title: Carm1_WT_Input_Rep2

data_processing:
Data quality was checked with FastQC and MultiQC.
Reads were aligned to the mm10 reference genome using Bowtie2 with default setting.
MACS2 was used for peak calling ( -f BAMPE --nomodel --extsize 200 -g mm -p 1e-5)
Diffbind was used to obtain the differentially bound peaks between reprogramming and mock samples.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Briefly, mosaic heart that contained AAV9-Cre infected Carm1KO or control AAV9-GFP infected cardiomyocytes was perfused with 20ml 1% PFA and then 20ml 0.25M Glycine to quench the excessive PFA. Then the heart was harvested. To obtain single nuclei suspension, the heart was cut into small pieces and then homogenized with an electric tissue homogenizer for 30sec on ice. Then the lysate was then washed with 1% BSA/PBS and then filtered through one 70 micrometer strainer and one 40 micrometer strainer. Then the nuclei were stained with PCM1+ antibody (1:500, Sigma, HPA023370) and subjected to FACS to enrich the cardiomyocytes nuclei for H3R17me2a ChIP.  The isolated cardiomyocyte nuclei were incubated in nuclear isolation buffer (Sigma-Aldrich). Then the chromatin was fragmented for 5 min at 37ºC by using MNase before addition of EDTA to stop the reaction. The chromatins were then diluted in complete IP buffer(20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, 1 mM PMSF) and incubated at 4 ºC for 1 hour. After the incubation, the chromatins were precleared with Protein A Dynabeads (Invitrogen) and immunoprecipitated with 1 µg H3R17me2a (Active motif, 39707) antibody for overnight. Immunoprecipitated complexes were washed twice with low salt wash buffer I (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 2 mM EDTA and 150 mM NaCl) and twice with high salt wash buffer (20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 2 mM EDTA and 500 mM NaCl). Protein–DNA complexes were eluted in 30 μl of ChIP elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 68 °C. Immunoprecipitated DNA was purified and used for sequencing.
The libraries are constructed with Takara ThruPLEX DNA-seq kit.

tag: antibody

value: Cardiomyocyte

value: Mouse was Injected with AAV-GFP at Postnatal Day 1


title: Carm1_WT_Input_Rep1

status: Public on Dec 26 2023

type: SRA

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Heart

tag: tissue

value: Heart

tag: cell type

tag: genotype

tag: treatment


title: Carm1_WT_ChIP_Rep2


title: Carm1_WT_ChIP_Rep1


title: chronicRNAseq_7365_imKO

city: Chicago

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Alignment:  ChIP-seq reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters. RNA-seq and Ribo-seq reads were mapped to an mm10 reference genome using STAR version 2.4.0.
ChIP-seq Peaks. Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings.
RNA-seq gene expression was quantified using HOMER. Differnetially expressed RNA's were normalized and identified using DESeq2 version 1.14.1.
Ribo-seq data was processed via Homer and RiboDiff. Raw RPF and RNA read counts matrices were generated with Homer using the analyzerepeats.pl command with the -noadj option. Changes in translation efficiency were detected with RiboDiff.
Assembly: mm10
Supplementary files format and content: Tab-delimited text (txt) files with annotated peak lists

molecule: polyA RNA

source_name: skeletal muscle - quadricep

extract_protocol:
Skeletal muscle for ChIP-Seq was dissected and finely minced. ChIP-seq samples were subjected to cross linking in 1% formaldehyde for 30 minutes and quenched with glycine. Tissue was dounced to release nuclei. Nuclei were sonicated to shear the chromatin and subjected to immunoprecipitation. Precipitates were washed and DNA was purified by column (Qiagen Min-Elute). Tissues for RNA-Seq were homogenized in Trizol using a MoBio PowerLyzer 24. Lysates were purified via Qiagen RNAeasy purification column. RiboSeq samples pulverized in liquid nitrogen then lysed in polysome lysis buffer supplemnted with 100ug/ml cyclohexamide. Lysate were dounced, then cleared by centrifugation. Cleared lysates were next treated with 3000U of T1RNase and ribosomes immunoprecipitated with HA tag magnetic beads. RNA was extracted from the immunoprecipitated ribosomes and subjected to library prep.
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosciences). RNA-seq libraries were prepared with the Illumina Tru-seq stranded mRNA kit. Ribo-seq libraries were prepared with the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs).

value: skeletal muscle - quadricep

tag: strain

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: TMX


title: chronicRNAseq_7364_imKO


title: Carm1_KO_Input_Rep2

value: Mouse was Injected with AAV-CRE at Postnatal Day 1


title: mycelium, wt_cel_rep_1

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were first processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter sequences, reads containing poly-N, and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. These clean reads were then mapped to the reference genome sequence by STAR aligner (v2.5.2b) (Dobin et al. 2013). The percentage of uniquely mapped reads was at least 95% in all of the samples. HTSeq (v 0.5.4) (Anders et al. 2015) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).  Anders S, Pyl P T, Huber W. 2015. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169. Dobin A, Davis C A, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras T R. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21.
Assembly: T. harzianum CBS 226.95 strain from NCBI (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003025095.1/) (Druzhinina et al. 2018). Druzhinina I S, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi M J, Grujic M, Cai F, Pourmehdi S, Salim K A, Pretzer C, Kopchinskiy A G, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, et al. 2018. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genetics, 14, e1007322.
Supplementary files format and content: tab-delimited text file of counts for each sample
Supplementary files format and content: tab-delimited text file of FPKM values for each sample

molecule: total RNA

organism: Trichoderma harzianum

source_name: mycelium

growth_protocol: To inoculate pre-cultures, spores were harvested from a PDA plate using a 0.05% tween 20 solution, filtered with a nappy gauze, and inoculated into a 250 mL flask containing 50 mL minimal medium supplemented with 1% w/v D-fructose and 0.1% w/v peptone to give a 1x10^4/mL spore final concentration. The composition of the minimal medium (MM) used was 5 g/L (NH₄)₂SO₄, 15 g/L KH2PO4, 0.6 g/L MgSO₄, 0.6 g/L CaCl₂ and 2 mL/L Vishniac solution 500X stock, and adjusted to pH 5.5 with KH2PO4 or K2HPO4 (Penttilä, Nevalainen et al. 1987). The pre-cultures were incubated at 28°C and 200 RPM for 36 h in the dark. For transfer, the mycelia were collected using a 38 µm nylon net filter and washed twice with ~200 mL MM solution. Then 1 g wet weight of mycelia was transferred into 250 mL flasks containing 50 mL of MM with either 25 mM D-fructose, 1% w/v cellulose (microcrystalline from cotton linters) or without an added carbon source, and incubated for 18 h at 28°C with 200 RPM in the dark. For transcriptomic analysis, mycelia were collected from cultures from the 18 h time-point, flash-frozen in liquid nitrogen, and stored at -80°C. To take account of variability from different spore plates, separate spore plates were used to inoculate each of the three sets of replicate pre-cultures, and each set of replicate pre-cultures was transferred to their respective replicate cultures with various carbon sources.

extract_protocol:
Total RNA was extracted using the Magnetic Tissue/Cell/Blood Total RNA Kit (Tiangen, China) according to the manufacturer’s instructions. RNA purity and quantity were evaluated using a NanoDrop spectrophotometer (Thermo Scientific, USA), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
For the library preparation for transcriptome sequencing, a total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). To select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. The purified PCR products (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina NovaSeq 6000 platform by Beijing Allwegene Technology (China), and paired-end 150 bp reads were generated. About ~40 M raw reads for each sample were generated.

treatment_protocol: See the growth protocol section for information on the treatments.

value: mycelium

value: wild type (CBS 226.95)

value: cellulose


title: chronicRNAseq_7358_imKO


title: E13.5 EDNRB-GFP bowel, GFP negative cells 2

city: Philadelphia

first: Robert

middle: O

last: Heuckeroth

state: PA

address: 3615 Civic Center Blvd Rm 1115

institute: Children's Hospital of Philadelphia Research Institute

description: GFP-Neg 2

data_processing:
Sequencing reads were aligned with STAR v2.4.2a, then normalized with PORT v0.8.5-beta.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized CPM values for each gene and sample

source_name: E13.5 bowel

extract_protocol:
RNA was purified from frozen samples in QIAzol using the Qiagen miRNAeasy Mini Kit (Qiagen #217004); a total of 750pg was used to begin library preparation
Libraries were prepared with the Clontech SMARTer PCR cDNA Synthesis Kit (Clontech #634925) followed by the Illumina NexteraXT kit (Illumina #FC-131)

value: E13.5 bowel

value: Non-enteric neural crest-derived cells

value: Wild-type


title: MIA PaCa-2_H2O

type: RNA

city: Fukuoka

first: Zhong

last: pingshan

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Surgery and Oncology

country: Japan

institute: Kyushu University

description: Gene expression after 48hr in H2O- MIA PaCa-2

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

organism: Homo sapiens

source_name: MIA PaCa-2, control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: MIA PaCa-2 and KP-2 cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, the cultures were treated for 48 hours at 37 ºC in a humidified incubator with 10% CO2.

tag: cell line

value: MIA PaCa-2

value: 48hr in H2O


title: b.End3 co-culture w/ D4M.3A rep3

city: Charlottesville

first: Sarah

last: Wang

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

data_processing:
adapters sequences were identified and removed with cutadapt (https://cutadapt.readthedocs.io/en/stable/). Reads were mapped to the genome with STAR.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file for gene count of each sample

growth_protocol: D4M.3A and SM1WT1 cells were cultured in DMEM/F-12 (#11330032, Gibco, USA) supplemented with 5% fetal bovine serum (FBS) (#16000-044, Gibco). Brain endothelial cells (b.End3) were cultured on 0.5% gelatin-coated plates in 4.5g/L D-glucose DMEM (#11965092, Gibco) supplemented with 10% FBS. All medias were supplemented with antimycotic/antibiotic (Gibco) and plasmocin (InvivoGen, USA).

