title: RNA_seq_SingleCell_dpc16

value: gestation day16


title: RNA_seq_Bulk_WT_NP_ex1

status: Public on Feb 17 2021

type: SRA

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

library_source: transcriptomic

data_processing:
For bulk RNA-seq analysis, the sequenced reads were mapped to the mm10 mouse reference genome using Tophat2 (version 2.2.1) with the GENCODE M15 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-1.14. The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were calculated using Cuffdiff within Cufflinks version 2.2.1 package and the GENCODE M15 annotation file (protein coding).
For scRNA analysis, the 10X Genomics Cell Ranger pipeline (version 2.2.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the GFP sequence, barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10
Supplementary_files_format_and_content: For bulk RNAseq, a tsv file include FPKM values. For scRNAseq, tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

molecule: total RNA

organism: Mus musculus

source_name: interfollicular epidermal basal cells from abdominal skin

extract_protocol:
Subcutaneous fat was removed from the skin with a scalpel, and the whole skin was trypsinized at 37 °C for an hour to remove the dermis. The cell suspensions were filtered through strainers (70-μm, BD Falcon), collected by centrifugation (300 × g, 5 min) and suspended in Dulbecco’s modified Eagle’s medium (Ca−). Cell suspensions were incubated with Pacific Blue anti-human/mouse CD49f (Biolegend) antibody and eFluor660 anti-mouse CD34 (Biolegend) antibody for 30 min on ice, washed twice with PBS and subjected to flow cytometric analysis. Cell isolation was performed on a FACSAria Ⅲ sorter. RNA was extracted from CD49f positive and CD34 negative cells using the RNeasy Micro Kit (Qiagen). Quality RNA samples were selected (RIN>7).  For scRNAseq, single cell suspensions of all samples were resuspended in PBS-1% BSA at 1000cells/μL and barcoded with a 10x Chromium Controller (10x Genomics).
RNA-seq libraries were generated using the TruSeq Stranded mRNA library prep kit (Illumina) and the libraries were sequenced on NextSeq 500 (Illumina). For scRNAseq, RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v2 reagent kit (10x Genomics). Sequencing was performed with Illumina NextSeq 500 .

tag: strain

tag: genotype

value: WT

tag: perinatal date

value: non pregnant


title: RNA_seq_Bulk_WT_NP_ex2


title: RNA_seq_SingleCell_dpp42_dermis

description:
Dpp42
scRNAseq

data_processing:
The 10X Genomics Cell Ranger pipeline (version 2.2.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the GFP sequence, barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample.

source_name: abdominal skin dermis

extract_protocol:
Subcutaneous fat was removed from the skin with a scalpel, and the whole skin was incubated for 30 min in 0.25% trypsin to separate into epidermis and dermis. Dermal cells were dissociated into single cells by pipetting and filtrated on a 40μm (Falcon) and 20μm (PLS). Single cell suspensions were resuspended in 1% BSA/PBS at 1000 cells/µL and barcoded with a 10× Chromium Controller (10× Genomics).
RNA from the barcoded cells of each sample was subsequently reverse transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell v2 reagent kit (10× Genomics), according to the manufacturer’s instructions. Sequencing was performed with a NextSeq 500 (Illumina), according to the manufacturer’s instructions.

value: Col1a2creERT2; R26H2B EGFP

value: 8-12week (post partum day 42)

tag: cell type

value: abdominal skin dermal cells


title: RNA_seq_SingleCell_dpp40

source_name: abdominal skin epidermis

value: Tbx3creERT2; R26H2B EGFP

value: post partum day 40


title: RNA_seq_SingleCell_NP


title: RNA_seq_Bulk_Tbx3cKO_dpc16_ex3


title: WT aILC2s With ISO  [sample-18-BH191107]

city: Los Angeles

first: Georges Doumet

last: HELOU

state: California

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

country: USA

institute: University of Southern California

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M16 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M. Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: WT aILC2s With ISO

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted ILC2s after three intranasal administrations of rmIL-33 (0.5 μg per mouse), defined in this study as IL-33-activated ILC2s (aILC2s), were incubated with rmIL-2 (10 ng mL−1) and rmIL-7 (10 ng mL−1) with CD200 FC or the isotype control for 24 hours (5x104 mL−1).

value: BALB/cByJ

tag: age

value: 8 weeks

tag: treatment

value: ISO

tag: tissue

value: lung

value: sorted mouse pulmonary ILC2s


title: WT aILC2s With ISO  [sample-17-BH191107]


title: WT aILC2s With CD200 FC [sample-35-BH191107]

source_name: WT aILC2s With CD200 FC

value: CD200 FC


title: WT aILC2s With CD200 FC [sample-36-BH191107]


title: WT aILC2s With CD200 FC [sample-38-BH191107]


title: RNA_seq_Bulk_Tbx3cKO_dpc16_ex1


title: RNA_seq_SingleCell_dpc16_dermis

description:
Dpc16
scRNAseq

value: 8-12week (gestation day16)


title: RNA_seq_Bulk_WT_dpc16_ex1

value: gestation day 16


title: RNA_seq_Bulk_WT_dpc16_ex3


title: WT aILC2s With ISO  [sample-16-BH191107]


title: RNA_seq_Bulk_WT_dpc16_ex2


title: RNA_seq_Bulk_Tbx3cKO_dpc16_ex2


title: MC3T3-E1_NC_input_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

library_source: genomic

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
MACS version 1.4.2 was used to peakcalling
Genome_build: GRCm38
Supplementary_files_format_and_content: peaks

molecule: genomic DNA

source_name: Osteoblast

extract_protocol:
Samples were harvested with RIPA  buffer ( 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1 × PBS, 2% PMSF and 1 × Protease inhibitor Cocktail) followed by sonication on ice (15mins with 10 s pulse-on and 10 s pulse-off, 20% amplitude).DNA was sonicated to 200 – 500 bp.
The lysate was then incubated with anti-MACF1(Abcam,ab117418) at 4 ◦ C overnight. The immunuprecipitates were further incubated with Pierce™ Protein A/G Magnetic Beads (Thermo,26162) for 2 hours at 4 ℃. After applying to magnet and removing the supernatants, we washed beads once with Low Salt Immune Complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl) and added 1 ml of buffer to each tube, rotated at 4 ℃ for 5 min; we then placed the tube on the magnet for 30 s, then discarded supernatant. We repeated washing first with High Salt Immune Complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl) and LiCl Immune Complex wash buffer(0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris, pH 8.1) and second with TE Buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) for a total of 5 washes. The immunoprecipitates were eluted from the beads with elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS) and incubated at 65 oC overnight. After sequential RNase A and proteinase K treatment, DNA fragments were purified by phenol extraction and ethanol precipitation. ChIP-Seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer’s instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing.

tag: cell line

value: Osteoblast

value: Control

tag: chip antibody


title: RNA_seq_Bulk_WT_NP_ex3

value: WT


title: MC3T3-E1_NC_input_1


title: MC3T3-E1_NC_EB_size3

value: MACF1 (Abcam,catalog# ab117418, lot#s GR180962-1 and GR87583-10)


title: MC3T3-E1_KD_EB_size3

value: MACF1 knockdown


title: MC3T3-E1_KD_input_2


title: MC3T3-E1_KD_input_size3


title: MC3T3-E1_KD_EB_1


title: MC3T3-E1_KD_input_1


title: MC3T3-E1_NC_EB_2


title: MC3T3-E1_KD_EB_2


title: MC3T3-E1_NC_input_size3


title: MC3T3-E1_NC_3d_rep2

description:
expressed_gene_reads.txt
expressed_gene_RPKM.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue < =0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance measurements (reads, RPKMs)

molecule: polyA RNA

extract_protocol:
Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agrose gel electrophoresis.
For each sample, 5 μg total RNA was used for RNA-seq library preparation (Gnomegen K02421-T). Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Thermo Fisher Scientific, Inc.) prior to use for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95˚C followed by end repair and 5'-adaptor ligation. Next, reverse transcription was performed with RT primer harboring a 3'-adaptor sequence and randomized hexamer using RT Master mix (Gnomegen K02421-T), with the reaction conditions: 25˚C, 10min, 42˚C, 40min, 70˚C, 15min, cool to 4˚C. The cDNAs were purified and amplified, and polymerase chain reaction (PCR)  was performed using 2× HiFi PCR Master Mix  (Gnomegen K02421-T) with the reaction conditions as below: 98˚C 45s, 98˚C 15s, 60˚C 30s, 72˚C 30s, 13 cycle. PCR products corresponding to 200-500 bps were collected by Size Selector (Gnomegen K02421-T), quantified and stored at -80˚C until used for sequencing.


title: MC3T3-E1_NC_0d_rep1


title: MC3T3-E1_NC_10d_rep1


title: MC3T3-E1_sh_10d_rep1


title: MC3T3-E1_sh_3d_rep2


title: MC3T3-E1_NC_5d_rep1


title: MC3T3-E1_sh_0d_rep2


title: MC3T3-E1_sh_0d_rep1


title: MC3T3-E1_NC_0d_rep2


title: MC3T3-E1_NC_5d_rep2


title: MC3T3-E1_NC_3d_rep1


title: MC3T3-E1_sh_5d_rep1


title: MC3T3-E1_sh_5d_rep2


title: MC3T3-E1_NC_EB_1


title: MC3T3-E1_sh_3d_rep1


title: HPMEC_Cyclic stretch 2 hr, biological rep1

type: RNA

city: Ji'nan

first: wang

last: dong

state: Shandong

address: 44 Wenhua Xi Road

institute: shandong university

description: HPMECs subjected to 20% cyclic stretch for 2 hr

hyb_protocol: Following fragmentation, ss-cDNA were hybridized for 16 hr at 45°C on Human Transcriptome Array 2.0 according to Affymetrix®WT PLUS Reagent Kit User Manual. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The microarray data were pre-processed using the Robust Multi-array Average (RMA) method for background-corrected, normalization and summary on the GCBI bioinformatics platform

label: biotin

organism: Homo sapiens

source_name: HPMEC

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

growth_protocol: Human pulmonary microvascular endothelial cells (HPMECs, ScienCell, San Diego, CA, USA) were cultured in endothelial cell medium (ECM, ScienCell, San Diego, CA, USA) in a humidified 5% CO2 incubator at 37°C, and used at passage 3 to 5.

