title: WGBSseq_ESC_qko_mbd

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.1 (NextSeq 500) and bcl2fastq2 v2.17 or lllumina RTA 3.4.5 (NovaSeq 6000) and bcl2fastq2 v2.20 was used for basecalling and demultiplexing.
Assembly: hg19 and mm10
Supplementary files format and content: Human (single-end) or mouse (paired-end) WGBS-seq reads were aligned to hg19 or mm10, respectively, using qAlign from the QuasR package with default parameters (with bisulfite = ”dir”). Number of total and methylated counts for Cs in the CpG context (genome-wide) were calculated using the qMeth function from QuasR.

source_name: esc

growth_protocol: HA36 mouse ES cells (mixed 129-C57Bl/6 strain) were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), 1x GlutaMax (ThermoScientific) and 1x Non-essential amino acids (Gibco), 0.001% beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). HEK293 cells were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 10 % Fetal Calf Serum (Invitrogen) and 2 mM L-Glutamine (ThermoScientific).

extract_protocol:
Nuclei of neurons (day 8) were isolated as in Grand et al.(Grand et al. 2021) and sorted by flow cytometry (BD FACS Aria III). Genomic DNA was isolated (QIAamp DNA Micro Kit, catalog number 56304) from  mouse ES cells or sorted nuclei of neurons and 1 ug was fragmented (Covaris S220) to an average size of ~ 300 bp. HEK293 genomic DNA was isolated with QIAamp DNA mini kit (Qiagen catalog number 51306) and fragmented with Covaris S220.
Libraries of mouse DNA were prepared according to manufacturer's instructions: Adapter ligation was performed using NEBNext Ultra II DNA Library Prep Kit (catalog number E7645L) with methylated adapters (NEBNext, catalog number E7535S), bisulfite treated (EZ DNA Methylation-Gold™ Kit, Zymo catalog number D5006) and indexed (NEBNext® Multiplex Oligos for Illumina) using 11 cycles in the PCR reaction (KAPA HiFi HotStart Uracil+ ReadyMix, Roche catalog number 07959052001). For HEK293 DNA, 500 ng of fragmented DNA were used for library preparation (NEBNext Ultra DNA Library Prep Kit, NEB catalog number E7370) with methylated adapters (NEBNext, NEB catalog number E7535S) and bisulfite treated with EZ DNA methylation-lightning Kit (Zymo Research catalog number D5046). Final PCR amplification was performed using KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (Roche catalog number 07959052001) with 12 cycles of amplification.

treatment_protocol: For HA36 ES cells containing the pTRE-Ngn2 construct differentiation was carried out by inducing expression of NGN2 with doxycycline as previously described (Thoma et al., 2012) with modifications. In brief, cells were plated on poly-D-lysine/laminin coated plates and treated with DMEM/F12 with Glutamax (LifeTech, 31331-028) containing 1x B27 without VitaminA (LifeTech #12587-010), 1x N2 supplement (LifeTech #17502-048), 10 ng/ml hEGF (LifeTech, PHG0315), 10 ng/ml hFGF (LifeTech, CTP0261) and 1 μg/mL doxycycline (Sigma, D989) for three days with no media change. At day three after doxycycline induction, medium was exchanged to Neurobasal-Medium (LifeTech, 21103-049) supplemented with 1x B27 with Vitamin A (LifeTech, 17504-044) , 1x N2 (LifeTech #17502-048) and 10ng/ml BDNF (PeproTech, 450-02), 10ng/ml GDNF (PeproTech, 450-10) and 10ng/ml NT-3 (PeproTech, 450-03). Every second day half of the media was replaced with fresh media.

value: ebryonic stem cells

value: MBD quadruple knock-out

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: WGBSseq_Neurons_qko_mbd

status: Public on Sep 27 2022

type: SRA

country: Switzerland

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: neurons

tag: cell type

tag: genotype

tag: strain


title: WGBSseq_ESC_wt

value: wild-type


title: WGBSseq_Neurons_wt_rep1


title: KIF_4+#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: polyA RNA

source_name: Colon

extract_protocol: For flow-cytometrically sorted samples, cells  were isolated by first enzymatically digesting distal colon tissue and then purified by fluorescence-activated cell sorting (two times to achieve enhanced purity). A total of  1,000  CD4+ T cells (DAPI- CD19- CD4+ TCRβ+) were sorted using the BD Aria IIinto TCL buffer (QIAGEN) with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

tag: tissue

value: Colon

tag: cell line

value: CD4+ T cells isolated from Germ-Free monocolinzed with EcN kfiCD mutant Colonic tissue

value: CD4+ T cells

tag: treatment

value: Germ-free + E.coli Nissle kfiCD D14


title: BXD32_HFD

type: RNA

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

institute: Ecole Polytechnique Fédérale de Lausanne

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD32 mice fed on high fat diet in a fed state

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner.

data_processing: Intensities were processed using the apt-probeset-summarize script from the Array Power Tool suite (version 2.11.3, https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip) with the gc-sst-rma-sketch standard method. Data processing code deposited at https://doi.org/10.5281/zenodo.4899683.

label: biotin

molecule: total RNA

source_name: liver, high fat diet

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (part number 4411974) according to manufactures protocols, then 5500ng of cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice were housed 5 per cage, by strain and diet, in isolator cages with individual air filtration (500 cm2, GM500, Tecniplast) and provided water ad libitum.

extract_protocol: Total RNA was extracted from tissue samples using trizol. RNA concentration was assessed using a Nanodrop. RNA extracts from approximately 5 animals were pooled at equal mass concentration, representing a total of roughly 360 animals. Pooled RNA extracts were then cleaned up using the Qiagen RNEasy kit.

treatment_protocol: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks of age until euthanasia, about half of the mice were fed ad libitum a high-fat diet (HFD) and the rest continued to be fed a chow diet. To avoid multiple sacrifices at night, the light/dark cycle of the mice was inverted two weeks before the sacrifice to ensure their adaptation. At 29 weeks of age, mice were fasted overnight (their day) and refed with their respective diet for 4 hours before sacrifice. Mice were euthanized with isoflurane anesthesia. Tissue samples were then excised and stored in liquid nitrogen. Standard rodent chow (CD): 18% kCal fat, 24% kCal protein and 58% kCal of carbohydrates (Harlan, 2018, Indianapolis, IN, USA). High-fat diet (HFD): 60.3% kCal fat, 18.3% kCal protein and 21.4% kCal of carbohydrates (Harlan, 06414, Indianapolis, IN, USA).

tag: Sex

value: male

tag: age

value: 29 weeks

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until euthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: fat:60.3% kCal, protein:18.3% kCal, carbohydrate:21.4% kCal

value: Teklad Custom Diet TD.06414, Envigo, Indianapolis, IN, USA

value: liver

value: ng/ul

tag: rin


title: GF_4+#2

value: CD4+ T cells isolated from Germ-Free Colonic tissue

value: Germ-free


title: BXD12_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD12 mice fed on high fat diet in a fed state


title: BXD32_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD32 mice fed on chow diet in a fed state

source_name: liver, chow diet

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: fat:18% kCal, protein:24% kCal, carbohydrate:58% kCal

value: Teklad Global 18% Protein Rodent Diet 2018 , Envigo, Indianapolis, IN, USA


title: BXD11_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD11 mice fed on high fat diet in a fed state


title: BXD6_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD6 mice fed on high fat diet in a fed state


title: BXD27_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD27 mice fed on chow diet in a fed state


title: WGBSseq_Neurons_wt_rep2

value: wild-type

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: RNAseq_Neurons_qko_mbd_cl1_1

description: processed data file: totalRNA_knownGene_mm10_neurons.csv

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Alignments (first read for paired-end) overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All ES cell experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated for ES cells with the RNeasy mini kit (Qiagen) using on- column DNA digestion or of neurons with Direct-zol RNA Microprep (Zymo research) with on-column DNA digestion.
Sequencing libraries were prepared from purified RNA for a minimum of two biological replicates per condition using TruSeq stranded total RNA Library Prep (Illumina)

treatment_protocol: For HA36 cells containing the pTRE-Ngn2 construct differentiation was carried out by inducing expression of NGN2 with doxycycline as previously described (Thoma et al., 2012) with modifications. In brief, cells were plated on poly-D-lysine/laminin coated plates and treated with DMEM/F12 with Glutamax (LifeTech, 31331-028) containing 1x B27 without VitaminA (LifeTech #12587-010), 1x N2 supplement (LifeTech #17502-048), 10 ng/ml hEGF (LifeTech, PHG0315), 10 ng/ml hFGF (LifeTech, CTP0261) and 1 μg/mL doxycycline (Sigma, D989) for three days with no media change. At day three after doxycycline induction, medium was exchanged to Neurobasal-Medium (LifeTech, 21103-049) supplemented with 1x B27 with Vitamin A (LifeTech, 17504-044) , 1x N2 (LifeTech #17502-048) and 10ng/ml BDNF (PeproTech, 450-02), 10ng/ml GDNF (PeproTech, 450-10) and 10ng/ml NT-3 (PeproTech, 450-03). Every second day half of the media was replaced with fresh media.

value: MBD quadruple knock-out

tag: cell line/strain background


title: RNAseq_Neurons_tko_creb_ko_1

value: Dnmt triple knock-out and Creb1 knock-out


title: RNAseq_Neurons_tko_creb_ko_2


title: RNAseq_Neurons_qko_mbd_cl2_1


title: RNAseq_Neurons_qko_mbd_cl2_2


title: BXD11_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD11 mice fed on chow diet in a fed state

value: male

value: 29 weeks


title: RNAseq_Neurons_tko_2

value: Dnmt triple knock-out


title: RNAseq_Neurons_qko_mbd_cl1_2


title: RNAseq_Neurons_tko_1


title: BXD27_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD27 mice fed on high fat diet in a fed state

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until euthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: fat:60.3% kCal, protein:18.3% kCal, carbohydrate:21.4% kCal

value: Teklad Custom Diet TD.06414, Envigo, Indianapolis, IN, USA


title: BXD1_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD1 mice fed on high fat diet in a fed state

value: liver

value: ng/ul


title: BXD6_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD6 mice fed on chow diet in a fed state

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.


title: BXD12_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD12 mice fed on chow diet in a fed state

value: fat:18% kCal, protein:24% kCal, carbohydrate:58% kCal

value: Teklad Global 18% Protein Rodent Diet 2018 , Envigo, Indianapolis, IN, USA


title: RNAseq_Neurons_wt_2

value: wild-type

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: BXD8_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD8 mice fed on high fat diet in a fed state

value: male


title: BXD1_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD1 mice fed on chow diet in a fed state

value: 29 weeks


title: ChIPseq_neurons_WT_hnf6_input_r2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters (paired="fr"), allowing only for uniquely mapping reads.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6. The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library.

extract_protocol:
ChIP was carried out as previously described (Barisic et al., 2019) with the following modifications: (1) Tow 15 cm plates of embryonic stem cell derived Ngn2 neurons were harvested eight days after doxycycline induction (2) chromatin was sonicated for 20 cycles of 30 s using a Diagenode Bioruptor Pico, with 30 s breaks in between cycles; (3) protein A magnetic Dynabeads Magnetic beads (Invitrogen, catalog number 10008D) were used; and (4) DNA was purified using AMPure XP beads.
Immunoprecipitated DNA and input DNA were submitted to library preparation (NEB Next Ultra DNA Library Prep Kit, Illumina). In the library preparation protocol, input samples (200 ng) were amplified using 6 PCR cycles and immunoprecipitation samples using 12 cycles.

