title: T72_CTL_FC1_4


title: T72_LPS_FC1_4

status: Public on Sep 27 2018

type: SRA

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Read count estimates per gene were obtained using the alignment-free method STAR (2.4.1d).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMCs were isolated from whole blood by Ficoll-Paque centrifugation and cryopreserved.

extract_protocol:
Total RNA was extracted from the non-stimulated and stimulated cells using the  miRNeasy kit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the  quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
Indexed cDNA libraries were pooled (6 libraries per pool) in  equimolar amounts and sequenced with single-end 100bp reads on an Illumina  HiSeq2500.

treatment_protocol: PBMCs were cultured in RPMI-1640 (Fisher) supplemented with 10% heatinactivated  FBS (FBS premium, US origin, Wisent) and 1% L-glutamine (Fisher). For  each of the tested individuals, PBMCs (2 million per condition) were stimulated for 4  hours at 37° C with 5% CO2 with the immune challenges gardiquimod (GARD, 0.5μg/ml,  TLR7 and TLR8 agonist) or lipopolysaccharide-EB (LPS, 0.25 μg/ml, TLR4 agonist). A  control group of non-stimulated PBMCs were treated the same way but with only  medium.

tag: cell type

value: Peripheral blood mononuclear cells

tag: donor id

tag: treatment

value: LPS

tag: population

value: Batwa

tag: admixture

tag: fraction assigned

tag: flowcell

tag: Sex

value: Male

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14

tag: proportion of cd20

tag: proportion of cd56


title: T75_CTL_FC1_4

value: CTL

value: Female


title: T73_CTL_FC1_4


title: T72_GARD_BATCH_2

value: GARD


title: T73_GARD_BATCH_2


title: axo8.E10A

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

data_processing:
"freeIbis" was used for C1 and SmartSeq2 sample data as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.) Cellranger, version 2.0.0, as part of the 10x Genomics analysis pipeline was used to call bases for 10x experiments.
"leeHom" was used to trim adapters and merge Illumina sequencing reads for C1 and SmartSeq2 sample data. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to trim adapters for 10x experiments.
"deML" was used for robust demultiplexing of Illumina sequences for C1 and SmartSeq2 sample data using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to demultiplex reads.
Reads were aligned against the axolotl transcriptome (www.axolotl-omics.org, Download: 2015-07-29) using kallisto (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) for C1 and SmartSeq 2 sample data or using STAR (Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.) implemented in 10x' cell ranger software, version 2.0.0, for 10x data.
Transcript Per Million (TPM) values were computed using kallisto for C1 and SmartSeq2 samples. (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) Cellranger, version 2.0.0, implemented in the 10x Genomics analysis pipeline was used to obtain bam alignment files and gene count (UMI) matrices.
Gene expression values of different isoforms of the same gene were summed using custom Perl scripts.
Genome_build: Axolotl transcriptome (Am_2.2)
Supplementary_files_format_and_content: Master data frame including cell ID, cell type, timepoint, gene ID, and TPM values for each single cell.

organism: Ambystoma mexicanum

source_name: forelimb upper arm blastema 11 dpa

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v2 Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

treatment_protocol: FACS enrichment for connective tissue cells

tag: cre line

tag: sc-rna-seq method

value: Fluidigm C1

tag: development stage

value: blastema 11 dpa


title: T74_GARD_BATCH_2


title: T71_LPS_FC1_4


title: T71_GARD_BATCH_2


title: T73_LPS_FC1_4


title: T69_LPS_FC5


title: T71_CTL_FC1_4


title: axo8.D3A


title: axo8.D4A


title: axo8.D7A


title: axo8.D3B


title: axo8.D2B


title: T65_LPS_FC1_4


title: T69_CTL_FC5


title: T65_GARD_BATCH_2


title: axo8.D5A


title: axo8.C9A


title: axo8.D12B


title: axo8.C5A


title: axo8.D11A


title: axo8.C4B


title: axo8.C6A


title: axo8.D10A


title: axo8.C6B


title: T64_LPS_FC1_4


title: T62_LPS_FC1_4


title: T64_CTL_FC1_4


title: T65_CTL_FC1_4


title: T63_CTL_FC1_4


title: T63_LPS_FC1_4


title: T62_CTL_FC1_4


title: T50_LPS_FC5


title: axo8.C3A


title: axo8.C2B


title: T47_LPS_FC1_4


title: axo8.C2A


title: T47_GARD_BATCH_2


title: axo8.C1A


title: axo8.C1B


title: axo8.C12B


title: T46_GARD_BATCH_2


title: T47_CTL_FC1_4


title: axo8.C12A


title: T46_LPS_FC1_4


title: axo8.C11A


title: T46_CTL_FC1_4


title: axo8.C10B


title: axo8.B9A


title: axo8.B8A


title: axo8.B9B


title: axo8.B7A


title: T40_GARD_BATCH_2


title: T40_CTL_FC5


title: T36_GARD_BATCH_2


title: T43_GARD_BATCH_2


title: axo8.B7B


title: T36_CTL_FC1_4


title: T41_GARD_BATCH_2


title: T36_LPS_FC5


title: axo8.B5B


title: T34_LPS_FC1_4


title: axo8.B5A


title: axo8.B4A


title: T34_CTL_FC1_4


title: axo8.B3B


title: T33_GARD_BATCH_2


title: T31_GARD_BATCH_2


title: axo8.B1A


title: T30_LPS_FC1_4


title: axo8.B3A


title: T31_CTL_FC1_4


title: T30_GARD_BATCH_2


title: T28_CTL_FC1_4


title: T28_LPS_FC1_4


title: axo8.B11B


title: axo8.A5B


title: T27_LPS_FC1_4


title: axo8.A1A


title: axo8.B10B


title: axo8.A12B


title: axo8.A8B


title: T28_CTL_BATCH_2


title: axo8.A10B


title: T30_CTL_FC1_4


title: T28_GARD_BATCH_2


title: T27_GARD_BATCH_2


title: axo8.A3B


title: axo8.A4B


title: axo8.A3A


title: axo8.A7B


title: T27_CTL_B_BATCH_2


title: axo11.G2B

source_name: forelimb upper arm blastema 5 dpa

value: blastema 5 dpa


title: axo11.G1B


title: T15_LPS_FC1_4


title: T27_CTL_FC1_4


title: axo8.A2B


title: axo8.A1B


title: T18_LPS_FC1_4


title: axo11.F7B


title: T13_LPS_FC1_4


title: axo11.F3B


title: axo11.F2B


title: T13_GARD_BATCH_2


title: T18_CTL_FC1_4


title: T13_CTL_FC1_4


title: T12_CTL_FC1_4


title: axo11.G3B


title: T15_CTL_FC1_4


title: axo11.D8B


title: axo11.E2B


title: T12_CTL_B_BATCH_2


title: T18_GARD_BATCH_2


title: axo11.E5B


title: axo11.E11B


title: T15_GARD_BATCH_2


title: axo11.D7B


title: T12_LPS_FC1_4


title: T12_GARD_BATCH_2


title: axo11.D5B


title: axo11.D11B


title: T10_GARD_BATCH_2


title: T10_LPS_FC1_4


title: T10_CTL_FC1_4


title: axo11.C8B


title: axo11.D1B


title: T9_LPS_FC1_4


title: T7_LPS_FC1_4


title: T8_CTL_FC1_4


title: axo11.C2B


title: axo11.C6B


title: axo11.C4B


title: axo11.C3B


title: T7_CTL_FC1_4


title: axo11.C11B


title: axo11.C10B


title: axo11.B6B


title: T4_LPS_FC5


title: axo11.B9B


title: T6_LPS_FC5


title: T6_GARD_BATCH_2


title: T6_CTL_FC5


title: axo11.B8B


title: T9_CTL_FC1_4


title: T3_GARD_BATCH_2


title: axo11.B1B


title: T8_LPS_FC1_4


title: axo11.B7B


title: T5_GARD_BATCH_2


title: T5_LPS_FC5


title: T5_CTL_FC5


title: axo11.B5B


title: axo11.B10B


title: axo11.A8B


title: axo11.B4B


title: T4_GARD_BATCH_2


title: T4_CTL_FC5


title: axo11.A11B


title: axo11.B3B


title: axo11.A9B


title: axo10.H7


title: axo11.A4B


title: axo10.H9


title: axo10.H5


title: K50_LPS_FC5

value: Bakiga


title: T3_CTL_FC1_4


title: K53_GARD_BATCH_2


title: K52_CTL_FC1_4


title: K53_CTL_FC5


title: K49_LPS_FC1_4


title: K51_LPS_FC1_4


title: K51_CTL_FC1_4


title: axo10.H4


title: axo10.H6


title: axo10.H3


title: K49_CTL_FC1_4


title: K51_GARD_BATCH_2


title: K50_CTL_FC1_4


title: K53_LPS_FC1_4


title: axo11.A5B


title: K52_LPS_FC1_4


title: axo10.H2B


title: axo10.H2


title: K47_CTL_FC1_4


title: axo10.H11


title: axo10.H8


title: K46_LPS_FC1_4


title: axo10.H10


title: K46_GARD_BATCH_2


title: axo10.H1


title: axo10.G9B


title: K44_LPS_FC1_4


title: axo10.G9


title: K44_GARD_BATCH_2


title: K46_CTL_FC1_4


title: axo10.G7B


title: axo10.G6


title: K44_CTL_FC1_4


title: K47_LPS_FC1_4


title: K38_CTL_FC1_4


title: axo10.G8


title: K38_CTL_BATCH_2


title: K35_GARD_BATCH_2


title: K37_LPS_FC1_4


title: axo10.G4


title: axo10.G2B


title: K34_GARD_BATCH_2


title: K37_CTL_FC1_4


title: K34_CTL_FC1_4


title: axo10.G1B


title: axo10.G3


title: K33_LPS_FC1_4


title: axo10.G12


title: K33_GARD_BATCH_2


title: K33_CTL_FC1_4


title: axo10.G10


title: axo10.G8B


title: K38_LPS_FC1_4


title: axo10.G7


title: axo10.G1


title: K32_GARD_BATCH_2


title: axo10.G5


title: axo10.F8B


title: K31_LPS_FC1_4


title: K31_GARD_BATCH_2


title: K30_CTL_BATCH_2


title: axo10.F8


title: axo10.F6


title: axo10.F7


title: axo10.F9


title: axo10.F9B


title: K32_CTL_FC1_4


title: K30_CTL_FC1_4


title: axo10.F4


title: K29_LPS_FC1_4


title: axo10.F3


title: K30_GARD_BATCH_2


title: K29_CTL_FC1_4


title: axo10.F5


title: K28_LPS_FC1_4


title: K29_GARD_BATCH_2


title: axo10.F2B


title: axo10.F1B


title: axo10.G11


title: axo10.F11


title: axo10.F12


title: K28_CTL_FC1_4


title: K27_LPS_FC1_4


title: K27_GARD_BATCH_2


title: axo10.F1


title: K30_LPS_FC1_4


title: axo10.F10


title: K27_CTL_FC1_4


title: axo10.E9B


title: axo10.E9


title: axo10.E7


title: K26_CTL_FC1_4


title: K26_GARD_BATCH_2


title: WT4_IL1: ControlHSC_IL1stimulated_rep4

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Hematopoietic stem cells defined as lineage negative: removal of mature T cells, B cells, NK cells, dendritic cells, monocytes, granulocytes, erythroid cells: CD3-, CD4-, B220-, Ter119-, Gr1-

library_source: genomic

data_processing:
Reads were controlled for quality and trimmed of any remaining adapters with Trim Galore (v.1.8) and FastQC (v.0.11.3).
Reads were then aligned to the mouse genome (Mm10) with Bowtie (v.2.2.6) in "--sensitive-local" mode.
Aligned reads were filtered to remove low quality matches (MAPQ <= 10) or reads mapping to mitochondrial sequences. On average, 16 million uniquely mapped reads (13.4-24.6 million representing 60% of total) were retained per sample.
Alignment start positions were shifted in a strand-aware manner (+4bp, -5bp) prior to peak calling with MACS2 (v.2.1.1) with the following settings: --nomodel --extsize 147 -q 0.01 -m 5 50 -s 50 --call-summits.
Differentially bound regions were identified using DiffBind (v.2.4.8, 59,60) with peak centering (summits=100) and edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: peaks.narrowPeak files generated using peak calling with MACS2 (v.2.1.1) and containing  peak (regions of enrichment) information. Peaks generated using aligned reads that have been filtered to removed low quality matches (MAPQ <= 10) or reads mapping to mitochondrial sequences.

