title: not differentiated PA, rep6

description:
Hs_Diff_PA_not_differentiated_rep6
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 1week, rep1

status: Public on Apr 02 2019

type: SRA

city: Solna

first: Adil

last: Mardinoglu

address: Tomtebodavägen 23B

department: Systems biology

country: Sweden

institute: SciLifeLab, KTH

description:
Hs_Diff_PA_1_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.

library_source: transcriptomic

data_processing:
Quantification of the data was done using BCBIO version 1.0.1.
Hisat2 version 2.0.5 was used within BCBIO to align the data against the human hg38 assembly.
Sailfish 0.10.1 was used within BCBIO to quantify gene and exon counts.
Genome_build: hg38 (GRCh38) assembly
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count values for each sample, along with Ensembl IDs and gene symbols.

molecule: total RNA

organism: Homo sapiens

source_name: Adipose tissue

extract_protocol:
The adipose tissue was removed of fibrous material, finely minced, and digested in collagenase buffer containing HBSS +CaCl2+MgCl2 (Gibco 14065-49), 2% BSA, and 800U/g of tissue (~3mg/g of tissue) of type 2 collagenase (Worthington-LS004177) for approximately 40 min at 37°C. Digested material was passed through a 250 um strainer and washed 3 times with a total of 1L of KRHB buffer (1x KRH, 25mM HEPES, 2mM glucose, 2%BSA) using a separation funnel (VWR 527-0007) to separate the infranatant which contains the preadipocytes from the floating mature adipocytes.
RNA quality and quantity were assessed using a Fragment Analyzer standard sensitivity RNA kit (AATI # DNF-471) according to manufacturer’s instructions. Libraries were prepared using Illumina’s stranded total RNA library prep kit with “ribo-gold” rRNA depletion (catalog# RS-122-2303). The quality of the libraries were assessed using a Fragment Analyzer standard-sensitivity NGS kit (AATI # DNF-473). Samples were pooled so that they were present at an equal molarity. Pooled samples were sequenced 2x with NextSeq high output 150 cycle kits (Illumina # FC-404-2002), paired-end reads.

tag: tissue

value: Adipose

tag: sample type

value: Differentiated PA, 1 week


title: MAAC, 2week, rep2

description:
Hs_TW_2_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: MAAC, 2 week


title: MAAC, 1week, rep4

description:
Hs_TW_1_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.

value: MAAC, 1 week


title: MAAC, 2week, rep1

description:
Hs_TW_2_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: MAAC, 2week, rep3

description:
Hs_TW_2_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: MAAC, 1week, rep1

description:
Hs_TW_1_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: MAAC, 1week, rep2

description:
Hs_TW_1_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 2week, rep3

description:
Hs_float_2_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.

value: Floating 2 week


title: floating 2week, rep2

description:
Hs_float_2_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep2

description:
Hs_Diff_PA_2_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Differentiated PA, 2 week


title: Differentiated PA, 1week, rep3

description:
Hs_Diff_PA_1_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: explant 2week, rep4

description:
Hs_explant_2_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.

value: Explant 2 week


title: explant 2week, rep3

description:
Hs_explant_2_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: explant 1week, rep2

description:
Hs_explant_1_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Explant 1 week


title: floating 1week, rep2

description:
Hs_float_1_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Floating 1 week


title: explant 1week, rep1

description:
Hs_explant_1_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 1week, rep4

description:
Hs_float_1_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.


title: MAAC, 1week, rep3

description:
Hs_TW_1_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: packed D0 cells, rep2

description:
Hs_packed_cells_D0_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Packed D0 cells


title: packed D0 cells, rep1

description:
Hs_packed_cells_D0_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: packed D0 cells, rep3

description:
Hs_packed_cells_D0_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: fresh whole tissue, rep4

description:
Hs_whole_tissue_fresh_rep4
Raw data not provided due to patient privacy concerns and European Union law.

value: Fresh whole tissue


title: fresh whole tissue, rep5

description:
Hs_whole_tissue_fresh_rep5
Raw data not provided due to patient privacy concerns and European Union law.


title: fresh whole tissue, rep3

description:
Hs_whole_tissue_fresh_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 1week, rep1

description:
Hs_float_1_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: explant 1week, rep4

description:
Hs_explant_1_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.