tag: chip antibody

value: R&D systems, AF6277


title: BXD8_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD8 mice fed on chow diet in a fed state


title: ChIPseq_neurons_TKO_hnf6_input_r2

value: Dnmt triple knock-out


title: RNAseq_Neurons_wt_1


title: ChIPseq_neurons_WT_hnf6_r2


title: ChIPseq_neurons_TKO_hnf6_r1


title: ChIPseq_neurons_TKO_hnf6_r2


title: ChIPseq_neurons_TKO_hnf6_input_r1


title: ChIPseq_neurons_WT_pol2_input_1

value: SantaCruz, sc899X


title: ChIPseq_neurons_TKO_creb_input_r3

value: SantaCruz, sc377154X


title: ChIPseq_neurons_WT_pol2_1


title: ChIPseq_neurons_WT_hnf6_input_r1


title: ChIPseq_neurons_WT_creb_input_r3


title: ChIPseq_neurons_TKO_creb_r3


title: ChIPseq_neurons_TKO_creb_input_r2


title: ChIPseq_neurons_WT_hnf6_r1


title: ChIPseq_neurons_WT_creb_input_r2


title: ChIPseq_neurons_WT_creb_r1


title: ChIPseq_neurons_WT_creb_r3


title: ChIPseq_neurons_TKO_pol2_2

value: Abcam, ab8WG16


title: ChIPseq_neurons_TKO_pol2_input_2


title: ChIPseq_neurons_TKO_pol2_1


title: ChIPseq_neurons_TKO_creb_r2


title: ATACseq_Neurons_b2_TKO_CrebKO_3

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ATAC-seq reads were trimmed using cutadapt version 2.5, (Martin, M. EMBnet.journal 17, 10 (2011)) with parameters -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -m 5 --overlap=1 and then mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 and pairedAsSingle=TRUE . The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

extract_protocol: ATAC-seq was performed according to the previously described protocol for Omni-ATAC (Corces et al. 2017). Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen). The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 11-12 cycles of PCR.

treatment_protocol: For HA36 cells containing the pTRE-Ngn2 construct differentiation was carried out by inducing expression of NGN2 with doxycycline as previously described (Thoma et al., 2012) with modifications. In brief, ES cells were plated on poly-D-lysine/laminin coated plates and treated with DMEM/F12 with Glutamax (LifeTech, 31331-028) containing 1x B27 without VitaminA (LifeTech #12587-010), 1x N2 supplement (LifeTech #17502-048), 10 ng/ml hEGF (LifeTech, PHG0315), 10 ng/ml hFGF (LifeTech, CTP0261) and 1 μg/mL doxycycline (Sigma, D989) for three days with no media change. At day three after induction, medium was exchanged to Neurobasal-Medium (LifeTech, 21103-049) supplemented with 1x B27 with Vitamin A (LifeTech, 17504-044) , 1x N2 (LifeTech #17502-048) and 10ng/ml BDNF (PeproTech, 450-02), 10ng/ml GDNF (PeproTech, 450-10) and 10ng/ml NT-3 (PeproTech, 450-03). Every second day half of the media was replaced with fresh media.

value: Dnmt triple knock-out and Creb1 knock-out


title: ATACseq_Neurons_b2_WT_2


title: ATACseq_Neurons_b2_TKO_2


title: ChIPseq_neurons_TKO_creb_r1


title: ChIPseq_neurons_WT_pol2_input_2


title: ATACseq_Neurons_b2_TKO_CrebKO_1


title: ChIPseq_neurons_TKO_pol2_input_1


title: ChIPseq_neurons_WT_pol2_2


title: ChIPseq_neurons_WT_creb_r2


title: ATACseq_Neurons_b2_WT_3


title: ATACseq_Neurons_b1_QKO_MBD_cl2_1

value: MBD quadruple knock-out


title: ATACseq_Neurons_b1_QKO_MBD_cl2_2


title: ATACseq_Neurons_b2_WT_1


title: ATACseq_Neurons_b2_TKO_1


title: ATACseq_Neurons_b2_TKO_3


title: ATACseq_Neurons_b2_TKO_CrebKO_2


title: ATACseq_Neurons_b1_TKO_2


title: ATACseq_ESC_QKO_MBD_cl2_1

value: embryonic stem cells


title: ATACseq_Neurons_b1_WT_1


title: ATACseq_Neurons_b1_QKO_MBD_cl1_1


title: ATACseq_Neurons_b1_TKO_1


title: ATACseq_ESC_QKO_MBD_cl2_2


title: ATACseq_ESC_QKO_MBD_cl1_1


title: ATACseq_ESC_TKO_1


title: ATACseq_ESC_WT_2


title: M_Control_2

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

description:
Male flies - Control - replicate 2
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt

data_processing:
RNA-seq data analysis was performed using the PURR-CHURP pipeline by the University of Minnesota Informatics Institute (UMII) at the University of Minnesota (Baller et al., 2019).
A subsample of 10,000 reads or read pairs were sampled from each sample’s reads. This subsample of 10,000 reads was searched for contamination from ribosomal RNA using a representative rRNA sequence list from the SILVA database release 132. Trimmed reads were aligned to the reference Drosophila genome (version BDGP6.28) with HISAT2 (Kim et al., 2019).
Duplicate reads based on alignment position were marked with SAMTools. Processed alignments were filtered of reads that had a mapping quality of less than 60, and sorted by query name rather than position.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package (Liao et al., 2014).
Raw per-gene counts were imported into R, and differential gene expression analysis was carried out using the edgeR package (Robinson et al., 2010). Genes were filtered by expression from the counts matrix before differential expression testing using the filtByExp() function. Exact tests were performed, and genes with false discovery rate (FDR) < 0.05 and absolute values (log2(fold-changes)) > 1 were considered significant.
Genome_build: Drosophila genome (version BDGP6.28)
Supplementary_files_format_and_content: subread_counts_gene_symbol.txt : Matrix of raw expression counts for gene features (in gene symbol format) for all samples (quantified with featureCounts from subread package). Rows = genes, columns = samples
Supplementary_files_format_and_content: CPM_normalized_expression_allSamples.txt : Matrix of Count per Million (CPM) normalized expression of genes (gene symbol format). Rows = genes, columns = samples

organism: Drosophila melanogaster

source_name: whole flies

growth_protocol: Flies were reared at a standard density (~ 250-300 eggs per 200 mL bottle) using synchronized egges laid within 24 hours. Upon emerging, flies were transferred onto fresh SY10/10 medium and allowed 48 hours to mature and mate before sorted into single sexes under light CO2 anesthesia. Flies were transferred to fresh SY10/10 food three times a week, and kept at 25°C, 65% relative humidity in a 12 h light: 12 h dark cycle.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Cat#: 15596026) following manufacturer protocol. High quality of RNAs passed QC were subjected to RNA-seq analysis.
Unique dual-indexed (UDI) TruSeq stranded mRNA libraries were created and sequenced on NovaSeq 2x150-bp run with mean depth >= 20M reads, and mean quality scores are above Q30.

treatment_protocol: 20 adult flies per biological replicate x 3 replicates per condition were snap-frozen in liquid nitrogen before RNA extraction.

tag: developmental stage

value: adult

value: whole flies

value: control

tag: nutrient source

value: fed on SY10/10 food


title: M_Control_3

description:
Male flies - Control - replicate 3
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: ATACseq_ESC_TKO_2


title: ATACseq_ESC_WT_1


title: ATACseq_Neurons_b1_QKO_MBD_cl1_2


title: ATACseq_Neurons_b1_WT_2


title: M_Bmm_2

description:
Male flies - Bmm over-expression - replicate 2
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt

value: Bmm overexpression


title: M_Bmm_3

description:
Male flies - Bmm over-expression - replicate 3
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: F_Control_1

description:
Female flies - Control - replicate 1
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt

value: female


title: F_Control_3

description:
Female flies - Control - replicate 3
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: M_Bmm_1

description:
Male flies - Bmm over-expression - replicate 1
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: F_Control_2

description:
Female flies - Control - replicate 2
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: F_Bmm_3

description:
Female flies - Bmm over-expression - replicate 3
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: ATACseq_ESC_QKO_MBD_cl1_2

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: F_Bmm_1

description:
Female flies - Bmm over-expression - replicate 1
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt


title: M_Control_1

description:
Male flies - Control - replicate 1
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt

value: male


title: Leaf, artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 1

city: Guelph

first: Clarence

last: Swanton

state: Ontario

address: 50 Stone Road East

department: Plant Agriculture

country: Canada

institute: University of Guelph

data_processing:
RNA libraries were sequenced on an Illumina sequencer at the Genome Quebec Innovation Center (McGill University, Canada).
Differentially expressed gene (DEG) analysis was performed by Harvest Genomics Inc. (Guelph, Canada), where the quality control of raw .fastq.gz files was performed prior to sequence alignment to the reference genome. Seuqence alignment against the reference genome was performed using Bowtie2 v2.4.3.
Count data were retrieved using HTSeq (version 0.13.5). HTSeq counts have been filtered with counts per gene >10 among all treatments. DEGs were determined using DESeq2 (version 1.30.1). The Benjamini-Hochberg false discovery rate (FDR) correction was used within DESeq2 (version 1.30.1) to obtain adjusted p-values (padj).
Log2 fold change (lfc) tables were produced according to Zhu et al. (2018) https://doi.org/10.1093/bioinformatics/bty895. Log2 fold change tables were produced for each pairwise comparison: FR vs WF; W vs FR; W vs WF.
Assembly: reference genome (GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff and GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gtf) using Bowtie 2 v2.4.3
Supplementary files format and content: Normalized abundance measurements using DESeq, Log2 fold change (lfc) tables, TPM & FPKM values

organism: Zea mays

source_name: Maize seedlings, exposed to artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, (far-red 1; FR1)

growth_protocol: The University of Guelph maize hybrid (CG108 × CG102) plants were grown for 9 days in controlled environment growth chambers (Model CMP 3244 Conviron, Winnipeg, Canada) with a 16 h light/8 h dark photoperiod, a day/night temperature of 23°C/18°C, a relative humidity of 60%, and a red (R) to far-red (FR) ratio R:FR ≈ 1.5. Two systems consisting of a surrogate weed and far-red LEDs were used to generate biological and artificicial low R:FR light environments with a R:FR ≈ 0.6.

extract_protocol:
Total RNA was extracted from the second leaves of 9-day-old seedlings using TRIzol reagent and the contaminating DNA was removed using the RNase-Free DNase kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TrueSeq RNA kit following manufacturer's protocols.