extract_protocol:
RNA was extracted with Quick-RNA Microprep (Zymo Research R1050) and 1μg RNA/sample was used as input
NEBNext Ultra RNA Library prep for Illumina (NEB, USA), following manufacture's protocol

treatment_protocol: For co-culture experiments, ECs were allowed to adhere for 2 days prior to seeding with melanoma cells. FACS/RNA extraction was performed 24hrs after co-culture in 4.5g/L D-glucose DMEM (#11965092, Gibco) supplemented with 10% FBS. Mono-culture controls were plated at the appropriate time points (Day0=b.End3, Day2=melanoma)

value: brain endothelial cell

value: co-coculture with D4M.3A


title: KP-2_H2O

description: Gene expression after 48hr in H2O- KP-2

source_name: KP-2, control


title: SM1WT1 mono-culture rep4

value: melanoma

value: BrafV600E, Pten-expressing

value: mono-culture


title: b.End3 mono-culture rep3


title: D4M.3A co-culture w/ b.End3 rep4

value: BrafV600E, Pten-null

value: co-coculture with b.End3


title: SM1WT1 co-culture w/ b.End3 rep4


title: b.End3 co-culture w/ D4M.3A rep4


title: D4M.3A mono-culture rep4


title: MIA PaCa-2_Az

description: Gene expression after 48hr in Az- MIA PaCa-2

source_name: MIA PaCa-2, treatment

value: 48hr in Az


title: b.End3 mono-culture rep4


title: SM1WT1 co-culture w/ b.End3 rep3


title: b.End3 co-culture w/ SM1WT1 rep4

value: co-culture with SM1WT1


title: KP-2_Az

description: Gene expression after 48hr in Az- KP-2

source_name: KP-2, treatment


title: GC8

city: Seocho-gu

first: Kim

last: Tae-Min

address: Banpo-daero

country: South Korea

institute: The Catholic University of Korea

data_processing:
FASTQ file were processed using SpaceRanger (V1.1.0)  with the GRCh38 genome assembly as reference.
Assembly: GRCH38
Supplementary files format and content: Tar archives contain compressed directories containing spaceranger output (filtered_feature_bc_matrix.h5, barcodes.tsv, features.tsv, and matrix.mtx, aligned_fiducials.jpg, scaledfactors_json.json, detected_tissue_image.jpg, tissue_hires_image.jpg, tissue_lowres_image.jpg, tissue_positions_list.csv).
Library strategy: Spatial transcriptomics

source_name: Gastric Cancer

extract_protocol:
Spatial transcriptomics were performed using Visium assay (10X Genomics) as manufacturer's recommendation. Surgical sections were prepared and stored in OCT. 10um tissue sections were prepared for HE stain to determine the regions of interests (6.5umX6.5um) and further subject to permeabilization to capture RNA molecules onto barcoded spots.
Sequencing library construction as manufacturer's protocol.

value: Gastric Cancer


title: Carm1_KO_ChIP_Rep2

value: Heart

value: Cardiomyocyte

value: Mouse was Injected with AAV-CRE at Postnatal Day 1


title: GC7


title: chronicRNAseq_7363_ctr

value: skeletal muscle - quadricep

value: Bcl6 fl/fl

value: TMX


title: b.End3 co-culture w/ SM1WT1 rep3


title: D4M.3A co-culture w/ b.End3 rep3


title: GC9


title: SM1WT1 mono-culture rep3


title: GC6-PM

source_name: Gastric Cancer Metastasis

value: Gastric Cancer Metastasis


title: Carm1_KO_ChIP_Rep1


title: Carm1_KO_Input_Rep1


title: D4M.3A mono-culture rep3


title: carm1_2_ATACseq

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
Genome_build: mm10 genome
Supplementary_files_format_and_content: one csv file containing raw count values for ATAC-seq peaks of WT and carm1 samples

source_name: Cardiac tissue

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol: ATAC-seq libraries were prepared for each sample by Active Motif Inc.

tag: age

value: Carm1 mutant


title: GC6


title: chronicRNAseq_7335_imKO

value: AEC-Esr Cre (+):Bcl6 fl/fl


title: chronicRNAseq_1800_ctr


title: WT_2_ATACseq

value: wild type


title: b.End3 co-culture w/ D4M.3A rep2

value: brain endothelial cell

value: co-coculture with D4M.3A


title: carm1_1_ATACseq


title: chronicRNAseq_1809_ctr


title: GC4


title: chronicRNAseq_7333_ctr


title: GC5


title: b.End3 mono-culture rep2

value: mono-culture


title: WT_1_ATACseq


title: K27Ac-Quad_WT

data_processing:
Alignment:  ChIP-seq reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters. RNA-seq and Ribo-seq reads were mapped to an mm10 reference genome using STAR version 2.4.0.
ChIP-seq Peaks. Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings.
RNA-seq gene expression was quantified using HOMER. Differnetially expressed RNA's were normalized and identified using DESeq2 version 1.14.1.
Ribo-seq data was processed via Homer and RiboDiff. Raw RPF and RNA read counts matrices were generated with Homer using the analyzerepeats.pl command with the -noadj option. Changes in translation efficiency were detected with RiboDiff.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists. bedGraph files.

tag: chip antibody (primary)

value: rabbit anti-H3K27Ac, Active Motif 39133


title: mKO-Bcl6_Quad_RNA_11722

description:
mKO_riboDiff_results.txt
mKO_AllCounts_countFile.txt

data_processing:
Library strategy: Ribo-seq
Alignment:  ChIP-seq reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters. RNA-seq and Ribo-seq reads were mapped to an mm10 reference genome using STAR version 2.4.0.
ChIP-seq Peaks. Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings.
RNA-seq gene expression was quantified using HOMER. Differnetially expressed RNA's were normalized and identified using DESeq2 version 1.14.1.
Ribo-seq data was processed via Homer and RiboDiff. Raw RPF and RNA read counts matrices were generated with Homer using the analyzerepeats.pl command with the -noadj option. Changes in translation efficiency were detected with RiboDiff.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists. bedGraph files.

value: AEC-Esr Cre (+):Bcl6 fl/fl; RiboTag (+)

tag: rna fraction

value: polyA RNA

tag: ribo-seq antibody

value: mouse anti-HA, magnetic bead bound, Pierce 88845


title: GC3

value: Gastric Cancer


title: mKO-Bcl6_Quad_RNA_11718


title: GC1


title: K27Ac-Quad_mKO_Input


title: mKO-Bcl6_Quad_RNA_11688


title: mKO-Bcl6_Quad_RNA_11721


title: D4M.3A co-culture w/ b.End3 rep2

value: melanoma

value: BrafV600E, Pten-null

value: co-coculture with b.End3


title: Ctr-Quad_RNA_11745

value: skeletal muscle - quadricep

value: AEC-Esr Cre (+); RiboTag (+)


title: D4M.3A mono-culture rep2


title: NC2

city: xuzhou

first: qiang

last: li

address: No. 99 Huaihai West Road, Xuzhou City

institute: Xuzhou Medical University

data_processing:
Apoptosis of human umbilical cord mesenchymal stem cells was determined by TUNEL staining kit (KeyGen Biotech). The apoptotic ratio was analyzed.
LncRNAs with significant differentially expressed expression were screened by fold change > 2 or < -2 and P value < 0.05.
Bioinformatics data analysis was provided by NewCore BioTech (Shanghai, China). fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38).
HTSeq software (v0.13.5) was used to get the raw transcript level lncRNA read counts as the lncRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups. Ensembl GTF gene annotation database (v104) was used to annotate the lncRNA. Gene Ontology and KEGG pathway enrichment analysis were performed with clusterProfiler R package (v3.18.1) based on the nearby mRNAs of differentially expressed lncRNAs.
The fold change and Pvalue were calculated using the DESeq2 R package, with fold change (fold change)> =2.0 and Pvalue <0.05 as the differential LncRNA screening threshold
Assembly: hg38
Supplementary files format and content: LncRNA Expression Profiling.xlsx

source_name: Mesenchymal stem cells

extract_protocol:
The stem cells in a high-glucose environment, treatment with high levels of glucose for 48 hours, hUCMSCs were subjected to high-throughput RNA sequencing to obtain the transcription profile of these cells under high-glucose conditions.  Sample preparation and microarray hybridization are carried out according to Arraystar's standard protocol. Simply put, the total RNA isolated from each sample is amplified and transcribed into fluorescent RNA using random primers, and the array is scanned with an Axon GenePix microarray scanner. Then the scanned images were imported into GenePix and data extraction was carried out. LncRNAs with significant differentially expressed expression were screened by fold change > 2 or < -2 and P value < 0.05
RNA-seq libraries were constructed by NewCore Biotech (Shanghai, China). Firstly, RNA was isolated with TRIZOL reagent (Invitrogen, Grand Island, NY), total RNA was purified by the Qiagen RNeasy mini kit (Qiagen, Valencia, CA). Purified RNA was analyzed on an ND-8000 spectropho tometer (Nanodrop Technologies, Wilmington, DE). High quality total RNA was used as the starting material. Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies,Inc., USA). Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 151 bp paired end reads.

value: Mesenchymal stem cells

value: stem cell

value: control


title: b.End3 co-culture w/ SM1WT1 rep2

value: co-culture with SM1WT1


title: K27Ac-Quad_mKO_1907

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: TMX


title: K27Ac_Quad_Ctr_Input

value: Bcl6 fl/fl


title: Ctr-Quad_RNA_11735


title: SM1WT1 co-culture w/ b.End3 rep2

value: BrafV600E, Pten-expressing


title: NC1


title: Ctr-Quad_RNA_11734


title: K27Ac-Quad_mKO_1900

value: rabbit anti-H3K27Ac, Active Motif 39133


title: T3

value: high levels of glucose for 48 hours


title: Ctr-Quad_RNA_11673

value: polyA RNA

value: mouse anti-HA, magnetic bead bound, Pierce 88845


title: b.End3 co-culture w/ SM1WT1 rep1

value: brain endothelial cell


title: K27Ac-Quad_mKO_1896


title: b.End3 co-culture w/ D4M.3A rep1

value: co-coculture with D4M.3A


title: SM1WT1 mono-culture rep2

value: melanoma

value: mono-culture


title: mKO-Bcl6_Quad_RPF_11722

value: skeletal muscle - quadricep

value: AEC-Esr Cre (+):Bcl6 fl/fl; RiboTag (+)

value: Ribosome footprint RNA


title: b.End3 mono-culture rep1


title: T1

value: Mesenchymal stem cells

value: stem cell


title: SM1WT1 co-culture w/ b.End3 rep1

value: co-coculture with b.End3


title: T2


title: K27Ac-Quad_Ctr_1899

value: TMX


title: K27Ac-Quad_Ctr_1906

value: Bcl6 fl/fl


title: GC2

value: Gastric Cancer


title: NC3

value: control


title: mKO-Bcl6_Quad_RPF_11721


title: K27Ac-Quad_Ctr_1898

value: rabbit anti-H3K27Ac, Active Motif 39133


title: SM1WT1 mono-culture rep1

value: BrafV600E, Pten-expressing


title: mKO-Bcl6_Quad_RPF_11718

value: mouse anti-HA, magnetic bead bound, Pierce 88845


title: D4M.3A co-culture w/ b.End3 rep1

value: BrafV600E, Pten-null


title: Oil_Ctr_RNA_P1910

description: PosOilVsPosTmx-diffexp-annotated.txt

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: Oil

value: polyA RNA


title: total_RNAPII_ChOR-seq_G1

city: Seville

first: Cristina

last: González-Aguilera

state: Seville

address: Avenida Américo Vespucio, 24

country: Spain

institute: CABIMER - CSIC

data_processing:
library strategy: ChOR-seq and EdU-seq
NovaSeq Control Software v1.8 was used for basecalling
Libraries were de-multiplexed, trimmed and UMI identified using Illumina BCL Converter (version 2.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server.Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) and the April 2006D. melanogastergenome assembly (BDGP R5/dm3) using Bowtie (v.1.2.0) with parameters -m1--best.
PCR duplicates were removed using ‘RmDup’ (Galaxy version 2.0.1) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
For ChOR-seq, genome coverage was calculated with ‘Genome Coverage’(v.2.30.0) from bedtools using default parameters but normalizing reads to Counts per million (CPM). For EdU-seq, genome coverage was calculated using bamCoverage (v.3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in CPM.
To identify replicated areas of the genome in our experiments, peak calling was performed with MACS2 bdgbroadcall(v.2.2.7.1+galaxy0) using --cutoff 0.85, --min-length 3000 and --max-gap 20000.
Assembly: hg38 and dm3
Supplementary files format and content: Bedgraph files include HeLa S3 CPM values for each sample without Drosophila melanogaster spike-in normalization and Bed file of EdU-seq includes positions of replicated regions.