title: fresh whole tissue, rep1

description:
Hs_whole_tissue_fresh_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: fresh whole tissue, rep2

description:
Hs_whole_tissue_fresh_rep2
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 2week, rep4

description:
Hs_float_2_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.


title: explant 2week, rep1

description:
Hs_explant_2_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 2week, rep1

description:
Hs_float_2_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: floating 1week, rep3

description:
Hs_float_1_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: H3K9me3 WT LSK cells

city: Copenhagen

first: Karl

last: Agger

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
Trimmed with Trimmomatic: IlluminaClip; Crop to 73; SLIDINGWINDOW across 4 bases, average quality required 20
Mapped with Bowtie2 against mm10 using using (--sensitive) preset settings. Duplicates removed with rmdup.
H3K4me3 data was taken from GSE55850 (i.e., third-party reanalysis of Samples GSM1347235 GSM1347236).
H3K9me3 reads were quantified +/- 500bp from H3K4me3 positive TSSs using EaSeq software (http://easeq.net). Reads from WT and knockout were divided to get the fold change in H3K9me3 levels after induction of knockout.
Genome_build: mm10
Supplementary_files_format_and_content: An excel file containing the positions of the H3K4me3 peaks and quantified H3K9me3 levels at H3K4me3 positive TSSs.

molecule: genomic DNA

organism: Mus musculus

source_name: Haematopoietic stem cell

extract_protocol:
Extraction protocol: Immunoprecipitation of formaldehyde cross-linked and sonicated cell lysate
Library construction protocol: NEBNext Ultra II protocol (NEB, E7645S)

treatment_protocol: Conditional knockout mice and control mice were injected with tamoxifen. After two weeks LSK cells were FACS sorted from the bone marrow

tag: strain

tag: genotype

value: WT control

tag: cell type

value: LSK cell

tag: chip antibody

value: anti_H3K9me3 (Abcam:ab9898)


title: H3K9me3 knockout LSK cells

value: Kdm4a, b c triple knockout


title: primary somatosensory cortex 1

city: Worcester

first: Georgia

last: Gunner

state: Massachusetts

address: 364 Plantation Street, LRB 770 Y-Z

department: Neurobiology

country: USA

institute: UMass Medical School

description: polyA RNA

data_processing:
The raw fastq files uploaded here were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):   *_R1_001.fastq.gz   : contains the 3' UTR cDNA read  *_R2_001.fastq.gz   : contains the first half of the cell barcode  *_R3_001.fastq.gz   : contains the library index for demultiplexing libraries  *_R4_001.fastq.gz   : contains the second half of the barcode and the UMI.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops).  The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrops.py custom pipeline are given in the yaml files.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.88) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > N; ii) mitochondrial gene content <M. For mouse samples N = 1500 and M = 20%. Counts were normalized as described in methods, and combined into a single genes x cells normalized filtered matrix  (counts.norm.csv).
Genome_build: GRCm38.88
Supplementary_files_format_and_content: counts.norm.csv: Gene Expression Matrix of count data normalized by total counts in each cell; [SAMPLE_ID].counts.tsv:  Raw cell/counts tables by sample; seuratClusters.csv: Metadata for individual cells: cell barcode, assigned cell type.

molecule: polyA RNA

source_name: primary somatosensory cortex

extract_protocol:
RNA was isolated within the droplets according to the inDrops protocol (Klein et al Cell 2015)(Zilionis et al Nature Protocols 2017).
1 to 2 libraries of approximately 3000 cells was collected from each animal. inDrops library preparation was performed as previously described (Klein et al., 2015)(Zilionis et al., 2017) Libraries were sequenced on the Illumina NextSeq system.
custom inDrops single-cell RNA-Seq

value: mixed sample (non-demultiplexed)

tag: Sex

value: Male and Female

tag: treatment

value: Whisker-deprived and Control

tag: age


title: explant 2week, rep2

description:
Hs_explant_2_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Adipose


title: packed D0 cells, rep5

description:
Hs_packed_cells_D0_rep5
Raw data not provided due to patient privacy concerns and European Union law.


title: primary somatosensory cortex 2

description: polyA RNA


title: explant 1week, rep3

description:
Hs_explant_1_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: packed D0 cells, rep4

description:
Hs_packed_cells_D0_rep4
Raw data not provided due to patient privacy concerns and European Union law.