treatment_protocol:
Maize seedlings were exposed to 3 red to far-red (R:FR) light ratios, while maintaining a consistent incoming PPFD (≈ 500-600 micromol m2 s-1) for the duration of experiments (9 days). A weed-free (WF) control with a R:FR ≈ 1.6, a biological low R:FR ≈ 0.6 (weedy; W), and an artificial low R:FR ≈ 0.6 (far-red; FR).
In total, 9 samples were analyzed. Samples consisted of 3 treatments. A weed-free control (WF), a biological (weedy) low R:FR (W), and an artificial low R:FR (FR) with 3 replicates. Each replicate consisted of a pool of second leaves from 3 individual plants (9-day-old).
[Detailed protocol]   All experiments were conducted in controlled environment growth chambers (Model CMP 6050 Conviron, Winnipeg, Canada). Growth conditions were 16 h light/8 h dark photoperiod, a day/night temperature of 23°C/18°C, and a relative humidity of 60%. Overhead radiation was supplied using a combination of white fluorescent tubes and 100 W incandescent bulbs (Sylvania, Washington, USA). Far-red light was supplied using a combination of 13W FR bulbs (Philips, Koninklijke, N.V.) and Ray44 Fluence Bars (Fluence, Texas, USA). Experimental design consisted of three treatments. A weed-free control treatment (WF) with high red to far-red ratio (R:FR ? 1.5), a biological low red to far-red (R:FR ? 0.6) treatment using a surrogate weed (W), and a simulated low red to far-red (R:FR ? 0.6) treatment (FR). The incoming light quantity (PPFD) was approximately 500-600 micromol m2 s-1 in all treatments. The reflected red to far-red ratios (R:FR) were approximately 1.5, 0.6, and 0.6 in the weed-free control, biological low R:FR, and simulated low R:FR treatments, respectively. Light quantity (PPFD) was measured using a LI-190 Quantum line sensor (LI-COR, Lincoln, USA). Light quality (R:FR) was measured using an R/FR sensor (Model SKR 100 with SKR 110 sensor, SKye instrument). Light quantity and quality were measured 5 cm above the soil level. Treatments were established by placing plastic tubes (8×18 cm, 1 L) into the center of plastic pots (16x15 cm, 3.36 L) (Airlite Plastics Company, Omaha, USA). Drainage holes were drilled into tubes and pots. The surrounding area outside the plastic tube was filled with a potting mix. The potting mix consisted of peat moss and perlite (sunshine #4 Aggergate Plus, Sungro Horticulture, Agawam MA). In the weed-free control and simulated low R:FR treatment, the potting mix surrounding the central tube remained intact. In the biological low R:FR treatment, the potting mix surrounding the central tube was seeded with a commercial mixture of perennial ryegrass (Lolium perenne L.), creeping red fescue (Festuca rubra L.), Kentucky bluegrass (Poa pratensis L.), and chewing fescue (Festuca rubra L.) (The Scotts Company LLC, Marysville, USA). A surrounding dense grass was established within approximately 2 months, which simulated a biological source of reflected FR light. Prior to planting maize seeds, the grass was cut to a 3 to 5 cm height and remained uncut for the duration of the experiment (9 days) to minimize potential volatile organic compounds that may interfere with maize development. Additionally, an upward airflow of 1.5 m3 min-1 within the growth chamber provided a homogenous mixture of air across the growth chamber. Experimental pots in the weed-free control and biological low R:FR treatments were separated using opaque corrugated plastic to minimize light interference between each treatment. Maize seeds (a University of Guelph hybrid CG108 × CG102) were planted in potting mix (Sungro, Massachusetts, USA) in plastic cups (8×10 cm; W × H/355 mL) (Dart Container Corp, Mason, USA), and placed inside the 1 L plastic tubes. This prevented direct resource competition between the maize roots and the surrounding grass. Maize seedlings were grown for 9 days to 4-leaf tip (i.e., Zadoks stage 4), and fertilized with 50 ml of full-strength Hoagland solution every other day. Treatments were randomized across the growth chamber between each replication. Total RNA was extracted by TRIzol reagent from the second leaf of 9-day-old maize seedlings. RNA cleanup and DNA removal were conducted using an RNeasy MinElute (Qiagen) and an RNase free DNase (Qiagen) kit according to the manufacturer's instructions. In total, 9 leaf RNA samples from 3 treatments with 3 replicates were analyzed. Each replicate consisted of a pool of second leaves from 3 individual 9-day-old seedlings.

value: 9-day-old maize seedlings

value: Second leaf of 9-day-old maize seedlings

value: A University of Guelph maize hybrid, CG108 x CG102

value: FR


title: XENLA_scCapSt27

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
We downloaded the genome of Xenopus laevis from XenBase (RRID: SCR_003280; also available at NCBI GenBank accession number GCA_001663975.1).
We used the annotation from the GitLab repository (https://gitlab.com/Xenbase/genomics/XENLA_9.2; 2018-May version) which is also maintained by the XenBase.
We mapped our raw sequencing data against this database using the CellRanger (version 2.1.1)  with the default option for 3’ Gene Expression v2 Libraries (‘SC3Pv2’).
Genome_build: xenLae2 (X. laevis genome 9.2)
Supplementary_files_format_and_content: cellranger_output

organism: Xenopus laevis

source_name: NF Stage 27 Animal Cap

growth_protocol: We maintained the animal cap explant under MMR buffer.

extract_protocol:
We followed the standard 10X Genomics 3'-seq protocol, and sequenced it with Illumina NextSeq 550.
10X single cell 3'-seq

treatment_protocol: No treatment (wild-type)

value: NF stage 27


title: Leaf, biological low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 3

source_name: Maize seedlings, exposed to biological (weedy) low red to far-red ratio (R:FR ≈ 0.6), 9 days, (weedy 3; W3)

value: W


title: XENLA_scCapSt24

source_name: NF Stage 24 Animal Cap

value: NF stage 24


title: Leaf, biological low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 2

source_name: Maize seedlings, exposed to biological (weedy) low red to far-red ratio (R:FR ≈ 0.6), 9 days, (weedy 2; W2)


title: Leaf, high red to far-red ratio (R:FR ≈ 1.5), 9 days, rep 2

source_name: Maize seedlings, grown weed-free, high red to far-red ratio (R:FR ≈ 1.5), 9 days, (weed-free 2; WF2)

value: WF


title: Leaf, high red to far-red ratio (R:FR ≈ 1.5), 9 days, rep 3

source_name: Maize seedlings, grown weed-free, high red to far-red ratio (R:FR ≈ 1.5), 9 days, (weed-free 3; WF3)


title: Leaf, artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 2

source_name: Maize seedlings, exposed artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, (far-red 2; FR2)


title: XENLA_scCapSt22

source_name: NF Stage 22 Animal Cap

value: NF stage 22


title: Leaf, biological low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 1

source_name: Maize seedlings, exposed to biological (weedy) low red to far-red ratio (R:FR ≈ 0.6), 9 days, (weedy 1; W1)


title: XENLA_scCapSt16

source_name: NF Stage 16 Animal Cap

value: NF stage 16


title: XENLA_scCapSt12

source_name: NF Stage 12 Animal Cap

value: NF stage 12


title: Leaf, artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, rep 3

source_name: Maize seedlings, exposed to artificial low red to far-red ratio (R:FR ≈ 0.6), 9 days, (far-red 3; FR3)


title: XENLA_scCapSt20

source_name: NF Stage 20 Animal Cap

value: NF stage 20


title: XENLA_scCapSt105

source_name: NF Stage 10.5 Animal Cap

value: NF stage 10.5


title: XENLA_scCapSt08

source_name: NF Stage 08 Animal Cap

value: NF stage 08


title: NGT PAL 30h i08

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) Reads were trimmed using Trim_Galore! (v0.4.3) on default settings
2) Trimmed reads were aligned using STAR (v2.5.3a) aligner with Ensembl human annotation (GRCh38, release 92)
3) Gene read coverages were counted using featureCounts from subread (v1.5.2) package
4) The lowly expressed genes were discarded from downstream analysis using filterByExpr function from edgeR package (v3.32.1) resulting 16,229 genes for downstream analysis
5) Batch effect caused by "individuals" are removed from CPM values by using removeBatchEffect function from limma (v3.46.0)
6) Batch effect removed logCPM values are used for rhythmicity and differential rhythmicity analysis by RAIN (v1.20.0) and DODR (v0.99.3), respectively
Assembly: hg38
Supplementary files format and content: Text file in tab separated format with gene coverages in units of read counts and logCPM (log counts per million) values (batch effect caused by individuals are removed)

organism: Homo sapiens

source_name: Primary myotubes from vastus lateralis

growth_protocol: Primary myoblasts from skeletal muscle biopsies from healthy men were grown in DMEM/F12+Glutamax with 16% FBS and 1% Antibiotic-Antimycotic (100X). Differentiation was induced at 80% confluence, by incubating the cells for 4-5 days in fusion medium consisting of 76% DMEM Glutamax with 25 mmol/l glucose, 20% M199 (5.5 mmol/l), 2% HEPES and 1% Antibiotic-Antimycotic (100X), with 0.03 μg/ml zinc sulfate and 1.4 mg/ml Vitamin B12, with a further addition of 100 μg/ml apo-transferrin and 0.286 IU/ml insulin prior to use. Experiments were performed on differentiated myotubes after an additional 3-5 days incubation in the same media containing 2% FBS (post fusion media).

extract_protocol:
Cells were lysed and RNA extracted using Trizol Reagent (Life Technologies; Cat #15596-018) and miRNAeasy kit (Qiagen; Cat #217004). RNA was checked for quality using the Agilent RNA 600 nano kit and Bioanalyser instrument (Agilent Technologies, Santa Clara, CA). Aliquots of RNA (1 µg) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina).
Ribosomal RNA was removed from the sample using 35 µl rRNA removal beads (Illumina) on a magnetic plate followed by clean-up of the ribosomal-depleted RNA with 193 µl Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash and elution into 10 µl Elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first strand cDNA synthesis with 1 µl Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min and 70°C for 15 min. Second strand cDNA was synthesized by addition of Second Strand Marking Master Mix and samples were incubated at 16°C for 60 min. Samples were subject to another bead clean up prior to A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead clean-up, samples were enriched for DNA fragments by amplification using the Illumina PCR Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a pre-defined cycle (98°C for 10 s, 60°C for 30 s and 72°C for 30 s) that was repeated 3-15 times, based on each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned, and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyser instrument.
Libraries were subjected to 100-bp paired-end sequencing on the X Ten platform (Illumina) at the Beijing Genomics Institute (BGI), Hong Kong, China. Approximately 18 million reads/sample were assigned to genes with 16,229 genes surviving the expression threshold.

treatment_protocol: After post fusion, DMEM with 5.5 mmol/l glucose was used in the post fusion medium to create a low glucose condition. After 22 hrs, cells were synchronized by serum shock (media containing 50% FBS, 2 hrs) and then switched back to low glucose media with or without 0.4 mM of BSA-conjugated palmitate. Skeletal muscle myotubes were lysed at 6-hr intervals from 12 hrs to 54 hrs.