source_name: HeLa S3

growth_protocol: Human HeLa S3 cells (female) were grown in DMEM medium (Sigma-Aldrich) supplemented with dialyzed FBS (HyClone), penicillin, and streptomycin at 37°C and 5% CO2.  Drosophila S2-DRSC cells were grown in M3+BPYE media with 10% heat-inactivated FBS, penicillin and streptomycin at 25°C. Both cells were grown in suspension in spinners.

extract_protocol:
HeLa S3 cells from each labeling set-up were fixed in 1% formaldehyde during 10 min and reaction stopped adding glycine (0.125 M) for 5 min at room temperature (RT). Fixed cells were lysed for 20 min at RT in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with protease inhibitors; passed through a 21G needle and sonicated using a Bioruptor UCD 200 TM-EX (Diagenode) to obtain chromatin fragment size of 250-500 bp. Sonicated chromatin was centrifuged at 19,000 x g at 4°C for 10 min and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were fixed, lysed and sonicated as described above. After sonication, equal amount of HeLa S3 sonicated chromatin from the two labeling set-ups was mixed. Then, Drosophila S2 sonicated chromatin was added to HeLa S3 chromatin in a proportion of 0.05% of total HeLa S3 chromatin as internal control. Chromatin associated to each RNAPII was obtained by incubating sonicated chromatin with the corresponding antibody. DNA from ChIPs was purified using MiniElute PCR purification kit (QIAGEN) where the five ChIPs from each condition were purified together in the first step. 17 ng of immunoprecipitated DNA for each time point sample were used to perform libraries with KAPA Hyperprep kit following manufacturer’s instructions, except that 7.5 μM xGen Methyl UDI-UMI Adapters (IDT) were ligated during 4 h. Later, indexed samples for the same time course (T0, T1, T2) were pooled together and biotinylated performing Click IT reaction during 45min at RT. Then, MyOne Streptavidin T1 beads (Thermo Fisher Scientific) were used to capture biotinylated libraries and subjected to PCR amplification following KAPA Hyperprep kit protocol (13 and 12 PCR cycles were used for Total RNAPII and S2P ChOR-seq experiments, respectively). For EdU-seq, HeLa S3 andDrosophilaS2 mixed chromatin (0.05% of total volume)from T0 was de-crosslinked and purified with QIAquickPCR Purification kit (QIAGEN). Libraries and streptavidin pull downs of EdU-seq experiments were performed as described above but using 100 ng of purified EdU labeled DNA, 15 μM of xGen Methyl UDI-UMI Adapters and performing 11 cycles of PCR amplification.
Library construction is performed during the chromatin extraction

treatment_protocol: For total and S2P RNAPII ChOR-seq, cells with newly-replicated chromatin labeled in two different moments of the S phase were mixed and analyzed together to maximize the purification of chromatin replicated in early S phase. In each of the labeling set-up, HeLa S3 were synchronized at the G1/S border by a single thymidine block (2mM, 17hr) and released into S phase using fresh medium containing deoxycytidine (24μM). Newly replicated chromatin was labeled during 15 min with 5-ethynyl-2′-deoxyuridine (EdU, 10μM) but in one case, labeling was performed after 1 hour of the release from the thymidine block while in the other, the labeling was done 2 hours and 15 min after release. Then, in both cases, cells were collected immediately after the labeling to get the nascent chromatin (T0). For mature time points, remaining cells were washed twice in 1X PBS and further incubated in fresh medium containing 10 μM thymidine for 1 hour (T1) and 2 hours (T2) after the labeling. Finally, ChOR-seq experiments in each time point were done mixing equal chromatin amount of the two labeling set-ups. To identify replicated regions in our experiments, mixed cells at T0 were also collected to performed EdU-seq analysis. For spike-in normalizations, asynchronousDrosophilaS2 cells were labeled with EdU (10μM) for 39hr and purified chromatin used as an internal control.

value: HeLa S3

value: Cervix adenocarcinoma

tag: cell cycle

value: Early S (13h after release)

value: Rpb1 NTD (D8L4Y) (Cell Signaling Technology, Cat No. 14958; RRID:AB_2687876)

tag: hydroxyurea (hu)_treatment

value: Non treated

tag: spike-in

value: YES


title: mKO-Bcl6_Quad_RPF_11688

value: skeletal muscle - quadricep

value: AEC-Esr Cre (+):Bcl6 fl/fl; RiboTag (+)

value: TMX

value: Ribosome footprint RNA


title: EdUseq_ChOR_G1

value: Early S (1h+2h 15min after release)


title: D4M.3A mono-culture rep1

value: melanoma

value: mono-culture


title: Oil_Ctr_RNA_P1905

description: PosOilVsPosTmx-diffexp-annotated.txt


title: Ctr-Quad_RPF_11745

value: AEC-Esr Cre (+); RiboTag (+)

value: mouse anti-HA, magnetic bead bound, Pierce 88845


title: Oil_Ctr_RNA_P1904

description: PosOilVsPosTmx-diffexp-annotated.txt

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: Oil


title: HU_S2P_RNAPII_T1

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Libraries were de-multiplexed, trimmed and UMI identified using Illumina BCL Converter (version 2.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) and the April 2006 D. melanogaster genome assembly (BDGP R5/dm3) using Bowtie (v.1.2.0) with parameters -m1--best.
PCR duplicates were removed using ‘UMI-tools extract’ (v.1.1.2+galaxy2) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
For ChOR-seq, genome coverage was calculated with ‘Genome Coverage’ (v.2.30.0) from bedtools using default parameters but normalizing reads to Counts per million (CPM).  For EdU-seq, genome coverage was calculated using bamCoverage (v.3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in CPM.
To identify replicated areas of the genome in our experiments, peak calling was performed with MACS2 bdgbroadcall (v.2.2.7.1+galaxy0) using --cutoff 0.85, --min-length 3000 and --max-gap 20000.
Assembly: hg38 and dm3
Supplementary files format and content: Bedgraph files include HeLa S3 CPM values for each sample without Drosophila melanogaster spike-in normalization and Bed file of EdU-seq includes positions of replicated regions.
Library strategy: ChOR-seq

extract_protocol:
HeLa S3 cells from each labeling set-up were fixed in 1% formaldehyde during 10 min and reaction stopped adding glycine (0.125 M) for 5 min at room temperature (RT). Fixed cells were lysed for 20 min at RT in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with protease inhibitors and phosphatase inhibitors; passed through a 21G needle and sonicated using a Bioruptor UCD 200 TM-EX (Diagenode) to obtain chromatin fragment size of 250-500 bp. Sonicated chromatin was centrifuged at 19,000 x g at 4°C for 10 min and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were fixed, lysed and sonicated as described above. After sonication, Drosophila S2 sonicated chromatin was added to HeLa S3 chromatin in a proportion of 0.05% of total HeLa S3 chromatin as internal control. Chromatin associated to S2P RNAPII was obtained by incubating sonicated chromatin with the corresponding antibody. DNA from ChIPs was purified using MiniElute PCR purification kit (QIAGEN) where the five ChIPs from each condition were purified together in the first step. 17 ng of immunoprecipitated DNA for each time point sample were used to perform libraries with KAPA Hyperprep kit following manufacturer’s instructions, except that 7.5 μM xGen Methyl UDI-UMI Adapters (IDT) were ligated during 4 h. Later, indexed samples from both biological replicates (T0 rep1, T1 rep1, T0 rep2, T1 rep2) were pooled together and biotinylated performing Click IT reaction during 45 min at RT. Then, MyOne Streptavidin T1 beads (Thermo Fisher Scientific) were used to capture biotinylated libraries and subjected to PCR amplification following KAPA Hyperprep kit protocol (14 PCR cycles were used). For EdU-seq, HeLa S3 and Drosophila S2 mixed chromatin (0.05% of total volume) from T0 was de-crosslinked and purified with QIAquick PCR Purification kit (QIAGEN). Libraries and streptavidin pull downs of EdU-seq experiments were performed as described above but using 100 ng of purified EdU labeled DNA, 15 μM of xGen Methyl UDI-UMI Adapters and performing 11 cycles of PCR amplification.
Library construction is performed during the chromatin extraction

treatment_protocol: HeLa S3 were synchronized at the G1/S border by a single thymidine block (2 mM, 17 hr) and released into S phase using fresh medium containing deoxycytidine (24 μM). After 1 hour of release, 5-ethynyl-2′-deoxyuridine (EdU, 10 μM) and HU (Sigma-Aldrich; 0.2mM) were added to the medium during 30min. Then, cells were collected to obtain the nascent chromatin (T0) and for EdU-seq. The remaining cells were washed twice in 1X PBS and further incubated in fresh medium containing 10 μM thymidine and HU (0.2mM) for 1 more hour (T1). For spike-in normalizations, asynchronous Drosophila S2 cells were labeled with EdU (10 μM) for 39 hr and purified chromatin was used as an internal control.

value: HeLa S3

value: Early S (1h after T0)

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) (ab5095)

value: Treated


title: Ctr-Quad_RPF_11735


title: HU_S2P_RNAPII_T0

value: Cervix adenocarcinoma

value: Early S (1h after release)


title: TMX_Ctr_RNA_P1909

description: NegTmxVsPosTmx-diffexp-annotated.txt

value: skeletal muscle - quadricep

value: Bcl6 fl/fl

value: polyA RNA


title: vd-48h-2

city: zhengzhou

first: yuzhi

last: zhang

state: henan

address: No. 218, Ping'an Avenue, Zhengdong New District, Jinshui District, Zhengzhou City, Henan Province

department: agronomy

institute: Henan Agricultural University

data_processing:
mRNA was isolated by Oligo(dT)-attached magnetic beads
mRNA was then randomly fragmented in fragmentation buffer.
First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.
Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within certain size range.
cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.
Assembly: https://www.cottongen.org/species/Gossypium_hirsutum/UTX-TM1_v2.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

organism: Gossypium hirsutum

source_name: root

extract_protocol:
1 μg of total RNA was used to generate the sequencing libraries, which were sequenced using the Illumina platform by Beijing Biomarker Biotechnology Co., Ltd. (www.biomarker.com.cn, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: root

value: Treatment with V592-GFP for 48 hours


title: EdUseq_ChrRNA

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Libraries were de-multiplexed, trimmed and UMI identified using Illumina BCL Converter (version 2.0.0) from BaseSpace using default parameters. Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) using Bowtie (v.1.2.0) using parameters -m1--best.
PCR duplicates were removed with RmDup (v.12.0.1) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Genome Coverage was calculated using bamCoverage (v. 3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in Counts Per Million (CPM). Bedgraph files from each time point generated with bamCoverage were strand specific.
To identify replicated areas of the genome in our experiments, peak calling was performed with MACS2 bdgbroadcall (v.2.2.7.1+galaxy0) using --cutoff 0.85, --min-length 3000 and --max-gap 20000.
Assembly: hg38
Supplementary files format and content: Bed file includes replicated regions
Library strategy: EdU-seq

growth_protocol: Human HeLa S3 cells (female) were grown in DMEM medium supplemented with dialyzed FBS, penicillin, and streptomycin at 37°C and 5% CO2. Cells were grown in suspension in spinners.