title: HSC_Kdm4abc KO mouse 2

data_processing:
Reads where mapped using RNA STAR (Galaxy Version 2.4.0d-2)
htseq-count (Galaxy Version 0.6.1galaxy1)
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count matrix in tabular format

growth_protocol: Cells were FACS sorted from bone morrow of mice.

extract_protocol:
Total RNA was extracted using Quiagen micro RNA purification kit
The RNA was pre-amplified and converted to cDNA using Nugen Ovation RNA-seq System V2. Amplified cDNA was sonicated 10 cycles on a BioRupture (30sec on, 30sec off, High setting) and RNA-seq libraries were generated. Quantity and quality of the libraries was performed using Qubit HS assay, KAPA Biosystems library quantification kit for Illumina platforms and Agilent High Sensitivity DNA Assay. Next generation sequencing of the libraries was performed on a Nextseq 500 (Illumina). Reads where mapped using RNA STAR16 (Galaxy Version 2.4.0d-2) mapped reads where counted using htseq-count17 (Galaxy Version 0.6.1galaxy1). Differentially expressed genes were identified using DESeq218 (Galaxy Version 2.1.8.3).

value: Haematopoietic stem cell


title: HSC_Kdm4abc KO mouse 1


title: HSC_Kdm4abc KO mouse 4


title: HSC_WT mouse 1


title: HSC_WT mouse 3


title: HSC_WT mouse 4


title: HSC_Kdm4abc KO mouse 3


title: HSC_WT mouse 2


title: MI+FG-3149 rep4

city: San Francisco

first: Todd

last: Seeley

state: CA

address: 409 Illinois St

department: Molecular Biology

institute: FibroGen, Inc.

data_processing:
Sequences were de-multiplexed and FASTQ generation was performed (Basespace, Illumina) Sequences were aligned to mm10, annotated using RefSeq Gene 2013.04.01 build and gene expression levels were quantitated using reads per kilobase of transcript, per million mapped reads (RPKM, Strand NGS).  Genes with a raw read count of >20 in at least 1 sample were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: 1 tab-delimited text file (RawCounts.tsv) include raw counts values for each Sample and 1 tab-delimited text file (RPKM.txt) includes RPKM values for each sample.

source_name: cardiac muscle

extract_protocol:
Total RNA was extracted from non-ischemic LV cardiac tissue with Trizol.
500ng of total RNA was used to generate libraries using the Illumina TruSeq LS Stranded mRNA Sample Prep kit.  Samples were individually barcoded and all 13 samples were run on one Nextseq 500 high output flow cell.  Sequencing was 1x75bp

value: cardiac muscle

tag: age at tx start

value: 8-10 week

tag: experimental time point

tag: surgery

value: Permanent ligation of the LAD

value: mouse anti CTGF mAb (FG-3149)

tag: dose


title: MI+IgG rep4

value: mouse anti IgG ab


title: MI+IgG rep5


title: MI+FG-3149 rep5


title: MI+IgG rep3


title: MI+FG-3149 rep2


title: MI+FG-3149 rep1


title: Sham rep2

value: Sham


title: Sham rep3


title: MI+IgG rep2


title: Sham rep1


title: Lgr5_NI_5

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

country: Germany

institute: Max Planck Institute for Infection Biology

data_processing:
We used STAR 2.4.0d to align sample de-multiplexed reads using a sparse STAR index (--genomeSAsparseD 2) prepared from the mm10 reference with ERCC spike-in sequences. We ran STAR with --outSAMstrandField intronMotif for cufflinks/cuffdiff compatibility and clip3pAdapterSeq with sample-appropriate sequences to trim 3’ end adapter sequence from short templates.
We used Cuffdiff for transcript assembly, gene and isoform expression and differential expression tests on the two sets of triplicates using quartile normalization of FPKMs, fragment bias correction, and mm10 for gene definitions and annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Quantile normalized FPKM estimates on gene level as generated by Cufflinks

source_name: Lgr5+ cells of non-infected stomach antrum

growth_protocol: 6-8 weeks old, male Lgr5eGFP-IRES-CreErt2 were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.