tag: disease

value: NGT

value: PAL

tag: group

tag: time

tag: individual


title: NGT PAL 42h i08


title: NGT CTL 18h i08

value: CTL


title: NGT PAL 18h i08


title: NGT CTL 54h i08


title: NGT PAL 48h i08


title: XENLA_scCapSt18

source_name: NF Stage 18 Animal Cap

value: NF stage 18


title: Leaf, high red to far-red ratio (R:FR ≈ 1.5), 9 days, rep 1

source_name: Maize seedlings, grown weed-free, high red to far-red ratio (R:FR ≈ 1.5), 9 days, (weed-free 1; WF1)

value: 9-day-old maize seedlings

value: Second leaf of 9-day-old maize seedlings


title: XENLA_scCapSt13

source_name: NF Stage 13 Animal Cap

value: NF stage 13


title: NGT PAL 36h i08


title: NGT PAL 54h i08


title: NGT PAL 24h i08


title: NGT CTL 30h i08


title: NGT CTL 42h i08


title: NGT CTL 48h i08


title: NGT PAL 42h i09


title: NGT PAL 54h i09


title: NGT PAL 54h i12


title: NGT PAL 12h i08


title: NGT PAL 18h i12


title: NGT CTL 12h i08


title: NGT PAL 42h i12


title: NGT CTL 54h i12


title: NGT PAL 30h i12


title: NGT CTL 36h i08


title: NGT CTL 24h i08


title: NGT PAL 30h i09


title: NGT PAL 18h i09


title: NGT CTL 54h i09


title: NGT CTL 30h i09


title: NGT PAL 48h i09


title: NGT CTL 18h i09


title: NGT CTL 30h i12


title: NGT CTL 42h i12


title: NGT PAL 24h i09


title: NGT CTL 36h i09


title: NGT CTL 48h i09


title: NGT CTL 24h i09


title: NGT PAL 30h i10


title: NGT PAL 42h i10


title: NGT CTL 12h i09


title: NGT PAL 36h i09


title: NGT PAL 12h i12


title: NGT CTL 42h i10


title: NGT PAL 42h i04


title: NGT CTL 18h i10


title: NGT PAL 18h i10


title: NGT CTL 36h i12


title: NGT PAL 48h i12


title: NGT CTL 30h i10


title: NGT CTL 54h i10


title: NGT CTL 48h i12


title: F_Bmm_2

description:
Female flies - Bmm over-expression - replicate 2
subread_counts_gene_symbol.txt
CPM_normalized_expression_allSamples.txt

source_name: whole flies

value: adult

value: whole flies

value: Bmm overexpression

value: female

value: fed on SY10/10 food


title: NGT PAL 24h i12


title: NGT CTL 12h i12


title: NGT PAL 18h i04


title: NGT CTL 42h i04


title: NGT CTL 30h i04


title: NGT CTL 54h i04


title: NGT PAL 30h i04


title: NGT PAL 48h i04


title: NGT CTL 18h i04


title: NGT PAL 12h i04


title: NGT PAL 36h i12


title: NGT PAL 24h i04


title: NGT PAL 36h i04


title: NGT CTL 24h i12


title: NGT PAL 12h i10


title: NGT PAL 48h i10


title: NGT CTL 48h i04


title: NGT CTL 36h i04


title: NGT PAL 54h i01


title: NGT PAL 42h i01


title: NGT CTL 12h i10


title: NGT PAL 18h i01


title: NGT CTL 12h i04


title: NGT PAL 24h i10


title: NGT CTL 24h i10


title: NGT CTL 36h i10


title: NGT PAL 30h i01


title: NGT CTL 48h i10


title: NGT PAL 36h i01


title: NGT CTL 24h i04


title: NGT PAL 12h i01


title: NGT CTL 54h i01


title: NGT PAL 36h i10


title: NGT CTL 18h i01


title: NGT CTL 48h i01


title: NGT PAL 24h i01


title: NGT CTL 36h i01


title: NGT CTL 30h i01


title: NGT PAL 30h i11


title: NGT CTL 12h i01


title: NGT PAL 54h i11


title: NGT PAL 48h i01


title: NGT PAL 18h i11


title: NGT CTL 30h i11


title: NGT PAL 42h i11


title: NGT PAL 24h i11


title: NGT PAL 36h i11


title: NGT CTL 54h i11


title: NGT CTL 18h i11


title: NGT CTL 42h i11


title: NGT CTL 24h i11


title: NGT CTL 48h i11


title: NGT CTL 36h i11


title: NGT CTL 12h i11


title: RAB5A overexpression Replicate 3 SAMMY-seq fraction S4

city: Milan

first: Giorgio

last: Scita

state: Mi

address: via Adamello, 16

country: Italy

institute: IFOM, The AIRC Institute of Molecular Oncology

description: Chromatin fraction S4 as per the original SAMMY-seq protocol (Sebestyén et al, Nature Communication 2020)

data_processing:
Library strategy: SAMMY-seq
Alignment: Sequencing reads were trimmed and adapters removed by using Trimmomatic (v0.39) using the following parameters for SAMMY-seq: 2 for seed_mismatch, 30 for palindrome_threshold, 10 for simple_threshold, 3 for leading, 3 for trailing and 4:15 for sliding window and sequence minimum length threshold of 35. As clip file has been used the trimmomatic provided dataset “TruSeq3-SE.fa” (for single end). All reads were cropped to 75 bp reads length (if longer) by setting the crop option of Trimmomatic (v0.39) to 75. After trimming, the reads were aligned using BWA (v0.7.17-r1188) etting –k parameter as 2 and using as reference genome the UCSC hg38 one (only canonical chromosomes have been taken into consideration). The alignment duplicates have been marked with Picard (v2.22) (http://broadinstitute.github.io/picard/) MarkDuplicates option. And then filtered using Samtools (v1.9), in addition we filtered all the reads with mapping quality lower than 1, unmapped and read fails platform/vendor quality checks (-F 1540 -q 1).     Each sequencing lane has been analysed separately up to this point and then merged.
Genomic tracks: The comparison between sequencing reads enrichment in ChIP-seq was performed using the SPP (v1.16.0)  R (v3.5.2) library. The reads have been imported from the (previously filtered) bam files using the “read.bam.tags” function, then they were filtered using “remove.local.tag.anomalies” and finally the normalized log2 reads density ratio was computed using the function “get.smoothed.enrichment.mle” setting “tag.shift = 0” and “background.density.scaling = TRUE” to exclude enriched regions from the calculation of normalization scaling factor.
Genome_build: UCSC hg38 one (only canonical chromosomes have been taken into consideration)
Supplementary_files_format_and_content: BigWig (.bw) files contains genomic tracks information.
Supplementary_files_format_and_content: Bed (.bed) files contains peak information (ChIP over INPUT enriched regions)

growth_protocol: MCF10.DCIS.com cells were provided by J. F. Marshall (Barts Cancer Institute, Queen Mary University of London, UK) and maintained in DMEM/F12 (Biowest) supplemented with 5% horse serum (Life Technologies), 2 mM L-Glutamine (EuroClone), 0.5 mg/ml Hydrocortisone (Sigma-Aldrich), 10 μg/ml Human insulin (Sigma-Aldrich) and 20 ng/ml EGF (Peprotech).

extract_protocol:
Three distinct biological replicas of control and RAB5A expressing MCF10.DCIS.com monolayers were processed for chromatin fractionation. 3 million cells were washed in PBS 1X, and extracted in 600 ml of cytoskeleton buffer (CSK: 10 mM PIPES pH 6,8; 100 mM NaCl; 1 mM EGTA; 300 mM Sucrose; 3 mM MgCl2; 1X protease Inhibitors by Roche Diagnostics; 1 mM PMSF) supplemented with 1 mM DTT and 0,5% Triton X-100. After 10 min on wheel at 4°C the cytoskeletal structure was separated from soluble proteins by centrifugation at 900g for 3’ at 4°C, and the supernatant was labeled as S1 fraction. The pellets were resuspended with 600 ml of cytoskeleton buffer, put 10 min on wheel at 4°C followed by centrifugation at 900g for 3’ at 4°C. Chromatin was solubilized by DNA digestion with 25U of RNase–free DNase (Turbo DNAse; Invitrogen AM2238) in 100 ml of CSK buffer for 60 min at 37°C. To stop digestion, ammonium sulphate was added in CSK buffer to a final concentration of 250 mM and, after 5’ in ice samples were pelleted at 900g for 3 min at 4°C and the supernatant was labeled as S2 fraction. The pellets were resuspended with 200 ml of CSK buffer, put 10 min on wheel at 4°C followed by centrifugation at 3000g for 3 min at 4°C. The pellet was further extracted with 100 l of CSK buffer with 2M NaCl for 5 min at 4°C, centrifuged at 2300g 3 min at 4°C and the supernatant was labeled as S3 fraction. This treatment removed the majority of histones from chromatin. The pellets were washed twice with 200 ml of CSK buffer with 2M NaCl, put 10 min on wheel at 4°C followed by centrifugation at 3000g for 3 min at 4°C., The pellets were solubilized in 100 ml of 8M urea buffer for 10 min at room temperature to remove any remaining protein component by applying highly denaturing conditions. This fraction was labeled as S4. DNA was extracted from S2, S3 and S4 fractions. All fractions were quantified and analyzed by SDS-PAGE and immunoblotting. Anti-tubulin alpha (Sigma T5168, mouse 1:10000), H3 (Abcam ab1791, rabbit 1:4000), Beta-Actin (Santa-Cruz sc1616, rabbit 1:4000), were used as primary antibodies. HRP-conjugated secondary antibodies were revealed with the ECL chemiluminescence kit (Thermo Fisher Scientific).    After incubation 90 min at 37°C with 6 l of RNAse cocktail (Invitrogen AM2286) followed by 150 min at 55°C with 40 mg of Proteinase K (Invitrogen, AM2548), DNA was extracted by standard phenol/chloroform extraction, precipitated and resuspended in 15μl milliQ H2O. The S2 fraction was further purified with PCR DNA Purification Kit (Qiagen, 28106). After Qubit HS DNA quantification then samples were evaluated by capillary electrophoresis (Agilent 2100 Bioanalyzer) and then sonicated with a Covaris M220 Focused-ultrasonicator using screw cap microTUBEs with the parameters: water bath 20°C, peak power 30.0, duty factor 20.0, cycle/burst 50, duration: 125 seconds for S2 and S3 fractions, 150 seconds for S4 fraction. The DNA profiles were checked again by capillary electrophoresis (Agilent 2100 Bioanalyzer).
For fractions S2, S3 and S4 obtained from chromatin fractionation procedure, at least 2.5 ng DNA were used to generate an indexed library (Kapa HyperPrep kit; Roche KK8504, KK8727). Indexed DNA libraries were purified (AmpureXP, Beckman, A63881), quantitated (Qubit dsDNA HS Assay, Q32851), checked for size distribution on Agilent Bioanalyzer 2100 (DNA HS kit, Agilent, 5067-4626) and normalized for pooling. 1% PhiX control was added to the sequencing pool, to serve as a positive run control. Sequencing was performed in SR mode (1x75nt) on an Illumina NextSeq550 platform, generating at least 30 million SR reads per sample.

treatment_protocol: MCF10.DCIS.com were infected with pSLIK-hygro-RAB5B, pSLIK-neo-RAB5C, pSLIK-neo-EV (empty vector, CTR) or pSLIK-neo-RAB5A lentiviruses and selected with the appropriate antibiotic to obtain stable inducible cell lines. Constitutive expression of mCherry H2B was achieved by retroviruses infection of MCF10DCIS.com cells with pBABE-puro-mCherry-H2B vector. pLL5.0 E-Cadherin shRNA/mEcad-GFP vector was a gift from Alpha S. Yap (Division of Molecular Cell Biology, Institute for Molecular Bioscience, The University of Queensland, Australia). pTRIP-CMV-GFP-FLAG-cGAS GFP vector was from Addgene (plasmid# 86675). pTRIP-SFFV-EGFP-NLS vector was from Addgene (plasmid# 86677).     Transfections were performed using either calcium phosphate or FuGENE HD Transfection Reagent (Promega, Cat# E2311), according to the manufacturer’s instructions.