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

treatment_protocol: HPMECs were subjected to 20% cyclic stretch for 0 or 2 hr (n = 3 per group).

value: Pulmonary microvascular endothelial cells

value: 20% cyclic stretch


title: HPMEC_Cyclic stretch 2 hr, biological rep3


title: TKO_TS1.4_rep1

city: Kobe

first: Yuichi

last: Kumaki

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor, line 1.4

hyb_protocol: 1.65 ug of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17.4 hours at 65 degrees C and 10 rpm according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7).

scan_protocol: Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 5 um resolution and 20-bit dynamic range.

data_processing: The scanned images were processed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 014868_D_F_20100123) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) removal of data of outlier probes (gIsFeatNonUnifOL flag = 1 or  gIsFeatPopnfOL flag = 1 in any of samples), c) log2 transformation, and d) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.

molecule: cytoplasmic RNA

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, line 1.4, replicate 1

label_protocol: Amplification and Cy3 labeling of RNA was prepared from 200 ng of RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7). Purification of Cy3-labeled cRNA was performed using the RNeasy Mini Kit (Qiagen). Quantity, quality and dye incorporation of Cy3-labeled cRNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

growth_protocol: ntTS cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 25 ng/ml FGF4, and 1 micro-g/ml heparin with mouse embryonic fibroblast feeder cells.

extract_protocol: Cytoplasmic RNA was isolated by using the RNeasy Mini Kit (Qiagen) according to the manufacture's cytoplasmic RNA protocol with DNase digestion option. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

treatment_protocol: The cells were recovered by trypsinization. To remove feeder cells, the ntTS cells were purified by sorting GFP positive cells with FACS-Aria (BD Biosciences).

value: Line 1.4

tag: genotype/variation

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst


title: HPMEC_Cyclic stretch 0 hr, biological rep3

description: HPMECs subjected to 20% cyclic stretch for 0 hr


title: HPMEC_Cyclic stretch 0 hr, biological rep2


title: WT_TS4.2_rep1

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor, line 4.2

source_name: mouse wild-type (WT) ntTS cells, line 4.2, replicate 1

value: Line 4.2

value: wild-type, carrying the CAG-GFP transgene


title: HPMEC_Cyclic stretch 2 hr, biological rep2


title: TKO_TS1_rep1

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor, line 1

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, line 1, replicate 1

value: Line 1


title: TKO_Flk1_rep1

description: Gene expression data from Flk1+ mesoderm cells derived from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

growth_protocol: ES cells were plated onto a 10-cm dish with confluent OP9 stromal cells in the differentiation medium (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4.5-5 days.

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1 antibody. Stained cells were sorted by FACS-Aria (BD Biosciences).

value: Line 19-1

value: Flk1+ mesoderm cells derived from embryonic stem (ES) cells


title: TKO_Flk1_rep2

source_name: Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2


title: WT_Flk1_rep2

description: Gene expression data from Flk1+ mesoderm cells derived from wild-type ES cells

source_name: Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 2

value: Line J1

value: wild-type


title: HPMEC_Cyclic stretch 0 hr, biological rep1


title: WT_TS9.2_rep2

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor, line 9.2

source_name: mouse wild-type (WT) ntTS cells, line 9.2, replicate 2

value: Line 9.2


title: NFFSE-cultured cells, biological rep3

first: Makoto

last: Takeo

state: Hyogo

department: BDR

description: gene expression data from hair follicle bulge cells cultured in NFFSE condition

hyb_protocol: Following fragmentation using GeneChip Hybridization, Wash and Stain Kit, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G, Thermo Fisher Scientific.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software and normalized using MAS5 algorithm. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Bulge cells cultured in NFFSE culture condition

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

growth_protocol: Cells were suspended in atelocollagen and cultured in the different media for 6 days before RNA extraction.

extract_protocol: Extraction of total RNA was performed using RNeasy mini kit  according to the manufacturer's instructions.

value: hair follicle bulge cells

tag: culture condition

value: NFFSE


title: NFFS-cultured cells, biological rep2

description: gene expression data from hair follicle bulge cells cultured in NFFS condition

source_name: Bulge cells cultured in NFFS culture condition

value: NFFS


title: WT_ES_rep1

description: Gene expression data from wild-type ES cells

source_name: mouse wild-type (WT) ES cells, replicate 1

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% KNOCKOUT Serum Replacement (Invitrogen), 10 micro-M human adrenocorticotrophic hormone (Kurabo), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor, on gelatinized culture dishes without feeder cells.

treatment_protocol: The cells were recovered by trypsinization and used for RNA preparation.

value: embryonic stem (ES) cells


title: WT_ES_rep2

source_name: mouse wild-type (WT) ES cells, replicate 2


title: WT_TS9.2_rep1

source_name: mouse wild-type (WT) ntTS cells, line 9.2, replicate 1


title: WT_TS4.2_rep2

source_name: mouse wild-type (WT) ntTS cells, line 4.2, replicate 2


title: WT_Flk1_rep1

source_name: Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 1


title: young mice 3 replicate 2

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-3_2_S13

data_processing:
UMI+CB were deconvoluted with UMI-Tools 1.0.0 (whitelist and extract)
Alignment was performed with STAR 2.7
Feature counts were done with Subread 2.0.0's FeatureCounts
Matrix generation was performed with UMI-Tools 1.0.0 (count)
Genome_build: GRCm38
Supplementary_files_format_and_content: TSVs of the cell X gene matrices, RDS of the processed Seurat object

source_name: Young_Esophageal epithelium

extract_protocol:
The inDrop™ System and single-cell RNA sequencing kit (1CellBio, Watertown MA) were used for single cell encapsulation.  Approximately 2,000 cells were co-encapsulated in 1-3 nL droplets with barcode-labeled hydrogel beads and reverse transcription/cell lysis reagents. Oligonucleotide primers with cell barcodes were released from the beads by an UV light exposure and reverse transcription was performed in the emulsion of droplets in oil.  Barcoded cDNA was released by breaking the droplets after reverse transcription and stored at -80°C.
Library preparation was performed following the 1CellBio protocol version 2.3. The steps were as follows: second strand synthesis, in vitro transcription using T7 RNA polymerase, fragmentation of amplified RNA, reverse transcription, and PCR amplification. Size-selected libraries were sequenced on an Illumina HiSeq 2500 instrument using paired-end 2 x 50 base pairs.
Smart-Seq2 modified protocol

value: Young

value: Esophageal epithelium


title: TKO_TS1_rep2

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, line 1, replicate 2


title: young mice 2 replicate 2

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-2_2_S5


title: young mice 3 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-3_1_S12


title: aged mice 3 replicate 2

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-3_2_S11

source_name: Aged_Esophageal epithelium

value: Aged


title: NFFS-cultured cells, biological rep1


title: TKO_ES_rep2

description: Gene expression data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 15% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.


title: NFFS-cultured cells, biological rep3


title: TKO_ES_rep1

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1


title: P10_65_Str

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

description: counts.csv

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
Reads were mapped to the mouse reference genome (GRCm38) with the Ensembl 92 genome annotation using STAR  v2.5.4b (parameters: --alignIntronMax 100000 --outSJfilterReads Unique --outSAMmultNmax 1 --outFilterMismatchNoverLmax 0.04)
Reads were counted with FeatureCounts v1.5.0 (meta-feature mode, stranded mode “2”, Ensembl 92), only uniquely mapping reads were counted
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

source_name: Striatum

growth_protocol: Mice were group housed and maintained in a specific pathogen-free animal facility in Leibniz Institute on Aging - Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
RNA was extracted using the RNAeasy Lipid Tissue Mini Kit (Qiagen), following the manufacturer's instructions.
Total RNA library preparation was done by use of Illumina’sTruSeq Stranded mRNA, following the manufacturer’s instructions.

tag: Sex

value: male

value: 10 days

value: Trrap Fl/+; Camk2-Cre tg


title: aged mice 3 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-3_1_S10


title: P10_64_Str

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

description: counts.csv


title: aged mice 1 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-1_1_S6


title: young mice 2 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-2_1_S4


title: young mice 1 replicate 2

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-1_2_S2


title: young mice 1 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
young-1_1_S1


title: aged mice 2 replicate 2

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-2_2_S9


title: TKO_TS1.4_rep2

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor, line 1.4

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, line 1.4, replicate 2

value: Line 1.4

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst


title: P10_61_Str

description: counts.csv

value: female

value: Trrap Fl/Fl; Camk2-Cre tg


title: aged mice 2 replicate 1

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-2_1_S8


title: P10_60_Str

description: counts.csv


title: NFFSE-cultured cells, biological rep2


title: P10_60_Ctx

description: counts.csv

source_name: Cortex


title: aged mice 1 replicate 2

description:
InDrop single cell sequenced data. Barcodes on read 1.
aged-1_2_S7


title: NFFSE-cultured cells, biological rep1

description: gene expression data from hair follicle bulge cells cultured in NFFSE condition


title: P10_57_Ctx

description: counts.csv


title: P10_55_Ctx

description: counts.csv


title: 39_OHT

description: counts.csv

source_name: primary adult neural stem cells

growth_protocol: Young ( around 2-4 months old)  mice were group housed and maintained in a specific pathogen-free animal facility in Leibniz Institute on Aging - Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
RNA was extracted using the RNAeasy Mini Kit (Qiagen), following the manufacturer's instructions.
Total RNA library preparation was done by use of Illumina’sTruSeq Stranded mRNA, following the manufacturer’s instructions.

treatment_protocol: Cells were treated with 4-OHT (1mM) for 5 days before the DNA isolation.