molecule: genomic DNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Nuclei from 50,000 cells per replicate were isolated and lysed (10 mmol/L Tris-Cl (pH 7.4), 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.05% NP-40) on ice.
Isolated nuclei were put through transposition reaction using Tn5 transposase and TD buffer (Illumina, USA) and DNA purified with MinElute PCR Purification Kit (Qiagen). Library amplification (NEBNext High Fidelity 2x PCR master mix, New England Biolabs, USA) was performed using cutom Nextera primers, followed by SPRI size selection to exclude fragments larger than 1,200 bp. Libraries were sequenced using the Illumina HiSeq 3000/4000 platform and the 50-bp single-read configuration.

treatment_protocol: IL-1β samples were cultured for 6hrs. Baseline cells were immediately lysed.

value: haematopoietic stem cell

tag: mouse phenotype

value: Control

tag: background strain

tag: stimulation

value: 10 ng/mL IL-1β


title: WT1_IL1: ControlHSC_IL1stimulated_rep1

tag: cell type

tag: treatment


title: WT1: ControlHSC_baseline_rep1

value: Unstimulated


title: axo10.E6


title: WT3_IL1: ControlHSC_IL1stimulated_rep3


title: axo10.E5B


title: WT2: ControlHSC_baseline_rep2


title: STZ4: DiabeticHSC_baseline_rep4

value: Diabetic

value: Streptozotocin (STZ) induction of diabetes


title: K28_GARD_BATCH_2

value: Peripheral blood mononuclear cells

tag: donor id

tag: population

tag: admixture


title: K24_GARD_BATCH_2

tag: fraction assigned

tag: flowcell

tag: Sex


title: K24_LPS_FC1_4

value: LPS

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: STZ3_IL1: DiabeticHSC_IL1stimulated_rep3


title: axo10.E5

tag: cre line


title: STZ3: DiabeticHSC_baseline_rep3


title: WT2_IL1: ControlHSC_IL1stimulated_rep2


title: STZ4_IL1: DiabeticHSC_IL1stimulated_rep4


title: axo10.E3B

tag: sc-rna-seq method


title: K23_LPS_FC1_4

tag: proportion of cd20

tag: proportion of cd56


title: STZ2: DiabeticHSC_baseline_rep2

tag: mouse phenotype

tag: background strain


title: STZ1_IL1: DiabeticHSC_IL1stimulated_rep1

tag: cell type

tag: stimulation


title: WT4: ControlHSC_baseline_rep4

tag: treatment


title: WT3: ControlHSC_baseline_rep3


title: STZ2_IL1: DiabeticHSC_IL1stimulated_rep2


title: K26_LPS_FC1_4

tag: donor id

tag: population


title: K24_CTL_FC1_4

tag: admixture

tag: fraction assigned


title: K23_GARD_BATCH_2

tag: flowcell

tag: Sex


title: axo10.E4

tag: development stage


title: axo10.E12


title: axo10.E2


title: K22_CTL_FC1_4

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: axo10.E1B

tag: cre line

tag: sc-rna-seq method


title: K22_LPS_FC1_4

tag: proportion of cd20

tag: proportion of cd56


title: RR681_P12-14_Tdrd12+/+;Exd1-/-_total small RNAs

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
small RNA
P12_14_small_RNA_counts.csv.gz

data_processing:
Analysis of reads originating from artificial piRNA precursor (Rosa26-pi) was done as previously (Wenda et al., 2017). Briefly, reads of at least 15 nucleotides were aligned to the Rosa26-pi sequence using bowtie (Langmead et al., 2009) allowing no mismatches. The abundance of reporter-derived piRNAs (24-30 nt reads) and 16-mer by-products was compared in between individual samples.
For the analysis of total small RNA libraries and libraries created from MILI and MIWI2 immunoprecpitated small RNAs, the reads were sorted into individual libraries based on the barcodes, the 3′ adapter sequences were removed and mapped to the mouse genome (mm10). The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome, and of minimum 15 nt in length, were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The files contain the counts of individual piRNAs and small RNAs in each sample.

source_name: testes

growth_protocol: The mouse knockout mutants for Tdrd12 (RIKEN Bio Resource Centre; BRC no. RBRC02326) (Pandey et al., 2013) and the Exd1 (The European Mouse Mutant Archive, EMMA; EM:08303) (Yang et al., 2016) are described. We crossed the fertile homozygous knockout Exd1-/- and heterozygous Tdrd12+/- animals to create fertile Exd1+/-; Tdrd12+/- animals. These were further intercrossed to generate animals of the Exd1-/- ; Tdrd12+/- genotype (referred to as the sensitized Exd1 mutant), which displays male-specific infertility. For studying the role of EXD1 in MILI slicing-triggered phased piRNA biogenesis, we brought the Rosa26-pi artificial piRNA precursor sequence (Yang et al., 2016) into the different Exd1 genetic backgrounds.

extract_protocol:
Immunoprecipitation of MILI and MIWI2 complexes from P0 (new-born pups) testes were carried out as previously described (Wenda et al., 2017). While MILI libraries were made directly from the immunoprecipitated RNAs, MIWI2-associated small RNAs (24-30nts) were purified from denaturing urea gel for library preparation. Deep sequencing libraries of P0 and P12-P14 testicular total small RNAs (19-40 nt) were prepared as described (Yang et al., 2016).
Sequencing libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina HiSeq 2000 platform (EMBL Heidelberg Gene core facility).

tag: age

tag: genotype

tag: purification

value: total small RNAs


title: RR679_P12-14_Tdrd12+/+;Exd1+/+_total small RNAs


title: RR686_P12-14_Tdrd12+/-;Exd1-/-_total small RNAs


title: RR683_P12-14_Tdrd12+/+;Exd1-/-_total small RNAs


title: RR682_P12-14_Tdrd12+/+;Exd1-/-_total small RNAs


title: RR685_P12-14_Tdrd12+/-;Exd1-/-_total small RNAs


title: RR680_P12-14_Tdrd12+/+;Exd1+/+_total small RNAs


title: K23_CTL_FC1_4

tag: cell type

tag: donor id

tag: treatment


title: K22_GARD_BATCH_2

tag: population

tag: admixture

tag: fraction assigned


title: STZ1: DiabeticHSC_baseline_rep1

tag: mouse phenotype

tag: Sex

value: Male

tag: background strain

tag: stimulation


title: axo10.E3

tag: cre line

tag: development stage


title: RR684_P12-14_Tdrd12+/-;Exd1-/-_total small RNAs


title: axo10.E11

tag: sc-rna-seq method


title: RR598_P0_Tdrd12+/-;Exd1-/-_MIWI2 IP

description:
small RNA
P0_IP_counts.csv.gz

value: MIWI2 IP

tag: antibody for ip

value: MIWI2 (rabbit polyclonal) (Pandey et al., 2013;PMID:24067652)


title: RR597_P0_Tdrd12+/+;Exd1-/-_MIWI2 IP

description:
small RNA
P0_IP_counts.csv.gz

tag: age


title: RR596_P0_Tdrd12+/+;Exd1-/-_MIWI2 IP

description:
small RNA
P0_IP_counts.csv.gz

tag: genotype


title: RR678_P12-14_Tdrd12+/+;Exd1+/+_total small RNAs

tag: purification


title: RR594_P0_Tdrd12+/+;Exd1+/-_MIWI2 IP

description:
small RNA
P0_IP_counts.csv.gz


title: axo10.E1


title: axo10.E10


title: RR595_P0_Tdrd12+/+;Exd1+/-_MIWI2 IP

description:
small RNA
P0_IP_counts.csv.gz


title: K20_GARD_BATCH_2

tag: cell type

value: GARD

tag: flowcell

value: Female

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14

tag: proportion of cd20

tag: proportion of cd56


title: K19_GARD_BATCH_2

tag: donor id

tag: treatment

tag: population

tag: admixture

tag: fraction assigned

tag: Sex


title: RR593_P0_Tdrd12+/-;Exd1-/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz

value: MILI IP

tag: antibody for ip

value: MILI (mouse monoclonal) (Reuter et al., 2009;PMID:19465913)


title: axo10.D9B

tag: cre line

tag: sc-rna-seq method

value: Fluidigm C1

tag: development stage

value: blastema 5 dpa


title: K19_LPS_FC1_4

tag: cell type

value: Bakiga


title: RR592_P0_Tdrd12+/-;Exd1-/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz

tag: age

tag: genotype

tag: purification


title: K19_CTL_FC1_4

value: CTL

tag: flowcell

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: RR591_P0_Tdrd12+/+;Exd1-/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz


title: axo10.D9


title: RR590_P0_Tdrd12+/+;Exd1-/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz


title: RR589_P0_Tdrd12+/+;Exd1+/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz


title: axo10.D6B


title: K18_LPS_FC1_4

tag: donor id

tag: treatment

tag: proportion of cd20

tag: proportion of cd56


title: K18_GARD_BATCH_2

tag: population

tag: admixture

tag: fraction assigned

tag: Sex


title: axo10.D7

tag: cre line

tag: sc-rna-seq method

tag: development stage


title: K18_CTL_FC1_4

tag: cell type


title: axo10.D6


title: RR568_P0_Tdrd12+/-;Exd1+/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz

tag: age

tag: genotype

tag: purification


title: RR570_P0_Tdrd12+/-;Exd1-/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz


title: K17_LPS_FC1_4

tag: flowcell

tag: proportion of cd4

tag: proportion of cd8


title: RR571_P0_Tdrd12+/-;Exd1-/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz


title: RR588_P0_Tdrd12+/+;Exd1+/-_MILI IP

description:
small RNA
P0_IP_counts.csv.gz

tag: antibody for ip


title: RR567_P0_Tdrd12+/-;Exd1+/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz


title: axo10.D5


title: RR569_P0_Tdrd12+/-;Exd1-/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz


title: K17_GARD_BATCH_2

tag: donor id

tag: treatment

tag: proportion of cd14

tag: proportion of cd20


title: RR566_P0_Tdrd12+/-;Exd1+/-_total small RNAs

description:
small RNA
P0_small_RNA_counts.csv.gz


title: RR425_P0_Exd1+/-; Rosa26-pi/+_MILI IP

description:
small RNA
Rosa26_counts.csv.gz


title: RR426_P0_Exd1-/-; Rosa26-pi/+_MILI IP

description:
small RNA
Rosa26_counts.csv.gz


title: axo10.D4


title: axo10.D3B


title: K17_CTL_FC1_4

tag: population

tag: admixture

tag: fraction assigned

tag: proportion of cd56


title: RR424_P0_Exd1+/+; Rosa26-pi/+_MILI IP

description:
small RNA
Rosa26_counts.csv.gz


title: RR422_P0_Exd1+/-; Rosa26-pi/+_MIWI2 IP

description:
small RNA
Rosa26_counts.csv.gz


title: RR423_P0_Exd1-/-; Rosa26-pi/+_MIWI2 IP

description:
small RNA
Rosa26_counts.csv.gz


title: axo10.D3

tag: cre line

tag: sc-rna-seq method

tag: development stage


title: RR421_P0_Exd1+/+; Rosa26-pi/+_MIWI2 IP

description:
small RNA
Rosa26_counts.csv.gz

tag: age

tag: genotype


title: K15_GARD_BATCH_2

tag: cell type

tag: flowcell

tag: Sex


title: axo10.D2B


title: K15_CTL_FC1_4

tag: proportion of cd4

tag: proportion of cd8


title: axo10.D2


title: axo10.D1B


title: K14_LPS_FC1_4

tag: donor id

tag: treatment


title: K14_GARD_BATCH_2

tag: proportion of cd14

tag: proportion of cd20


title: axo10.D10


title: fM14;Viral-GFP m6A-RNA-seq Rep3

city: Chicago

first: Jessica

last: Koranda

state: IL

address: 974 E 57th Street

country: USA

institute: University of Chicago

description:
Sample 29
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx

data_processing:
m6A-seq: Reads were aligned to the reference genome using Tophat v2.0. The longest isoform was used if the gene had multiple isoforms. The peak calling method was modified from published work (Dominissini, et al., 2013).
mRNA-seq: Reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the RPKM of each gene to represent their mRNA expression level (Trapnell et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: (1) rpkm table of RNA-seq or input samples; (2) m6A peak list, including gene ID, gene symbol, Ref_seq number, m6A peak coordinates and location on the transcript, m6A enrichment score, whether the peak is present in the paired samples, m6A enrichment score ratio compared to the paired sample, m6A and m6A motif information.