value: RAB5A overexpression

tag: fraction

value: Chromatin fraction S4


title: RAB5A overexpression Replicate 3 SAMMY-seq fraction S2

description: Chromatin fraction S2 as per the original SAMMY-seq protocol (Sebestyén et al, Nature Communication 2020)

value: Chromatin fraction S2


title: NGT PAL 48h i11


title: RAB5A overexpression Replicate 2 SAMMY-seq fraction S3

description: Chromatin fraction S3 as per the original SAMMY-seq protocol (Sebestyén et al, Nature Communication 2020)

value: Chromatin fraction S3


title: RAB5A overexpression Replicate 2 SAMMY-seq fraction S4


title: RAB5A overexpression Replicate 2 SAMMY-seq fraction S2


title: RAB5A overexpression Replicate 1 SAMMY-seq fraction S3


title: RAB5A overexpression Replicate 1 SAMMY-seq fraction S2


title: RAB5A overexpression Replicate 3 SAMMY-seq fraction S3


title: RAB5A overexpression Replicate 1 SAMMY-seq fraction S4


title: MCF10A RAB5A 3

data_processing:
Reads were aligned to the GRCh38/hg38 assembly human reference genome using the STAR aligner (Dobin et al. 2013) with default settings with the parameter --quantMode GeneCounts in order to obtain gene counts.
Genome_build: GRCh38/hg38 assembly
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest (genes)

source_name: MCF10A RAB5A

growth_protocol: MCF10.DCIS.com cells were maintained in DMEM/F12 (Biowest) supplemented with 5% horse serum (Life Technologies), 2 mM L-Glutamine (EuroClone), 0.5 mg/ml Hydrocortisone (Sigma-Aldrich), 10 μg/ml Human insulin (Sigma-Aldrich) and 20 ng/ml EGF (Peprotech).   MCF10A cells were maintained in DMEM/F12 (Biowest) supplemented with 5% horse serum (Life Technologies), 2 mM L-Glutamine (EuroClone), 0.5 mg/ml Hydrocortisone (Sigma-Aldrich), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 μg/ml Human insulin (Sigma-Aldrich) and 20 ng/ml EGF (Peprotech).

extract_protocol:
Monolayers were processed for RNA extraction using RNeasy Plus Mini Kit (Qiagen), according to manufacturer’s instructions.
Library preparation was performed starting from 500 ng of total mRNA (Illumina, TruSeq Stranded mRNA, 20020594) according to the manufacturer’s instructions. Indexed libraries were quality controlled on Agilent Bioanalyzer 2100 (High Sensitivity DNA kit), quantified (Qubit dsDNA HS Assay, Q32851), normalized and pooled to perform a multiplexed sequencing run.

treatment_protocol: Cells were infected with pSLIK-neo-EV (empty vector, CTR) or pSLIK-neo-RAB5A lentiviruses and selected with the appropriate antibiotic to obtain stable inducible cell lines.

tag: cell type

value: MCF10A cells


title: Control Replicate 3 SAMMY-seq fraction S3

value: Control


title: MCF10A RAB5A 2


title: Control Replicate 1 SAMMY-seq fraction S3


title: Control Replicate 1 SAMMY-seq fraction S4


title: Control Replicate 2 SAMMY-seq fraction S2


title: Control Replicate 1 SAMMY-seq fraction S2


title: Control Replicate 2 SAMMY-seq fraction S3


title: Control Replicate 2 SAMMY-seq fraction S4


title: MCF10A CTR 1

source_name: MCF10A CTR

value: pSLIK-neo empty vector, CTR


title: Control Replicate 3 SAMMY-seq fraction S2


title: MCF10A CTR 2


title: MCF10.DCIS.com CTR 3

source_name: MCF10.DCIS.com CTR

value: MCF10.DCIS.com cells


title: MCF10.DCIS.com RAB5A 2

source_name: MCF10.DCIS.com RAB5A


title: Control Replicate 3 SAMMY-seq fraction S4


title: MCF10.DCIS.com RAB5A 1


title: MCF10A RAB5A 1


title: MCF10.DCIS.com RAB5A 3


title: MCF10A CTR 3


title: MCF10.DCIS.com CTR 1


title: RAB5A_INPUT: RAB5A overexpression INPUT ChIP-seq

data_processing:
Alignment: Sequencing reads were trimmed and adapters removed by using Trimmomatic (v0.39) using the following parameters: 2 for seed_mismatch, 30 for palindrome_threshold, 10 for simple_threshold, 3 for leading, 3 for trailing and 4:15 for sliding window and sequence minimum length threshold of 35. As clip file has been used the trimmomatic provided dataset “TruSeq3-SE.fa” (for single end). After trimming, the reads were aligned using BWA (v0.7.17-r1188) setting –k parameter as 2 and using as reference genome the UCSC hg38 one (only canonical chromosomes have been taken into consideration). The alignment duplicates have been marked with Picard (v2.22) (http://broadinstitute.github.io/picard/) MarkDuplicates option. And then filtered using Samtools (v1.9), in addition we filtered all the reads with mapping quality lower than 1, unmapped and read fails platform/vendor quality checks (-F 1540 -q 1).     Each sequencing lane has been analysed separately up to this point and then merged.
Genomic tracks: The comparison between sequencing reads enrichment in ChIP-seq (ChIP over input control reads enrichment) was performed using the SPP (v1.16.0)  R (v3.5.2) library. The reads have been imported from the (previously filtered) bam files using the “read.bam.tags” function, then they were filtered using “remove.local.tag.anomalies” and finally the normalized log2 reads density ratio was computed using the function “get.smoothed.enrichment.mle” setting “tag.shift = 0” and “background.density.scaling = TRUE” to exclude enriched regions from the calculation of normalization scaling factor.
Peaks: Peaks were defined using the EDD (v1.1.19)  software with parameters (binsize = 200 Kb and gap penalty = 25) processing the filtered bam files obtained as described above. The “required_fraction_of_informative_bins” parameter was set to 0.98. The unalignable regions were defined with the ENCODE Unified GRCh38 Exclusion List (previously "blacklist") and downloaded from (https://www.encodeproject.org/files/ENCFF356LFX/).
Genome_build: UCSC hg38 one (only canonical chromosomes have been taken into consideration).
Supplementary_files_format_and_content: BigWig (.bw) files contains genomic tracks information (ChIP over INPUT).
Supplementary_files_format_and_content: Bed (.bed) files contains peak information (ChIP over INPUT enriched regions)

extract_protocol:
Control or RAB5A-expressing MCF10 DCIS.com monolayers were treated with Formaldheyde (F8775 SIGMA) in a PBS-solution (final 1%) for 10 min while rocking at room temperature and quenched with 0.125 M Glycine for 5 min. Cells were washed twice with cold PBS and scraped off the plates. PBS-washed cells were transferred to 15 ml tubes and spun down at 400g at 4C. The pellet was lysed with 1X sonication lysis buffer (10 mM Tris pH 8.0, 0.25% SDS, 2 mM EDTA, plus protease inhibitors) and incubated for at least 10 min at 4°C. Lysed chromatin was sheared at the average size of 300 bp fragments using Covaris® E220 evolution ultrasonicator (settings: duty factor 20%, peak incidence power 75 Watt, cycles per burst 200, 5 minutes). Sonicated chromatin (3 mg) was incubated overnight at 4°C with 3 mg of the following histone mark antibodies: H3K9me3 ab176916, H3K9me3 ab8898. Immunocomplexes were recovered with 20 μl of pre-blocked Protein G-Dynabeads (Thermo Fisher) for 2 h, at 4°C, and washed twice with RIPA-low salt, twice with RIPA-high salt, twice with RIPA-LiCl and once with 10 mM Tris pH 8.0 and once with 1X TE, as previously reported90. The washed immunocomplexes were incubated with ChIP elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 300 mM NaCl, 0.4% SDS) supplemented with 0.8 mg/ml Proteinase K for 1 h at 55°C and overnight at 65°C, for reverse crosslinking. The immunoprecipitated DNA was then purified by Qiagen MinElute kit (Qiagen) and eluted in 22 μl EB buffer.
ChIP-seq libraries were constructed with TruSeq ChIP Library Preparation Kit (Illumina), according to the manufacturer’s instructions. 2 ng of DNA having fragment size 350-400bp were used to syntfhesize libraries for Chromatin Immunoprecipitation profiles (Kapa HyperPrep kit; Roche KK8504, KK8727). Indexed DNA libraries were size-selected and purified (AmpureXP, Beckman, A63881), quantitated (Qubit dsDNA HS Assay, Q32851), checked for size distribution on Agilent Bioanalyzer 2100 (DNA HS kit, Agilent, 5067-4626) and normalized for pooling. 1% PhiX control was added to the sequencing pool, to serve as a positive run control.

tag: antibody


title: RAB5A_H3K9me3_2: RAB5A overexpression H3K9me3 ChIP-seq (ab8898-Abcam)


title: CTR_INPUT: Control INPUT ChIP-seq


title: CTR_H3K9me3_1: Control H3K9me3 ChIP-seq (ab176916-Abcam)


title: RAB5A_H3K9me3_1: RAB5A overexpression H3K9me3 ChIP-seq (ab176916-Abcam)


title: CTR_H3K9me3_2: Control H3K9me3 ChIP-seq (ab8898-Abcam)


title: MCF10.DCIS.com CTR 2


title: Primary myotube_PA48h_i4

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

data_processing:
Samples quality was assessed using FASTQC software and quality trimmed with trimmomatic (v0.32)
Reads were mapped to H. sapiens reference genome using Bowtie2 (v2.3.2-foss-2016b)
Duplicate removal was performed using samtools (v1.5-foss-2016b)
BAM files were subjected to peak count using MACS2 software (v2.1.0)
Called peaks were quantified with featureCounts (v1.6.3)
Assembly: GRCh38
Supplementary files format and content: Raw counts for peaks for the palmitate and BSA vehicle

source_name: Primary myotube

growth_protocol: Primary myoblasts were grown in DMEM/F12+Glutamax with 16% FBS and 1% Antibiotic-Antimycotic. At 80% confluence, myoblasts were differentiated into myotubes by culturing in fusion medium consisting of 76% DMEM Glutamax with 25 mM glucose, 20% M199 (5.5 mM), 2% HEPES, and 1% Antibiotic-Antimycotic (100X), with 0.03 μg/mL zinc sulfate and 1.4 mg/mL Vitamin B12. Apo-transferrin (100 μg/mL) and insulin (0.286 IU/mL) was added to the fusion medium. After 4-5 days, the medium was switched to the same medium without apo-transferrin or insulin, with 2% FBS (post-fusion media) and the cultures were continued for 3-5 days.

extract_protocol:
Myotubes were cross-linked in 1% formaldehyde and lyzed in SDS buffer. Nuclei were pelleted by centriguation and sonicated to an average length of 200-500 bp. 2-10 μg DNA was combined with 2.5 μg antibody for H3K27ac (Ab4729) and immunoprecipitated with Protein G Sepharose beads. Chromatin was de-cross-linked in 1% SDS and 0.1 M NaHCO3 and DNA was purified using Qiagen MinElute PCR purification kit.
3-10 ng of immunoprecipitated DNA was used to generate adapter-ligated DNA libraries using the NEBNext® Ultra DNA library kit for Illumina (New England Biolabs, E7370L) and indexed multiplex primers for Illumina sequencing (New England Biolabs, E7335)

treatment_protocol: Fatty acid stock solution (200 mM) were prepared in 50% ethanol and then diluted 25 times in a 10.5% BSA solution. BSA in serum-free essential alpha medium (αMEM) was used as a carrier and control. Myotubes were incubated in 5.5 mM glucose media for 22h prior to the experiments. Myotubes were synchronized by serum shock (50% FBS, 2h), washed with PBS, and incubated in 5.5 mM glucose medium containing fatty acids (0.4 mM) or BSA (vehicle). Cultures were collected every 8h starting from 24h after synchronization.