value: 2 months

value: Trrap Fl/Fl; Rosa26-CreERT2 tg


title: P10_64_Ctx

description: counts.csv


title: 37_OHT

description: counts.csv


title: P10_63_Str

description: counts.csv


title: P10_63_Ctx

description: counts.csv


title: 35_OHT

description: counts.csv

value: Trrap Fl/+; Rosa26-CreERT2 tg


title: 28_OHT

description: counts.csv


title: P10_61_Ctx

description: counts.csv


title: P10_59_Ctx

description: counts.csv


title: P10_58_Str

description: counts.csv


title: P10_57_Str

description: counts.csv


title: P10_58_Ctx

description: counts.csv


title: 26_OHT

description: counts.csv


title: 36_OHT

description: counts.csv


title: 24

description: counts.csv

value: no treatment


title: P10_59_Str

description: counts.csv


title: 27_OHT

description: counts.csv


title: 19_OHT

description: counts.csv


title: 24_OHT

description: counts.csv


title: 36

description: counts.csv


title: 26

description: counts.csv


title: 35

description: counts.csv


title: 19

description: counts.csv


title: KRAS, senescent cells, rep 3

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

data_processing:
Reads were demultiplexed using the CEL-Seq2 scripts. Quality filtering and trimming of adapters and poly-A tail was done using Cutadapt, version 1.12, with parameters -e 0 -q 10 -a A{100} -a A{15}N{100} -a GATCGTCGGACT -n 3 -m 28.
Processed reads were aligned using Tophat2, v2.0.14, with parameters -N 2 --read-edit-dist 2 -G genes.gtf.
Counting of raw reads per gene was done with the CEL-Seq2 wrapper script for htseq-count.
Differentially expressed genes were determined by DESeq2, using default parameters. Genes with average expression below 2 were filterd out. Significance threshold was padj < 0.1 (default).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file with a single header line. First 6 columns are general gene details, then raw counts for each sample (6 columns), then normalized counts for each sample (6 columns), then a column of average expression (baseMean), then the results of differential expression analysis (5 columns). A question mark (?) denotes missing value.

source_name: Acinar cells

growth_protocol: The following mouse lines were obtained from The Jackson Laboratory, maintained ina specific pathogen-free environment throughout the study,and crossed as indicated:Ptf1a-CreER(C57Bl6), PDX-Cre(C57Bl6), Kras+/lsl-G12D(C57Bl6, 129sv),Rosalsl- tdTomato(C57Bl6). Both males and females were used. For inducible Kras activation in acinar cells,Ptf1a-CreER; Kras+/lsl-G12D;Rosalsl- tdTomatotriple transgenics (3 mice) were injected at 6 weeks of age subcutaneously with two doses of 400 mg/Kg.90 days after Kras activation.

extract_protocol:
For mRNA-seq we isolated tdTomato+SA-bGal– and tdTomato+SA-bGalhigh fractions from 3 mice. Total RNA from FACS-sorted cells was isolated by TRIzol (Invitrogen) extraction followed by Rneasy Plus Micro Kit (Qiagen), using >10,000 cells of each sample.
Profiling was conducted using an adapted CEL-Seq2 protocol:  3’ cDNA was synthesized and barcoded, followed by RNA synthesis, amplification by in vitro transcription and library generation for sequencing.

treatment_protocol: For mouse pancreas dissociation into single cell suspensions, pancreata were manually cut with scissors into small pieces and incubated with trypsin-EDTA treatment for 10 min at 37 °C, followed by treatment with collagenase P (Sigma, 11213857001) 1 mg/ml for 20–30 min at 37 °C and filtered through 70 and 40 micron. We incubated purified cells with the fluorescent β-galactosidase substrate C12FDG (Invitrogen D-2893) at 33 μM for 1h at 37°C, followed by sorting based on C12FDG and tdTomato fluorescence and CD45- fluorescence, using an Aria III sorter (BD Biosciences). The SA-bGal+fraction out of total tdTomato+was calculated.

value: senescent


title: KRAS, non-senescent, rep 3

value: non-senescent


title: KRAS, senescent cells, rep 2


title: KRAS, non-senescent, rep 1


title: KRAS, senescent cells, rep 1


title: KRAS, non-senescent, rep 2


title: 29_OHT

description: counts.csv


title: Input

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

data_processing:
Bases were called using the Real Time Analysis 2 software of the NextSeq 500.
Reads were trimmed using Trim Galore (version 0.4.0) with default parameter settings.
Unmapped reads were filtered out and multiplexed subsamples were merged with samtools (version 1.9).
Redundant reads were filtered out using Picard (version 2.18.27) for peak calling (but were kept for differential peak change analysis).
Peak calling was done using the MUSIC (multiscale enrichment calling) software (Harmanci et al., 2014). A mappability profile was generated using the Oryza sativa ssp. japonica (build MSU7.0) genome with a read length parameter of 76. For peak calling samples were merged per histone modification (excluding the input sample). For histone modifications H3K9me2 and H3K27me3 the broad peak subroutine was used while for histone modification H3K9ac punctate peaks were called , adhering to the classification of the ENCODE project that denominates H3K9me2 and H3K27me3 as broad marks and H3K9ac as a narrow mark  . Otherwise default parameters were used.
To assess significant changes in peak regions between galls and roots, count tables of read counts in peak regions were generated by the summarizeOverlaps function in the GenomicAlignments R package (version 1.16.0). Differential peaks were identified using the DESeq2 package (version 1.22.2) (Love et al., 2014).
Genome_build: Oryza sativa IRGSP-1.0
Supplementary_files_format_and_content: BED files containing peak locations per histone mark
Supplementary_files_format_and_content: CSV files containg the results of the differential peak change analysis per histone mark

organism: Oryza sativa Japonica Group

source_name: Mixture of infected roots and uninfected roots

growth_protocol: Oryza sativa L. cv. ‘Nipponbare’ (GSOR-100, USDA) seeds were germinated for 5 days in darkness at 30 °C, after which they were transferred to synthetic absorbent polymer (SAP) substrate in polyvinylchloride (PVC) tubes (Reversat et al., 1999) and grown at 28 °C (16 h light/8 h darkness). Plants were watered by Hoagland solution every other day.

extract_protocol:
Two-week-old rice plants (cv. Nipponbare) were grown as described above and inoculated by 300 J2 nematodes per plant or mock-inoculated with water as a control. After 36 hours, they were transferred to 50 % Hoagland solution in glass tubes to synchronize the infection process. Three days after inoculation (3 dai), galls of infected plants and uninfected roots tips were harvested and snap frozen in liquid nitrogen. The chromatin extraction and shearing was performed according to the Diagenode Chromatin Shearing Optimization Kit for Universal Plant ChIP-seq Kit (Cat. No. C01020014) and precipitation according to Plant ChIP-seq kit (Cat. No. C011010150) with some modifications. Briefly, collected galls and root tips (for each three biological replicates), were cross-linked in a buffer containing 1 % formaldehyde for 15 minutes on ice in a desiccator under vacuum condition. After that, gGlycine was added to stop crosslinking under an additional 5 minutes of vacuum. Then, root materials were ground to a fine powder in liquid nitrogen. The chromatin was extracted using three extraction buffers as in protocol and the final pellet was collected and dissolved in 600 µLl of sonication buffer supplemented with Protease Inhibitor Cocktail (Sigma, P9599). Sonication was performed using a Covaris M220 Focused-Ultrasonicator TM under the following settings: Peak power of 75, duty factor of 10 and cycle/burst of 200 for 15 minutes. The sonicated plant materials were centrifuged (16000 g for 5 minutes) and the supernatant was collected to proceed with immunoprecipitation. Chromatin precipitation was performed using three antibodies purchased from Diagenode (Belgium), H3K9ac (C15410004), H3K9me2 (C15410060) and H3K27me3 (C15410195). For chromatin precipitation, magnetic beads (DiaMag protein A-coated magnetic beads: Diagenode, C03010020) were incubated with each antibody overnight, after which they were washed with ChIP dilution buffer to remove unbound antibodies. Then beads were incubated for 10h with 50 µL of sheared chromatin diluted in ChIP dilution buffer (Diagenode, Belgium). One tenth of the diluted chromatin was collected and kept aside as an input sample before incubation with antibody (un-precipitated chromatin). After incubation, beads were washed with washing buffers to remove unbound DNA fragments as in protocol (Cat. No. C011010150). DNA was eluted from the beads using elution buffer. The input and precipitated DNA were washed in absolute ethanol and the pellet was dissolved in 20 µLl of DNase free water.
Library preparation was done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). To prepare samples, 34 µL of DNase-free water was added to 16 µL of precipitated DNA   and then adaptors were ligated to DNA fragments according to the manufacturer’s instructions (NEBNext Multiplex Oligos for Illumina kit NEB, E7335L). After ligation, the DNA samples were cleaned up using AMPure XP beads (0.9x) (Beckman Coulter). Then, the fragments were amplified for 14 cycles using NEBNext Ultra II PCR protocol (New England BioLabs). The quality of the libraries was assessed with Agilent High sensitivity DNA kit. The amplicons were excised from 2 % agarose gel (200-800 bp fragments were excised) and then purified from gel using the Gel DNA recovery kit (Zymo Research). After purification, the quality was assessed again using the Agilent High Sensitivity DNA Kit. The library concentrations were measured with qPCR according to Illumina’s Sequencing Library qPCR Quantification Guide. Sequencing was done on a NextSeq500 using single reads (76 bp). A 2.3 pM library was loaded on the flowcell with 2 % Phix spike-in.

treatment_protocol: A pure culture of M. graminicola was originally obtained from the Philippines (Prof. Dirk De Waele, Catholic University Leuven). The nematodes were cultured on susceptible rice and grasses (Echinocloa crus-galli). Nematodes were extracted from 3-4 month old cultures using tray method (Whitehead and Hemming, 1965). After 2-3 days nematode suspension was collected and concentrated using 20 µm sieves. Two-week-old plants were inoculated by around 300 second-stage juveniles per plants or mock inoculated with water.