extract_protocol:
HeLa S3 cells were fixed in 1% formaldehyde during 10 min and reaction stopped adding glycine (0.125 M) for 5 min at room temperature (RT). Fixed cells were lysed for 20 min at RT in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with protease inhibitors; passed through a 21G needle and sonicated using a Bioruptor UCD 200 TM-EX (Diagenode) to obtain chromatin fragment size of 250-500 bp. Sonicated chromatin was centrifuged at 19,000 x g at 4°C for 10 min and the supernatant was isolated for subsequent steps. DNA was de-crosslinked and purified with QIAquick PCR Purification kit (QIAGEN). 100 ng of purified EdU labeled DNA were used to perform libraries with KAPA Hyperprep kit following manufacturer’s instructions, except that 15 μM xGen Methyl UDI-UMI Adapters (IDT) were ligated during 4 h. Samples were biotinylated performing Click IT reaction during 45 min at RT. Then, MyOne Streptavidin T1 beads (Thermo Fisher Scientific) were used to capture biotinylated libraries and subjected to PCR amplification following KAPA Hyperprep kit protocol (11 PCR cycles).
Library construction is performed during the chromatin extraction

treatment_protocol: Newly-replicated chromatin was labeled 1 hour after the release into S phase. HeLa S3 were synchronized at the G1/S border by a single thymidine block (2 mM, 17 hr) and released into S phase using fresh medium containing deoxycytidine (24 μM). Newly replicated chromatin was labeled during 15 min with 5-ethynyl-2′-deoxyuridine (EdU, 10 μM). Then, cells were collected immediately after the labeling to get the nascent chromatin (T0).

value: Non treated


title: Ctr-Quad_RPF_11673

value: TMX

value: Ribosome footprint RNA


title: Ctr-Quad_RPF_11734

value: AEC-Esr Cre (+); RiboTag (+)

value: mouse anti-HA, magnetic bead bound, Pierce 88845


title: vd-24h-3

value: Treatment with V592-GFP for 24 hours


title: ChrRNA_T2

description: Chromatine associated RNA

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ Generation based on bcl2fastq with default parameters. Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to December 2013 human genome assembly (GRCh38/hg38) using HISAT2 (v.2.2.1+galaxy1) using default parameters but specifying --rna-strandness RF and paired.end parameters --fr.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Genome Coverage was calculated using bamCoverage (v. 3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in Counts Per Million (CPM). Bedgraph files from each time point generated with bamCoverage were strand specific and converted to Bed format adding the forth column with 'name' in each row with R custom script.
Assembly: hg38
Supplementary files format and content: Bed files include CPM values for each sample
Library strategy: ChrRNA-seq

growth_protocol: Human HeLa S3 cells (female) were grown in DMEM medium (Sigma-Aldrich) supplemented with dialyzed FBS (HyClone), penicillin, and streptomycin at 37°C and 5% CO2. Cells were grown in suspension in spinners.

extract_protocol:
HeLa S3 cells from T0, T1, T2 and their cytoplasmic, nucleoplasmic and chromatin-associated RNA fractions were harvested. Two independent replicates for each time point were performed.  For that, cell pellets were lysed in 400 μl of cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 min. The lysates were layered onto 1 ml cold sucrose buffer (10 mM Tris pH 7.5, 150 mM NaCl, 24% sucrose w/v), and centrifuged at 3500 g for 10 min. Supernatant from lysates was centrifuged again at 14,000 x g for 1 min and its supernatant frozen as cytoplasmatic RNA fraction. Nuclear pellets from lysates were resuspended into 250 μl cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol). Then, 250 μl of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40, 1 mM DTT) was added to the samples, followed by a pulsed vortexing and incubated on ice for 2 min. Samples were then centrifuged for 2 min at 13,000 × g. The supernatant was frozen as nucleoplasmic RNA fraction and the pellet, representing the chromatin-associated RNA fraction, was rinsed with 1 ml of cold PBS and resuspended in 50 μl of PBS-EDTA. All buffer were suplemented with RNase inhibitors (RNasinPlus, Promega). Finally, only chromatin-associated RNA was extracted using TRIZOL and 5 μg of RNA was treated with TURBO DNA-free kit for DNA removal according to manufacturer’s instructions.
Libraries preparation of chromatin-associated RNA were realized using Illumina Stranded Total RNA prep ligation with Ribo-Zero plus kit, according to its reference guide.

treatment_protocol: For ChrRNA-seq, newly-replicated chromatin was labeled 1 hour after the release into S phase. HeLa S3 were synchronized at the G1/S border by a single thymidine block (2 mM, 17 hr) and released into S phase using fresh medium containing deoxycytidine (24 μM). Newly replicated chromatin was labeled during 15 min with 5-ethynyl-2′-deoxyuridine (EdU, 10 μM). Then, cells were collected immediately after the labeling to get the nascent chromatin (T0). For mature time points, remaining cells were washed twice in 1X PBS and further incubated in fresh medium containing 10 μM thymidine for 1 hour (T1) and 2 hours (T2) after the labeling.

value: HeLa S3

value: Early S (2h after T0)


title: Oil_Ctr_RNA_P1897

description: PosOilVsPosTmx-diffexp-annotated.txt

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: Oil


title: TMX_Ctr_RNA_P1906

description: NegTmxVsPosTmx-diffexp-annotated.txt


title: ChrRNA_T1

description: Chromatine associated RNA

value: Cervix adenocarcinoma

value: Early S (1h after T0)


title: Primary fibroblasts, patient 3

city: Istanbul

first: Nathalie

last: Billard

state: Istanbul

address: Istanbul- Bayrampasa

country: Turkey

institute: Koc university

data_processing:
Illumina BaseSpace Apps
Quality control of raw fastq data obtained as a result of sequencing was performed by the FastQC tool. Then, trimmomatic tool was used (i) to trim the reads with a Phred score less than 20 and (ii) to filter out the reads shorter than 20 bases long
Reads that passed quality filtering were aligned by the STAR aligner to the human reference genome hg19.
FeatureCounts tool was used to count reads aligned to each gene, and raw count values were obtained.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: fibroblast

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit V3.0 following manufacturer's protocols.

value: fibroblast

value: SNUPN mutation

value: no treatment


title: vd-48h-1

value: root


title: vd-24h-2


title: Primary fibroblasts, patient 2


title: TMX_Ctr_RNA_P1899

description: NegTmxVsPosTmx-diffexp-annotated.txt

value: skeletal muscle - quadricep

value: Bcl6 fl/fl

value: polyA RNA


title: TMX_Ctr_RNA_P1898

description: NegTmxVsPosTmx-diffexp-annotated.txt

value: TMX


title: EdUseq_HU_ChORseq

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Libraries were de-multiplexed, trimmed and UMI identified using Illumina BCL Converter (version 2.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) and the April 2006 D. melanogaster genome assembly (BDGP R5/dm3) using Bowtie (v.1.2.0) with parameters -m1--best.
PCR duplicates were removed using ‘UMI-tools extract’ (v.1.1.2+galaxy2) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
For ChOR-seq, genome coverage was calculated with ‘Genome Coverage’ (v.2.30.0) from bedtools using default parameters but normalizing reads to Counts per million (CPM).  For EdU-seq, genome coverage was calculated using bamCoverage (v.3.5.1.0.0) from deepTools with default parameters but dividing genome in 1 bp bin size and normalizing mapped reads in CPM.
To identify replicated areas of the genome in our experiments, peak calling was performed with MACS2 bdgbroadcall (v.2.2.7.1+galaxy0) using --cutoff 0.85, --min-length 3000 and --max-gap 20000.
Assembly: hg38 and dm3
Supplementary files format and content: Bedgraph files include HeLa S3 CPM values for each sample without Drosophila melanogaster spike-in normalization and Bed file of EdU-seq includes positions of replicated regions.
Library strategy: EdU-seq

value: Early S (1h after release)

value: Treated


title: ChrRNA_T0

description: Chromatine associated RNA

value: Non treated


title: vd-24h-1

value: Treatment with V592-GFP for 24 hours


title: Primary fibroblasts, patient 1


title: EdUseq_ChOR-seq

extract_protocol:
HeLa S3 cells from each labeling set-up were fixed in 1% formaldehyde during 10 min and reaction stopped adding glycine (0.125 M) for 5 min at room temperature (RT). Fixed cells were lysed for 20 min at RT in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with protease inhibitors and, in case of S2P RNAPII, also phosphatase inhibitors; passed through a 21G needle and sonicated using a Bioruptor UCD 200 TM-EX (Diagenode) to obtain chromatin fragment size of 250-500 bp. Sonicated chromatin was centrifuged at 19,000 x g at 4°C for 10 min and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were fixed, lysed and sonicated as described above. After sonication, equal amount of HeLa S3 sonicated chromatin from the two labeling set-ups was mixed. Then, Drosophila S2 sonicated chromatin was added to HeLa S3 chromatin in a proportion of 0.05% of total HeLa S3 chromatin as internal control. Chromatin associated to each RNAPII was obtained by incubating sonicated chromatin with the corresponding antibody. DNA from ChIPs was purified using MiniElute PCR purification kit (QIAGEN) where the five ChIPs from each condition were purified together in the first step. 17 ng of immunoprecipitated DNA for each time point sample were used to perform libraries with KAPA Hyperprep kit following manufacturer’s instructions, except that 7.5 μM xGen Methyl UDI-UMI Adapters (IDT) were ligated during 4 h. Later, indexed samples for the same time course (T0, T1, T2) were pooled together and biotinylated performing Click IT reaction during 45 min at RT. Then, MyOne Streptavidin T1 beads (Thermo Fisher Scientific) were used to capture biotinylated libraries and subjected to PCR amplification following KAPA Hyperprep kit protocol (13 and 12 PCR cycles were used for Total RNAPII and S2P ChOR-seq experiments, respectively). For EdU-seq, HeLa S3 and Drosophila S2 mixed chromatin (0.05% of total volume) from T0 was de-crosslinked and purified with QIAquick PCR Purification kit (QIAGEN). Libraries and streptavidin pull downs of EdU-seq experiments were performed as described above but using 100 ng of purified EdU labeled DNA, 15 μM of xGen Methyl UDI-UMI Adapters and performing 11 cycles of PCR amplification.
Library construction is performed during the chromatin extraction

treatment_protocol: For total and S2P RNAPII ChOR-seq, cells with newly-replicated chromatin labeled in two different moments of the S phase were mixed and analyzed together to maximize the purification of chromatin replicated in early S phase. In each of the labeling set-up, HeLa S3 were synchronized at the G1/S border by a single thymidine block (2 mM, 17 hr) and released into S phase using fresh medium containing deoxycytidine (24 μM). Newly replicated chromatin was labeled during 15 min with 5-ethynyl-2′-deoxyuridine (EdU, 10 μM) but in one case, labeling was performed after 1 hour of the release from the thymidine block while in the other, the labeling was done 2 hours and 15 min after release. Then, in both cases, cells were collected immediately after the labeling to get the nascent chromatin (T0). For mature time points, remaining cells were washed twice in 1X PBS and further incubated in fresh medium containing 10 μM thymidine for 1 hour (T1) and 2 hours (T2) after the labeling. Finally, ChOR-seq experiments in each time point were done mixing equal chromatin amount of the two labeling set-ups. To identify replicated regions in our experiments, mixed cells at T0 were also collected to performed EdU-seq analysis. For spike-in normalizations, asynchronous Drosophila S2 cells were labeled with EdU (10 μM) for 39 hr and purified chromatin used as an internal control.