value: Human primary skeletal myotubes

value: PA

tag: subjectid


title: Primary myotube_PA40h_i4


title: Primary myotube_PA48h_i3


title: Primary myotube_PA40h_i3


title: Primary myotube_PA32h_i4


title: Primary myotube_PA40h_i1


title: Primary myotube_PA32h_i3


title: Primary myotube_PA32h_i1


title: Primary myotube_PA32h_i2


title: Primary myotube_PA24h_i4


title: Primary myotube_PA40h_i2


title: Primary myotube_PA48h_i2


title: SU SSC uninjured

city: PALO ALTO

first: yuting

last: wang

state: California

address: 265 campus drive, lokey stem cell research building, RM-G3105-SIM1

institute: Stanford University

description: FACs sorted SSC from sham female

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: FACs sorted SSC from sham female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: sham

tag: gender


title: SIB sham callus BCSP

description: FACs sorted BCSP from sham female callus

tag: treatment

value: sham+fracture


title: SS sham callus SSC

description: FACs sorted SSC from female sham callus

source_name: FACs sorted SSC from female sham callus


title: SUS sham Uninjured SSC

description: FACs sorted SSC from sham female


title: ES E2 callus SSC

description: FACs sorted SSC from female E2 rescued callus


title: EB E2 callus BCSP

description: FACs sorted BCSP from female E2 rescued callus


title: OB OVX callus BCSP

description: FACs sorted BCSP from female OVX callus

source_name: FACs sorted BCSP from female OVX callus

value: OVX+fracture


title: OIB OVX callus BCSP

description: FACs sorted BCSP from female OVX callus


title: OUS OVX SSC

description: FACs sorted SSC from OVX female mice

source_name: FACs sorted SSC from OVX female mice

value: OVX


title: Primary myotube_PA24h_i1


title: OIS OVX callus SSC

description: FACs sorted SSC from female OVX callus

source_name: FACs sorted SSC from female OVX callus


title: Primary myotube_BSA48h_i2

value: BSA


title: Primary myotube_BSA32h_i4


title: Primary myotube_BSA48h_i3


title: Primary myotube_BSA48h_i4


title: Primary myotube_BSA40h_i3


title: Primary myotube_PA24h_i2


title: NGT CTL 42h i01

value: NGT

value: CTL


title: Primary myotube_BSA40h_i2


title: Primary myotube_PA24h_i3


title: OS OVX callus SSC

description: FACs sorted SSC from female OVX callus

value: female


title: Primary myotube_BSA48h_i1


title: SIS sham callus SSC

description: FACs sorted SSC from sham female callus

source_name: FACs sorted SSC from sham female callus


title: BU BCSP Uninjured

description: FACs sorted BCSP from sham female mice

source_name: FACs sorted BCSP from sham female mice


title: SI SSC injured

description: FACs sorted SSC from  female callus

source_name: FACs sorted SSC from  female callus

value: fracture


title: SB sham callus BCSP

description: FACs sorted BCSP from female sham callus


title: BI BCSP Injured

description: FACs sorted BCSP from  female callus

source_name: FACs sorted BCSP from  female callus


title: OUB OVX BCSP

description: FACs sorted BCSP from OVX female mice

source_name: FACs sorted BCSP from OVX female mice


title: Primary myotube_BSA40h_i1


title: Primary myotube_BSA32h_i3


title: Primary myotube_BSA40h_i4


title: Primary myotube_BSA32h_i1


title: Primary myotube_BSA32h_i2


title: Primary myotube_BSA24h_i4


title: Primary myotube_BSA24h_i1


title: Primary myotube_BSA24h_i3


title: Primary myotube_BSA24h_i2


title: MR354_CD14

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

institute: Gothenburg University

description:
MR354
mapped to HG38

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Assembly: HG38
Supplementary files format and content: matrix with ENS number and samples in each one column

source_name: Primary activated CD14 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD14 cells,

extract_protocol: Total RNA purification (Norgen, Ontario, Canada)

treatment_protocol: culture activated with LPS, 2h total

tag: agent

value: LPS, 5ug/ml

value: Rheumatoid arthritis

tag: Sex


title: MR353_CD14

description:
MR353
mapped to HG38


title: MR351_CD14

description:
MR351
mapped to HG38


title: MR349_CD14

description:
MR349
mapped to HG38


title: MR347_CD14

description:
MR347
mapped to HG38


title: MR343_CD14

description:
MR343
mapped to HG38


title: MR344_CD14

description:
MR344
mapped to HG38


title: MR342_CD14

description:
MR342
mapped to HG38


title: MR345_CD14

description:
MR345
mapped to HG38


title: MR340_CD14

description:
MR340
mapped to HG38


title: MR336_CD14

description:
MR336
mapped to HG38


title: MR341_CD14

description:
MR341
mapped to HG38


title: MR332_CD14

description:
MR332
mapped to HG38


title: MR338_CD14

description:
MR338
mapped to HG38


title: MR333_CD14

description:
MR333
mapped to HG38


title: MR335_CD14

description:
MR335
mapped to HG38


title: MR334_CD14

description:
MR334
mapped to HG38


title: MR339_CD14

description:
MR339
mapped to HG38


title: MR337_CD14

description:
MR337
mapped to HG38


title: MR350_CD14

description:
MR350
mapped to HG38


title: MR328_CD14

description:
MR328
mapped to HG38


title: MR329_CD14

description:
MR329
mapped to HG38


title: MR327_CD14

description:
MR327
mapped to HG38


title: MR331_CD14

description:
MR331
mapped to HG38


title: MR326_CD14

description:
MR326
mapped to HG38


title: MR330_CD14

description:
MR330
mapped to HG38


title: MR352_CD14

description:
MR352
mapped to HG38


title: MR321_CD14

description:
MR321
mapped to HG38


title: MR325_CD14

description:
MR325
mapped to HG38


title: MR322_CD14

description:
MR322
mapped to HG38


title: MR319_CD14

description:
MR319
mapped to HG38


title: MR320_CD14

description:
MR320
mapped to HG38


title: MR313_CD14

description:
MR313
mapped to HG38


title: MR318_CD14

description:
MR318
mapped to HG38


title: MR308_CD14

description:
MR308
mapped to HG38


title: MR314_CD14

description:
MR314
mapped to HG38


title: MR304_CD14

description:
MR304
mapped to HG38


title: MR305_CD14

description:
MR305
mapped to HG38


title: MR311_CD14

description:
MR311
mapped to HG38


title: MR317_CD14

description:
MR317
mapped to HG38


title: MR316_CD14

description:
MR316
mapped to HG38


title: MR312_CD14

description:
MR312
mapped to HG38


title: MR307_CD14

description:
MR307
mapped to HG38


title: MR306_CD14

description:
MR306
mapped to HG38


title: MR310_CD14

description:
MR310
mapped to HG38


title: MR348_CD14

description:
MR348
mapped to HG38


title: MR303_CD14

description:
MR303
mapped to HG38


title: MR324_CD14

description:
MR324
mapped to HG38


title: MR302_CD14

description:
MR302
mapped to HG38


title: MR295_CD14

description:
MR295
mapped to HG38


title: MR301_CD14

description:
MR301
mapped to HG38


title: MR323_CD14

description:
MR323
mapped to HG38


title: MR298_CD14

description:
MR298
mapped to HG38


title: MR297_CD14

description:
MR297
mapped to HG38


title: MR299_CD14

description:
MR299
mapped to HG38


title: MR300_CD14

description:
MR300
mapped to HG38


title: MR296_CD14

description:
MR296
mapped to HG38


title: MR315_CD14

description:
MR315
mapped to HG38


title: MR309_CD14

description:
MR309
mapped to HG38


title: P18

city: Amsterdam

first: Niels

last: Verstegen

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

library_source: transcriptomic single cell

data_processing: The quality of the retrieved sequencing data was assessed using FastQC (Andrews, 2010). Reads were pseudo-aligned to the human transcriptome (gencode version v27) using kallisto (Bray et al., 2016). Quantification of gene expression was obtained by gene-level summarization of transcripts abundance using the R package tximport (Soneson et al., 2015), without any scaling (countsFromAbundance option set to “no”). Counts were then normalized using the Transcript per Million (TPM) method (Li et al., 2010) with the following approach: a) gene length scaling, b) removal of all immunoglobulins genes and pseudogenes, and c) sequencing depth scaling (Figure1—figure supplement 1a). Removal of immunoglobulin genes at this stage prevented the artificial skewing of other genes expressed in the antibody-secreting cell clusters, due to the high content of immunoglobulins RNA present in this cell type. The scaled TPM matrix was used for downstream analysis.

source_name: differentiated human B cells starting from naive, scRNAseq

extract_protocol:
CD40L-expressing 3T3 cells were harvested, irradiated with 30 Gy, and 1 × 104 CD40L-expressing 3T3 cells were seeded in B cell medium (RPMI 1640 (Gibco) without phenol red containing 5% FCS, 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine, 50 μM β-mercaptoethanol and 20 μg/ml human apotransferrin (Sigma Aldrich; depleted for human IgG with protein G sepharose)) in 96-well flat-bottom plates (NUNC) to allow adherence overnight. The next day, 2.5 × 104 human naive (CD19+CD27-IgG-IgD+) B cells were sorted on a FACS Aria and activated using the irradiated CD40L-expressing 3T3 cells in the presence of IL-4 (100 ng/ml; Cellgenix) for six days.  After six days, activated B cells were collected and co-cultured with 1 × 104 CD40L-expressing 3T3 cells or 1 × 104 WT together with CD40L-expressing 3T3 cells (ratio 9:1) that were irradiated and seeded one day in advance (as described above), together with IL-4 (100 ng/ml) and IL-21 (50 ng/ml; Invitrogen) for five days.
Sorted cells were processed using the Smart-seq2 protocol (Picelli et al., 2014) adjusted for 384-well plates. In short, 384-well plates containing single cells were thawed and cells were lysed and mRNA denatured by incubating the plates at 95°C for 3 minutes and put back on ice. Subsequently, 2.7 μl of first-strand cDNA reagent mix, containing 1x First-strand buffer, 5 mM DTT, 1 M betaine, 14 mM MgCl2, 5 U RNase inhibitor, 25 U Superscript II Reverse Transcriptase, and 1 μM Template-Switching oligonucleotides in nuclease-free water, was added to each well. Plates were incubated at 42°C for 90 minutes, 70°C for 15 minutes, and kept on hold at 4°C. Afterward, 7.5 μl of the pre-amplification mix, consisting of 1x KAPA HiFi HotStart Readymix and 0.12 μM ISPCR primers in nuclease-free water, was added to each well. Plates were then incubated as followed: 98°C for 3 minutes, 23 cycles of 98°C for 20 seconds; 67°C for 15 seconds; and 72°C for 6 minutes, then at 72°C for 5 minutes and kept on hold at 4°C. Purification of the resulting cDNA was performed using SeraMag SpeedBeads containing 19% w/v PEG 8,000 and a 1:0.8 ratio of cDNA/beads was used for cDNA precipitation. Purified cDNA was eluted in 14 μl of nuclease-free water. The quality of cDNA was randomly checked in 5% of the wells using the Tapestation High-Sensitivity D5000 assay. For the tagmentation reaction, 0.5 μl of 50-150 pg cDNA was mixed with a 1.5 μl Tagmentation mix containing 1x Tagment DNA buffer and Amplicon Tagment mix (Nextera XT DNA sample preparation kit). Plates were incubated at 55°C for 8 minutes and kept on hold at 4°C. 0.5 μl Neutralize Tagment buffer was added and incubated at room temperature for 5 minutes to inactivate Tn5. PCR amplification of adapter-ligated cDNA fragments was performed in a final volume of 5 μl containing the two index primers (Nextera XT Index kit) in a 1:5 dilution and Nextera PCR master mix. Plates were then incubated as followed: 72°C for 3 minutes, 95°C for 30 seconds, then 14-15 cycles of 95°C for 10 seconds; 55°C for 30 seconds; and 72°C for 30 seconds, then 72°C for 5 minutes and kept on hold at 4°C. 384 wells (the entire plate, including negative controls) were pooled in a single 2 ml tube (Eppendorf). Purification of cDNA was performed by adding 400 μl of cDNA in a 1:1 ratio with SeraMag SpeedBeads in 19% w/v PEG 8,000 in a 1.5 ml LoBind tube. Beads were washed with 1 ml of 80% ethanol. Purified cDNA was eluted in 200 μl of nuclease-free water. The concentration of the library was measured by Qubit according to the manufacturer’s instructions. The size distribution of the library was measured using the Tapestation High-Sensitivity D1000 or D5000 assay. The cDNA library pool was stored at -20°C until ready for sequencing.   cDNA library pool was diluted to 2 nM and prepared for sequencing using the NextSeq 500 High Output Kit v2 (75 cycles) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 500 instrument.