extract_protocol:
The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 ⁰C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 μM mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. We prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system.
Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT.

treatment_protocol: We infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group)

value: male

value: stomach antrum

value: Lgr5+ cells

tag: condition

value: Non-infected


title: Lgr5_Hp_2

source_name: Lgr5+ cells of H.pylori-infected stomach antrum

value: H.pylori infected


title: Lgr5_NI_3


title: Lgr5_NI_1


title: Lgr5_Hp_6


title: fetalOvary_RUNX1, rep1

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description:
RUNX1 ChIP-seq on pools of E14.5 mouse ovaries.
processed data file: fetalOvary_RUNX1.bigWig
processed data file: RUNX1_ChIP.peaks.bed

data_processing:
Sequenced reads were filtered to retain only those with average base quality score >20.
Filtered reads were mapped against the mm10 reference genome via bowtie v1.2 with parameter "-m 1".
Alignments were deduplicated with MarkDuplicates.jar from the Picard tools suite v1.110.
For visualization of read depth, each uniquely-mapped non-duplicate read was extended to a length of 200nt. Depth tracks were generated via BEDTools genomeCoverageBed v2.24.0, normalized to 10 million reads, then converted to bigWig format with UCSC utility bedGraphToBigWig.
Peaks were identified by HOMER v4.9 with parameters "-style factor -fdr 0.00001 -tbp 0 -inputtbp 0" using merged replicates. Peaks were then re-defined as 300mers centered on the called peak midpoint.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Depth tracks in bigWig format.
Supplementary_files_format_and_content: Peaks in BED format.

source_name: E14.5 XX gonads

growth_protocol: CD1 mice were time-mated overnight and checked for a vaginal plug the next morning. Noon of the day when the vaginal plug was detected was considered as embryonic day E0.5. Pregnant females were euthanized at E14.5 and embryos were collected.

extract_protocol:
Ovaries from E14.5 CD1 embryos were separated from the mesonephros, snap-frozen, and stored at -80°C. Two independent ChIP-seq experiments were performed by Active Motif Inc. using 20-30 ug of shared chromatin from different pools of embryonic ovaries (n=80-100 ovaries/ChIP), and 10 ul of RUNX1 antibody (a kind gift from Dr. Yoram Groner and Dr. Ditsa Levanon, the Weizmann Institute of Science, Israel).
Libraries were prepared by Active Motif Inc.

tag: strain/background

tag: gender

value: Female

tag: developmental stage

value: Ovaries


title: fetalOvary_Input, rep1

description:
Input ChIP-seq on pools of E14.5 mouse ovaries.
processed data file: fetalOvary_Input.bigWig

tag: tissue


title: fetalOvary_RUNX1, rep2


title: TIL.IL10.2

city: Pittsburgh

first: Maria

last: Chikina

state: PA

address: 3501 5th ave

institute: University of Pittsburgh

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_TIL_IL10001Aligned.sortedByCoord.out.bam

data_processing:
adapter trimmed
aligned with STAR default parameters
quantified with featureCounts (subread)
counts processed by limma voom
qunatile normalized log(counts+0.5)
Genome_build: mm10
Supplementary_files_format_and_content: all counts and normalized counts after filtering for genes with low expression

source_name: Tumor

growth_protocol: CD8 and regulatory Tcell cDNAs were prepared using the SMARTer®

extract_protocol:
Each cell fraction was double-sorted to ensure high purity (>95%) and directly lysed using the Clontech SMART-Seq v4 (T regs ) or v3 (CD8) kit for cDNA synthesis
Libraries were prepared using Nextera XT DNA Library Preparation kit (Illumina), normalized at 2nM using Tris-HCl (10mM, pH 8.5) with 0.1% Tween20, diluted and denatured to a final concentration of 1.8nM.