value: HeLa S3

value: Early S (1h+2h 15min after release)

value: YES


title: vd-48h-3

value: Treatment with V592-GFP for 48 hours


title: Primary fibroblasts, control 2

value: WT


title: TMX_Bcl6mKO_RNA_P1907

description:
NegTmxVsPosTmx-diffexp-annotated.txt
PosOilVsPosTmx-diffexp-annotated.txt

value: AEC-Esr Cre (+):Bcl6 fl/fl


title: total_RNAPII_ChOR-seq_T2

value: Cervix adenocarcinoma

value: Early S (2h after T0)

value: Rpb1 NTD (D8L4Y) (Cell Signaling Technology, Cat No. 14958; RRID:AB_2687876)


title: ck-48h-3

value: root

value: Unhandled


title: Primary fibroblasts, control 1

value: fibroblast

value: no treatment


title: ck-48h-2


title: TMX_Bcl6mKO_RNA_P1895

value: skeletal muscle - quadricep

value: TMX

value: polyA RNA


title: TMX_Bcl6mKO_RNA_P1911


title: carm1_2_RNAseq

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using hisat2.
Genome_build: mm10 genome
Supplementary_files_format_and_content: one csv file containing raw count values for RNA-seq of WT and carm1 samples

extract_protocol:
Hearts were extracted according to standard protocol
RNA-seq libraries were prepared for each sample by BGI Inc.

value: Heart

value: Carm1 mutant


title: total_RNAPII_ChOR-seq_T0

value: HeLa S3

value: Early S (1h+2h 15min after release)

value: Non treated


title: WT_2_RNAseq

value: wild type


title: ck-24h-2


title: TMX_Bcl6mKO_RNA_P1896

value: AEC-Esr Cre (+):Bcl6 fl/fl


title: Quad_Input_ChIP


title: S2P_RNAPII_ChOR-seq_T1

value: Cervix adenocarcinoma

value: Early S (1h after T0)

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) (abcam, Cat No. ab5095; RRID:AB_304749)

value: YES


title: ck-24h-1

value: root

value: Unhandled


title: WT_1_RNAseq


title: S2P_RNAPII_ChOR-seq_T0


title: Quad_Bcl6_ChIP

value: guinnea-pig anti-Bcl6 (in-house monoclonal)


title: TMX_Bcl6mKO_RNA_P1900

value: skeletal muscle - quadricep


title: FluVax6

status: Public on Dec 25 2023

first: Amanda

last: Marzo

state: IL

address: 1620 W Harrison St

institute: Rush University

hyb_protocol: Nanostring Murine Immune Exhaustion Kit Protocol

scan_protocol: nCounter Digital Analyzer

data_processing: ROSALIND webtool software normalized using house keeping genes

source_name: Tumor Tissue

growth_protocol: Tumor induced in vivo with 200,000 4T1 cells in mammary fat pad

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit from tumor tissues. RNA was evaluated by Bioanalyzer

treatment_protocol: Intratumoral influenza vaccine administration

tag: fluvax treatment

value: Treated

value: Balb/c

tag: gender

value: Female

value: Adult


title: FluVax2

label_protocol: Nanostring Murine Immune Exhaustion Kit Protocol


title: FluVax4


title: FluVax5


title: FluVax3


title: PBS5

value: Control


title: total_RNAPII_ChOR-seq_T1

value: HeLa S3

value: Rpb1 NTD (D8L4Y) (Cell Signaling Technology, Cat No. 14958; RRID:AB_2687876)


title: PBS6


title: FluVax1


title: PBS4


title: ck-48h-1


title: ck-24h-3


title: S2P_RNAPII_ChOR-seq_T2

value: Early S (2h after T0)

value: Non treated


title: PBS3


title: carm1_1_RNAseq

value: Heart

value: Carm1 mutant


title: PBS2


title: PBS1


title: ID_SetDB1-KO_Su(var)39-KO-2

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: ID RNA-seq in SetDB1/Su(var)3-9 double mutants

data_processing:
RNA-seq raw data were trimmed using Cutadapt with -u 15 -U 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT parameters. Then processed reads were aligned to BDGP6 (Ensembl 95) using HISAT2 aligner in paired-end mode with "no-discordant" parameter. Reads aligned to genomic locations were counted gene-wise according Ensemle annotation (https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/genes/dm6.ensGene.gtf.gz) using FeatureCounts tool with -p -P -d 50 -D 1000 -B -s 2 parameters. Expression of mobile elements for each sample were calculated using SalmonTE with standart parameters.
Assembly: BDGP R6/dm5
Supplementary files format and content: Read counts per gene

organism: Drosophila melanogaster

source_name: wing imaginal discs

growth_protocol: The flies were kept at 25°C

extract_protocol:
Total RNA from 25 salivary glands or 25 pairs of wing imaginal discs was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
To construct RNA-seq libraries, we used NEBNext Ultra II RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 1000 ng of RNA was used as a starting material. For imaginal discs, we followed the manufacturer's protocol, but for salivary glands it was modified, because the standard protocol did not allow for complete removal of the ribosomal RNA. To address this issue, mRNA enrichment procedure using oligo-dT beads was repeated twice. Specifically, following the first round of enrichment, mRNA was eluted in 50 ul of TE buffer preheated to 80°С and incubated with beads for 2 minutes (rather than eluted into the First Strand Synthesis Reaction Buffer as in the manufacturer’s protocol). The eluate was used for the second round of enrichment on oligo dT beads and processed as described in the protocol. Constructed RNA-seq libraries were sequenced with DNBSeq-G400 platform using 2x150bp paired-end mode (BGI, China). Three technical replicates were run.

tag: developmental stage


title: ID_oregon_wt-2

description: ID RNA-seq control

value: OregonR


title: ID_oregon_wt-3

description: ID RNA-seq control


title: ID_oregon_wt-1

description: ID RNA-seq control


title: ID_SetDB1-KO_Su(var)39-KO-3


title: SG_SetDB1-KO_Su(var)39-KO-3

description: SG RNA-seq in SetDB1/Su(var)3-9 double mutants

source_name: salivary glands


title: SG_SetDB1-KO_Su(var)39-KO-2


title: SG_oregon_wt-3

description: SG RNA-seq control


title: SG_oregon_wt-2

description: SG RNA-seq control


title: NSCLC tissue mouse 1, total RNA, miRNA-seq, biological rep 1 [NSCLC_2A]

city: Austin

first: Eleftherios

last: Bochalis

state: Texas

address: 2515 Speedway

department: College of Pharmacy

institute: The University of Texas at Austin

data_processing:
In house miRNA-seq analysis pipeline was employed. Firstly, adapters and UMIs were extracted for each sample and reads were length filtered so that all reads were above 18nt. Mature and hairpin miRNA reads were aligned to both the miRBase mature and hairpin sequences and the hg38 genome. Differentially expressed miRNAs were obtained with the use of DESeq2 using an adjusted p-value < 0.05 and a log2fold change cutoff of plus-minus 1.
Assembly: hg38
Assembly: miRBase release 22.1
Assembly: mm10
Supplementary files format and content: Comma-separated values files and matrix files

source_name: Lung tumor tissue

extract_protocol:
Total RNA was extracted using QIAGEN miRNA minikit (REF 1038703) and RNA samples were forwarded to library construction.
Libraries were constructed from RNA samples with the QIAseq miRNA sequencing kit (REF 1103677) combined with the QIAseq miRNA NGS 12 Index IL (REF 331592). As an initial step, adapters were ligated to the 3’ and 5’ ends of miRNAs and subsequently, universal cDNA synthesis with Unique Molecular Indices (UMI) assignment, cDNA cleanup, library amplification and library cleanup were performed.

value: Lung tumor tissue

value: Epithelial

value: Urethane


title: NSCLC tissue mouse 2, total RNA, miRNA-seq, biological rep 2 [NSCLC_3B]


title: NSCLC tissue mouse 1, total RNA, miRNA-seq, biological rep 2 [NSCLC_2B]


title: Healthy lung tissue mouse 1, total RNA, miRNA-seq, biological rep 4 [NLT_4]

source_name: Lung normal tissue

value: Lung normal tissue


title: Healthy lung tissue mouse 1, total RNA, miRNA-seq, biological rep 2 [NLT_2]


title: NSCLC tissue mouse 3, total RNA, miRNA-seq, biological rep 1 [NSCLC_4A]


title: NSCLC tissue mouse 3, total RNA, miRNA-seq, biological rep 2 [NSCLC_4B]


title: SG_oregon_wt-1

description: SG RNA-seq control


title: Healthy lung tissue mouse 1, total RNA, miRNA-seq, biological rep 1 [NLT_1]


title: NSCLC tissue mouse 2, total RNA, miRNA-seq, biological rep 1 [NSCLC_3A]


title: H5

city: Wuhan

first: yingying

last: zhou

address: NO.169.Donghu Road, Wuhan

institute: Zhongnan Hospital of Wuhan university

data_processing:
The raw reads were trimmed of low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx_toolkit/). Then, the clean reads were evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Clean reads were aligned to the human GRch38 genome by tophat2[17], allowing 4 mismatches. Uniquely mapped reads were used to calculate read number and reads per kilobase of exon per million fragments mapped (RPKM) for each gene. The expression levels of genes were evaluated using RPKM.
Clean reads were aligned to the human GRch38 genome by tophat2, allowing 4 mismatches. Uniquely mapped reads were used to calculate read number and reads per kilobase of exon per million fragments mapped (RPKM) for each gene. The expression levels of genes were evaluated using RPKM. The software edgeR[18], which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and p value (p value≤0.05) to determine whether a gene was differentially expressed.
To systematically analyze the lncRNA expression pattern, we used a pipeline for lncRNA identification similar to that previously reported, which was constructed based on cufflinks software.
To explore the regulatory mode between lncRNAs and mRNAs, we calculated the Pearson’s correlation coefficients (PCCs) between them with a correlation of 0.6 and a p value of 0.05. Then, the distance between lncRNAs and genes (10 kb) was used as the threshold to determine the cis- and trans-regulatory relationships. A distance between lncRNAs and genes less than 10 kb was defined as cis regulation, and a distance greater than 10 kb or on other chromosomes was considered trans regulation.
We first identified all the coexpression pairs of lncRNAs and genes in each sample by calculating Pearson’s correlation coefficients (|r| >0.6 and P value <0.05) between the expression levels of differential lncRNAs and all genes. Then, with a threshold distance of 10 kb between lncRNA and gene pairs, cis-acting genes were identified. The other lncRNA and gene pairs with distances greater than 10 kb or in the different chromosomes were regarded as trans-acting pairs.
To sort out functional categories of genes, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified using the KOBAS 2.0 server. Hypergeometric tests and Benjamini-Hochberg FDR controlling procedures were used to define the enrichment of each term. Reactome (http://reactome.org) pathway profiling was also used for functional enrichment analysis of the sets of selected genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peripheral blood monocytes