tag: plant age

value: 14 days

tag: cultivar

value: Nipponbare

tag: antibody


title: H3K9ac Control 2

description:
H3K9ac_peaks.bed
H3K9ac_peak_changes.csv

source_name: Uninfected roots

tag: replicate number


title: 7-TG3

city: Paris

first: Maharajah

last: Ponnaiah

state: Île-de-France

address: 47-83 Boulevard de l'Hôpital

country: France

institute: Institute for Cardiometabolism and Nutrition

description: gene expression data from CD 103+ CD11b+ sorted dendritic cells

hyb_protocol: cDNA hybridization was performed using the GeneChip® Mouse Gene 2.0 ST (Affymetrix) following the manufacturer’s instructions.

scan_protocol: The scanned images are then analyzed with Expression Console software (Thermofischer) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.

data_processing: RMA normalization is performed using PartekGenomicSuite version 7 software . All subsequent analyses were based on the log (base 2) transformed data in Partek Genomics Suite: non-supervised analysis and Anova were used to detect eventual outlier samples and to identify differentially expressed genes. Statistical and Hierarchial clustering was performed using the TIGR Multiple Experiment Viewer (MeV 4.9.0).

source_name: cDC CD103+ CD11b+ from DChBcl-2

label_protocol: Total RNA (2.5 ng) was reverse transcribed following the Ovation Pico WTA System V2 (Nugen).

growth_protocol: 8 wks-old mice were killed by cervical dislocation and mesenteric lymph nodes harvested for further cell preparation.

extract_protocol: After FACS-cell sorting, cells were counted and resuspended in Trizol lysis reagent (Thermo Fisher Scientific), frozen in liquid nitrogen, and stored at −80°C. RNA extraction was performed using the RNeasy micro kit (Qiagen) following the manufacturer’s instructions

treatment_protocol: To obtain cells from mesenteric lymph nodes organs were manually smashed on cell strainer, and after washing step the cells were stained for subsequent cDC CD103+ CD11b+ FACS-cell sorting

tag: gender

value: Male

value: 8 weeks-old

value: mesenteric lymph nodes

value: hBcl-2 transgene


title: 6-TG2

tag: strain


title: 5-TG1

tag: genotype


title: 2-WT2

source_name: cDC CD103+ CD11b+ from WT

value: wild type


title: TKO_Flk1_rep1

description: Gene expression data from Flk1+ mesoderm cells derived from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

hyb_protocol: 600 ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 degrees C and 10 rpm according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5).

scan_protocol: Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 3 um resolution and 20-bit dynamic range.

data_processing: The scanned images were processed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20110406) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) removal of data of outlier probes (gIsFeatNonUnifOL flag = 1 or  gIsFeatPopnfOL flag = 1 in any of samples), c) log2 transformation, and d) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.

source_name: Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

label_protocol: Amplification and Cy3 labeling of RNA was prepared from 50 ng of RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5). Purification of Cy3-labeled cRNA was performed using the RNeasy Mini Kit (Qiagen). Quantity, quality and dye incorporation of Cy3-labeled cRNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

value: Line 19-1

value: Flk1+ mesoderm cells derived from embryonic stem (ES) cells


title: 4-WT4


title: HuH7 EGOT gapmer. Replicate 1

city: Pamplona

first: Puri

last: Fortes

address: Pio XII 55

country: Spain

institute: CIMA/UNAV

description: Cell transfected with PKR and pIC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Genome Array.

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

data_processing: Both background correction and normalization were done using RMA (Robust Multichip Average) algorithm. Then, a filtering process was performed to eliminate low expression probe sets. We selected 33732 probe sets with an expression value greater than 16 in at least two samples for each experimental condition. R/Bioconductor was used for preprocessing and statistical analysis

source_name: HuH7 cells transfected with gapmer targeting EGOT

label_protocol: Cy3 cRNAs were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: HuH7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) enriched with 10% fetal bovine serum (Invitrogen), 100 µg/ml streptomycin and 100 IU/ml penicillin (Invitrogen), and 2 mM glutamine (Invitrogen) at 37°C in a 5% CO2 atmosphere.

extract_protocol: Cellular RNA was extracted with the MaxWell 16 research system from Promega following the manufacturer’s recommendations. RNA concentration was measured using NanoDrop 1000 Spectrophotometer. The quality of the RNA used for microarray hybridization was analyzed by Bioanalyzer (AgilentTechnologies).

treatment_protocol: HuH7 cells were seeded in 6-well plates at 100,000 cell/well. One day later, cells were transfected with lipofectamine 2000 (Invitrogen) in Opti-MEM (Gibco) according to the manufacturer’s recommendations. Six hours after transfection fresh complete medium was added. Each 6-well-plate well received 1 µg of plasmid DNA containing a carrier plasmid and 0.3 µg of the plasmid expressing PKR (EMBO Rep. 17: 1013–1028.2016). For the transfection of LNA GapmeR oligonucleotides (EXIQON), each well of a 6-well-plate received 50 pmol of gapmers targeting the sequence AGAGACACTTAGAAGA (ga·1αEGOT), or AACACGTCTATACGC (gaCtrl).


title: WT_TS_rep2

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor

source_name: mouse wild-type (WT) ntTS cells, replicate 2

value: Line 9.2

value: wild-type, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst


title: WT_Flk1_rep1

description: Gene expression data from Flk1+ mesoderm cells derived from wild-type ES cells

source_name: Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 1

value: Line J1

value: wild-type


title: HuH7 EGOT gapmer. Replicate 3

description: Cell transfected with PKR and pIC


title: WT_TS_rep1

source_name: mouse wild-type (WT) ntTS cells, replicate 1


title: HuH7 control gapmer. Replicate 3

description: Cell transfected with PKR and pIC

source_name: HuH7 cells transfected with control gapmer


title: TKO_TS_rep2

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 2

value: Line 1

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene


title: 8-TG4


title: TKO_Flk1_rep2

source_name: Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2


title: 3-WT3


title: HuH7 EGOT gapmer. Replicate 2

description: Cell transfected with PKR and pIC


title: HuH7 control gapmer. Replicate 1

description: Cell transfected with PKR and pIC


title: H3K9ac Infected 2

source_name: Infected roots


title: TKO_ES_rep2

description: Gene expression data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

value: embryonic stem (ES) cells


title: TKO_ES_rep1

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1


title: H3K9ac Control 1

value: 14 days


title: WT_ES_rep2

description: Gene expression data from wild-type ES cells

source_name: mouse wild-type (WT) ES cells, replicate 2


title: TKO_TS_rep1

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 1


title: H3K9ac Infected 1

value: Nipponbare


title: HuH7 control gapmer. Replicate 2

description: Cell transfected with PKR and pIC


title: H3K9me2 Control 3

description:
H3K9me2_peaks.bed
H3K9me2_peak_changes.csv


title: 1-WT1

value: Male


title: H3K9me2 Control 1


title: WT_ES_rep1

source_name: mouse wild-type (WT) ES cells, replicate 1


title: H3K9me2 Control 2

source_name: Uninfected roots


title: H3K9me2 Infected 2


title: YPL245_WT_Sfp1_ChEC

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

country: Switzerland

institute: Univeristy of Geneva

data_processing:
Library strategy: ChEC-Seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive" through HTSStation (http://htsstation.epfl.ch)
Data were filtered to retain only the mapped reads with at most 5 hits in the reference
The mapped reads were extended by 1 bp only to indicate cut sites
All densities were normalized by total number of reads (in units of 10 millions)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to OD600=0.6

extract_protocol:
DNA was prepared as described in Kubik S. et al., 2018 (PMID: 29979971 )
Libraries were constructed as described in Kubik S. et al., 2018 (PMID: 29979971 )

treatment_protocol: At OD600 ~0.6, cells were washed and resuspended in a buffer containing 15 mM Tris, pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1× Roche EDTA-free mini protease inhibitors, 1 mM PMSF and 0.1% digitonin and incubated for 5 min at 30°C. CaCl2 was added to the final concentration of 5 mM and reactions were stopped after 10, 30, 60 seconds for Esa1 and Gcn5 ChEC, 60 seconds for Sfp1 ChEC and 20 minutes for free MNase ChEC by adding EGTA to a final concentration of 50 mM.

value: W303 MATa pGUA1-mut SFP1-3XFLAGMNase::hphMX4


title: H3K9me2 Infected 3


title: H3K9me2 Infected 1


title: YPL245_MT_Sfp1_ChEC

value: W303 MATa pYPL245W-mut SFP1-3XFLAGMNase::hphMX4


title: YPL245_WT_free_MNase_ChEC

value: W303 MATa pGUA1-mut pREB1-3XFLAG-Mnase::URA3


title: recurrent low glucose  exp 2

type: genomic

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

description: recurrent low glucose

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina HiScan

data_processing:
WateRmelon
Normalized (dasen) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Astrocyte Primary Cell Line

label_protocol: DNA methylation was measured using the Infinium MethylationEPIC BeadChip platform

extract_protocol: DNA was extracted using a modified phenol:chloroform protocol.

value: Recurrent hypo

tag: experiment

tag: hypo

tag: status

tag: ID


title: antecedent RLG  exp 2

description: antecedent RLG

tag: treatment

value: Antecedent hypo


title: control exp 2

description: control

value: Control

value: ctrl


title: YPL245_MT_free_MNase_ChEC

value: W303 MATa pYPL245W-mut pREB1-3XFLAG-Mnase::URA3


title: H3K27me3 Control 3

description:
H3K27me3_peaks.bed
H3K27me3_peak_changes.csv


title: H3K27me3 Control 2


title: WT_Flk1_rep2

source_name: Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 2

tag: cell line

tag: cell type

value: Flk1+ mesoderm cells derived from embryonic stem (ES) cells


title: recurrent low glucose  exp 1

description: recurrent low glucose


title: DNMT3BKO_rep2

description: Gene expression data from Dnmt3b-/- ES cells

data_processing: The scanned images were processed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20110406) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) log2 transformation, and c) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.

source_name: mouse Dnmt3b-/- ES cells, replicate 2

growth_protocol: ES cells were cultured in feeder-free conditions in Glasgow Minimum Essential Medium (GMEM) (WAKO) containing 10% FCS (Invitrogen), 1 mM glutamine (WAKO), nonessential amino acid (WAKO) and 0.1 mM mercaptoethanol (WAKO) and supplemented with LIF (WAKO).