value: Cultured naive B cells

tag: tissue

value: Peripheral blood

tag: condition

value: CD40L and IL-4/IL-21 stimulated

tag: time point

value: 11 days cultured


title: P24


title: P21


title: P3


title: P8


title: P9


title: P7


title: P22


title: P23


title: P6


title: P5


title: P4


title: P2


title: P19


title: P17


title: P20


title: P15


title: P16


title: Untreated macrophages, biological rep1

city: Frederick

first: Jun

last: Yang

state: MD

address: P. O. Box B

institute: Leidos Biomedical

description: Gene expression data from untreated macrophages, donor 1

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip huamn GeneArray 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using Affymetrix GeneArray scanner 3000

data_processing: The data were analyzed with Partek Genomic suite. RMA as normalized method

source_name: Human monocytes derived macrophages

label_protocol: Biotinylated cRNA were prepared according to the WT plus Affymetrix protocol from 100ng total RNA

growth_protocol: To generate monocyte-derived macrophages (MDMs), isolated CD14+ monocytes were plated in 10 cm Petri dishes at 1.0 × 107 cells/dish. Monocytes were stimulated with 25 ng/ml M-CSF (R&D Systems, Minneapolis, MN) in macrophage serum-free medium (Thermo Fisher Scientific, Waltham, MA) for seven days. MDMs were then maintained in DMEM (Invitrogen, Thermo Fisher Scientific,) containing 10% FBS (HyClone Laboratories, Logan, UT), 25 mM HEPES (Quality Biology, Gaithersburg, MD), and 5 µg/ml Gentamicin (Thermo Fisher Scientific) before use in experiments.

extract_protocol: Total cellular RNA was isolated from cells using the RNeasy isolation kit (QIAGEN). RNA was quantitated and qualified with a Nanodrop 1000 (Thermo Fisher Scientific) and an Agilent Bioanalyzer RNA Nano 6000 chip (Agilent, Santa Clara, CA).

treatment_protocol: Macrophages were pretreated with MnCl2 at 25 µM for 24 h, and then transfected with DNA. Total RNA was extracted at 24 h after DNA transfection.

value: macrophage

tag: donor

value: untreated


title: Untreated macrophages, biological rep3

description: Gene expression data from untreated macrophages, donor 3


title: Mn pretreated and DNA transfected Macrophages, biological rep3

description: Gene experission data from Mn pretreated and DNA transfected macrophages, donor 3

value: Mn pretreated and DNA transfected


title: DNA transfected macrophages, biological rep1

description: Gene experission data from DNA transfected macrophages, donor 1

value: DNA transfected


title: DNA transfected macrophages, biological rep3

description: Gene experission data from DNA transfected macrophages, donor 3


title: Mn pretreated Macrophages, biological rep2

description: Gene experission data from Mn treated macrophages, donor 2

value: Mn treated


title: Mn pretreated and DNA transfected Macrophages, biological rep2

description: Gene experission data from Mn pretreated and DNA transfected macrophages, donor 2


title: DNA transfected macrophages, biological rep2

description: Gene experission data from DNA transfected macrophages, donor 2


title: Mn pretreated Macrophages, biological rep3

description: Gene experission data from Mn treated macrophages, donor 3


title: Untreated macrophages, biological rep2

description: Gene expression data from untreated macrophages, donor 2


title: Mn pretreated Macrophages, biological rep1

description: Gene experission data from Mn treated macrophages, donor 1


title: P14


title: P11


title: O3


title: P1


title: O6


title: P12


title: O9


title: O23


title: O4


title: O5


title: O22


title: O8


title: O12


title: P13


title: O19


title: O21


title: O24


title: O14


title: O15


title: P10


title: O11


title: O18


title: O10


title: O17


title: O2


title: O7


title: O13


title: O16


title: N9


title: N8


title: O20


title: N7


title: O1


title: N6


title: N5


title: N21


title: N23


title: N22


title: N14


title: N12


title: N16


title: N19


title: N18


title: N20


title: N4


title: N3


title: N11


title: N1


title: M9


title: M5


title: M8


title: N10


title: M6


title: N24


title: M7


title: N2


title: M3


title: M22


title: M4


title: M24


title: N15


title: N17


title: M20


title: M2


title: M21


title: M19


title: M17


title: M23


title: M16


title: M18


title: N13


title: M12


title: M14


title: Mn pretreated and DNA transfected Macrophages, biological rep1

description: Gene experission data from Mn pretreated and DNA transfected macrophages, donor 1


title: M13


title: L8


title: M1


title: L9


title: M10


title: L7


title: M15


title: L5


title: L4


title: L3


title: L22


title: L17


title: L24


title: L23


title: L20


title: L18


title: L6


title: L2


title: L21


title: L19


title: M11


title: L15


title: L16


title: L12


title: L14


title: L13


title: L1


title: L10


title: K9


title: K7


title: K5


title: K8


title: K4


title: K3


title: K23


title: K24


title: K6


title: K22


title: K21


title: K20


title: L11


title: K19


title: K17


title: K16


title: K14


title: K15


title: K13


title: K12


title: K1


title: K10


title: J9


title: J8


title: K2


title: K11


title: J6


title: K18


title: J5


title: J23


title: J4


title: J22


title: J21


title: J3


title: J24


title: J20


title: J7


title: J16


title: J19


title: I9


title: J14


title: J15


title: J18


title: J17


title: J2


title: J12


title: I7


title: J11


title: J13


title: I8


title: I4


title: I5


title: J10


title: I22


title: I23


title: J1


title: I24


title: I18


title: I16


title: I19


title: I17


title: I20


title: I21


title: I15


title: I6


title: I3


title: I14


title: I1


title: I11


title: I12


title: I10


title: H8


title: H9


title: H5


title: I13


title: H7


title: H6


title: H3


title: H4


title: I2


title: H23


title: H20


title: H24


title: H22


title: H21


title: H15


title: H2


title: H17


title: H14


title: H18


title: H13


title: H19


title: H12


title: H11


title: H1


title: H10


title: G4


title: G5


title: G9


title: G8


title: G6


title: G7


title: H16


title: G3


title: G23


title: G24


title: G21


title: G22


title: G20


title: G19


title: G2


title: G18


title: G17


title: WT, NK, rep1

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq files were analysed using Fastqc, trimmed and aligned to Mm9 genome using the STAR aligner v 2.5.0
Read counts for each gene were generated using the --quantMode GeneCounts option in the STAR aligner v 2.5.0
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleens of mixed bone marrow chimeric animals reconstituted with ~1:1 mixtures of WT and Bach2-KO bone marrow cells (CI056).

extract_protocol:
Cells were stored in RNAlater (Ambion/Sigma) and total RNA purified using Qiagen Rneasy Plus Mini kit. RNA quality was assessed using bioanalyser analysis
Libraries were generated using the Clontech SMARTer protocols following the manufacturer's instructions

value: Spleen

value: NK cells

tag: genotype

value: WT


title: WT, mNK2 KLRG1-, rep4

source_name: Spleens of WT animals


title: WT, NK, rep3


title: KO, NK, rep3


title: WT, NK, rep2


title: WT, mNK2 KLRG1+, rep4


title: KO, NK, rep2


title: WT, mNK1, rep4


title: WT, NK, rep4


title: KO, NK, rep4


title: WT, iNK, rep4


title: WT, mNK2 KLRG1-, rep3


title: KO, NK, rep1


title: WT, mNK2 KLRG1+, rep3


title: G15


title: G16


title: G14


title: G13


title: G12


title: WT, mNK2 KLRG1+, rep2


title: WT, mNK1, rep3


title: WT, iNK, rep3


title: F9


title: G11


title: WT, mNK2 KLRG1-, rep2


title: G1


title: WT, mNK2 KLRG1-, rep1


title: G10


title: WT, iNK, rep2


title: WT, mNK2, KLRG1+, rep1


title: WT, mNK1, rep2


title: F5


title: F8


title: WT, mNK1, rep1


title: F3


title: F6


title: F4


title: F23


title: F24


title: F7


title: GXNI3

city: Tianjin

first: Guangxu

last: Xiao

address: Beihua South Road, JingHai District

country: China

institute: Tianjin University of Traditional Chinese Medicine

data_processing:
To ensure the quality and reliability of data processing, reads containing adapter and ploy-N, and low-quality reads in the original Illumina sequencing data were deleted.
The HISAT2 alignment software was utilized to compare the processed reads with the Mus musculus genome, and the featureCounts tool of subread software was used to quantify gene expression levels.
Differential expression analysis between groups was performed using DESeq2 software.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from heart tissue using TRIzol Reagent.
RNA libraries for RNA-seq were prepared using Transcriptor First Strand cDNA Synthesis Kit following manufacturer's protocols.

value: heart

value: Cardiomyocytes

value: MIRI+GXNI


title: MIRI2

value: MIRI


title: GXNI1


title: sham2

value: not


title: WT, iNK, rep1


title: F20

value: Cultured naive B cells


title: GXNI2


title: MIRI3


title: sham1


title: MIRI1


title: F22

value: Peripheral blood


title: F18

value: CD40L and IL-4/IL-21 stimulated


title: F21

value: 11 days cultured


title: F2


title: F19


title: F17


title: F15


title: RNA-seq_HIBD

city: beijing

first: shan

address: 2yabao road

institute: Capital Institute of Pediatrics

description: Rat Brain tissue,10 day

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: Excel file includes RPKM values for each Sample

organism: Rattus norvegicus

source_name: brain

growth_protocol: Wistar rats, 8–10 weeks old, SPF grade,  housed in a 12-h light/dark cycle, with free access to food and water.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Briefy, after deeply anesthetized with chloral hydrate(200 mg/kg), the rats pups in Sham, HIBD, HIBD+SAL and HIBD+SB groups were perfused with physiological saline from the right auricle until the liver turns white. The brain of rats was removed on ice, put into an ice-cold PBS and rapidly separated the infarct side cerebral cortex

value: brain

value: Wistar

value: HIBD  operation

value: Day 10


title: sham3


title: RNA-seq_HIBD-SB

description: Rat Brain tissue,10 day

value: Butyrate (SB) intervention


title: smallRNA-seq CTRL Spc 4

city: Turku

first: Matthieu

last: Bourgery

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description:
counts_piRNA_cluster_smallRNAseq.txt
counts_piRNA_rmsk_smallRNAseq.txt
merge_miRNAs_smallRNAseq.txt