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit (QIAGEN), and during the purification process of the sample, DNA enzyme (QIAGEN) was used for on-column digestion of the DNA. RNA quality and concentration were measured using an Agilent 2100 biological analyzer.
Ribosomal RNA molecules (rRNA) were eliminated using Ribo-Zero rRNA removal kits (Illumina). RNA sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer's instructions, and purified library products were evaluated using 2200 Tapestation (Agilent Technologies) and Qubit®2.0 (Thermo Fisher Scientific). Finally, single-stranded DNA molecules were clustered and sequenced for 150 cycles on an Illumina HiSeq 3000 system (Illumina).

value: Peripheral blood monocytes

value: healthy


title: H4


title: H3


title: ID_SetDB1-KO_Su(var)39-KO-1


title: H2


title: H1


title: Healthy lung tissue mouse 1, total RNA, miRNA-seq, biological rep 3 [NLT_3]


title: A6

value: after treatment


title: SG_SetDB1-KO_Su(var)39-KO-1


title: Liver endothelial cells, high iron 3

city: Boston

first: Allison

last: Fisher

state: MA

address: 50 Blossom Street, Thier Research Building, 1117A

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
Base calling was performed using Illumina HiSeq software
Reads were mapped to reference genome using STAR aligner
Read counts for individual transcripts from ENSEMBL annotation were obtained using HTSeq
Differentially expressed genes were identified using EdgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM and CPM values

source_name: Liver

growth_protocol: 3-week-old wild-type 129S6/SvEvTac male mice were fed purified AIN-93G rodent diet formulated to contain 37 ppm iron as ferric citrate (Research Diets D08090806) or 10,000 ppm carbonyl iron (Research Diets D08090805) for 4 weeks.

extract_protocol:
Total RNA from FACS-sorted liver endothelial cells was isolated using PicoPure RNA Isolation Kit (Applied Biosystems). RNA quality and concentration were assessed by Agilent 2100 Bioanalyzer. 70 ng total RNA was used for library construction.
Libraries were constructed using Clontech SMARTer Ultra Low Input RNA Kit

treatment_protocol: Liver endothelial cells were sorted from 7-week-old mice by FACS on a FACSAriaII (BD Biosciences). Cells were first gated using FSC/SSC characteristics, and doublets were sequentially excluded by comparing FSC and SSC height and area signals. Endothelial cells were identified as CD45-, CD31+, lineage-, MHCII-, CD64-, CD146+.

value: Liver

value: Primary cells

value: Endothelial cell

value: Wildtype 129S6/SvEvTac

value: High iron diet (10,000 ppm)


title: A3


title: A1


title: Liver endothelial cells, high iron 2


title: Liver endothelial cells, high iron 1


title: B6

value: before treatment


title: A4


title: A2


title: Liver endothelial cells, control iron 2

value: Control iron diet (37 ppm)


title: A5


title: Transgenic plant with complementation of RPOTmp functions in chloroplasts

city: Irkutsk

first: Igor

middle: V

last: Gorbenko

address: Lermontova st., 132

department: Cell biology and engineering

institute: SIPPB SB RAS

description: 3 analytical replicates of TP1 transgenic plant vs Col-0 WT

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and linear-LOWESS normalization. rDyeNormSignal and gDyeNormSignal were used for analyses with limma R package [version 3.58.1].

organism: Arabidopsis thaliana

source_name: Transgenic plant

label_protocol: cDNA labelling was perfored according to Agilent labelling protocol for 2 color arrays

growth_protocol: After 3 days at 4°C, seeds were sown onto Petri plates containing 0.5X Murashige and Skoog salts (Sigma-Aldrich) and 0.8% (w/v) Phytagel (Sigma-Aldrich) and grown at 22°C in a KBW720 growth chamber (Binder) at a photon flux density of 150 μmol•m –2 •s –1 and with a 16 h light / 8 h dark photoperiod.

extract_protocol: Total RNA extracted using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: transgene targetting

value: Pt

tag: phenotype

value: Mut

tag: transgene insertions number

tag: line used for transfection

value: 12 Days old seedling

source_name: Wild type plant Col-0


title: Overexpressor plant with chloroplast targetting of recombinant RPOTmp, 1

description: 3 analytical replicates of P12 transgenic plant vs Col-0 WT

value: WT


title: Overexpressor plant with chloroplast targetting of recombinant RPOTmp, 2

description: 3 analytical replicates of P5 transgenic plant vs Col-0 WT


title: Transgenic plant with complementation of RPOTmp functions in mitochondria, 2

description: 3 analytical replicates of TM3 transgenic plant vs Col-0 WT

value: Mt


title: B4

tag: tissue

tag: treatment


title: Liver endothelial cells, control iron 1

tag: cell type

tag: genotype


title: Transgenic plant with complementation of RPOTmp functions in mitochondria, 1

description: 3 analytical replicates of TM11 transgenic plant vs Col-0 WT

tag: age


title: Overexpressor plant with mitochondrial targetting of recombinant RPOTmp, 2

description: 3 analytical replicates of M20 transgenic plant vs Col-0 WT


title: rpot2-knockout mutant plant, GABI_286E07

description: 3 analytical replicates of GABI_286E07 mutant plant vs Col-0 WT

source_name: Mutant plant


title: Overexpressor plant with mitochondrial targetting of recombinant RPOTmp, 1

description: 3 analytical replicates of M15 transgenic plant vs Col-0 WT


title: B3


title: si-NC2

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

data_processing:
Convert Illumina high-throughput sequencing results to Raw Reads and store them in the FASTQ file format. Removal of low-quality sequences and linker contamination from Raw Reads by the fastp (version 0.18.0) platform for analysis of Clean Reads. Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database and removed the rRNA mapped reads.
The filtered-sequencing sequence of each sample was compared to a reference genome (GRCh38) and localized to the genome by the improved BWT algorithm of HISAT2 2.4 software with “-rna-strandness RF” and other parameters set as a default.
The number and proportion of genes compared to the genome are called mapping reads and mapping rate. The fragment per kilobase of transcript per million mapped reads (FPKM) value was calculated to quantify its expression abundance, using RSEM software. The differentially expressed genes (DEGs) were identified by DESeq2 software[21] (|log2 Fold Change|>log2 (1.5) and p-value < 0.05).
Assembly: Homo sapiens Ensembl_release106
Supplementary files format and content: all.genes.group.expression.annot include Read Count and FPKM for each Sample.

growth_protocol: The human HCC cell line HepG2 used in this study was purchased from the Shanghai Cell Bank of the Chinese Academy of Sciences. HepG2 cells are cultured in Dulbecco’s modified Eagle’s medium (HyClone, Logan, UT, USA) containing 10% fetal bovine serum (HyClone), 1% penicillin/streptomycin at an incubator temperature of 37 °C and CO2 concentration of 5%.

extract_protocol:
Sample RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol, obtaining 1.5 μg of RNA separately for each sample. The purity and concentration of RNA was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
Once the total RNA sample is up to standard, it is enriched with Oligo (dT) beads. Then the purified mRNA was fragmented into short fragments using fragmentation buffer. The first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system using fragmented mRNA as a template and random oligonucleotides as primers. Add buffer, dNTPs, Rnase H and DNA Polymerase I to synthesize the second strand of cDNA. The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: HepG2 cells were divided into 2 groups, including the negative control group (si-NC) and the si-Girdin group. Based on the human Girdin gene sequence and small interfering RNA (siRNA) sequence with high transfection rate provided by GenBank, Huzhou Hippo Biotechnology Co., Ltd. was commissioned to design the siRNA sequence (5'-3', GCAAGCUAAGCAAGAUUGAAUTT) and negative control sequence for Girdin. The transient transfection of siRNA was performed using the GenMute™ siRNA Transfection Reagent (SignaGen Laboratories, Maryland, USA) according to the manufacturer's instructions.

tag: cell line

value: hepatoma carcinoma cell

value: si-NC


title: si-NC1


title: si-NC3


title: B2

value: Peripheral blood monocytes


title: si-Girdin3

value: Girdin Knockdown

value: si-Girdin


title: B1


title: B5


title: Liver endothelial cells, control iron 3

value: Liver


title: si-Girdin1


title: si-Girdin2


title: AG25367_g4_DOX_d4

city: Worcester

first: Hong

last: Zhang

address: 55 Lake Avenue North

department: Pediatrics

institute: University of Massachusetts Chan Medical School

data_processing:
Sequence reads were aligned using STAR v2.7.10b and samtools v1.15.1 to acquire bam files
Read counts were obtained using FeatureCounts in Subread v2.0.3
Normalized counts were genereated by log2-transforming read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized log2-transformed read count values for each sample

growth_protocol: Human iPSCs were maintained in TeSR-E8 media in humidied atmosphere with 5% CO2 at 37°C. Cells were passaged every 4 days at 1:4 ratio.

extract_protocol:
Total RNA was extracted with TRI reagent (Millipore Sigma) and treated with DNase I (Qiagen) using a RNeasy MinElute Cleanup Kit (Qiagen). RNA integrity was determined using Agilent 4200 TapeStation.
Library preparation was performed with 1 µg of total RNA. Ribosomal RNA was removed by an RNase-H method using the RiboErase kit (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94°C for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III reverse transcriptase enzyme and random hexamers (Life Technologies) per manufacturer’s instructions. A second strand reaction was performed to yield double stranded cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases targeting 30M clusters.

treatment_protocol: The day before treatment, iPSC colonies were dissociated with TrypLE and seeded with TeSR-E8 supplemented with 10 µM Y-27632. On the day of treatment, cells were fed with fresh media with or without 0.3 µg/mL doxycycline (DOX).