source_name: fM14;Viral-GFP m6A-RNA-seq

extract_protocol:
Striata were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. mRNA was further purified using Dynabeads mRNA purification kit and column (Invitrogen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Striatum

value: 3-6 months

tag: m6a antibody

value: anti-m6A; Synaptic Systems Cat# 202-203, RRID:AB_2279214


title: fM14;Viral-Cre m6A-RNA-seq Rep3

description:
Sample 32
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx

source_name: fM14;Viral-Cre m6A-RNA-seq


title: fM14;Viral-Cre m6A-RNA-seq Rep2

description:
Sample 31
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx


title: H3K27me3_mouse_bone_marrow_N1dE

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Read sequences were aligned to NCBI Build 37 (mm9) mouse reference genome using BWA-backtrack v0.5.7 and default parameters.
Custom java program (BAM2WIG) was used to generate wig files for downstream analysis and visualization in genome browser. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Peak enrichment was computed using MACS2 v2.1.0 with a false discovery rate (FDR) value of 0.05 and “-- broad” option. Input sample was used as control background.
Duplicate reads were marked using Picard Tools MarkDuplicates v1.52
Bam files from 3 sequencing lanes were merged using Picard Tools MergeSamFiles v1.52
Genome_build: mm9
Supplementary_files_format_and_content: Bed files generated using MACS2 v2.1.0 (https://github.com/taoliu/MACS)

source_name: adult lin- bone marrow cells transduced with N1dE

growth_protocol: Single cell suspensions were generated by manual disaggregation of embryonic day 14.5 fetal livers (FL) or flushing of bone marrow (BM) from long bones of 8 week old C57BL/6 mice with PBS/3% FBS. Cells were then stained with a lineage panel comprising antibodies against CD3, CD8, Gr1, Ter119, B220, CD11b, CD11c, and NK1.1 (eBioscience, Biolegend). Lin− cells were isolated by fluorescence activated cell sorting (FACS), and then prestimulated overnight in StemPro-34 media (Gibco) supplemented with 10% FCS, antibiotics, and cytokines IL-3, IL-6, and FLT3 ligand (10 ng/ml each), and SCF (100 ng/ml) (Peprotech).

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. H3K27me3 antibody was incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG. The PCR program included an initial denaturation step at 98C for 30 sec, followed by 8 cycles at 98C for 15 sec, 65C for 30 sec, and 72C for 30 sec, and ending with a final step at 72C for 5 min.
We performed native chromatin immunoprecipitation (ChIP) as described previously (Lorzadeh et al., 2016) using a validated anti-H3K27me3 antibody (cat #pAB-195-050,Diagenode). Libraries were constructed using an Agilent Bravo automated liquid handling platform. Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol: Cells were transduced by spinoculation with NOTCH1ΔE (N1dE) lentivirus at 300xg for 2h, and cultured for 3 days in the same media. Virally transduced (GFP+) cells were then FACS sorted prior to ChIP assay.

value: adult bone marrow (lin-)

value: 8 weeks

tag: antibody

value: anti-H3K27me3, cat #pAB-195-050, Diagenode

tag: genotype/variation

value: transduced with N1dE lentivirus


title: Input_mouse_fetal_liver_N1dE

source_name: lin- fetal liver cells transduced with N1dE

value: fetal liver (lin-)

value: 14.5 embryonic days


title: H3K27me3_mouse_fetal_liver_N1dE


title: Input_mouse_bone_marrow_N1dE


title: K14_CTL_FC1_4

value: Peripheral blood mononuclear cells

tag: population

tag: admixture

tag: fraction assigned

tag: proportion of cd56


title: fM14;Viral-GFP m6A-RNA-seq Rep1

description:
Sample 27
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx

tag: age


title: K13_GARD_BATCH_2

tag: cell type

value: GARD

tag: flowcell

tag: Sex

value: Male


title: axo10.D1

tag: cre line

tag: sc-rna-seq method

tag: development stage


title: fM14;Viral-Cre RNA-seq Rep3

description:
Sample 26
mRNA
input sample of Sample 32
C_fM14_Viral.xlsx

source_name: fM14;Viral-Cre RNA-seq


title: K15_LPS_FC5

tag: donor id

tag: treatment

value: LPS

value: Female

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14

tag: proportion of cd20


title: axo10.C9B

value: Fluidigm C1

value: blastema 5 dpa


title: fM14;Viral-Cre RNA-seq Rep2

description:
Sample 25
mRNA
input sample of Sample 31
C_fM14_Viral.xlsx

tag: strain

tag: tissue

tag: m6a antibody


title: K12_LPS_FC1_4

tag: population

value: Bakiga

tag: admixture

tag: fraction assigned

tag: proportion of cd56


title: fM14;Viral-GFP m6A-RNA-seq Rep2

description:
Sample 28
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx

value: Striatum

tag: age


title: fM14;Viral-GFP RNA-seq Rep3

description:
Sample 23
mRNA
input sample of Sample 29
C_fM14_Viral.xlsx

source_name: fM14;Viral-GFP RNA-seq

value: 3-6 months


title: axo10.C9

tag: cre line


title: axo10.C8B

tag: sc-rna-seq method


title: K12_GARD_BATCH_2

tag: cell type

tag: flowcell

tag: Sex


title: fM14;Viral-GFP RNA-seq Rep1

description:
Sample 21
mRNA
input sample of Sample 27
C_fM14_Viral.xlsx


title: fM14;Viral-Cre RNA-seq Rep1

description:
Sample 24
mRNA
input sample of Sample 30
C_fM14_Viral.xlsx


title: fM14;Viral-Cre m6A-RNA-seq Rep1

description:
Sample 30
mRNA, m6A antibody enriched
C_fM14_Viral.xlsx

value: anti-m6A; Synaptic Systems Cat# 202-203, RRID:AB_2279214


title: K12_CTL_FC1_4

tag: donor id

tag: treatment

value: CTL

tag: proportion of cd4


title: fM14;A2AR-KO m6A-RNA-seq Rep3

description:
Sample 20
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx

source_name: fM14;A2AR-KO m6A-RNA-seq


title: axo10.C8

tag: development stage


title: fM14;A2AR-KO m6A-RNA-seq Rep2

description:
Sample 19
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx

tag: strain


title: K11_CTL_FC1_4

tag: proportion of cd8

tag: proportion of cd14

tag: proportion of cd20


title: fM14;A2AR-KO m6A-RNA-seq Rep1

description:
Sample 18
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx

tag: tissue

tag: m6a antibody


title: axo10.C7B


title: K11_LPS_FC1_4

tag: population

tag: admixture

tag: fraction assigned

tag: proportion of cd56


title: axo10.C7

tag: cre line

tag: sc-rna-seq method


title: fM14;A2AR-WT m6A-RNA-seq Rep3

description:
Sample 17
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx

source_name: fM14;A2AR-WT m6A-RNA-seq

tag: age


title: fM14;A2AR-KO RNA-seq Rep3

description:
Sample 14
mRNA
input sample of Sample 20
B_fM14_A2AR.xlsx

source_name: fM14;A2AR-KO RNA-seq


title: fM14;A2AR-WT m6A-RNA-seq Rep2

description:
Sample 16
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx


title: K10_GARD_BATCH_2

tag: cell type

tag: donor id

tag: flowcell

tag: Sex


title: axo10.C6B

tag: development stage


title: fM14;A2AR-KO RNA-seq Rep2

description:
Sample 13
mRNA
input sample of Sample 19
B_fM14_A2AR.xlsx

tag: strain


title: axo10.C6


title: fM14;A2AR-KO RNA-seq Rep1

description:
Sample 12
mRNA
input sample of Sample 18
B_fM14_A2AR.xlsx


title: fM14;A2AR-WT m6A-RNA-seq Rep1

description:
Sample 15
mRNA, m6A antibody enriched
B_fM14_A2AR.xlsx


title: fM14;Viral-GFP RNA-seq Rep2

description:
Sample 22
mRNA
input sample of Sample 28
C_fM14_Viral.xlsx


title: axo10.C5B


title: fM14;A2AR-WT RNA-seq Rep2

description:
Sample 10
mRNA
input sample of Sample 16
B_fM14_A2AR.xlsx

source_name: fM14;A2AR-WT RNA-seq


title: fM14;A2AR-WT RNA-seq Rep1

description:
Sample 9
mRNA
input sample of Sample 15
B_fM14_A2AR.xlsx


title: fM14;A2AR-WT RNA-seq Rep3

description:
Sample 11
mRNA
input sample of Sample 17
B_fM14_A2AR.xlsx


title: K9_GARD_BATCH_2

tag: treatment

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: axo10.C4


title: K8_LPS_FC1_4

tag: population

tag: proportion of cd20


title: fM14;D1R-KO RNA-seq Rep3

description:
Sample 6
mRNA
input sample of sample 8
A_fM14_D1R.xlsx

source_name: fM14;D1R-KO RNA-seq

tag: tissue

tag: m6a antibody


title: axo10.C3B

tag: cre line


title: fM14;D1R-WT m6A-RNA-seq Rep1

description:
Sample 7
mRNA, m6A antibody enriched
A_fM14_D1R.xlsx

source_name: fM14;D1R-WT m6A-RNA-seq


title: K8_GARD_BATCH_2

source_name: Peripheral blood mononuclear cells

tag: admixture

tag: fraction assigned

tag: proportion of cd56


title: fM14;D1R-KO RNA-seq Rep2

description:
Sample 5
mRNA
input sample of sample 8
A_fM14_D1R.xlsx

tag: age


title: fM14;D1R-KO RNA-seq Rep1

description:
Sample 4
mRNA
input sample of sample 8
A_fM14_D1R.xlsx


title: K10_CTL_FC1_4

tag: cell type

tag: donor id

tag: flowcell


title: fM14;D1R-WT RNA-seq Rep3

description:
Sample 3
mRNA
input sample of sample 7
A_fM14_D1R.xlsx

source_name: fM14;D1R-WT RNA-seq

tag: strain


title: K8_CTL_FC1_4

tag: treatment

tag: Sex


title: axo10.C3

source_name: forelimb upper arm blastema 5 dpa

tag: sc-rna-seq method

tag: development stage


title: fM14;D1R-WT RNA-seq Rep2

description:
Sample 2
mRNA
input sample of sample 7
A_fM14_D1R.xlsx


title: axo10.C2B


title: fM14;D1R-WT RNA-seq Rep1

description:
Sample 1
mRNA
input sample of sample 7
A_fM14_D1R.xlsx


title: axo10.C2


title: K10_LPS_FC1_4

tag: population

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: K7_LPS_FC5

tag: proportion of cd20


title: D1166-1

city: Toronto

first: Donghyun

last: Lee

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

data_processing:
Quality score of bases were determined using Phred score system
Reads underwent filters with unconverted C filter to remove all reads that originated from non bisulfite-converted strands
BS-Seeker2 was used to align the reads and obtain raw methylation values (ranging from 0.0 - 1.0)
Genome_build: hg19
Supplementary_files_format_and_content: .xls file was generated by collecting data from output files of each sample after appropriate processing. Values represent methylation percentage at each CpG site in genomic coordinate Chr5:XXXXXXX (hg19)