extract_protocol: Total RNA was isolated by TRIZOL Reagent (Invitrogen) and purified using the RNeasy Plus Micro Kit with gDNA Eliminator column (Qiagen) according to the manufacturer's protocols. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

value: Line 8bb

value: embryonic stem cells (ESCs)


title: J1_PRDM14OE_DNMT3B_rep1

description: Gene expression data from PRDM14 and DNMT3B1 overexpressing ES cells

source_name: mouse PRDM14 and DNMT3B1 overexpressing wild-type ES cells, replicate 1

value: Line JP-23+3b-3

value: wild-type, stably expressing Prdm14 and Dnmt3b1 gene


title: J1_rep1

source_name: mouse wild-type ES cells, replicate 1

value: Line J1

value: wild-type


title: Dnmts TKO

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/-  ES cells

value: Line 19-1


title: low glucose  exp 2

description: low glucose

value: Acute Hypo


title: H3K27me3 Infected 3

value: 14 days

value: Nipponbare


title: DNMT3BKO_rep1

source_name: mouse Dnmt3b-/- ES cells, replicate 1


title: J1_PRDM14OE_DNMT3B_rep2

source_name: mouse PRDM14 and DNMT3B1 overexpressing wild-type ES cells, replicate 2


title: recurrent low glucose  exp 6

description: recurrent low glucose


title: H3K27me3 Infected 2


title: DNMT1KO

description: Gene expression data from Dnmt1-/- ES cells

source_name: mouse Dnmt1-/- ES cells

value: Line 36


title: H3K27me3 Control 1


title: J1_PRDM14OE_rep1

description: Gene expression data from PRDM14-overexpressing wild-type ES cells

source_name: mouse PRDM14-overexpressing wild-type ES cells, replicate1

value: Line JP-23

value: wild-type, stably expressing Prdm14 gene


title: J1_PRDM14OE_rep2

source_name: mouse PRDM14-overexpressing wild-type ES cells, replicate2


title: antecedent RLG  exp 1

description: antecedent RLG

value: Antecedent hypo


title: J1_rep2

source_name: mouse wild-type ES cells, replicate 2


title: low glucose  exp 1

description: low glucose


title: control exp 1

description: control

value: Control

value: ctrl


title: RPL4_mutant_Ribo_seq

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
The adaptor of all sequencing data was removed by Cutadapt.
The clean reads were aligned to human transcriptome using STAR aligner with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab separated RPKM table. The first column is the Ensembl transcript ID, the second column is the RPKM value.

source_name: Human embryonic kidney cells

growth_protocol: HEK293 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
Sucrose solutions were prepared in polysome gradient buffer (10 mM Hepes, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 5 mM DTT, and 20 U/ml SUPERase_In (Ambion)). Sucrose density gradients (15% - 45% (wt/vol)) were freshly made in SW41 ultracentrifuge tubes (Fisher) using a BioComp Gradient Master (BioComp) according to the manufacturer's instructions. Cells were plated to four 10-cm dishes before ribosome profiling. HEK293 cells were first treated with CHX (100 μM) or LTM (50 μM) for 30 min at 37 °C to freeze the translating ribosomes or initiating ribosomes, respectively. After ice-cold PBS solution wash, cells were then harvested by ice-cold polysome lysis buffer (10 mM Hepes, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 5 mM DTT, 20 U/ml SUPERase_In, and 2% (vol/vol) Triton X-100). After centrifugation at 4 °C and 10 000× g for 10 min, approximately 650 μl supernatant was loaded onto sucrose gradients, followed by centrifugation for 100 min at 38 000 rpm, 4 °C, in an SW41 rotor. Separated samples were fractionated at 0.375 ml/min by using a fractionation system (Isco) that continually monitored OD254 values. Fractions were collected into tubes at 1-min intervals. To convert the polysome into monosome, E. coli RNase I (Ambion) was added into the pooled polysome samples (750 U per 100 A260 units) and incubated at 4 °C for 1 h. SUPERase_In (50 U per 100 U RNase I) was then added to stop digestion. Total RNA extraction was performed using TRIzol reagent.
Purified RNA samples were dephosphorylated in a 15 μl reaction containing 1× T4 polynucleotide kinase buffer, 10 U SUPERase_In, and 20 U T4 polynucleotide kinase (NEB). Dephosphorylation was carried out for 1 h at 37 °C, and the enzyme was then heat inactivated for 20 min at 65 °C. Dephosphorylated samples were then mixed with 2 Novex TBE-Urea sample buffer (Invitrogen) and loaded on a Novex denaturing 15% polyacrylamide TBE-urea gel (Invitrogen). The gel was stained with SYBR Gold (Invitrogen) to visualize the RNA fragments. Gel bands containing RNA species corresponding to 28 nt were excised and physically disrupted by centrifugation through the holes of the tube. RNA fragments were dissolved by soaking overnight in gel elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U/ml SUPERase_In). The gel debris was removed using a Spin-X column (Corning) and RNA was purified by using ethanol precipitation. Purified RNA fragments were resuspended in 10 mM Tris (pH 8) and denatured briefly at 65 °C for 30 s. Poly-(A) tailing reaction was performed in a 8 μl buffer with 1× poly-(A) polymerase, 1 mM ATP, 0.75 U/μl SUPERase_In, and 3 U E. coli poly-(A) polymerase (NEB). Tailing was carried out for 45 min at 37 °C. For reverse transcription, the following oligos containing barcodes were synthesized:    MCA02, 5′-pCAGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3′; LGT03, 5′-pGTGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3′; YAG04, 5′-pTCGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3′; HTC05, 5′-pAGGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3′.    In brief, the tailed RNA product was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 65 °C for 5 min, followed by incubation on ice for 5 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III (Invitrogen). Reverse transcription reaction was performed according to the manufacturer's instructions. RNA was eliminated from cDNA by adding 1.8 μl of 1 M NaOH and incubating at 98 °C for 20 min. The reaction was then neutralized with 1.8 μl of 1 M HCl. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 100 nt, and the corresponding region was excised. The cDNA was recovered by using DNA gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine, and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 h, and the reaction was heat inactivated at 80 °C for 10 min. Circular single-strand DNA was relinearized with 20 mM Tris-acetate, 50 mM potassium acetate, 10 mM magnesium acetate, 1 mM DTT, and 7.5 U APE 1 (NEB). The reaction was carried out at 37 °C for 1 h. The linearized single-strand DNA was separated on a Novex 10% polyacrylamide TBE-urea gel (Invitrogen) as described earlier. The expected 100-nt product bands were excised and recovered as described earlier.

treatment_protocol: HEK293 stable cell lines expressing GFP control, L4 wild type, or Δloop mutant were infected with lentiviruses encoding shRNA targeting RPL4 or scramble control.

value: RPL4 mutant

value: no erythromycin


title: H3K27me3 Infected 1

source_name: Infected roots


title: TKO_TS_K9_rep1

description: H3K9me2 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor

hyb_protocol: Approximately 4 ug each of Cy3 and Cy5 labeled DNA were hybridized in Agilent hybridization chambers for 40.5-41.0 hours at 65 degrees C and 20 rpm according to the manufacturer's instructions (G4481-90010 Agilent Mammalian ChIP-on-chip Protocol Version 10.11).

data_processing: The scanned images were processed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol ChIP_107_Sep09 and Grid 027128_D_F_20100129) to generate background subtracted and spatially detrended Processed Signal intensities and log 10 ratios with the linear normalization.  Data was processed by a) change log base from 10 to 2, b) removal of data of control probes, c) removal of data of outlier probes (gIsFeatNonUnifOL flag = 1,  gIsFeatPopnfOL flag = 1, gIsPosAndSignif flag = 0, rIsFeatNonUnifOL = 1 or rIsFeatPopnfOL = 1 in any of samples).

source_name: H3K9me2 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 1

label_protocol: Without amplification, ChIP DNA and input MNase digested DNA were labeled with Cy5 and Cy3, respectively, using the Genomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions (G4481-90010 Agilent Mammalian ChIP-on-chip Protocol Version 10.11). Purification of labeled DNA was performed using the Amicon Ultra-0.5, Ultracel-30, 30kDa (Millipore). Quantity and dye incorporation of labeled DNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

extract_protocol: Approximately 3-5 x 10^6 cells were collected and washed twice with ice-cold PBS. The cells were suspended in 50 ul of 0.3 M sucrose containing buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5mM dithiothreitol, 0.5 % Protease Inhibitor Cocktail (SIGMA P8340) , 15 mM Tris-HCl pH7.5). The cells were lysed by adding 50 ul of 0.8 % NP-40 and 0.3 M sucrose containing buffer 1 and put on ice for 10 min. The lysate was layered over 0.8 ml of 1.2 M sucrose containing buffer 1. The nuclear pellets were collected by centrifuge 8.5 k rpm 10 min, and resuspended in 250 ul of micrococcal nuclease (MNase) digestion buffer (4 mM MgCl2, 1 mM CaCl2, 0.32 M sucrose, 0.5 % Protease Inhibitor Cocktail (SIGMA P8340) , 50 mM Tris-HCl pH7.5). MNase digestion was performed at 37 degrees C for 20 min with 0.8 U MNase (Takara), then stopped by addition of EDTA to final 20 mM. The chromatin extract was obtained as the supernatant of centrifugation at 13 k rpm 10 min. 60 x 2 (duplicate), 30 and 80 ul of the chromatin extracts were used for immunoprecipitation for H3K4me2, H3K9me2 and H3K27me3, respectively, and remained extract was served for the input sample (MNase digested input DNA). 60 x 2 (duplicate), 30, 80 ul of Dynabeads M-280 Sheep anti-Mouse IgG (Invitorogen), pre-equilibrated with incubation buffer (50 mM NaCl, 5 mM EDTA, 0.1 % NP-40, 0.1 mM PMSF, 20 mM Tris-HCl pH 7.5), were incubated overnight with 3, 1.5 and 4 ug of mouse monoclonal antibodies against H3K4me2 (Monoclonal antibody institute, MABI0303), H3K9me2 (Monoclonal antibody institute, MABI0307) and H3K27me3 (Abcam, ab6002), respectively, in 200 ul of incubation buffer. Beads-antibody complexes were collected and resuspend in 540 x 2 (duplicate), 270 and 720 ul, for H3K4me2, H3K9me2 and H3K27me3, respectively, of incubation buffer and incubated 4 hours with the chromatin extract. The immune complexes were sequentially washed with 75, 125 and 175 mM NaCl containing buffer A (10 mM EDTA, 0.1 % NP-40, 50 mM Tris-HCl pH 7.5). Both input and immunoprecipitated samples were treated with RNase and proteinase K, and purified with MinElute Reaction Cleanup kit (Qiagen).