value: Induced pluripotent stem cells

value: AD

value: DOX-treated for 4 days


title: AG25367_g2_DOX_d4


title: 35L11_g4_CTL_d6

value: Healthy

value: Untreated for 6 days


title: 35L11_g4_DOX_d6

value: DOX-treated for 6 days


title: AG25367_g4_DOX_d6


title: 35L11_g2_CTL_d6


title: 35L11_g2_DOX_d4


title: AG25367_g2_DOX_d6


title: 35L11_g4_DOX_d4


title: In vitro sample 1 Control

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
Bacillus subtilis/RNase R expressed in E.coli
read 2 sequence

library_source: other

data_processing:
The data was aligned using Novoalign (www.novocraft.com; version 3.06) to the B. subtilis 16S rRNA sequence (16S_rRNA.fs file). After generating the bam files, bed-graph files were generated using bedtools and visualized using the IGV genome brows-er.
Assembly: Bacillus/1-1554 subtilis 168 | BSU_rRNA_4 | rrnA-16S
Supplementary files format and content: BAM files of reads mapped to 16S rRNA
Supplementary files format and content: bedgraph files of reads mapped to 16S rRNA

molecule: other

organism: Bacillus subtilis

source_name: delta-rnr strain / BL21-CodonPlus(DE3)-RIL

growth_protocol: For the in vivo experiments B. subtilis 168 wild type cells (BGSC strain 1A1 wild type: trpC2) expressing RNase R-FLAG from pHT01 p43 wRBS RNase R-GS5-FLAG tGyrA were grown at 37 °C in Lysogeny broth (LB) medium (Roth) supplemented with 5 μg/mL chloramphenicol and shaking at 145 rpm until OD600 of 1.5. For the in vitro experiments BL21-CodonPlus(DE3)-RIL cells (Stratagene) transformed with expression vectors were grown in Lysogeny broth (LB) medium (Roth) supplemented with antibiotics (30 μg/mL kanamycin and 34 μg/mL chloramphenicol. His6-TEV tagged RNase R wt was expressed by induction with isopropyl β-D-1-thiogalactopyranoside (IPTG) for 16 h at 18°C. To isolate ribosomes, the Δrnr strain (BGSC BKE33610 trpC2; Δrnr::erm) was grown in 2 L LB media until OD600= 0.8.

extract_protocol:
To extract the RNA from the Flag-IP or from the in vitro reaction 1 ml of Trizol reagent (Invitrogen) was used according to the manufacturer’s instructions with an additional 75% EtOH wash step at the end.
The samples were then taken into a modified NextFlex small RNA seq v4 protocol. Inputs were standardized to 206 ng as measured by RNA Qubit HS. Samples had 3’ adapters ligated with an adapter dilution of 1:1, followed by an adapter inactivation step (Steps A and B). Samples were cleaned up with Adapter Depletion Solution, beads, and isopro-panol following Step E but with reagent volumes adjusted for the smaller reactions. Sam-ples were resuspended in 12 µl water, and 11.2 µl were taken, added with 4 µl of 5X T4PNK buffer (NEB), and fragmented at 94°C for 1 min. 4 µl of 10 mM ATP and 0.8 µl of T4PNK were added, and samples were incubated at 37°C for 30 mins, followed by deac-tivation at 65°C for 20 mins. Then samples were taken into the 5’ ligation step from the Nextflex protocol with adapters diluted 1:3 (Step C), and the remainder of the protocol was followed as per manufacturer instructions. The positive control was amplified with 16 PCR cycles, while the DP samples were amplified with 25 PCR cycles. Samples were cleaned up individually with a 1.3x bead ratio, and checked on the bioanalyzer. Samples were pooled equimolarly, and cleaned up once more with a 1x bead ratio. Samples were sequenced using the MiSeq 50 bp v2 kit with the following read mode: 5-8-0-61. Sam-ples were demultiplexed using bcl2fastq, adapter trimming was performed with cutadapt, sequences from Read 2 were reverse-complemented (_rc) and taken forward into alignments.

treatment_protocol: For the in vivo reactions, cells were harvested in 25 mM Hepes-KOH pH 7.5, 100 mM KOAc, 15 mM Mg(OAc)2, 0.1% NP-40, 0.5 mM Tris Carboxy Ethyl Phosphene (TCEP) buffer supplemented with protease inhibitor cocktail (Roche), flash frozen in liquid nitrogen and lysed under cryogenic conditions using a Retsch MM400 (Retsch). The lysate was cleared at 16,000 rpm for 15 min and incubated with anti-FLAG M2 affinity beads (Merck) for 1.5 hours at 4°C on a turning wheel. After in-batch wash with 20 ml lysis buffer without protease inhibitors, the beads were transferred to a mobicol column and washed with 4 ml of 25 mM Hepes-KOH, pH 7.5, 100 mM KOAc, 15 mM Mg(OAc)2, 0.01% DDM  (Dodecylmaltoside), 0.5 mM Tris Carboxy Ethyl Phosphene (TCEP) buffer after which the RNase R complexes were eluted using 0.2 mg/ml 3X FLAG peptide (Sigma) in wash buffer. To sequence the in vitro degradation reactions, 5 µM RNase R was mixed with 1,5 µM 30S subunits in a 10 µl volume at 37°C and the reaction was stopped at 4 min with the addition of 1 ml Trizol.

value: BGSC BKE33610 trpC2; delta-rnr::erm / Stratagen

value: Reaction stopped at 0 min with trizol


title: 35L11_g2_DOX_d6


title: AG25367_g4_CTL_d6


title: In vivo sample 3

description:
Bacillus subtilis
read 2 sequence

source_name: 168 wild type

value: 168 wild type

value: BGSC strain 1A1 wild type:trpC2

value: grown to OD 1.5


title: In vitro sample 2 Treated

value: delta-rnr strain / BL21-CodonPlus(DE3)-RIL

value: mixed at 37  C for 4 min


title: In vitro sample 1 Treated


title: DH_E14

city: Chengdu

first: Xiong

middle: Zhi

last: Li

address: Wuhou District

institute: Southwest Minzu University

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was analyzed by the Cell Ranger software (v3.1.0) provided by 10×Genomics to ensure the availability and validity of data for subsequent analysis. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (v3.1.1).The STAR software was used to align sequences to the reference genome (GRCg6a).
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: leg musculature

extract_protocol:
The muscle tissues isolated of E10, E14 and E18 were digested with collagenase I for 30 min and then mechanically dissociated into single cell suspension by pipetting. The cell suspensions were filtered through a 40 μm nylon cell strainer for single cell library construction.
Single cell barcoding and library preparation were performed based on 10×Genomics single-cell RNA sequencing platform (10×Genomics, Pleasanton, CA, USA). The filtrated single cells prepared above were assessed using a hemocytometer (Thermo Fisher Scientific) and the cell concentration was adjusted to 1,000 cells/μl. Reverse transcription and 10×barcoded cDNA library was performed by the 10×Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2 (10×Genomics, Pleasanton, CA, USA) and 10×Genomics Chromium barcoding system following the instructions provided by the manufacturer. The sequencing of prepared libraries was performed using Illumina Next-Seq500 sequencer (Illumina, San Diego, CA, USA) as per the manufacturer’s instructions.

value: leg musculature

value: skeletal muscle tissue cells

value: embryonic 14


title: TC_E18

value: embryonic 18


title: DH_E10

value: embryonic 10


title: TC_E14


title: In vitro sample 3 Treated


title: In vitro sample 2 Control


title: In vitro sample 3 Control


title: TC_E10


title: DH_E18


title: H6

value: Peripheral blood monocytes

value: healthy


title: AG25367_g2_CTL_d6

value: Induced pluripotent stem cells

value: AD


title: In vivo sample 2

description:
Bacillus subtilis
read 2 sequence


title: 35L11_g4_CTL_d4

value: Healthy

value: Untreated for 4 days


title: 35L11_g2_CTL_d4


title: AG25367_g2_CTL_d4


title: AG25367_g4_CTL_d4


title: In vivo sample 1

description:
Bacillus subtilis
read 2 sequence


title: Central forebrain, sleep deprived 6h & recovery 8h, rep3 [R8-3]

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

institute: Washington State Univ. Spokane

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022

data_processing:
*library strategy: WTTS-seq (whole transcriptome termini site sequencing) targeting alternative polyA sites
Raw read processing: Raw data were obtained from 55 samples and stored in FASTQ format. We filtered raw reads with the FASTQ quality filter in the FASTX Toolkit (v0.0.13), allowing for a minimum score of ≥10 for ≥50% of bases (http://hannonlab.cshl.edu/fastx_toolkit/). We trimmed T nucleotides or T-rich sequences located at the 5’ ends of the reads using Perl scripts, as described in a previous study30. Trimmed reads of at least 16 bp in length were kept for further analysis.
Read mapping and poly(A) site clustering: For each data set, we aligned the processed reads to the Rattus norvegicus genome (mRatBN7.2/rn7) using the torrent mapping program (TMAP, v3.4.1; http://github.com/iontorrent/tmap) with the unique best hits parameter (-a 0). We then extracted raw PASs supported by the uniquely mapped reads from SAM files and obtained a polyadenylation tag (PAT) file using an in-house script. After that, we merged all the PAT files to determine the final PASs for all samples. PASs within 25 nucleotides of one another were grouped into one polyadenylation site cluster (PAC) using GetPolyaSiteCluster31. PACs with few reads were rejected according to different criteria depending on library size. For libraries that had less than 1.7M reads, clusters were retained only if a group of 5 biological replicates had at least 3 samples with ≥3 reads. For libraries with more than 1.7M reads, at least 3 samples with ≥4 reads were required.
Gene annotation and usage of poly(A) sites: We annotated all the final PACs for PAS_ID, gene symbol, functional region, and other factors, as indicated, using Cuffcompare (v2.2.1)32, Perl scripts, and annotation file (GCF_000001895.5_Rnor_6.0_genomic.gtf; https://ftp.ncbi.nlm.nih.gov/). Clusters that mapped to mitochondrial genes were removed, then the number of PAS-covered reads was normalized33 to the total number of covered reads within each library and rescaled by a factor of 107.
Circadian/ultradian PAS discovery: Based on input, unnormalized PAS read counts, rhythmic patterns were identified using the MetaCycle34 R package meta2d, which synthesizes the results of three cycle analysis algorithms (ARSER, JTK_Cycle, and Lomb-Scargle). The analysis was run 5 times with different replicates inserted into each of the appropriate ZT time slots, and the average p-value, FDR, phase, and other statistics were calculated. Only the highly corroborated PASs that were significant (p<0.05) in all 5 trials were used for all analyses.
Differential expression analysis of sleep deprivation/recovery: To evaluate the expression of PASs in sleep homeostasis experiments, PAS counts from rats recovering from 6 h SD were contrasted with time-matched controls (R0 vs ZT6, R2 vs ZT8, R4 vs ZT10, R8 vs ZT14). We removed high variation from the first principal component systematically, resulting in improved variance estimates for low read counts. Prcomp (in R) was used to perform principal component analysis (PCA) and find eigenvectors by way of singular value decomposition. DESeq-2 with "Apeglm" Shrinkage36 and the Wald Test were used to generate test statistics in R software. The FDRtool was used to determine the Local FDR
Assembly: Rattus norvegicus genome  build mRatBN7.2/rn7
Supplementary files format and content: the details in the processed_data_readme.txt

organism: Rattus norvegicus

source_name: central forebrain

growth_protocol: Male Long Evans rats (7-9 weeks old) were housed in pairs at 22 ± 2 °C on a 12:12 h light-dark cycle. The rats were acclimated to this light cycle for at least 10 days prior to tissue collection, with water and chow ad libitum. Cages were cleaned weekly (between 8 and 11 AM) unless the rats were being euthanized within 24 h.