source_name: Human tumor

growth_protocol: Human cancer cell lines were cultured under ATCC-recommended conditions

extract_protocol:
DNA from cultured human cancer cell lines were extracted using QIAGEN Dneasy Blood & Tissue Kit. Tumor and normal DNA samples from human were extracted from other collaborating centers
For NGS using the HiSeq platform, the PCR products were first purified using the QIAquick Gel Purification Kit (Qiagen), followed by sequencing library preparation using Nextera XT DNA Library Preparation Kit (Illumina) according to standard single-end sequencing protocol provided and sequenced following the manufacturer’s instructions for the HiSeq 2500 Rapid Run (Illumina) mode to obtain 126 nucleotide read lengths.
For NGS using the MiSeq platform, the resulting PCR products were prepared in accordance to the 16S Metagenomic Sequencing Library Preparation guide (15044223 B, Illumina) and were sequenced following the manufacturer’s instructions for the MiSeq Reagent Kit v3 (Illumina) to obtain single-end 125 nucleotide read lengths.
Bisulfite-Seq (Targeted)

tag: tissue type

value: Cancer (Skin-melanoma)


title: D1165-1


title: K7_GARD_BATCH_2

tag: admixture

tag: fraction assigned


title: D1164-1


title: axo10.C12B

tag: cre line


title: axo10.C1B


title: fM14;D1R-KO m6A-RNA-seq Rep1

description:
Sample 8
mRNA, m6A antibody enriched
A_fM14_D1R.xlsx

source_name: fM14;D1R-KO m6A-RNA-seq

tag: tissue

tag: age

tag: m6a antibody


title: D1162-1


title: D1163-1


title: K7_CTL_FC5

tag: cell type

tag: donor id

tag: flowcell

tag: proportion of cd56


title: D1161-1


title: D1160-1


title: K6_LPS_FC5

tag: treatment

tag: Sex


title: axo10.C12

tag: sc-rna-seq method

tag: development stage


title: D1159-1


title: D1158-1


title: K6_GARD_BATCH_2

tag: population

tag: proportion of cd4

tag: proportion of cd8

tag: proportion of cd14


title: axo10.C11


title: Ca gDNA2_18 (22133)

tag: tissue type

value: Cancer (Prostate)


title: axo10.C10

tag: cre line


title: K6_CTL_FC1_4

tag: admixture

tag: fraction assigned

tag: proportion of cd20


title: D1157-1


title: K5_LPS_FC1_4

tag: cell type


title: 4868c


title: K5_CTL_FC1_4

tag: donor id


title: Ca gDNA15 (21280)


title: Ca gDNA6 (2195)


title: 2226c


title: 486 Irma Sottsas


title: 1669c


title: 517 Irma Sottsas


title: axo10.B9


title: K2_GARD_BATCH_2

tag: flowcell


title: axo10.B9B


title: K1_LPS_FC1_4

tag: proportion of cd56


title: 415 Irma Sottsas


title: K1_GARD_BATCH_2

tag: treatment


title: axo10.B7


title: 341 Irma Sottsas


title: 253 Irma Sottsas


title: axo10.B8


title: axo10.B6B


title: 160 Irma Sottsas


title: 196 Irma Sottsas


title: Ca gDNA2_17 (18035)


title: axo10.B5


title: axo10.C1


title: 150 Irma Sottsas


title: 122 Irma Sottsas


title: axo10.B4B


title: wt_YPD_log_TOTAL_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
After adapter and quality trimming using Trim Galore (v0.5.0), ChIPseq data was mapped to yeast genome R64-1-1 and Drosophila genome BDGP6 using Bowtie 2 (v2.3.2) by the Babraham Institute Bioinformatics Facility. Reads that mapped to the Drosophila genome were then remapped against the yeast genome and all cross-mapping reads discarded. Similarly cross-mapping reads from yeast to Drosophila were also discarded. For normalisation, in each dataset counts were performed of the total number of reads mapping to non-rDNA and non-mitochondrial regions of the yeast genome (Y) and the total number of reads mapping exclusively to the Drosophila genome (D). Normalisation factors were calculated using the formula (1 / DChIP ) x (Dinput / Yinput ) and applied to yeast ChIP read counts. Mapped data was analysed using SeqMonk (v1.39.0, https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: R64-2-1
Supplementary_files_format_and_content: ChIP-Seq report: raw read counts of 500b tiles across the genome for reads mapping exclusively to the yeast genome (tab delimited text)
Supplementary_files_format_and_content: total Drosophila reads: total read counts for reads mapping exclusively to the Drosophila genome (tab delimited text)

organism: Saccharomyces cerevisiae

source_name: Mother Enrichment Project diploid

growth_protocol: Cells were inoculated in 4ml YPD and grown for 6-8 hours then diluted in 25ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml. If required, cells were labelled (see below), then cells were inoculated in YPD at 2x104 cells/ml containing 5µg/ml ampicillin (Melford A0104) and 1µM β-estradiol (Sigma E2758).

extract_protocol:
Percoll gradients (1 for 7.5 hour or 2 for 24/48 hour time points) were formed by vortexing 1.16ml Percoll (Sigma P1644) with 42 µl 5 M NaCl, 98 µl water in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Cells were defrosted on ice, re-suspended in ~250 µl cold PBSE per gradient and layered on the pre-formed gradients. Gradients were centrifuged for 20 min at 1,000 g, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g to pellet the cells, which were then re-suspended in 1ml PBSE per time point (re-uniting samples split across two gradients). 25 µl Streptavidin magnetic beads were added (Miltenyi Biotech 1010007) and cells incubated for 30 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 8 ml cold PBSE and eluted with 1ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. Final elution was to 1.5 ml tubes (Treff 1130153). 50 µl cells were set aside for quality control, while the remainder were pelleted by centrifugation and processed directly for ChIP.  Cells were re-suspended in 50 μl cold CLB (50mM HEPES pH 7.0, 140mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, cOmplete Protease Inhibitors (Roche 1836170)) with 3ng Drosophila melanogaster spike-in chromatin (Active Motif 02317006) and 50 µl zirconium beads and lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater then transferred to a Covaris 520045 microTUBE and topped up to 130 µl with CLB. Sonication was performed on a Covaris 220: Duty Factor 5 %, PIP 130 W, 900s, 200 cycles per burst, 8.9 ºC. Samples were decanted to a 1.5 ml tube,   centrifuged 5 min top speed at 4 ºC and the pellet discarded. Lysate was pre-cleared by incubation with 15 μl of pre-equilibrated Protein-G magnetic beads (Life Technologies 10004D) 2 hrs at 4 ºC on a wheel, then 30 μl set aside for total DNA extraction and 50 μl used per immunoprecipitation (IP). Antibodies were added at 1:50 dilution (rabbit anti-H3, CST 2650 or rabbit anti-H3K4me3, CST 9751) and to every IP 0.8µg of spike-in antibody (Active Motif 61686) was added. IPs were incubated over night at 4 ºC on a wheel.
Libraries were synthesised using a NEBNext DNA Ultra II kit (NEB E7645) with modifications: Concentration of DNA was increased by reducing the volumes of the end repair and ligation steps 5-fold, with reagent quantities reduced in kind. After clean-up with 0.9x AMPure beads, PCR was performed in 50 μl volumes according to manufacturer’s instructions. Libraries were purified with 0.9x AMPure beads and eluted in 30μl, then a size selection was performed by incubating first with 15μl AMPure beads, discarding the beads then purifying the remaining DNA from the supernatant with an additional 12 μl AMPure beads.

treatment_protocol: 0.25x107 cells per sample were harvested by centrifugation (15 s at 13,000 g), washed twice with 125µl PBS and re-suspended in 125µl of PBS containing ~3mg/ml Biotin-NHS (Sigma B1022 or Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125µl PBS and re-suspended in YPD. For 7.5 hr time points, cells were inoculated in 15ml YPD + 5µg/ml ampicillin and grown for 2 hours before addition of 1µM β-estradiol (Sigma E2758). For 24 and 48 hr time points, cells were directly inoculated in 125ml YPD containing 5µg/ml ampicillin and 1mm β-estradiol. For 24/48 hr time points, no contamination of labelled non-aged cells was observed by bud scar staining as these cells presumably lyse, and this strategy helped keep the culture density low (cultures did not exceed 0.75x107 cells/ml in 48 hr). Cells were harvested by centrifugation for 1 min, 4600 rpm in 15/50 ml tubes and immediately fixed by resuspension in 70% ethanol and storage at -80°C. Alternatively, formaldehyde (Thermo 11586711) was added to 1% and cells incubated at room temperature for 15 min before quenching with 125 mM glycine, harvested by centrifugation as above and washed three times with PBS before freezing on N2 and storage at -80°.

tag: strain

value: Mother Enrichment Project diploid

tag: age

value: log

tag: chip antibody


title: wt_YPD_log_H3K4me3_2

value: Cell Signalling Technologies, 9751


title: 102 Irma Sottsas


title: axo10.B4

tag: sc-rna-seq method

tag: development stage


title: 423 Irma Sottsas


title: wt_YPD_log_H3K4me3_1


title: 349 Irma Sottsas


title: 321 Irma Sottsas


title: axo10.B3B


title: 361 Irma Sottsas


title: 393 Irma Sottsas


title: axo10.B3


title: wt_YPD_log_H3_1

value: Cell Signalling Technologies, 2650


title: wt_YPD_48h_TOTAL_2

value: 48 hour


title: wt_YPD_log_H3_2


title: T1688

value: Cancer (Lungs)


title: 353 Irma Sottsas


title: wt_YPD_log_TOTAL_1


title: T1684


title: T1678


title: T1676


title: axo10.B2


title: wt_YPD_48h_H3K4me3_2


title: axo10.B1B


title: T1668


title: wt_YPD_48h_H3K4me3_1


title: axo10.B12


title: T1680


title: T1651


title: T1664


title: wt_YPD_48h_H3_2


title: T1647


title: axo10.B11B


title: T1686


title: T1645


title: wt_YPD_48h_H3_1


title: wt_YPD_24h_TOTAL_2

value: 24 hour


title: T1641


title: axo10.B2B


title: T1634


title: wt_YPD_48h_TOTAL_1


title: axo10.B10


title: T1617


title: T1618


title: wt_YPD_24h_H3K4me3_2


title: T1613


title: axo10.B1


title: wt_YPD_24h_H3K4me3_1


title: T1653


title: T1643


title: T1656


title: T1636


title: wt_YPD_24h_H3_2


title: axo10.A9


title: T1626


title: wt_YPD_24h_H3_1


title: 149

value: Cancer (Bladder)


title: 59


title: T1628


title: axo10.A8B

value: Fluidigm C1


title: 47


title: T1620


title: axo10.B11

value: blastema 5 dpa


title: axo10.B10B


title: 123


title: wt_YPD_24h_TOTAL_1


title: 20M


title: axo10.A8


title: axo10.A7


title: 24M


title: 125


title: Human_HC_2

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

data_processing:
Basecalling was performed using Illumina Casava software
Samples were demultiplexed using Illumina bcl2fasq software
Sequenced reads were processed, aligned and counts summarised using Cellranger 2.1 pipeline
Seurat r package was used to process raw UMI matrices and procude UMI counts per 10,000 unique molecules identified per cell
Genome_build: hg38, mm10
Supplementary_files_format_and_content: tab-delimited UMI counts per  10,000 unique molecules detected

source_name: Colon

extract_protocol:
Single cell suspension derived from enzymatic digestion of colonic biopsies and enrichment for stromal fraction by MACS-depletion of epithelial and immune cells and red blood cells.
Libraruy construction by 3’ prime V2 chemistry Chromium single cell gene expression kit.