value: Line 1

tag: genotype/variation

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst

tag: chip antibody

tag: chip antibody vendor

value: Monoclonal antibody institute

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K9me2 ChIP, replicate 1

value: none, MNase digested input DNA


title: TKO_TS_K27_rep1

description: H3K27me3 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor

source_name: H3K27me3 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 1

value: Abcam

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K27me3 ChIP, replicate 1


title: antecedent RLG  exp 5

description: antecedent RLG

source_name: Astrocyte Primary Cell Line


title: TKO_TS_K27_rep2

source_name: H3K27me3 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 2

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K27me3 ChIP, replicate 2


title: TKO_TS_K9_rep2

source_name: H3K9me2 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 2

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K9me2 ChIP, replicate 2


title: RPL4_mutant_with_erythromycin_Ribo_seq

description: ribosome protected RNA

value: erythromycin


title: antecedent RLG  exp 6

description: antecedent RLG


title: Wild_type_Ribo_seq

description: ribosome protected RNA

value: Wild type


title: antecedent RLG  exp 4

description: antecedent RLG


title: antecedent RLG  exp 3

description: antecedent RLG


title: recurrent low glucose  exp 5

description: recurrent low glucose

value: Recurrent hypo


title: recurrent low glucose  RH_3

description: recurrent low glucose

data_processing:
fastq sequence quality was checked using MultiQC
Alignment to the human genome using STAR
Mapped reads were counted using the FeatureCounts function of the subread package
Differential gene expression was calculated using DESeq2
Genome_build: Build GRCh38.p12
Supplementary_files_format_and_content: csv file of counts

extract_protocol:
RNA was extracted using TRIzol and Direct-zol miniprep kit (Invitrogen, Carlsbad, CA, USA).
cDNA libraries were generated using the TruSeq DNA HT Library Preparation Kit (Illumina Inc., San Diego, CA, USA)

value: RH

tag: pretreatment

tag: glucose


title: low glucose  exp 5

description: low glucose

value: Acute Hypo


title: Wild_type_with_erythromycin_Ribo_seq

description: ribosome protected RNA


title: low glucose  exp 6

description: low glucose


title: recurrent low glucose  RH_6

description: recurrent low glucose


title: control exp 5

description: control


title: low glucose  exp 4

description: low glucose


title: WT_TS_K27_rep2

description: H3K27me3 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor

source_name: H3K27me3 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 2

value: Line 9.2

value: wild-type, carrying the CAG-GFP transgene

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K27me3 ChIP, replicate 2


title: control exp 3

description: control

value: Control


title: recurrent low glucose  RH_1

description: recurrent low glucose


title: control exp 4

description: control

value: ctrl


title: control exp 6

description: control


title: TKO_TS_K4_rep2

description: H3K4me2 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor

source_name: H3K4me2 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 2

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K4me2 ChIP, replicate 2


title: recurrent low glucose  RH_5

description: recurrent low glucose


title: Control, RNA-seq

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

institute: Yamaguchi University School of Medicine

description: no treatment

data_processing:
RNA-Seq; After the quality of the library was validated using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), the samples were subjected to sequencing with a next-generation sequencer (Genome Analyzer GAIIx, Illumina, San Diego, CA).  Then, gene expression values were calculated as “reads per kilobase of exon unit per million mapped reads” (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: In RNA-Seq, RPKM was calculated with TopHat.

source_name: endometrial stromal cells

extract_protocol:
Total RNA was isolated from the cultured cells from one patient with an RNeasy® Mini Kit. (QIAGEN, Inc., Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocol.

treatment_protocol: ESCs were transfected with control or C/EBPb siRNA and then treated with or without cAMP for 4 days.

value: endometrial stromal cells

tag: transfection

tag: agent

value: no treatment


title: low glucose  exp 3

description: low glucose


title: WT_TS_K9_rep1

description: H3K9me2 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor

source_name: H3K9me2 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 1

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K9me2 ChIP, replicate 1


title: recurrent low glucose  exp 3

description: recurrent low glucose


title: WT_TS_K27_rep1

source_name: H3K27me3 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 1

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K27me3 ChIP, replicate 1


title: WT_TS_K4_rep2

description: H3K4me2 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor

source_name: H3K4me2 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 2

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K4me2 ChIP, replicate 2


title: TKO_TS_K4_rep1

source_name: H3K4me2 ChIP DNA mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells, replicate 1

value: Line 1

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS cells for H3K4me2 ChIP, replicate 1


title: recurrent low glucose  RH_2

description: recurrent low glucose

source_name: Astrocyte Primary Cell Line


title: cAMP_under_C/EBPb-knockdown, RNA-seq

description: cAMP treatment under C/EBPb-knockdown

value: C/EBPb siRNA

value: cAMP treatment


title: low glucose  HYPO_6

description: low glucose

value: H

value: control


title: Control

description: no treatment

data_processing:
ChIP-Seq; After the quality of the library was validated using the Agilent Bioanalyzer 2100 (Agilent Technology), the ChIP-sequence library was sequenced by the Genome Analyzer GAIIx.  The obtained reads from the sequencing platform was first applied for quality checking by the fastx quality stats program in the FASTX-Toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/).  The reads that passed the quality checking were then mapped to the human reference genome sequence (hg19) by using the bowtie program followed by Model-Based Analysis of ChIP-Sequence (MACS) to detect the H3K27ac regions.
Genome_build: hg19
Supplementary_files_format_and_content: For peal calling, MACS was used.

extract_protocol:
See library construction protocol
Cultured cells were cross-linked by adding formaldehyde to the medium at a final concentration of 1% and incubated for 10 min at 37 °C.  Cross-linking was terminated by addition of glycine (0.125 M, final concentration).  ChIP was performed with H3K27ac antibody.  An unimmunoprecipitated control and immunoprecipitated DNA were used to prepare the ChIP-seq library with NEBNext DNA sample prep master mix set 1 (New England BioLabs, Ipswich, MA) and DNA sample prep kit, oligo only (Illumina) according to the manufacturer’s instructions.

tag: antibody


title: cAMP

description: cAMP treatment


title: cAMP_under_C/EBPb-knockdown

description: cAMP treatment under C/EBPb-knockdown


title: cAMP, RNA-seq

description: cAMP treatment


title: low glucose  HYPO_3

description: low glucose


title: low glucose  HYPO_5

description: low glucose


title: degradome S4

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

data_processing:
The putative miRNA:target pairs were predicted by different algorithms: targetSeek approach or PAREsnip2 approach.
PAREsnip2 approach: firstly raw sequencing reads were processed by CLC Genomics Workbench
Trim settings: removal - low quality sequence (limit = 0.02), ambiguous nucleotides: maximal 2 nucleotides allowed, adapter sequences, removal of sequences on length - minimum length 15 nucleotides.
The putative miRNA:target pairs were predicted by PAREsnip2 software (Thody et al., 2018) to generate t-plots in conjunction with five databases (miRNAs, small RNAs, differentially expressed mRNAs, cDNAs from Ensembl Plants, and degradome profiles from roots and shoots). We set the Fahlgren and Carrington targeting rules that permit a mismatch or G:U wobble at position 10. Thody J, Folkes L, Medina-Calzada Z, Xu P, Dalmay T, Moulton V. PAREsnip2 : a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules. Nucleic Acids Res. 2018;46(17):8730–39.
In the second approach, TargetSeek: the raw sequencing reads were processed by Cutadpt program (https://cutadapt.readthedocs.io/en/stable/) to trim low-quality and adapter sequences. Only sequences of length 15 nt and above were selected for further analyses. The processed sequencing reads were aligned to the reference sequences using bowtie. The count of 5'-end marked cleavage sites was scored by Perl script and normalized to the depth of sequencing and total signal for each of the reference transcripts.
TargetSeek cont.: The putative miRNA:target pairs were predicted by a custom program (targetSeek) which included the following steps: (i) calculation of perfect match MFE (minimum free energy); (ii) RNAplex-based (Vienna package) screening for sRNA:transcript pairs; (iii) filtering number of bulges and length of sequence overhangs by MFE (percent of the perfect MFE match); and (iv) calculation of prediction score using a penalty schema for loops, bulges, and G:U wobble pairing.
Genome_build: miRBase release 22 and Hordeum vulgare, Ensembl Plants database v.40
Supplementary_files_format_and_content: Degradome_analysis.xlsx file which has been generated using PAREsnip2 software (The UEA Small RNA Workbench) using three databases:   A. microRNA_set.fasta file (162 sequences from barley shoot);   B. transcripts.fasta file (cDNA from barley shoot);   C. submitted degradome data (Degradome_S4_JDG-2-2.fastq.gz);

organism: Hordeum vulgare

source_name: shoot

growth_protocol: Barley seeds were germinated on wet, sterile Whatman filter paper for 3 days in a growth chamber under long-day (16 h) conditions at 23 °C until white hypocotyls were visible. Three seedlings were then transferred to a single pot that contained a mixture of sterile low-Pi soil (8 mg P/kg) and sand (7:2 ratio). The plants were subsequently grown under controlled conditions, which included a 16 h day/8 h night photoperiod at a temperature of 22 °C. Plant material was obtained from low-Pi regime.