tag: population

tag: mouse genotype

value: WT

tag: batch

value: Treg


title: TIL.DN.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_TIL_DN001Aligned.sortedByCoord.out.bam

value: DoubleNeg

tag: cell type


title: MI+FG-3149 rep3

tag: strain


title: ndLN.Ebi3.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_ndLN_Ebi3001Aligned.sortedByCoord.out.bam

source_name: NonDrainingLymphNode


title: ndLN.IL10.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_ndLN_IL10001Aligned.sortedByCoord.out.bam


title: MI+IgG rep1


title: fetalOvary_Input, rep2

tag: chip antibody


title: Naive.Ebi3.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_Naive_Ebi3001Aligned.sortedByCoord.out.bam

source_name: NaiveTcell


title: ndLN.DN.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_ndLN_DN001Aligned.sortedByCoord.out.bam


title: Naive.IL10.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_Naive_IL10001Aligned.sortedByCoord.out.bam


title: TIL.IL10.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_9001Aligned.sortedByCoord.out.bam


title: ndLN.Ebi3.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_7001Aligned.sortedByCoord.out.bam


title: Naive.Ebi3.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_4001Aligned.sortedByCoord.out.bam


title: ndLN.IL10.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_6001Aligned.sortedByCoord.out.bam


title: ndLN.DN.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_5001Aligned.sortedByCoord.out.bam


title: Naive.Teff.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_Naive_Teff001Aligned.sortedByCoord.out.bam

value: Teff

value: effectorTcell


title: Naive.DN.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_Naive_DN001Aligned.sortedByCoord.out.bam


title: TIL.DN.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_8001Aligned.sortedByCoord.out.bam


title: Naive.IL10.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_3001Aligned.sortedByCoord.out.bam


title: Lgr5_Hp_4

tag: Sex


title: TIL.Ebi3.2

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
Set_AKA3_TIL_Ebi3001Aligned.sortedByCoord.out.bam


title: Naive.DN.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_2001Aligned.sortedByCoord.out.bam


title: TIL.IL10

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_TIL_IL10001Aligned.sortedByCoord.out.bam


title: Naive.Teff.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_1001Aligned.sortedByCoord.out.bam


title: TIL.Ebi3

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_TIL_Ebi3001Aligned.sortedByCoord.out.bam


title: ndLN.IL10

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_ndLN_IL10001Aligned.sortedByCoord.out.bam


title: ndLN.Ebi3

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_ndLN_Ebi3001Aligned.sortedByCoord.out.bam


title: TIL.DN

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_TIL_DN001Aligned.sortedByCoord.out.bam


title: ndLN.DN

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_ndLN_DN001Aligned.sortedByCoord.out.bam


title: Naive.Ebi3

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_Naive_Ebi3001Aligned.sortedByCoord.out.bam


title: DP.Ebi3L.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_20_S10_R1_001Aligned.sortedByCoord.out.bam


title: Naive.IL10

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_Naive_IL10001Aligned.sortedByCoord.out.bam


title: SP.Ebi3L.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_19_S9_R1_001Aligned.sortedByCoord.out.bam


title: Naive.DN

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_Naive_DN001Aligned.sortedByCoord.out.bam


title: INT.Ebi3L.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_18_S8_R1_001Aligned.sortedByCoord.out.bam


title: TIL.Ebi3.1

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA2_10001Aligned.sortedByCoord.out.bam


title: NEG.Ebi3L.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_17_S7_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.Ebi3L.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_16_S6_R1_001Aligned.sortedByCoord.out.bam

value: NDLN


title: Naive.Teff

description:
processed data file:
TregNormFiltered.txt
sample name in processed data file:
SetAKA1_Naive_Teff001Aligned.sortedByCoord.out.bam


title: SP.yfp.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_09_S4_R1_001Aligned.sortedByCoord.out.bam

value: yfp


title: INT.yfp.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_08_S3_R1_001Aligned.sortedByCoord.out.bam


title: NEG.yfp.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_07_S2_R1_001Aligned.sortedByCoord.out.bam


title: SP.Ebi3L.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_14_S9_R1_001Aligned.sortedByCoord.out.bam


title: INT.Ebi3L.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_13_S8_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.Ebi3L.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_11_S6_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.yfp.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_06_S1_R1_001Aligned.sortedByCoord.out.bam


title: DP.yfp.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_05_S5_R1_001Aligned.sortedByCoord.out.bam


title: DP.yfp.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_13_10_S5_R1_001Aligned.sortedByCoord.out.bam


title: DP.Ebi3L.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_15_S10_R1_001Aligned.sortedByCoord.out.bam


title: INT.yfp.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_03_S3_R1_001Aligned.sortedByCoord.out.bam