treatment_protocol: Cells isolated from colonic tissues, untreated, directly used for chip loading.

tag: tissue

value: Colon

tag: disease state

value: Healthy


title: axo10.A9B


title: Human_UC_2

value: Ulcerative Colitis


title: axo10.A6B


title: Human_UC_1


title: axo10.A6


title: 14M

tag: tissue type


title: 1915


title: 1911


title: axo10.A5

tag: cre line


title: 245


title: axo10.A4B


title: 65


title: 97


title: 40M


title: cell line MM1s-pLenti6-EV

city: Singapore

first: Wee

middle: Joo

last: Chng

address: 5 Lower Kent Ridge Road

department: Haematology-Oncology

country: Singapore

institute: National University Cancer Institute, Singapore

description:
editing_sites_in_mm1s_cell_line_annotated.txt
strand-specific RNA-Seq

data_processing:
Raw reads were mapped to reference genome (hg19) using bwa (0.7.16a-r1181). PCR duplicates were removed with samtools (v1.5). The reads with mapping quality score less than 20 were discarded.
Variants were called with an in-house variant caller (Perl script) from the samtools mpileup data.
Candidate editing sites were filtered as the following: SNPs from different databases (1000 Genomes Project, NHLBI GO Exome Sequencing Project (http://evs.gs.washington.edu/EVS/), dbSNP v138) were removed, sites within the first 6 bases of the reads were excluded. For sites not located in Alu elements, the candidates within the 4 bases of a splice junction on the intronic side, and those residing in the homopolymeric regions and in the simple repeats were all removed. Candidate variants located in the reads that map to the non-unique regions of the genome by using BLAT were also excluded. Only A-to-G editing sites based on the strand information were retained.
To obtain high confidence editing events, the candidate sites were required to be supported by at least 20 reads and having more than 10% absolute editing frequency.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include all editing events before filtering annotated with ANNOVAR (2017-07-17) and merged for each editing site across all the samples in the comparison group

source_name: Human myeloma cell line

growth_protocol: Human myeloma cell lines were grown in RPMI-1650 supplemented with 10% FBS and 1% Penicillin and Streptomycin. 5 million cells were harvested for RNA extraction when they were growing at the log- phase.

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: ADAR1 shRNA and pLenti6 overexpressing plasmids were introduced into the myeloma cell lines via lentivirus infection method.

tag: cell line

value: Human myeloma cell line MM1s

tag: disease stage

value: Malignant

value: Lentivirus delivery of empty vector of pLenti6


title: cell line MM1s-pLenti6-ADAR1-Mutant

value: Lentivirus delivery of pLenti6 overexpressing ADAR1-deaminase mutant


title: cell line MM1s-pLenti6-ADAR1-WT

value: Lentivirus delivery of pLenti6 overexpressing ADAR1-WT


title: 35M


title: cell line U266-shADAR1-3

description:
editing_sites_in_u266_cell_line_annotated.txt
strand-specific RNA-Seq

value: Human myeloma cell line U266

value: Lentivirus delivery of shADAR1 #3


title: axo10.A3B


title: 267


title: axo10.A4


title: 39


title: 269


title: cell line U266-shADAR1-1

value: Lentivirus delivery of shADAR1 #1


title: 41


title: 22M


title: axo10.A3


title: cell line U266-shCtrl

value: Lentivirus delivery of shRNA scrambled


title: 311


title: Human_HC_1


title: axo10.A2


title: patient sample R-196

description:
editing_sites_in_mm_patients_annotated.txt
strand-specific RNA-Seq

source_name: Bone marrow

value: plasma cells


title: axo10.A1B


title: axo10.A12B


title: 1492

source_name: Normal human blood

value: Blood


title: 233

value: Cancer (Bladder)


title: patient sample R-146


title: 1490


title: 1462


title: patient sample R-134


title: 1403


title: axo10.A12

value: Fluidigm C1


title: patient sample R-106


title: axo10.A11B

value: blastema 5 dpa


title: 1266


title: GBP7067


title: patient sample R-094


title: GBP7061


title: axo10.A11


title: 149012


title: 213


title: patient sample ND-079


title: patient sample ND-177


title: 149016


title: axo10.A10


title: axo10.A10B


title: axo10.A1


title: 148916


title: 63


title: patient sample ND-051


title: UW228

source_name: Cancer Cell Line

value: Cancer cell line (Brain)


title: patient sample ND-049


title: axo4.H9

source_name: Stage 44 forelimb limb bud

treatment_protocol: no connective tissue enrichment

value: stage 44 limb bud


title: U87


title: axo4.H8


title: U118


title: GBP7063


title: PRMT1-cKO2

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

description: processed data file: PRMT1-WT_vs_PRMT1-CKO.xlsx

data_processing:
Reads were mapped on GRCm38 mouse reference genome and quantified using CLC Genomics Workbench (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software (Qiagen).
Genome_build: GRCm38
Supplementary_files_format_and_content: PRMT1-WT_vs_PRMT1-CKO.xlsx: Excel file

source_name: Heart

extract_protocol:
Cardiac total RNA was extracted using ISOGEN II (Nippon Gene, #311-07361) according to manufacturer's instruction. Ribosomal RNA (rRNA) was removed using RiboMinus Eukaryote Kit (Thermo Fisher Scientific, #A1083708).
cDNA libraries were prepared using SOLiD total RNA-Seq kit (Thermo Fisher Scientific, #4445374) according to manufacturer's instruction.

tag: strain/background

tag: genotype/variation

value: Heart

value: 6 weeks


title: 149537


title: LN229


title: axo4.H7


title: PRMT1-cKO1


title: axo4.H6


title: WT1

value: WT


title: MDA-MB-231

value: Cancer cell line (Breast)


title: WT2


title: patient sample HV7

tag: cell type

value: Normal


title: 148656


title: axo4.H4


title: patient sample MGUS-023

value: Pre-malignant


title: axo4.H12


title: RT112

value: Cancer cell line (Bladder)


title: MCF7


title: patient sample HV6


title: patient sample HV3


title: axo4.H11


title: patient sample HV2


title: wt_log_YPD_6

description: report_of_all_averaged_genes_across_age_in_wt_and_compass_mutants.txt

data_processing:
All reads had poor qualities and read-through adapter contamination removed with Trim Galore (v0.4.2) in default mode prior to mapping.
ChIP-Seq reads were aligned using Bowtie 2 (v2.3.2) with default parameters.
RNA-Seq reads were mapped to genome R64-2-1 using HISAT2 v2.0.5 (parameters: --sp 1000,1000 ). BAM files were imported into Seqmonk v0.39.0 and normalised based on the number of reads mapping to the antisense strand of annotated open reading frames, excluding the rDNA locus and the mtDNA.
Genome_build: R64-2-1
ChIP-Seq report: Quantitated ChIP-Seq data files are tab delimited SeqMonk reports containing the following columns: 1) Probe (chromosomal location), 2) Chromosome, 3) Start, 4) End, 5-30) raw read count 1 kb tiles
Quantitated RNA-Seq data files are tab delimited SeqMonk reports containing the following relevant columns: (1) CDS name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (8) Description (Ensembl); (12-13) log2 RPKM value

extract_protocol:
Percoll gradients (1 for 7.5 hr or 2 for 24/48 hr time points) were formed by vortexing 1ml Percoll (Sigma P1644) with 110µl 10x PBS in 2ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed 1x with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~250 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g to pellet the cells, which were then re-suspended in 1ml PBSE per timepoint (re-uniting samples split across two gradients). Cells were briefly sonicated in a chilled Bioruptor 30 s on low power, then 25 µl Streptavidin microbeads added (Miltenyi Biotech 1010007) and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 2 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. Cells were re-suspended in 50µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater, then 250µl Lysis buffer added followed by 15µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 13,000 g, 4 °C. Pellet was washed with cold 70% ethanol and re-suspended in 10 µl water.
500ng RNA was used to prepare libraries using the NEBNext Ultra Directional mRNAseq kit (NEB E7420, E7490, E7335, E7500, E7710) as described with modifications: Reagent volumes for RT, second strand synthesis, tailing and ligation were reduced by 50%, while libraries were amplified for 12 cycles using 2 µl each primer per reaction before two rounds of AMPure bead purification as described in the kit at 0.9x ratio prior to analysis by quality control using a Bioanalyzer.

value: Mother Enrichment Project diploid

value: log


title: wt_log_YPD_5


title: patient sample MGUS-052


title: patient sample ND-024

value: Malignant


title: wt_log_YPD_1


title: patient sample HV1

value: plasma cells


title: axo4.H10


title: NT2D1_CT_H3K27me3_+RA

city: Marburg

first: Uta

middle: Maria

last: Bauer

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research

institute: Philipps University Marburg

description: CRISPR/Cas9 control NT2/D1 cells

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2
Aligned files (bam) were filtered for duplicated aligned reads
MACS 1.4 was used to perform the peak calling
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function with binsize=50, peak files incorporate the number of peaks after filtering for given sample; bigwig files were normalized with CPM (Count Per Million)

source_name: embryonal carcinoma cell line

growth_protocol: NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS

extract_protocol:
Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonified  and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies.
Libraries were prepared according to the manufacturer’s protocol (Diagenode, MicroPlex Library Preparation Kit)

treatment_protocol: 1 µM all trans retinoic acid (ATRA) for 3 days

value: pluripotent

value: rabbit (Millipore, 07-449)


title: NT2D1_KO_H3K27me3_+RA

description: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells and PRMT6 re-expression with doxy


title: LN18 (Nuno)

value: LN18 (Nuno)


title: NT2D1_KO_H3K27me3_-RA


title: wt_7.5h_YPD_6

value: 7.5 hour


title: axo4.H1

value: Fluidigm C1


title: wt_7.5h_YPD_5


title: NT2D1_CT_H3K27me3_-RA

description: CRISPR/Cas9 control NT2/D1 cells


title: axo4.G9

value: stage 44 limb bud


title: axo4.G3


title: D20-oocyte-Stella-Het-RRBS.rep1

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
RRBS sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: CpG methylation levels were generated with Bismark, and only sites with depth greater than 5 were kept. Methylation levels of 100-bp tiles along the genome (mm9) were calculated as total C / total C+T within each tile.

source_name: Dpp 20 oocytes from Stella+/- mouse

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
RRBS for oocyte and PGC samples: For oocytes, before MspI digestion, 5 µl of lysis buffer (20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, 1 mg/ml QIAGEN Protease) was directly added to the frozen samples (in < 1µl PBS) followed by 3 hours of incubation at 50 ℃ and 30 minutes of inactivation at 75 ℃. Then to the same tube, 13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) and 0.5pg unmethylated λ DNA (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃. For PGCs, the purified genomic DNA was directly digested with MspI in an 18 µl total volume. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 0.2 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 20 minutes of incubation at 30 ℃, 20 min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5 mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where -s- indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by size selection of 150-500 bp DNA fragments using AMPure XP beads (Beckman Coulter).
RRBS for sperm: 100ng genomic DNA was digested with 10 units of MspI in a 18 µl total volume at 37 ℃ overnight. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment exo- , 0.2 µl of 10x Buffer Tango, 5 mM dATP, and 0.5 mM each of dGTP and dCTP, followed by 20 minutes of incubation at 30 ℃, 20min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed at 20 ℃ for 15min using NEBNext Ultra Ligation Module (NEB) by adding 15 µl of ligase master mix, 1 µl of ligation enhancer, 2.5 µl of 1.5 µM methylated custom adaptor and ddH2O to a total volume of 80 µl. The reaction mix was then size selected of 150-500 bp DNA fragments using AMPure XP beads. The size-selected sample was then subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by AMPure XP beads clean-up of the PCR product.
RNA-seq for oocyte samples: cDNA libraries were synthesized and amplified using SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech) following manufacturer’s instructions. The purified cDNA was fragmented with Covaris M220 sonicator, and then subjected to Illumina sequencing library construction with KAPA Hyper Prep kits (Kapa Biosystems) following manufacturer’s instructions.