extract_protocol:
Shoots and roots of 23 old barley were harvested and frozen in liquid nitrogen. Total RNA was extracted from 1.5 g of grinded organ using RNA extraction buffer: 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate pH 5.0, 5% v/v glycerol, 38% v/v saturated acidic phenol, 5 mM EDTA, 0.5% sodium lauroylsarcosine, in diethylpyrocarbonate-treated water (DEPC).
Degradome libraries have been prepared according protocols described by German et al., 2009 and Alaba et al., 2015. Total RNA from barley root (R4) and shoot (S4) was isolated using RNA extraction buffer. PolyA RNA fraction was isolated using NucleoTrap® mRNA Mini kit (Macherey-Nagel). Then 5’ RNA adapter containing site recognized by MmeI restriction enzyme was ligated to isolated polyA RNA fragments using T4 RNA Ligase (ssRNA Ligase, NEB). Biotinylated oligo (dT)18 was attached to Dynabeads™ M-280 Streptavidin (Invitrogen) and used for purification of the ligation product. In next step reverse transcription was carried out using specific RT-oligo dT (41 nt) oligo and SuperScript™ II reverse transcriptase (Invitrogen). cDNA was purified using phenol/chloroform and resuspended in water. Then PCR was performed using Q5® High-Fidelity DNA Polymerase (NEB), followed by treatment by Exonuclease I (NEB) and phenol/chloroform purification. Then purified PCR products were digested using MmeI, followed by FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and Proteinase K (invitrogen) treatment. Digested fragments were separated on 12% polyacrlamide gel, excised from the gel and purified. Then 3’ double stranded DNA adapters were ligated using Rapid DNA Ligation kit (Roche). Ligation products were purified using phenol/chloroform, separated on polyacrylamid gel and excised from the gel. Finally PCR was performed using indexed primers, PCR products were gel purified and used for NGS sequencing.  Final degradome library structure is given below, N – denotes cleaved or RNA degradation fragment ligated between 5’ and 3’ adapters, X – denotes index sequence:  5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGACNNNNNNNNNNNNNNNNNNNNNTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACXXXXXXATCTCGTATGCCGTCTTCTGCTTG 3’  Quantity of the purified libraries were performed using Qubit® dsDNA HS Assay kit (Invitrogen, Thermo Fisher Scientific) and Qubit 3.0 Fluorometer (Invitrogen, Thermo Fisher Scientific). Finally, the quality of the libraries was analyzed using High Sensitivity D1000 ScreenTape Assay (Agilent Technologies) and 2200 TapeStation (Agilent Technologies). Reference: German MA, Luo S, Schroth G, Meyers BC, Green PJ. (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc. 4(3):356-62.  Alaba S, Piszczalka P, Pietrykowska H, Pacak AM, Sierocka I, Nuc PW, Singh K, Plewka P, Sulkowska A, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. (2015) The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. New Phytol. 206(1):352-67.

treatment_protocol: Stressed plants were growing on soil (low-Pi contaning 8 mg of P/kg).

tag: line

value: Rolap

tag: protocol

value: low Pi condition


title: WT_TS_K4_rep1

source_name: H3K4me2 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 1

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst

value: Monoclonal antibody institute

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K4me2 ChIP, replicate 1

value: none, MNase digested input DNA


title: S17 RNA-Seq

data_processing:
Raw reads where trimmed (first 9 nucleotides) using CLC Genomics Workbech (Qiagen).
Quality trim (quality limit=0.01), automatic removal of read-through adapter sequences.
Following parameters were used during gene expression analysis using CLC Genomics Workbech:  Reference type = Genome annotated with genes and transcripts  Reference sequence = Hordeum_vulgare.IBSC_v2.dna.toplevel (Genome)  Gene track = Hordeum_vulgare.IBSC_v2.42_Gene  mRNA track = Hordeum_vulgare.IBSC_v2.42_mRNA  Use spike-in controls = yes  Spike-in controls = ERCC Spike-ins  Auto-detect paired distances = Yes  Strand specific = Both  Expression value = TPM
Statistical comparison of gene expression between samples derived from low-Pi vs. Control conditions was performed using CLC Genomics Workbench.
Genome_build: Hordeum vulgare, Ensembl Plants database v.42
Supplementary_files_format_and_content: Gene expression fold changes upon Pi starvation as a table in Excel file, created using CLC Genomics Workbench.

growth_protocol: Barley seeds were germinated on wet, sterile Whatman filter paper for 3 days in a growth chamber under long-day (16 h) conditions at 23 °C until white hypocotyls were visible. Three seedlings were then transferred to a single pot that contained a mixture of sterile low-Pi soil (8 mg P/kg) and sand (7:2 ratio). The plants were subsequently grown under controlled conditions, which included a 16 h day/8 h night photoperiod at a temperature of 22 °C. Plant material was obtained from two different Pi regimes: low-Pi and Pi-sufficient (control).

extract_protocol:
Shoots of 23 old barley were harvested and frozen in liquid nitrogen. Total RNA was extracted from 100 mg of grinded tissue using Direct-Zol RNA MiniPrep (Zymo Reserach). RNA quality was analyzed using Plant RNA Nano assay and 2100 Bioanalyzer (Agilent).
To 1500 ng of total RNA 420 pg of Spike-In RNA Variants SIRV-set3 (Lexogen) was added. This RNA was used for library construction for each sample. Libraries were prepared using mRNA-seq Library Prep kit V2 for Illumina® (Lexogen). Quantity of the purified libraries were performed using Qubit® dsDNA HS Assay kit (Invitrogen, Thermo Fisher Scientific) and Qubit 3.0 Fluorometer (Invitrogen, Thermo Fisher Scientific). Finally, the quality of the libraries was analyzed using High Sensitivity DNA assay (Agilent Technologies) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Stressed plants and control plants were growing on same soil (low-Pi contaning 8 mg of P/kg). To control plants additional 60 mg of P/kg (using KH2PO4) was added to provide Pi-sufficient conditions.

tag: condition

value: Pi sufficient condition


title: S18 RNA-Seq


title: degradome R4

source_name: root


title: low glucose  HYPO_2

description: low glucose


title: low glucose  HYPO_1

description: low glucose


title: TKO_Flk1_K27_rep2

description: H3K27me3 ChIP-chip data from Flk1+ mesoderm cells derived from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K27me3 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

value: Line 19-1

value: Flk1+ mesoderm cells derived from embryonic stem (ES) cells

value: Abcam

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K27me3 ChIP, replicate 2


title: S16 RNA-Seq


title: S6 RNA-Seq


title: Sample 4_PGC;Ras;APC FF-4

city: Singapore

first: Daisuke

last: Douchi

address: 14 Medical Drive

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

description: 1 mouse

data_processing:
Sequenced reads were aligned with the STAR software to mm10, and mapped counts were employed to generate the raw expression counts using the FeatureCounts with GENCODE transcriptome annotation.
The raw expression counts were then further normalized using the Cross-Correlation method (Nucleic Acids Res 2006;34:e38).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: PGC;Ras;APC FF_stomach

extract_protocol:
RNA was extracted from mouse stomach corpus using the RNeasy Mini Kit (QIAGEN) with on-column genomic DNA digestion using the RNase-free DNase Set (QIAGEN).
RNA were sent to Beijing Genomics Institute (BGI) for transcriptome library preparation and sequencing.

tag: strain background

tag: genotype

value: PGC;Ras;APC FF

tag: tissue

value: Stomach (corpus)


title: Sample 5_PGC;Ras;APC FF-5

description: 1 mouse


title: TKO_Flk1_K9_rep2

description: H3K9me2 ChIP-chip data from Flk1+ mesoderm cells derived from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K9me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

tag: cell line

tag: cell type

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K9me2 ChIP, replicate 2


title: TKO_Flk1_K27_rep1

source_name: H3K27me3 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

tag: genotype/variation

tag: chip antibody

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K27me3 ChIP, replicate 1


title: S5 RNA-Seq


title: Sample 3_Ras;APC FF-3

description: 1 mouse

source_name: Control (Ras;APC FF)_stomach

value: Control (Ras;APC FF)


title: control CONT_6

description: control

tag: treatment

value: C


title: control CONT_5

description: control


title: S4 RNA-Seq


title: Sample 2_Ras;APC FF-2

description: 1 mouse


title: control CONT_4

description: control


title: Sample 6_PGC;Ras;APC FF-6

description: 1 mouse


title: control CONT_3

description: control


title: R18 smallRNAs

data_processing:
Raw reads where trimmed using CLC Genomics Workbech (Qiagen)
Trim settings: removal - low quality sequence (limit = 0.02), ambiguous nucleotides: maximal 2 nucleotides allowed, adapter sequences, removal of sequences on length: minimum length 18 nucleotides and maximum length 25 nucleotides.
Extract and count was performed using CLC Genomics Workbench.
Empirical analysis of (EDGE) was used to find significant fold changes in small RNA expression levels between samples derived from different treated barley. Moreover we performed EDGE Bonferroni and EDGE FDR p-value correction calculation.
Unique sequences were annotated in a two-step process: firstly were mapped to miRBase to extract data about known microRNAs.
Secondly, unannotated to miRBase reads were maped to the Ensembl Plants database v.40 to annotate other small RNAs to different types of barley cDNAs.
Genome_build: miRBase release 22 and Hordeum vulgare, Ensembl Plants database v.40
Supplementary_files_format_and_content: Small RNA which are annotated to miRBase, small RNA which expression is changed significantly (Bonferroni p-value correction < 0.05).