title: SP.yfp.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_04_S4_R1_001Aligned.sortedByCoord.out.bam


title: NEG.yfp.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_02_S2_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.yfp.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_01_S1_R1_001Aligned.sortedByCoord.out.bam


title: DP.DKO.CD8.3

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_20_S10_R1_001Aligned.sortedByCoord.out.bam

value: DKO


title: NDLN.DKO.CD8.3

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_16_S6_R1_001Aligned.sortedByCoord.out.bam


title: SP.DKO.CD8.3

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_19_S9_R1_001Aligned.sortedByCoord.out.bam


title: DP.Ebi3L.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_15_S5_R1_001Aligned.sortedByCoord.out.bam


title: INT.DKO.CD8.3

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_18_S8_R1_001Aligned.sortedByCoord.out.bam


title: SP.Ebi3L.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_14_S4_R1_001Aligned.sortedByCoord.out.bam


title: NEG.Ebi3L.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_12_S2_R1_001Aligned.sortedByCoord.out.bam


title: INT.Ebi3L.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_13_S3_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.Ebi3L.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_11_S1_R1_001Aligned.sortedByCoord.out.bam


title: DP.DKO.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_010_S10_R1_001Aligned.sortedByCoord.out.bam


title: SP.DKO.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_009_S9_R1_001Aligned.sortedByCoord.out.bam


title: NEG.Ebi3L.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_12_12_S7_R1_001Aligned.sortedByCoord.out.bam


title: NEG.DKO.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_007_S7_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.DKO.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_006_S6_R1_001Aligned.sortedByCoord.out.bam


title: DP.Il10.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_005_S5_R1_001Aligned.sortedByCoord.out.bam


title: NEG.Il10.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_002_S2_R1_001Aligned.sortedByCoord.out.bam


title: INT.DKO.CD8.2

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_008_S8_R1_001Aligned.sortedByCoord.out.bam


title: INT.Il10.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_003_S3_R1_001Aligned.sortedByCoord.out.bam


title: SP.Il10.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_004_S4_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.Il10.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set9_001_S1_R1_001Aligned.sortedByCoord.out.bam


title: INT.DKO.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___8__DKO_CD8_TIL_INT_S8_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.DKO.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___6__DKO_CD8_ndLN_S6_R1_001Aligned.sortedByCoord.out.bam


title: SP.DKO.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___9__DKO_CD8_TIL_SP_S9_R1_001Aligned.sortedByCoord.out.bam


title: NEG.DKO.CD8.3

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set10_17_S7_R1_001Aligned.sortedByCoord.out.bam


title: DP.Il10.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___5__IL10L_CD8_TIL_DP_S5_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.Il10.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___1__IL10L_CD8_ndLN_S1_R1_001Aligned.sortedByCoord.out.bam


title: NEG.DKO.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___7__DKO_CD8_TIL_NEG_S7_R1_001Aligned.sortedByCoord.out.bam


title: DP.DKO.CD8.1

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___10__DKO_CD8_TIL_DP_S10_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.DKO.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___6__DKO_CD8_ndLN__S6_ALL_R1_001Aligned.sortedByCoord.out.bam


title: SP.DKO.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___9__DKO_CD8_TIL_SP_S9_ALL_R1_001Aligned.sortedByCoord.out.bam


title: NEG.DKO.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___7__DKO_CD8_TIL_NEG_S7_ALL_R1_001Aligned.sortedByCoord.out.bam


title: INT.DKO.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___8__DKO_CD8_TIL_INT_S8_ALL_R1_001Aligned.sortedByCoord.out.bam


title: NEG.Il10.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___2__IL10L_CD8_TIL_NEG_S2_R1_001Aligned.sortedByCoord.out.bam


title: SP.yfp.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___4__YFP_CD8_TIL_SP_S4_ALL_R1_001Aligned.sortedByCoord.out.bam


title: INT.yfp.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___3__YFP_CD8_TIL_INT_S3_ALL_R1_001Aligned.sortedByCoord.out.bam


title: DP.DKO.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___10__DKO_CD8_TIL_DP_S10_ALL_R1_001Aligned.sortedByCoord.out.bam


title: NEG.yfp.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___2__YFP_CD8_TIL_NEG_S2_ALL_R1_001Aligned.sortedByCoord.out.bam