tag: strain background

value: primary cells isolated from mouse

value: growing oocyte

value: stella+/-

value: ovary

tag: developmental stage

value: day 20 postpartum


title: axo4.F4


title: MII-oocyte-Stella-Het-RRBS.rep1

source_name: MII oocytes from Stella+/- mouse

value: MII oocyte

value: week 7 postpartum


title: D5-oocyte-Stella-Null-RRBS.rep3

source_name: Dpp 5 oocytes from Stella-/- mouse

value: stella-/-

value: day 5 postpartum


title: axo4.G2


title: axo4.F2


title: D20-oocyte-Stella-Null-RRBS.rep1

source_name: Dpp 20 oocytes from Stella-/- mouse


title: MII-oocyte-Stella-Null-RRBS.rep1

source_name: MII oocytes from Stella-/- mouse


title: wt_48h_YPD_2

value: Mother Enrichment Project diploid

value: 48 hour


title: NT2D1_CT_KMT2D_-RA_abgent

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2
Aligned files (bam) were filtered for duplicated aligned reads
MACS 1.4 was used to perform the peak calling
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function with binsize=50, peak files incorporate the number of peaks after filtering for given sample; bigwig files were normalized with CPM

growth_protocol: NT2/D1 and U2OS cells were cultured in DMEMI supplemented with 10% FCS

treatment_protocol: 1 µM all trans retinoic acid (ATRA) for 3 days; 16 µM MS049 (PRMT6 inhibitor) 3 days; PRMT6 rescue with Doxy treatment 6 days

value: embryonal carcinoma cell line

tag: cell status

value: pluripotent

value: CRISPR/Cas9 control NT2/D1 cells

value: rabbit (AP6183a, abgent)


title: NT2D1_CT_KMT2D_-RA_santacruz

value: rabbit (SC-293217, santa cruz)


title: wt_48h_YPD_5

tag: strain


title: NT2D1_KO_H3R2me2a_-Doxy_R2

value: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells

value: rat monoclonal generated in the laboratory


title: D5-oocyte-Stella-Null-RRBS.rep2

value: primary cells isolated from mouse

value: growing oocyte


title: wt_48h_YPD_1

tag: age


title: wt_48h_YPD_7


title: NT2D1_KO_KMT2D_-RA_santacruz

tag: chip antibody


title: NT2D1_KO_Input_-Doxy


title: axo4.F12

tag: sc-rna-seq method

value: Fluidigm C1

value: stage 44 limb bud


title: axo4.F1

tag: development stage


title: D5-oocyte-Stella-Null-RRBS.rep1

tag: tissue

value: ovary


title: NT2D1_KO_H3R2me2a_+Doxy_R1

value: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells and PRMT6 re-expression with doxy


title: wt_24h_YPD_6

value: 24 hour


title: D5-oocyte-Stella-Het-RRBS.rep3

source_name: Dpp 5 oocytes from Stella+/- mouse

value: stella+/-

value: day 5 postpartum


title: wt_24h_YPD_2

value: Mother Enrichment Project diploid


title: wt_24h_YPD_5


title: axo4.D11


title: NT2D1_CT_H3R2me2a_+Inh_R2

value: embryonal carcinoma cell line

value: CRISPR/Cas9 control NT2/D1 cells and treatment with PRMT6 inhibitor


title: D5-oocyte-Stella-Het-RRBS.rep1


title: D5-oocyte-Stella-Het-RRBS.rep2


title: NT2D1_KO_KMT2D_-RA_abgent

value: pluripotent


title: swd1_log_YPD_6

source_name: Mother Enrichment Project swd1 diploid

value: Mother Enrichment Project swd1 diploid

value: log


title: wt_24h_YPD_1


title: swd1_log_YPD_5


title: NT2D1_KO_Input_+Doxy


title: Mouse_DSS_2

value: Colon

tag: disease state

value: DSS-induced Colitis


title: axo3.H8


title: NT2D1_CT_H3R2me2a_+Inh_R1

value: rat monoclonal generated in the laboratory


title: axo3.H5


title: axo3.H9


title: axo4.B5


title: Mouse_DSS_1


title: axo3.H7


title: swd1_7.5h_YPD_5

value: 7.5 hour


title: swd1_48h_YPD_5

value: 48 hour


title: NT2D1_KO_H3R2me2a_+Doxy_R2


title: NT2D1_CT_KMT2D_+RA_santacruz

value: CRISPR/Cas9 control NT2/D1 cells

value: rabbit (SC-293217, santa cruz)


title: Mouse_HC_3

value: Healthy


title: axo3.H2

value: Fluidigm C1

value: stage 44 limb bud


title: NT2D1_KO_KMT2D_+RA_abgent

value: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells

value: rabbit (AP6183a, abgent)


title: Mouse_HC_1


title: Mouse_HC_2


title: swd1_24h_YPD_6

value: 24 hour


title: swd1_48h_YPD_4


title: swd1_24h_YPD_5


title: Mouse_DSS_3


title: axo3.H10


title: NT2D1_CT_H3R2me2a_-RA_R2 | NT2D1_CT_H3R2me2a_-Inh_R2

value: embryonal carcinoma cell line


title: axo3.H1


title: NT2D1_KO_H3R2me2a_-Doxy_R1

value: pluripotent


title: axo3.H3


title: axo3.G9


title: NT2D1_CT_KMT2D_+RA_abgent


title: axo3.G7


title: NT2D1_KO_KMT2D_+RA_santacruz


title: U2932

type: RNA

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: As described in the user guide, appendix A, of the The Encore™Biotin Module  (NuGEN)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing:
RMA normalized using R (v3.3.2), the affy-package (v1.48.0) from Bioconductor, and probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_20.0.0].
Probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_20.0.0]

label: Biotin

source_name: cell line without treatment

label_protocol: The following two kits from NuGEN were used following manufactures guide lines: The WT-Ovation™ Exon Module Version 1.0 and The Encore™Biotin Module

growth_protocol: In tissue culture media supplemented with pen/strep and fetal calf serum (10-20 %). Incubated with 5% CO2 at 37 degrees celcius

extract_protocol: Total RNA was purified using Trizol and transferring to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction

treatment_protocol: not applicaple

tag: disease

value: Diffuse large_B-cell Lymphoma (DLBCL)


title: NT2D1_CT_H3R2me2a_-Inh_R1


title: spp1_7.5h_YPD_2

source_name: Mother Enrichment Project spp1 diploid

value: Mother Enrichment Project spp1 diploid


title: spp1_log_YPD_1

value: log


title: axo3.G6


title: spp1_7.5h_YPD_3


title: U2OS_KO_H3R2me2a

value: bone osteosarcoma

value: differentiated

value: CRISPR/Cas9-mediated deletion of PRMT6 inU2OS cells


title: axo3.G10


title: axo3.G12


title: U2OS_IgG

value: CRISPR/Cas9 control U2OS cells

value: IgG rabbit (I5006, Sigma)


title: SU-DHL-5


title: SU-DHL-4


title: U2OS_CT_H3R2me2a

value: rat monoclonal generated in the laboratory


title: spp1_48h_YPD_1

value: 48 hour


title: spp1_48h_YPD_2


title: spp1_log_YPD_2


title: SU-DHL-8


title: OCI-Ly7


title: axo3.G1

value: Fluidigm C1


title: spp1_24h_YPD_2


title: spp1_7.5h_YPD_1

value: 7.5 hour


title: OCI-Ly19


title: RIVA


title: spp1_24h_YPD_1


title: axo3.F8

value: stage 44 limb bud


title: axo3.F9


title: set1CD_log_YPD_2

source_name: Mother Enrichment Project set1-H1017L diploid


title: axo3.F6


title: axo3.F5


title: set1CD_log_YPD_1

value: Mother Enrichment Project set1-H1017L diploid


title: set1CD_7.5h_YPD_3


title: axo3.F4


title: FARAGE


title: DB


title: set1CD_7.5h_YPD_2


title: axo3.F3


title: set1CD_7.5h_YPD_1


title: axo3.F10


title: set1CD_48h_YPD_2


title: set1CD_48h_YPD_1


title: axo3.E8


title: set1CD_24h_YPD_2

value: 24 hour


title: set1CD_24h_YPD_1


title: axo3.E6


title: NU-DHL-1


title: axo3.E4


title: BB506_PC_CD19pos CD56neg

data_processing:
RMA normalized using R (v3.3.2), the affy-package (v1.48.0) from Bioconductor, and probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_20.0.0].
Probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_20.0.0]
Probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_20.0.0]

source_name: From patient BB506 - FACS as population PC note on population (in any): CD19pos CD56neg

growth_protocol: not applicable

extract_protocol: mRNA was isolated using the μMACS™ technology (Miltenyi Biotech, Bergisch-Gladbach, Germany), using μ Columns and elution with pure water. Amplification was performed using WT Ovation Pico RNA Amplificatio System (NuGEN Technologies, Inc., San Carlos, CA) following manufactures protocol.

treatment_protocol: Normal bone marrow (BM, n=7) was harvested from healthy volunteers. The normal B-cell subsets were directly phenotyped by multiparametric flow cytometry (MFC) and fluorescence-activated cell sorting (FACS) into six distinct B-cell subsets PreBI, PreBII, immature (Im), naïve (N), memory (M) B-cells, and plasma cells (PC) by a highly selected monoclonal antibody panel. The B-cell subset RNA was labeled for microarray analysis (MAA) and hybridized to the Human Exon 1.0 ST Array platform.

value: Healthy

tag: person id

value: Population of plasma cells purified with flow cytometry from mononoclear cells of bone marrow


title: BB504_PC_CD19pos CD56neg

source_name: From patient BB504 - FACS as population PC note on population (in any): CD19pos CD56neg


title: axo3.E3


title: BB504_preBII_

source_name: From patient BB504 - FACS as population preBII note on population (in any):