extract_protocol:
Rats were decapitated by guillotine under normal room light (ZT2–10) or under dim red light (ZT14–22). Following decapitation, forebrains were resected (Fig. 1A), frozen in 2-methylbutane suspended in dry ice, and then stored at -80 °C until homogenization for RNA extraction. Just before RNA isolation, forebrains were removed from -80 °C storage and placed on dry ice. Prior to use, a stainless-steel mortar and pestle were cleaned with RNase Zap (Thermo Fisher) and 70% ethanol. The mortar was then partially filled with liquid nitrogen before a forebrain was added, pulverized, and placed in a conical tube. Between each sample, the mortar and pestle were cleaned with 70% ethanol. A small aliquot of sample was removed for RNA isolation using Trizol Reagent (Invitrogen), according to the manufacturer’s instructions. Purified RNA was resuspended in water, and concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Fisher).
WTTS-Seq libraries were prepared as described by Zhou et al. https://doi.org/10.1534/genetics.116.188508. Briefly, total RNA (2.5 µg) was incubated at 70 °C with 10X Fragmentation buffer (Invitrogen) for 3 min. The fragmentation reaction was halted by the addition of Stop Solution and incubation on ice for at least 2 min. Next, poly(A)+ RNA was purified from the fragmented total RNA with Dynabeads Oligo (dT)25 (Invitrogen), according to the manufacturer’s directions, and used for first-strand cDNA synthesis in a 20 µL reaction mixture. First, 1.0 µL of barcode primer (100 µM) and 1.0 µL of a common SMART primer (100 µM) were annealed to the poly(A)+ RNA template by heating to 65 °C for 5 min and incubating on ice for at least 2 min. Next, 4.0 µL of 5X First-strand buffer (Invitrogen), 1.0 µL of SuperScript III reverse transcriptase (Invitrogen), 1.0 µL of 0.1 M dithiothreitol, 2.5 µL of 10 mM dNTP, and 1.0 µL of RNase OUT (Invitrogen) were added to the mixture. First-strand cDNA was synthesized by incubating the mixture at 40 °C for 90 min in the presence of library-specific adaptors. Synthesis was terminated by heating the mixture at 70 °C for 15 min. RNases I (100 U/µL; Invitrogen) and H (2 U/µL; Invitrogen) were subsequently added and incubated with the mixture at 37 °C for 30 min to hydrolyze the remaining single-stranded RNA molecules and ensure that only single-stranded cDNA remained. RNase activities were terminated by heating the samples at 70 °C for 20 min. Following purification with solid-phase reversible immobilization (SPRI) beads, second-strand cDNA was synthesized from first-strand cDNA by asymmetric PCR. In addition to the cDNA, the 50 µL PCR reaction contained 1.0 µL of Phusion Hi-Fidelity DNA polymerase, 10.0 µL of 5X HF buffer, 1.0 µL of 0.4 µM barcode primer, 1.0 µL of 0.8 µM common primer, 1.0 µL of 10 mM dNTP, and nuclease-free water. The PCR reaction was carried out by heating at 95 °C for 30 sec, followed by 20 cycles of 98 °C for 10 s, 50 °C for 30 s, and 72 °C for 30 s, with a final elongation step at 72 °C for 10 min. SPRI beads were used to purify and select 200 – 500 bp fragments from the final library.

treatment_protocol: Thirty rats were randomly assigned to one of six groups (n=5/group) that were sampled every 4 h, beginning 2 h after light onset (i.e., ZT2, 6, 10, 14, 18, and 22). For the sleep deprivation (SD) study, twenty rats were randomly assigned to 6 h SD from ZT0–6, wherein rats were kept awake by an automated bedding stir bar (Pinnacle) at the bottom of a cylindrical cage. The bar was set to rotate for 4 s, randomly changing rotation direction and stopped for a random interval ranging from 10 to 30 s28,29. Following SD, rats (n=5/time point) were euthanized immediately (R0) or were returned to their home cage for 2 h (R2), 4 h (R4), or 8 h (R8) under red light without disruption before sampling. Five additional rats were euthanized at ZT8 as undisturbed, time-matched controls.

value: central forebrain

value: age 7-9 weeks

value: male

value: Long Evans

value: sleep deprived 6h & recovery 8h


title: Central forebrain, sleep deprived 6h & recovery 8h, rep4 [R8-4]


title: Central forebrain, sleep deprived 6h & recovery 8h, rep5 [R8-5]


title: Central forebrain, sleep deprived 6h & recovery 8h, rep1 [R8-1]


title: Central forebrain, sleep deprived 6h & recovery 4h, rep5 [R4-5]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
ZT10vR4_25016_9-3-2023_apeglm

value: sleep deprived 6h & recovery 4h


title: H1 cells, TesR, rep2

city: Haining

first: Yaqi

last: Su

state: Zhejiang

address: ZJU-UoE Institute,718 East Haizhou Rd.

institute: Zhejiang University-University of Edinburgh Institute, Zhejiang University

data_processing:
Sequence reads were mapped to GRCh38 using minimap2 (parameters: -ax splice --MD)
Read counts extraction were performed using featureCounts basd on the GRCh38.105 reference annotation (parameters: -L -M -O -g: transcript_id -t: transcript)
Assembly: human NCBI genome build 38
Supplementary files format and content: tab-delimited text files include expression raw count values for each sample

extract_protocol:
RNA was harvested using Trizol reagent and purified.
Library was prepared according to theNanopore Ligation Sequencing Kit 1D (PM).

value: Embryonic stem cells

value: WT

value: Primed ESCs were grown in mTeSR till reaching 60-70% confluency


title: Central forebrain, sleep deprived 6h & recovery 4h, rep3 [R4-3]


title: H1 cells, TesR, rep1


title: MCF7 NF1-45 E2 Rep 3

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

data_processing:
Trim reads with trim_galore v0.6.0
Reads were mapped to GRCh38 with GENCODE release 33 with STAR v2.7.8a basic two-pass mode.
The raw counts were extracted from the reverse strand alignments.
Assembly: GRCh38
Supplementary files format and content: raw_counts.tsv contains raw read counts
Supplementary files format and content: counts_per_million.tsv contains counts per million mapped reads

source_name: breast

growth_protocol: Cells were grown in MEC media (phenol red-free DMEM/F12, 10% horse serum, 20ng/mL EGF, 0.5ug/mL hydrocortisone, 100ng/mL cholera toxin, and 10ug/mL insulin) in a 37°C humidified incubator in 5% CO2.

extract_protocol:
Buffer RLT (from RNeasy kit) containing betamercaptoethanol was added to each well of cells. The mix of buffer RLT and cells was then added to an MPbio lysing matrix E tube. Cells were homogenized for 20 seconds in an MPbio homogenizer, then the supernatant was added to a Qia Shredder column. An equal volume of 70% ethanol was added to the flow through, and the entire volume of liquid added to an RNeasy column. RNA was extracted according to the manufacturer’s instructions for the RNeasy kit (Qiagen).
KAPA mRNA Hyperprep kit (v7.21)

treatment_protocol: 10nM beta-estradiol for 24hr

value: breast

value: epithelial

value: beta-estradiol (10mM)


title: MCF7 NF1-EV E2 Rep 1


title: MCF7 NF1-EV E2 Rep 3


title: MCF7 NF1-EV E2 Rep 2


title: Endometrial samples from cows supplemented with methionine and became pregnant after AI -Rep4

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

country: Germany

institute: University of Bonn

data_processing:
Adapter and low-quality sequences were trimmed using Trim Galore (Babraham Bioinformatics, UK) by specifying the RRBS option.
Cleaned RRBS sequences were aligned to the bovine genome using Bismark Bisulfite Mapper (Babraham Bioinformatics, UK).
The BAM files generated from mapping were sorted and the replicate libraries from the same biological group were merged using the SAMtools.
Methylation calls were obtained from merged BAM files using the Bismark methylation extractor script integrated with the Bismark Bisulfite Mapper. Bismark coverage files
Quantification of methylation calls and identification of differentially methylated CpG sites was done using SeqMonk v1.48.0 tool (Babraham Bioinformatics, UK).
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: text delimited file (Data_Geo_RRBS_2023.txt).  Column names: S12, S16. S24, S28 indicate CON_noP_1, CON_noP_2, CON_noP_3, CON_noP_4 of CON_noP  group, respectively. Column names: S14, S18, S26, S30 indicate, CON_P_1, CON_P_2, CON_P_3, CON_P_4 of CON_P  group, respectively. Column names: S13, S17, S25, S29 indicate MET_noP_1, MET_noP_2, MET_noP_3, MET_noP_4 of MET_noP group, respectively. Column names: S15,  S19,  S27,  S31 indicate MET_P_1, MET_P_2, MET_P_3, MET_P_4 of MET_P  group, respectively.

organism: Bos taurus

extract_protocol:
DNA was isolated from each sample using AllPrep DNA/RNA/Protein (Qiagen).
2 µg genomic DNA was digested with MspI enzyme, end repaired, A-tailed and ligated with methylated adaptor sequences using TruSeq Nano DNA Sample Preparation kit (Illumina, San Diego, CA). Following this, 40–200 bp-sized DNA fragments were extracted using the Zyomclean™ Gel DNA Recovery Kit (Zymo Research). The samples were then treated with bisulfite using the EZ DNA Methylation-Gold Kit™ (Zymo Research).

treatment_protocol: Endometrial cytobrush samples collected from post-calving cows offered a control diet or rumen-protected methionine (RPM) were  classified based on the pregnancy. Endometrial samples collected from cows fed with control feed and that become pregnant and did not become were categorized as control pregnant (CON_P) and control non pregnant (CON_noP), respectively. Samples collected from cows supplemented with RPM and resulted in pregnancy or in no pregnancy were categorized as methionine pregnant (MET_P) and methionine non pregnant (MET_noP) groups, respectively.


title: MCF7 NF1-45 E2 Rep 2


title: H1 cells, FINE, rep2

value: Naïve ESCs were grown in FINE culture condition after research 50% confluency


title: Endometrial samples from cows supplemented with methionine and became pregnant after AI -Rep3


title: Central forebrain, sleep deprived 6h & recovery 8h, rep2 [R8-2]


title: Endometrial samples from cows supplemented with methionine and became pregnant after AI -Rep1