title: INT.Il10.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___3__IL10L_CD8_TIL_INT_S3_R1_001Aligned.sortedByCoord.out.bam


title: NDLN.yfp.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___1__YFP_CD8_ndLN__S1_ALL_R1_001Aligned.sortedByCoord.out.bam


title: Arhgef2-KO NT rep2

city: Dallas

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

department: Medicine

institute: University of Texas Southwestern Medical Center

data_processing:
Blc2fastq2 Conversion software (Illumina) was used to generate de-multiplexed Fastq files.
Illumina reads were post-processed and aligned to the mouse mm9 assembly using Tophatprogram with default parameters in the DNAnexus.
Expression values were normalized as Fragments per Kilobase Million reads after correction for gene length (FPKM) in Cuffdiff version v1.06 in the DNAnexus
Genome_build: mm10

source_name: Bone Marrow-derived Macrophage (BMDM)

growth_protocol: Bone marrow-derived macrophages (BMDMs) cells were generated by flushing bone marrow cells from femurs and tibia of WT or indicated knockout (KO) mice, depleting red blood cells using ACK lysis buffer, and resuspending cell in complete DMEM media supplemented with 10% FBS, 0.5% penicillin/streptomycin mixture, and 20 ng/ml M-CSF. Cells were maintained in culture at 37 °C, 5%CO2 for 6 days before experimentation.

extract_protocol:
500ng of total RNA was subjected to library synthesis using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adaptors according to the manufacturer’s protocol (Illumina).
Total RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2. BMDMs were stimulated in FCS free DMEM with or without N-Glycolyl-MDP (5μg/ml) for 18 hours.

tag: genotype/variation

tag: background strain

tag: treatment

value: No treatment


title: Arhgef2-KO MDP rep2

value: 5ug/ml of N-Glycolyl-MDP(MDP)


title: Arhgef2-KO MDP rep1


title: WT MDP rep2


title: WT NT rep1


title: Arhgef2-KO NT rep1


title: WT MDP rep1


title: Irf5-KO NT rep2


title: WT NT rep2


title: Irf5-KO MDP rep2


title: DP.yfp.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
Set_8___5__YFP_CD8_TIL_DP_S5_ALL_R1_001Aligned.sortedByCoord.out.bam


title: Irf5-KO NT rep1


title: SP.Il10.CD8

description:
processed data file:
CD8NormFiltered.txt
sample name in processed data file:
_Set_9___4__IL10L_CD8_TIL_SP_S4_R1_001Aligned.sortedByCoord.out.bam


title: scRNA data of B16 tumor from Foxp3Cre-YFP mouse

first: Wei

last: Chen

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

description: scRNA data from tumor

data_processing:
Standard 10X Genomics CellRanger pipeline
Genome_build: mm10
Supplementary_files_format_and_content: for each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

