’s instructions (Illumina). 16 paired-end libraries were constructed and sequenced according to the Illumina HiSeqTM platform sequencing protocols.

value: pellicle

value: 19-week-old pellicle tissues after pollination

tag: cultivar


title: RNA-Seq_RUVBL2_Dox_rep2

description: RUVBL2 degron

data_processing:
The paired-end sequencing fastq files were removed adaptors and low-quality reads with Cutadapt V1.18 (Martin, 2011), then the filtered reads were aligned to mm10 genome with STAR V 2.7.3a (Dobin et al., 2013).
And the bam files after removing duplicates were used to count the genes with annotation files from GENCODE (version M23) (Frankish et al., 2019) with RSEM V1.3.1  (Li and Dewey, 2011).
Differential analysis was performed with DESeq2 V1.24.0 (Love et al., 2014), and the significant genes were selected with foldchange >1.5 and FDR <0.05. For the clustering analysis of Ruvbl2 RNA-seq, a method like Gkountela et al., 2013 (Gkountela et al., 2013) was used.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq rawcount, TPM count and DESeq2 results

growth_protocol: For RNA- seq, Ruvbl2-mAID tagged cell lines were cultured in 0.2 % gelatin coated 6 well plates with irradiated mouse embryonic fibroblasts (MEF) in DMEM-KO (Gibco, 10829018) containing 15% FBS, 1000 U/ml mouse leukemia inhibiting factor (mLIF), 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1× nonessential amino acids, and 1× penicillin/ streptomycin at 37 °C with 5% CO2, as described previously (Jiang et al., 2020).

extract_protocol:
Cells were lysed in Trizol reagent and extracted RNA according to the manufacture’s protocol
examination the concentration and integrity of the total RNA, the untreated (Mock), doxycycline treatment (Dox), and time series auxin treated samples were delivered for poly A RNA library generation by Novogene Com

treatment_protocol: after two passages, 2 μg/ml Doxycycline (Dox) were added into the medium for 24 h to induce the OsTir1 expression, and then 500 μM auxin (3-indole acetic acid) were appended for 0.5h, 1h, 6h, 12h, 24h and 48h to induce the RUVBL2 degradation. Then cells were lysed by Trizol reagent for RNA extraction.

value: RUVBL2 degron Dox

value: embryonic stem cells


title: Control-11

value: female


title: RNA-Seq_RUVBL2_Mock_rep1

description: RUVBL2 degron

value: RUVBL2 degron Mock


title: P7 No6 Control heart


title: ChIP-Seq_mESCs_INO80_Auxin_0.5h_rep2

value: RUVBL2 degron


title: Control-9


title: RNA-Seq_RUVBL2_Mock_rep2

description: RUVBL2 degron


title: Control-16

value: male