data_processing:
RNA-seq: For transcript-level DE analysis, reads were trimmed off adapter contents using cutadapt (v2.8) and mapped to the mouse genome (Ensembl: Grcm38) using STAR (v2.7.1a) in two-pass mode. Then, reads were assigned and counted using FeatureCounts (v2.0.1) in paired-end mode. First, raw read counts were filtered in order to keep only transcripts with 20 or more normalized counts in at least three individual samples among six samples from a given cell type (3 x CTRL and 3 x cKO). Raw count reads were normalized and differential expression calculated using DESeq2 in R (v4.0.3). 2) To analyze transposable elements and piRNA precursors, reads were mapped to the mouse genome (UCSC: mm10) using STAR (v2.7.1a) in two-pass mode. For transposable elements, reads were assigned and counted using TEtranscripts in reverse stranded mode (v2.2.1). For piRNA precursor transcripts, reads were assigned and counted against the gtf file containing the 214 piRNA precursors using FeatureCounts. Raw count reads were filtered to keep only genes with at least 10 reads across all samples (Smg6-cKO and CTRL). Raw count reads were normalized and differential expression calculated using DESeq2 in R (v4.0.3).
Small RNA-seq: SPORTS1.1 was used to map small RNA reads successively rsRNA, miRNA, tsRNA and piRNA sequences extracted from mm10 UCSC genome files originating from rRNAdb, miRBase (v.22) GtRNAdb (v.2.0) and piRBase (v.2.0) using SPORTS default settings. Then, reads mapping to rsRNA, miRNA and tsRNA sequences were extracted from SPORTS output text file using R. Repeats from repeatMasker and piRNA precursor locations were mapped to the mouse genome (UCSC : mm10) using HISAT2 (v2.1.0); then, reads were assigned and counted using FeatureCounts (v2.0.1). Raw read counts were filtered to keep only genes with at least one occurrence found per sample. Raw read counts were normalized and differential expression calculated using DESeq2 (v4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts text files

source_name: testis

extract_protocol:
RNA was extracted from enriched fractions of Spc, RS or isolated CBs with the Trisure reagent (Bioline) using standard protocols. Isolated RNA was analyzed using NanoDrop (Thermo Scientific) and Bioanalyzer (Agilent).
1) CB RNA-seq: Total RNA libraries without ribosomal RNA removal were prepared by NEBNext® Ultra™ Directional RNA Library Prep Kit without fragmentation. Sequencing was performed with NovaSeq6000 (PE150) platform (Illlumina) at Novogene (www.en.novogene.com). 2) RNA-seq of Spc and RS samples: Libraries were constructed with Illumina TruSeq Stranded mRNA library preparation kit and sequenced with HiSeq3000 (read length 2 x 75 bp) sequencing system (Illumina, San Diego, CA, USA) at the Finnish Functional Genomics Centre (https://bioscience.fi/services/functional-genomics/services/). 3) SmallRNA-seq of Spc and RS samples: Libraries were constructed with QIAseq miRNA library preparation kit and sequenced with HiSeq2500 Rapid run sequencing platform (1 x 75bp) at the Finnish Functional Genomics Centre.

value: isolated pachytene spermatocytes

value: control

value: mixed C57Bl/6J and SV129


title: F14


title: F12


title: F13


title: E8


title: F11


title: F16


title: F1


title: smallRNA-seq CTRL Spc 5


title: E7


title: E6


title: F10


title: RNA-seq_sham

description: Rat Brain tissue,10 day

value: sham


title: smallRNA-seq cKO Spc 4


title: smallRNA-seq CTRL RS 3

value: isolated round spermatids


title: smallRNA-seq cKO Spc 3


title: smallRNA-seq cKO Spc 5


title: smallRNA-seq cKO Spc 2


title: smallRNA-seq CTRL Spc 1


title: smallRNA-seq CTRL Spc 2


title: E3


title: smallRNA-seq CTRL Spc 3


title: E5


title: smallRNA-seq cKO Spc 1


title: E4


title: smallRNA-seq CTRL RS 1


title: smallRNA-seq CTRL RS 2


title: E20


title: smallRNA-seq cKO RS 3


title: E9


title: E24


title: E23


title: smallRNA-seq cKO RS 1


title: smallRNA-seq cKO RS 2


title: RNA-seq cKO Spc 3

description:
mRNA_transcript_counts_ensembl_Spc_RNAseq.txt
Tetranscripts_out_UCSC_Spc_RNAseq.cntTable
counts_piRNA_precursor_Spc_RNAseq.txt


title: E18


title: E19


title: E17


title: RNA-seq cKO Spc 2


title: RNA-seq cKO Spc 1


title: E15


title: E21


title: E2


title: E13


title: E16


title: RNA-seq CTRL Spc 3


title: RNA-seq CTRL Spc 1


title: RNA-seq CTRL RS 2

description:
mRNA_transcript_counts_ensembl_RS_RNAseq.txt
Tetranscripts_out_UCSC_RS_RNAseq.cntTable
counts_piRNA_precursor_RS_RNAseq.txt


title: RNA-seq CTRL Spc 2


title: RNA-seq cKO RS 3


title: RNA-seq CTRL RS 1


title: RNA-seq cKO RS 2


title: RNA-seq cKO RS 1


title: E14


title: RNA-seq CTRL RS 3


title: HaCaT, KD, 3

city: Guangzhou

first: Huiting

last: Liu

state: Guangdong

address: Lujing road NO.2

institute: Dermatology Hospital, Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using hisat2 (v2.0.1)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for all Samples.

source_name: HaCaT

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

extract_protocol:
RNA was extracted using Trizol reagent. Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent  Technologies, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HaCaT

value: AHNAK knockdown


title: E22


title: E11


title: E1


title: D9


title: E10


title: E12


title: HaCaT, KD, 2


title: HaCaT, KD, 1


title: HaCaT, NC, 2


title: D6


title: D8


title: Subj_8 AR [S28]

city: BALTIMORE

first: Luigi

last: Ferrucci

address: 251 BAYVIEW BLVD.

department: Translational Gerontology Branch

institute: National Institute on Aging, National Institutes of Health

description: 31 totalRNA-Seq samples were pooled and sequenced on 2 lanes of a NovaSeq 6000 S4 XP run using Illumina(R) Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

data_processing:
Reads were trimmed using Cutadapt (v. 1.18) to remove sequencing adapters.
Reads were aligned to human reference genome hg38 using STAR (v. 2.7.0f)
Expression levels were quantified using RSEM (v. 1.3.0) with GENCODE annotation (v. 21)
Assembly: hg38
Supplementary files format and content: RSEM raw counts as tab-delimited file for 58,381 genes (rows) and 31 samples (columns).

source_name: skeletal muscle

extract_protocol:
In each participant, a vastus lateralis muscle biopsy (∼150 mg) was collected using a Weil–Blakesley conchotome at ∼2 cm from the motor point. Two ml of lidocaine (2%) were injected in the area of the sampling and a small incision of muscle and fascia was performed. Muscle samples were frozen in liquid nitrogen and stored at −80°C. RNA was extracted from the muscle tissues by REPROCELL (USA) using a Norgen Animal Tissue RNA Purification Kit #257 (Norgen Biotek Corp, Ontario, CA).
RNA-Seq was performed at the Frederick National Laboratory for Cancer Research Sequencing Facility, NIH.  The libraries were made using the TruSeq Stranded Total RNA Library Prep protocol from Illumina.

value: skeletal muscle

tag: subject

value: AR


title: Subj_9 AR [S29]


title: D24

value: Cultured naive B cells

value: Peripheral blood


title: D23

value: CD40L and IL-4/IL-21 stimulated

value: 11 days cultured


title: D7


title: D22


title: Subj_3 AR [S25]


title: Subj_11 AR [S31]


title: D4


title: Subj_6 AR [S26]


title: Subj_7 AR [S27]


title: D5


title: D21


title: D20


title: HaCaT, NC, 1


title: Subj_11 ULLS [S22]

value: ULLS


title: D19


title: D18


title: Subj_2 AR [S24]


title: D3


title: Subj_9 ULLS [S20]


title: Subj_10 AR [S30]


title: D17


title: Subj_6 ULLS [S17]


title: D2


title: NCIH838 KDSR KO-2

city: Worcester

first: Meghan

middle: E

last: Spears

address: 364 Plantation St, LRB

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
aligned to the reference genome assembly hg38 with star/2.5.3a (Dobin et al., 2013)
annotated with gencode.v29.primary_assembly (Harrow et al., 2012)
Aligned exon reads with mapping quality higher than 20 were counted toward gene expression with featureCounts_2.0.0 (Liao et al., 2014) with default settings except the following parameters ‘-Q 20 --minOverlap 1 --fracOverlap 0 -p -B -C’
Normalized expression values were calculated using the Transcripts Per Million (TPM) method.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, normalized expression values in TPM

source_name: Cancer cell line

growth_protocol: Cells were grown adhered to tissue culture plates at 37°C, under 5% CO2 and atmospheric oxygen. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100units/ml penicillin-streptomycin, and 2mM L-glutamine.

extract_protocol: Total RNA was extracted from each sample using the RNeasy Kit for total RNA isolation (Qiagen #74104).

treatment_protocol: Cells were transduced with lentivirus containing lentiCRISPR v2 containing either a control non-targeting guide (CTRL) or a guide targeting KDSR (KDSR g1). Cells were selected with puromycin for 5 days and collected for RNA extraction at day 8 (HUH7 and DLD1) or day 10 (NCIH838) after lentiviral infection.

value: lung

tag: disease

value: lung adenocarcinoma

value: CRISPR gene KO of KDSR


title: NCIH838 KDSR KO-3


title: Subj_10 ULLS [S21]


title: D13


title: Subj_8 ULLS [S19]


title: D16


title: Subj_1 AR [S23]


title: D14


title: Subj_5 ULLS [S16]


title: D11


title: Subj_7 ULLS [S18]


title: NCIH838 CTRL-2

value: CRISPR non-targeting guide


title: Subj_4 ULLS [S15]


title: D10


title: NCIH838 CTRL-3


title: C6


title: D1


title: Subj_3 ULLS [S14]


title: C4


title: D15


title: Subj_11 baseline [S11]

value: baseline


title: C3


title: DLD1 KDSR KO-3

value: colon

value: colon adenocarcinoma


title: DLD1 KDSR KO-2


title: Subj_10 baseline [S10]


title: C24


title: NCIH838 KDSR KO-1


title: C9


title: D12


title: Subj_2 ULLS [S13]


title: Subj_1 ULLS [S12]


title: C5


title: C7


title: NCIH838 CTRL-1


title: C23


title: C21


title: C8


title: DLD1 KDSR KO-1


title: Subj_8 baseline [S8]


title: Subj_9 baseline [S9]


title: C22


title: DLD1 CTRL-3


title: C2


title: C18


title: DLD1 CTRL-1


title: C20


title: Subj_7 baseline [S7]


title: Subj_6 baseline [S6]


title: DLD1 CTRL-2


title: C16


title: C17


title: C19


title: HUH7 KDSR KO-3

value: liver

value: hepatocellular carcinoma


title: C15


title: Subj_5 baseline [S5]


title: Subj_4 baseline [S4]


title: HUH7 KDSR KO-2


title: HUH7 CTRL-3


title: C14


title: HUH7 KDSR KO-1


title: Subj_3 baseline [S3]


title: C10


title: HUH7 CTRL-2


title: Subj_2 baseline [S2]


title: B9


title: C1


title: C12


title: C13


title: C11


title: B8


title: B7


title: B6


title: B5


title: B4