title: wt_YPD_log_TOTAL_1_no-spike-in

source_name: Mother Enrichment Project diploid

extract_protocol:
Percoll gradients (1 for 7.5 hr or 2 for 24/48 hr timepoints) were formed by vortexing 1.16ml Percoll (Sigma P1644) with 42µl 5M NaCl, 98 µl water in 2ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Cells were defrosted on ice, re-suspended in ~250 µl cold PBSE per gradient and layered on the pre-formed gradients. Gradients were centrifuged for 20 min at 1,000 g, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g to pellet the cells, which were then re-suspended in 1ml PBSE per timepoint (re-uniting samples split across two gradients). 25 µl Streptavidin magnetic beads were added (Miltenyi Biotech 1010007) and cells incubated for 30 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 8 ml cold PBSE and eluted with 1ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. Final elution was to 1.5 ml tubes (Treff 1130153). 50 µl cells were set aside for quality control, while the remainder were pelleted by centrifugation and processed directly for ChIP.  Cells were re-suspended in 50 μl cold CLB (50mM HEPES pH 7.0, 14mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, cOmplete Protease Inhibitors (Roche 1836170)) with 50 µl zirconium beads and lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater then decanted to a Covaris 520045 microTUBE and topped up to 130 µl with CLB. Sonication was performed on a Covaris 220: Duty Factor 5 %, PIP 130 W, 900s, 200 cycles per burst, 8.9 ºC. Samples were decanted to a 1.5 ml tube and Covaris tube washed with CLB and combined to give 180 μl total volume, which was centrifuged 5 min top speed at 4 ºC and the pellet discarded. Lysate was pre-cleared by incubation with 10μl of pre-equilibrated Protein-G magnetic beads (Life Technologies 10004D), then 30 μl set aside for total DNA extraction and 50 μl used per immunoprecipitation (IP). Antibodies were added at 1:50 dilution (rabbit anti-H3, CST 2650 or rabbit anti-H3K4me3, CST 9751), one IP was processed without antibody, and IPs were incubated over night at 4 ºC on a wheel.   10μl pre-equilibrated protein-G beads in 25μl CLB were added to each IP and incubated 2-3 hrs at 4 ºC on a wheel. Beads were then washed once each at room temperature for 5 minutes on a wheel with: CLB, CLB with 0,5 M NaCl, wash buffer (10 mM Tris pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), TE, then eluted overnight at 65 ºC with 200 μl elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS). Input samples were diluted to 200 μl with TE, treated with 1 μl 1 mg/ml RNase A at 37 ºC for 1 hour then incubated overnight at 65 ºC. Input and IP samples were treated with 1 μl proteinase K for 2 hours at 55 ºC, then purified by phenol:chloroform extraction, precipitated and re-suspended in 5 μl TE.
libraries were synthesised using a NEBNext DNA Ultra II kit (NEB E7645) with modifications: Concentration of DNA was increased by reducing the volumes of the end repair and ligation steps 5-fold, with reagent quantities reduced in kind. After clean-up with 0.9x AMPure beads, PCR in 50 μl volumes according to manufacturer’s instructions. Libraries were purified with 0.9x AMPure beads and eluted in 30μl, then a size selection was performed by incubating first with 18μl AMPure beads, discarding the beads then purifying the remaining DNA from the supernatant with an additional 9 μl AMPure beads.

value: Mother Enrichment Project diploid


title: BB504_PC_CD19 neg CD56 neg

source_name: From patient BB504 - FACS as population PC note on population (in any): CD19 neg CD56 neg


title: wt_YPD_log_H3_1_no-spike-in

value: Cell Signalling Technologies, 2650


title: axo3.E2

source_name: Stage 44 forelimb limb bud


title: axo3.E12


title: wt_YPD_log_H3K4me3_1_no-spike-in

value: log

value: Cell Signalling Technologies, 9751


title: axo3.E7


title: wt_YPD_24h_TOTAL_1_no-spike-in


title: axo3.E11


title: axo3.E10


title: wt_YPD_24h_H3K4me3_1_no-spike-in


title: BB506_Immature_

source_name: From patient BB506 - FACS as population Immature note on population (in any):


title: axo3.E5


title: wt_YPD_24h_H3_1_no-spike-in


title: axo3.D8


title: axo3.D7


title: sKO-3A.MII.RNA.rep2

molecule: polyA RNA

source_name: MII oocytes from Stella-KO/Dnmt3a-KO mouse

tag: cell line

value: primary cells isolated from mouse

value: MII oocyte

value: stella-/-, Dnmt3a-/-

value: ovary

value: week 7 postpartum


title: sKO-3A.MII.RNA.rep1


title: BB158-8_preBI_

source_name: From patient BB158 sample no 8 FACS as population preBI note on population (in any):


title: BB158-7_preBII_

source_name: From patient BB158 sample no 7 FACS as population preBII note on population (in any):


title: axo3.D6


title: BB158-6_Immature_

source_name: From patient BB158 sample no 6 FACS as population Immature note on population (in any):


title: BB163-5_Memory_

source_name: From patient BB163 sample no 5 FACS as population Memory note on population (in any):


title: sHet-3A.MII.RNA.rep1

source_name: MII oocytes from Stella-Het/Dnmt3a-KO mouse

value: stella+/-, Dnmt3a-/-


title: axo3.D4

value: Fluidigm C1


title: BB163-1_PC_CD19pos CD56neg

source_name: From patient BB163 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: axo3.D3


title: sKO-UKO.MII.RRBS.rep3

source_name: MII oocytes from Stella-KO/Uhrf1-KO mouse

value: stella-/-, Uhrf1-/-


title: BB158-5_Memory_

source_name: From patient BB158 sample no 5 FACS as population Memory note on population (in any):


title: sKO-pPN-RRBS.rep2

source_name: Paternal pronucleus from Stella-/- mouse

value: Paternal pronucleus

value: stella-/-

value: zygote

value: PN4-PN5 stage zygotes 11 hours post fertilization (hpf)


title: sHet-3A.MII.RNA.rep2


title: axo3.D11

value: stage 44 limb bud


title: sKO-UKO.MII.RRBS.rep2


title: axo3.D1


title: BB158-4_Naive_

source_name: From patient BB158 sample no 4 FACS as population Naive note on population (in any):

value: Healthy

value: Population of plasma cells purified with flow cytometry from mononoclear cells of bone marrow


title: BB163-4_Naive_

source_name: From patient BB163 sample no 4 FACS as population Naive note on population (in any):


title: BB163-6_Immature_

source_name: From patient BB163 sample no 6 FACS as population Immature note on population (in any):


title: BB149-6_Immature_

source_name: From patient BB149 sample no 6 FACS as population Immature note on population (in any):


title: BB158-1_PC_CD19pos CD56neg

source_name: From patient BB158 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: BB158-3_PC_CD19neg CD56pos

source_name: From patient BB158 sample no 3 FACS as population PC note on population (in any): CD19neg CD56pos


title: BB149-4_Naive_

source_name: From patient BB149 sample no 4 FACS as population Naive note on population (in any):


title: BB149-1_PC_CD19pos CD56neg

source_name: From patient BB149 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: BB149-3_PC_CD19neg CD56pos

source_name: From patient BB149 sample no 3 FACS as population PC note on population (in any): CD19neg CD56pos


title: BB149-7_preBII_

source_name: From patient BB149 sample no 7 FACS as population preBII note on population (in any):


title: axo3.C7

source_name: Stage 44 forelimb limb bud


title: axo3.C8


title: axo3.C6


title: axo3.D2


title: sKO-3A.MII.RRBS.rep2

source_name: MII oocytes from Stella-KO/Dnmt3a-KO mouse


title: sKO-D1.MII.RRBS.rep2

source_name: MII oocytes from Stella-KO/Dnmt1-KO mouse

value: stella-/-, Dnmt1-/-


title: axo3.C3


title: sKO-mPN-RRBS.rep2

source_name: Maternal pronucleus from Stella-/- mouse

value: Maternal pronucleus


title: sKO-3A.MII.RRBS.rep3

value: primary cells isolated from mouse


title: sHet-UKO.MII.RRBS.rep3

source_name: MII oocytes from Stella-Het/Uhrf1-KO mouse

value: MII oocyte

value: stella+/-, Uhrf1-/-


title: BB147-6_Immature_

source_name: From patient BB147 sample no 6 FACS as population Immature note on population (in any):


title: BB147-5_Memory_

source_name: From patient BB147 sample no 5 FACS as population Memory note on population (in any):


title: axo3.C12


title: axo3.C1


title: BB147-4_Naive_

source_name: From patient BB147 sample no 4 FACS as population Naive note on population (in any):


title: axo3.C4


title: sHet-D1.MII.RRBS.rep3

source_name: MII oocytes from Stella-Het/Dnmt1-KO mouse

value: stella+/-, Dnmt1-/-

value: ovary


title: sHet-UKO.MII.RRBS.rep2

value: week 7 postpartum


title: sHet-pPN-RRBS.rep2

source_name: Paternal pronucleus from Stella+/- mouse

value: stella+/-


title: sHet-mPN-RRBS.rep2

source_name: Maternal pronucleus from Stella+/- mouse


title: sKO-D1.MII.RRBS.rep3


title: BB163-7_preBII_

source_name: From patient BB163 sample no 7 FACS as population preBII note on population (in any):


title: axo3.C2

value: Fluidigm C1


title: BB147-3_PC_CD19neg CD56pos

source_name: From patient BB147 sample no 3 FACS as population PC note on population (in any): CD19neg CD56pos


title: BB145-1_PC_CD19pos CD56neg

source_name: From patient BB145 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: wt_log_YPD_4

source_name: Mother Enrichment Project diploid

value: Mother Enrichment Project diploid

value: log


title: sHet-D1.MII.RRBS.rep2


title: BB145-4_Naive_

source_name: From patient BB145 sample no 4 FACS as population Naive note on population (in any):


title: BB147-2_PC_CD19neg CD56neg

source_name: From patient BB147 sample no 2 FACS as population PC note on population (in any): CD19neg CD56neg


title: BB145-7_preBII_

source_name: From patient BB145 sample no 7 FACS as population preBII note on population (in any):


title: axo3.B9

source_name: Stage 44 forelimb limb bud


title: wt_log_YPD_3


title: sHet-3A.MII.RRBS.rep3

source_name: MII oocytes from Stella-Het/Dnmt3a-KO mouse

value: stella+/-, Dnmt3a-/-


title: BB147-1_PC_CD19pos CD56neg

source_name: From patient BB147 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: BB143-6_Immature_

source_name: From patient BB143 sample no 6 FACS as population Immature note on population (in any):


title: axo3.B8


title: axo3.C11


title: wt_7.5h_YPD_3

value: 7.5 hour


title: sHet-3A.MII.RRBS.rep2


title: axo3.B7

value: stage 44 limb bud


title: axo3.B5


title: wt_7.5h_YPD_2


title: ko2C.RRBS.rep3

source_name: 2-cell embryos derived from Stella-/- oocytes(C57BL/6) and WT sperm (DBA/2)

value: 2-cell embryo

value: stella-/-, WT

value: embryo

value: 2-cell stage


title: BB143-4_Naive_

source_name: From patient BB143 sample no 4 FACS as population Naive note on population (in any):

value: Healthy

value: Population of plasma cells purified with flow cytometry from mononoclear cells of bone marrow


title: ko2C.RRBS.rep2

value: primary cells isolated from mouse


title: BB143-5_Memory_

source_name: From patient BB143 sample no 5 FACS as population Memory note on population (in any):


title: wt_7.5h_YPD_1


title: axo3.B4


title: wt_48h_YPD_3

value: 48 hour


title: het2C.RRBS.rep3

source_name: 2-cell embryos derived from Stella+/- oocytes(C57BL/6) and WT sperm (DBA/2)

value: stella+/-, WT


title: U-266

description: gene expression data from untreated cell line

source_name: cell line without treatment

value: Multiple myeloma (MM)


title: wt_24h_YPD_3

value: 24 hour


title: swd1_log_YPD_3

source_name: Mother Enrichment Project swd1 diploid

value: Mother Enrichment Project swd1 diploid


title: het2C.RRBS.rep2


title: axo3.B12

value: Fluidigm C1


title: axo3.A8


title: swd1_7.5h_YPD_3


title: BB143-1_PC_CD19pos CD56neg

source_name: From patient BB143 sample no 1 FACS as population PC note on population (in any): CD19pos CD56neg


title: OPM-2


title: swd1_7.5h_YPD_2


title: RPMI-8226


title: MM.1S


title: swd1_log_YPD_2

value: log


title: swd1_48h_YPD_2


title: axo3.A9


title: axo3.A6


title: LP-1


title: KMS-12-BM


title: swd1_24h_YPD_3


title: axo3.A5


title: Lgr5_2

city: Taichung City

first: Yu-Ting

last: Yen

state: Taiwan

address: No. 2, Yude Road, North District,

country: Taiwan

institute: China Medical University

description: NER+DMBA+TAM 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads. The filtering process is as follows:
(1) Discard reads with adaptor contamination.
(2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%).
(3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: intestine tissue

growth_protocol: Culture condition: Noggin, EGF and R-spondin-1 (NER) in Matrigel

extract_protocol:
RNA was harvested using Trizol reagent. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. A total amount of 3 μg RNA per sample
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Treated：DMBA or/and tamoxifen