extract_protocol:
Shoots and roots of 23 old barley were harvested and frozen in liquid nitrogen. Total RNA was extracted from 100 mg of grinded organ using RNA extraction buffer: 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate pH 5.0, 5% v/v glycerol, 38% v/v saturated acidic phenol, 5 mM EDTA, 0.5% sodium lauroylsarcosine, in diethylpyrocarbonate-treated water (DEPC) (Smoczynska et al., 2019) and protocol that allow for enrichment of small RNAs (Kruszka et al., 2013). Quality of the isolated RNA was analyzed using Plant RNA Nano assay and 2100 Bioanalyzer (Agilent Technologies). Reference: Smoczynska A, Sega P, Stepien A, Knop K, Jarmolowski A, Pacak A, Szweykowska-Kulinska Z. (2019) miRNA Detection by Stem-Loop RT-qPCR in Studying microRNA Biogenesis and microRNA Responsiveness to Abiotic Stresses. Methods Mol Biol. 1932:131-150.  Kruszka K, Pacak A, Swida-Barteczka A, Stefaniak AK, Kaja E, Sierocka I,  Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. (2013) Developmentally regulated expression and complex processing of barley pri-microRNAs. BMC Genomics. 14:34.
Total RNA was separated on 15 % 8M urea polyacrylamide gel and small RNA fraction 15 nt -30 nt was excised from the gel, purified and was used for libraries construction. Libraries were prepared using TruSeq Small RNA Library Preparation Kit (Illumina). Quantity of the purified libraries were performed using Qubit® dsDNA HS Assay kit (Invitrogen, Thermo Fisher Scientific) and Qubit 3.0 Fluorometer (Invitrogen, Thermo Fisher Scientific). Finally, the quality of the libraries was analyzed using High Sensitivity D1000 ScreenTape Assay (Agilent Technologies) and 2200 TapeStation (Agilent Technologies).

tag: tag

value: root


title: TKO_Flk1_K4_rep2

description: H3K4me2 ChIP-chip data from Flk1+ mesoderm cells derived from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K4me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

tag: chip antibody vendor

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K4me2 ChIP, replicate 2


title: Sample 1_Ras;APC FF-1

description: 1 mouse


title: TKO_Flk1_K4_rep1

source_name: H3K4me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K4me2 ChIP, replicate 1


title: WT_Flk1_K27_rep2

description: H3K27me3 ChIP-chip data from Flk1+ mesoderm cells derived from wild-type ES cells

source_name: H3K27me3 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 2

value: Line J1

value: wild-type

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K27me3 ChIP, replicate 2


title: TKO_Flk1_K9_rep1

source_name: H3K9me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K9me2 ChIP, replicate 1


title: R17 smallRNAs

source_name: root


title: control CONT_1

description: control

source_name: Astrocyte Primary Cell Line

tag: pretreatment

value: control

tag: glucose


title: antecedent RLG  AH_6

description: antecedent RLG

value: AH

value: RH


title: Mtb_AG_3

city: Shanghai

first: xiangyang

last: wu

address: 507 Zhengmin Road, Shanghai, China

institute: Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data contained low quality reads, contaminated joints, and unspecified high N base reads. These reads need to be removed by using SOAPnuke v1.5.2 solfware with parameters -l 15 -q 0.2 -n 0.1 (BGI Platform: https://github.com/BGI-flexlab/SOAPnuke) before data analysis to ensure the reliability of the results (QC).
After we got clean reads, we used HISAT(Hierarchical Indexing for Spliced Alignment of Transcripts) (Kim, Langmead et al. 2015) v2.0.4 software with parameters -p 8 --phred64 --sensitive -I 1 -X 1000 (http://www.ccb.jhu.edu/software/hisat) to compare clean reads to the reference genome sequence (May need to QC of alignment).
Clean reads were aligned to the reference sequence by using Bowtie2 (Langmead and Salzberg 2012) v2.2.5 software with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 (http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml), and then RSEM (Li and Dewey 2011) v1.2.12 software with the default parameters (http://deweylab.biostat.wisc.edu/ RSEM) was used to calculate the expression levels of genes and transcripts.
We used DEGseq algorithm with parameters Fold Change >= 2 and Adjusted Pvalue <= 0.001  for differential gene analysis a protocol from (Wang, Feng et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: differential expression statistics

source_name: peritoneal macrophage

growth_protocol: Peritoneal macrophages were isolated as described (Kong et al, 2009). Briefly, mice received intraperitoneally 2.0 ml of 4% Brewer’s thioglycollate medium (B2551, Sigma-Aldrich). After 3 days, peritoneal exudate cells were collected from euthanized animals using 10 ml cold PBS. Subsequently, cells were plated in 12-well plates at 106 cells/well in RPMI 1640 supplemented with 10% FBS plus penicillin/streptomycin and were incubated at 37°C in 5% CO2 for 2 hours. Cultures were washed three times with PBS to remove non-adherent cells, and the remaining adherent monolayer cells were used as primary peritoneal macrophages.

extract_protocol:
Total RNA was isolated, its concentration, RIN value, and 28S/18S fragment size were measured, used for RNA-seq analysis. cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NT(no treatment); AG(arabinogalactan, 1μg/ml, 24h); Mtb(H37Rv, MOI=5,24h); Mtb_AG(H37Rv MOI 5 for 24, plus arabinogalactan, 1μg/ml for 24h). Before infection, Mtb organisms were suspended in a complete medium without antibiotics. Peritoneal macrophages were infected with Mtb at an MOI of 5.

tag: strain

value: peritoneal macrophage


title: antecedent RLG  AH_5

description: antecedent RLG


title: R16 smallRNAs

value: Rolap


title: Mtb_AG_2


title: R6 smallRNAs

value: low Pi condition


title: R5 smallRNAs


title: Mtb_AG_1


title: Mtb_3


title: R4 smallRNAs


title: WT_Flk1_K9_rep2

description: H3K9me2 ChIP-chip data from Flk1+ mesoderm cells derived from wild-type ES cells

source_name: H3K9me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 2

value: Monoclonal antibody institute

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K9me2 ChIP, replicate 2

value: none, MNase digested input DNA


title: WT_Flk1_K27_rep1

source_name: H3K27me3 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 1

value: Flk1+ mesoderm cells derived from embryonic stem (ES) cells

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K27me3 ChIP, replicate 1


title: WT_Flk1_K9_rep1

source_name: H3K9me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 1

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K9me2 ChIP, replicate 1


title: antecedent RLG  AH_2

description: antecedent RLG


title: WT_Flk1_K4_rep2

description: H3K4me2 ChIP-chip data from Flk1+ mesoderm cells derived from wild-type ES cells

source_name: H3K4me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 2

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K4me2 ChIP, replicate 2


title: Mtb_2


title: antecedent RLG  AH_1

description: antecedent RLG


title: AG_2


title: S18 smallRNAs

source_name: shoot

value: shoot

value: Pi sufficient condition


title: S17 smallRNAs


title: Sample_10_UsOS50_cont [control]

city: Tel Aviv

first: Yuval

last: Ebenstein

state: HaMerkaz (Central)

address: Ramat Aviv

institute: Tel Aviv University

description: processed data file: Control - no damage.bedgraph

data_processing:
library strategy: Repair Assisted Damage Detection sequencing (RADD-seq)
Sequencing reads were aligned to the hg38 human reference using Bowtie 2 (version 2.3.4.2) with default parameters
Following alignment, reads with MAPQ less than 30 were filtered with SAMtools, and the remaining reads were de-duplicated with MateCigar (version 2.18.2.1) to eliminate PCR duplication bias
Genomic coverage damaged DNA was calculated using BEDTools genomecov (version 2.27.1)
Each of the data sets, damage, repaired and input data, were generated using an in house sliding window script with 200 bp window size and 1bp length step size
Correlation of biological replicates was assessed using Pearson correlation in 1 kb bins
The two biological replicates for damage and repair data sets were combined by averaging the number of reads in each region
The data in both sample types (“damage” and “repaired”) was normalized to the input DNA, to eliminate any bias resulting from the pull-down assay and mis-alignment to repetitive areas in the genome. In the first step, we divided the input DNA into 200 bp sized-windows, and the read count in each window falling in the range of (mean+1Stdv - mean+2Stdv) was divided by mean+1Stdv (values were ranging between 1-1.14). In the second step, values lower than mean+1Stdv was set to 1, and all regions higher than mean+2Stdv were discarded from the data since they represent areas with high background level. Next, the read count for damage and repaired data in each 200 bp window was divided by the normalized input DNA respective windows
The regions discarded from the input data were discarded from these data sets as well. Finally, reads mapping to the ENCODE-defined blacklist regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph, Bed

source_name: control

growth_protocol: U2OS (human osteosarcoma) cells were cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (Gibco), L-glutamine (2 mM) and 1% Penicillin-Streptomycin (10,000 U/mL, Gibco). Cells were incubated at 37 °C with 5% CO2.

extract_protocol: DNA was extracted from approximately 106 cells using the “GenElute-Mammalian Genomic DNA Miniprep Kit” (Sigma) according to manufacturer's instructions.

treatment_protocol: Final concentration of 50 mM KBrO3 was added to culture medium for one hour. Cells were washed with PBS twice, and genomic DNA was immediately extracted (for damage samples). Alternatively,  cell medium was replaced, and cells were allowed to repair for one hour at 37 °C with 5% CO2 before DNA extraction (for repaired samples). Cells were allowed to grow up to a week post KBrO3 treatment, to validate their viability.

value: human osteosarcoma cell line

tag: treatment group


title: AG_1


title: antecedent RLG  AH_4

description: antecedent RLG


title: WT_Flk1_K4_rep1

source_name: H3K4me2 ChIP DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells, replicate 1

growth_protocol: ES cells were plated onto a 10-cm dish with confluent OP9 stromal cells in the differentiation medium (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4.5-5 days.

source_name: MNase digested input DNA from Flk1+ mesoderm cells derived from mouse wild-type (WT) ES cells for H3K4me2 ChIP, replicate 1


title: TKO_ES_K9_rep2

description: H3K4me2 ChIP-chip data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K9me2 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

value: Line 19-1

value: embryonic stem (ES) cells

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K9me2 ChIP, replicate 2

treatment_protocol: The cells were recovered by trypsinization and used for chromatin IP.


title: Sample_9_UsOS50_cont__hoGG1 [control]


title: TKO_ES_K27_rep2

description: H3K27me3 ChIP-chip data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K27me3 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

value: Abcam

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K27me3 ChIP, replicate 2


title: S6 smallRNAs

tag: condition