value: intestinal organoid

tag: days

value: 50-day period of culture

tag: protocol

value: NER+DMBA+TAM


title: DSS_S1

description: NER+ Dosage-sensitive TAM (short) 1

value: NER+ Dosage-sensitive TAM (short)


title: DSS_L2

description: NER+ Dosage-sensitive TAM (Long) 2

value: NER+ Dosage-sensitive TAM (Long)


title: Lgr5_1

description: NER+DMBA+TAM 1


title: DSS_L1

description: NER+ Dosage-sensitive TAM (Long) 1


title: DSS_S2

description: NER+ Dosage-sensitive TAM (short) 2


title: axo3.B1

data_processing:
"freeIbis" was used for C1 and SmartSeq2 sample data as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.) Cellranger, version 2.0.0, as part of the 10x Genomics analysis pipeline was used to call bases for 10x experiments.
"leeHom" was used to trim adapters and merge Illumina sequencing reads for C1 and SmartSeq2 sample data. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to trim adapters for 10x experiments.
"deML" was used for robust demultiplexing of Illumina sequences for C1 and SmartSeq2 sample data using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to demultiplex reads.
Reads were aligned against the axolotl transcriptome (www.axolotl-omics.org, Download: 2015-07-29) using kallisto (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) for C1 and SmartSeq 2 sample data or using STAR (Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.) implemented in 10x' cell ranger software, version 2.0.0, for 10x data.
Transcript Per Million (TPM) values were computed using kallisto for C1 and SmartSeq2 samples. (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) Cellranger, version 2.0.0, implemented in the 10x Genomics analysis pipeline was used to obtain bam alignment files and gene count (UMI) matrices.
Gene expression values of different isoforms of the same gene were summed using custom Perl scripts.
Genome_build: Axolotl transcriptome (Am_2.2)
Supplementary_files_format_and_content: Master data frame including cell ID, cell type, timepoint, gene ID, and TPM values for each single cell.

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v2 Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

value: stage 44 limb bud


title: axo3.A3


title: axo3.A7


title: KMS-12-PE


title: swd1_48h_YPD_3


title: KMS-11


title: NL1

description: NER culture medium +DMBA (Long) 1

value: NER culture medium +DMBA (Long)


title: KMM-1


title: spp1_log_YPD_4

source_name: Mother Enrichment Project spp1 diploid

value: Mother Enrichment Project spp1 diploid


title: axo3.A12


title: axo3.A11


title: NL2

description: NER culture medium +DMBA (Long) 2


title: spp1_log_YPD_3


title: spp1_log_YPD_5


title: wild-type untreated(6mA modification)

city: beijing

first: huang

last: tianxiao

address: yiheyuan

institute: peking university

data_processing:
low quality or N bases, and reads below 50 bases long are removed by Trimmomatic version 0.35 to optimize paired-end alignment.
The filtered sequencing reads were aligned to the Caenorhabditis elegans reference genome using the Bowtie2 version 2.2.6 with default settings.
Duplicated reads aligned to the same position with the same orientation were retained for only one read with highest mapping quality to avoid potential PCR bias by using picard.
The differential peaks are called by MACS2 bdgdiff with default parameters.
Genome_build: ce10
Supplementary_files_format_and_content: 364 peaks enrichment were changed in wild-type C.elegans genome by 6mA MeDIP-seq and  generated using MACS2 version 2.1.0

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: wild-type animals was raised at 22℃ with or without antimycin from eggs until they grow to L4

extract_protocol:
worm genomic DNA was extracted followed general gDNA extract protocol by phenol: chloroform: isopentanol (25:24:1) extraction.
library construction is followed protocol of NEBNEXT Ultra DNA Library Prep Kit for Illumina (E7370L)

treatment_protocol: antimycin A were diluted in M9 buffer and drop onto agar, air dry before eggs seeded. Antimycin concentration= umol of drug / agar volume

value: Bristol

tag: antibody

tag: treatment

value: untreated


title: wild-type 1.92uM antimycin treated

value: 1.92uM antimycin


title: axo3.A1


title: axo3.A4


title: spp1_48h_YPD_4

value: 48 hour


title: spp1_48h_YPD_5


title: AMO-1

value: Multiple myeloma (MM)


title: wild-type 1.93uM antimycin treated(6mA modification)


title: wt_YPD_log_TOTAL_3_no-spike-in

source_name: Mother Enrichment Project diploid

value: Mother Enrichment Project diploid


title: NS1

description: NER culture medium +saline 1

value: NER culture medium +saline


title: wt_YPD_log_TOTAL_2_no-spike-in


title: wild-type untreated (MeDIP-seq)


title: axo2.H5

value: Fluidigm C1


title: axo2.H6


title: damt-1 1.92uM antimycin treated(F2)

data_processing:
reads below 50 bases long are removed by Trimmomatic version 0.35 to optimize paired-end alignment.
the filtered sequencing reads were aligned to the Caenorhabditis elegans reference genome (ce10/WS220) using the HISAT2 version 2.0.5 with default settings.
duplicated reads aligned to the same position with the same orientation were retained for only one read with highest mapping quality to avoid potential PCR bias by using samtools version 1.3.1.
HTSeq version 0.9.1 was used by count with the sum of individual gene counts is greater than 10.
The counting matrix is merged by R version 3.5.0 package DESeq2 version 1.20.0.
Genome_build: ce10
Supplementary_files_format_and_content: the excel include the different expression genes (the gene counts have changed) and fold change value  in wild-type C.elegans transcriptome compared to DAMT-1 mutant upon mitochondrial stress.

growth_protocol: wild-type and damt-1 animals were raised at 22℃ with or without antimycin from eggs until they grow to L4

extract_protocol:
worm total RNA was extracted by phenol: chloroform: isopentanol (25:24:1) extraction.
RNA libraries were prepared for sequencing using Illumina (E7370L) protocols.

tag: genotype/variation

tag: replication


title: damt-1 untreated


title: damt-1 1.92uM antimycin treated(P0)


title: axo2.H12


title: spp1_48h_YPD_3


title: axo2.G8


title: axo2.H1


title: NS2

description: NER culture medium +saline 2


title: axo2.G6


title: wt_YPD_log_H3K4me3_2_no-spike-in

value: log

value: Cell Signalling Technologies, 9751


title: wild-type 1.92uM antimycin treated(F2)

value: wild type


title: axo2.G4


title: wild-type 1.92uM antimycin treated(P0)


title: wt_YPD_log_H3K4me3_3_no-spike-in


title: wild-type 1.92uM antimycin treated(F1)


title: wt_YPD_log_H3_3_no-spike-in

value: Cell Signalling Technologies, 2650


title: axo2.G3


title: axo2.G10


title: wt_YPD_log_H3_2_no-spike-in


title: damt-1 1.92uM antimycin treated(F1)


title: ATAC-Seq of BA treated arr1,10,12 roots; replicate 2

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 4144 Genome Sciences Building

department: Biology

institute: University of North Carolina

description: TypeB

data_processing:
All datasets were trimmed using the BBDuk tool from the BBMap 37.50 package with the following parameters 'k=13 ktrim=r'.
The trimmed ATAC-Seq reads were then mapped to the Arabidopsis genome (TAIR10) using bowtie 1.2.0 with the following parameters '-X 1000 -v 2'. These parameters keep unique aligning fragments with lengths up to 1000 bps and reads can have up to 2 mismatches.
The resulting SAM file containing mapped reads was converted to BAM format, sorted, indexed, and processed to remove duplicate and organellar reads using Samtools 1.5.
To normalize and visualize the datasets, the BAM files were converted to bigwig using the bamCoverage function within deepTools 2.5.2 with a bin size of 10 bp and normalized to 1x sequencing depth of the genome size of Arabidopsis (150 M).
The findPeaks script within HOMER 4.9.2 was used to call peaks on ATAC datasets with the following options '-region -size 200 -minDist 202 -gsize 135000000 -tbp 0', which allows for peak calling of variable lengths greater than 200 bps.
To do differential accessible region analysis of ATAC datasets, diffReps, a perl script, was used with the following parameters '-ns b -mo n -me nb'. These parameters find broadly enriched regions (Z-score cutoff = 2) greater than 200 bps using a negative binomial test to test for significance.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak files are in BED format, which includes genomic coordinates for called peaks. Genome browser tracks are in BIGWIG format. Identified differential ATAC regions are in BED format, which includes the genomic coordinates for these regions.
There are processed data files for merged ATAC-seq replicates on the series record:
Roots_NaOH_Merged.bw: ATAC-Seq of control treated roots; merged reps
Roots_BA_Merged.bw: ATAC-Seq of BA treated roots; merged reps
Shoots_NaOH_Merged.bw: ATAC-Seq of control treated shoots; merged reps
Shoots_BA_Merged.bw: ATAC-Seq of BA treated shoots; merged reps
TypeB_NaOH_Merged.bw: ATAC-Seq of control treated arr1,10,12 roots; merged reps
TypeB_BA_Merged.bw: ATAC-Seq of BA treated arr1,10,12 roots; merged reps
Roots_WT_All_diffRepsFC1.2.bed: Differential_ATAC_Regions
Shoots_WT_All_diffRepsFC1.2.bed: Differential_ATAC_Regions

organism: Arabidopsis thaliana

source_name: arr1,10,12 roots treated for 45 with benzyl adenine

extract_protocol:
For ATAC-Seq, crude nuclei were harvested on sucrose cushions and sorted by DAPI-staining and FANS.
For ATAC-Seq, the libraries were created by incubating nuclei with hyperactive Tn5 transposase and fragmented DNA was barcoded with indexing primers by PCR, as described by Buenrostro, et al., 2013.

treatment_protocol: Tissue were treated for 45 minutes with vehicle control or 5uM BA in MS liquid media.

value: Roots

value: BA

tag: replicate number

value: Rep 2

tag: genotype


title: axo2.G1

value: stage 44 limb bud


title: wild-type untreated

tag: strain


title: wt_YPD_7.5h_TOTAL_2_no-spike-in

tag: age

value: 7.5 hour


title: axo2.E7

tag: sc-rna-seq method


title: ATAC-Seq of BA treated arr1,10,12 roots; replicate 1

description: TypeB

value: Rep 1


title: wt_YPD_7.5h_TOTAL_1_no-spike-in


title: wt_YPD_7.5h_H3K4me3_2_no-spike-in

tag: chip antibody


title: wt_YPD_7.5h_H3K4me3_1_no-spike-in


title: ATAC-Seq of control treated arr1,10,12 roots; replicate 1

description: TypeB

source_name: arr1,10,12 roots treated for 45 with control

tag: tissue

value: Control


title: wt_YPD_7.5h_H3_2_no-spike-in


title: ATAC-Seq of BA treated shoots; replicate 1

source_name: Shoots treated for 45 minutes with benzyl adenine

value: Shoots


title: axo2.E4

source_name: Stage 44 forelimb limb bud

tag: development stage


title: axo2.E6


title: ATAC-Seq of BA treated shoots; replicate 2


title: wt_YPD_48h_TOTAL_2_no-spike-in

value: 48 hour


title: axo2.E11


title: ATAC-Seq of control treated shoots; replicate 2

source_name: Shoots treated for 45 minutes with control


title: axo2.E1


title: wt_YPD_48h_TOTAL_1_no-spike-in


title: ATAC-Seq of BA treated roots; replicate 4

source_name: Roots treated for 45 minutes with benzyl adenine

value: Rep 4


title: ATAC-Seq of control treated shoots; replicate 1


title: wt_YPD_48h_H3K4me3_1_no-spike-in

value: Mother Enrichment Project diploid


title: wt_YPD_48h_H3K4me3_2_no-spike-in


title: ATAC-Seq of BA treated roots; replicate 3

value: Rep 3


title: axo2.F1

value: Fluidigm C1


title: ATAC-Seq of BA treated roots; replicate 2