value: B16 tumor at day 14

tag: age

value: 5-8 week

tag: genotype


title: scRNA data of unchallenged lymph node from Foxp3Cre-YFP mouse

description: scRNA data from lymph node

source_name: Lymph node

value: Lymph node unchallenged


title: ChIP-seq Input WT FGO

city: Fukuoka

first: Wan Kin

last: Au Yeung

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

department: Department of Molecular and Structural Biology

country: Japan

institute: Kyushu University

data_processing:
ChIP-seq data analysis: Low quality bases in the 3’ portion and adapter sequences were removed from raw reads and trimmed reads were mapped to mouse genome mm10 by bowtie2 v2.2.9 with options ‘--end-to-end --no-1mm-upfront -N 0 -D 500 -X 1000 --no-mixed --no-discordant’. Duplicate and low quality reads (MapQ <5) were removed using Picard v2.6.0.
WGBS data analysis: Low quality bases in the 3’ portion (Q <30) and adapter sequences were removed from raw reads by Trim-Galore! v0.3.3 and trimmed reads were mapped to mouse genome mm10 by Bismark v0.14.5 with options ‘--bowtie2 --pbat -D 75’. For allelic-specific analysis, trimmed reads were mapped to N-masked mm10 genome using published SNP data of JF1 strain. Allelic reads were selected using SNPsplit v0.3.2.
RNA-seq data analysis: Low quality bases in the 3’ portion and adapter sequences were removed from raw reads and trimmed reads were mapped to mouse genome mm10 by HISAT2 v2.0.5 with options ‘--dta --pen-canintronlen G,-8,3 --pen-noncanintronlen G,-8,3 -k 50 --no-mixed --no-discordant’. Transcripts were assembled by StringTie v1.3.3. Repeat masker-annotated microRNA, rRNA, tRNA-like, snRNA and transcripts with CDS <200 bp were excluded in the downstream analyses. For allelic-specific analysis, trimmed reads were mapped to N-masked mm10 genome using published SNP data of JF1 strain. Allelic reads were selected using SNPsplit v0.3.2.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: [ChIP-seq] Normalized H3K9me2 profiles of rep1 and rep 2 are provided in 10-kb sliding windows and input-normalized.
Supplementary_files_format_and_content: [WGBS] The CG coverage files are tab-delimited, 1-based genomic coordinates for every covered CG site in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation level> <methylated cytosine> <unmethylated cytosine>.
Supplementary_files_format_and_content: [RNA-Seq] FPKM values are tab-delimited text files for each sample and are in the following format: <chromosome> <geneName> <start position> <end position> <Control rep1 FPKM> <Control rep2 FPKM> <mat-KO rep1 FPKM> <mat-KO rep2 FPKM> OR <chromosome> <geneName> <start position> <end position> <Control rep1 FPKM> <Control rep2 FPKM> <cKO rep1 FPKM> <cKO rep2 FPKM>

source_name: fully grown oocytes

growth_protocol: All animal experiments were performed under the ethical guidelines of Kyushu University, Kindai University, and The Canadian Council on Animal Care (CCAC). All mice used in this manuscript were aged 4 weeks or older and were euthanized by CO2 asphyxiation.

extract_protocol:
Total RNA was extracted from pooled FGOs and 2-cell embryos using Trizol reagent (Thermo Fisher Scientific).
ULI-NChIP-seq libraries were prepared from about 200 FGOs based on previous reports (Brind'Amour et al., 2015). ChIP was performed with 0.15 μg of anti-H3K9me2 (abcam ab1220) in 200-μl NChIP buffer. WGBS libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012). Pooled  GOs, FGOs, MII oocytes, 2-cell embryos and blastocysts were spiked with 1% unmethylated lambda phage DNA (Promega). Libraries were amplified with KAPA library amplification kit (KAPA) for 4 cycles using primers AATGATACGGCGACCACCGAGATCTACAC and CAAGCAGAAGACGGCATACGAGAT. For RNA-seq, libraries were constructed using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), NEBNext® RNA First Strand Synthesis Module, NEBNext® Ultra Directional RNA Second Strand Synthesis Module, and NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocols. Libraries were amplified by PCR for 10 cycles. WGBS libraries were sequenced on HiSeq 1500 or 2500 (Illumina) (FGOs and blastocysts: HCS v2.0.5 and RTA v1.17.20; MII oocytes and 2-cell embryos: HCS v2.2.68 and RTA v1.18.66.3) using TruSeq SBS kit v3-HS and HiSeq Rapid SBS Kit v2 (Illumina) according to manufacturer’s protocols. For ULI-ChIP-seq and RNA-seq, libraries were sequenced on NextSeq 500, HiSeq 1500, or HiSeq 2500 (Illumina) according to manufacturer’s protocols.

treatment_protocol: Growing oocytes (GOs) were harvested by sequential digestion of P10 ovaries in 1 mg/ml collagenase (Sigma-Aldrich), 0.25% trypsin-EDTA (Invitrogen), and 0.5% protease type XIV (C9891 Sigma-Aldrich). Fully grown oocytes (FGOs) were harvested from ovaries of 10 weeks or older by needle puncture. Superovulation was induced by injecting females at 10 weeks or older with 7.5 U of pregnant mare serum gonadotrophin (PMSG) and then 48 hour later with 7.5 U of human chorionic gonadotropin (hCG). Cumulus-oocyte complexes were collected from the oviducts and fertilized with C57BL/6J sperm for whole genome bisulfite sequencing (WGBS) of blastocysts; or with JF1 sperm for WGBS and RNA-seq of 2-cell embryos. MII oocytes were harvested by digestion in hyaluronidase (H4272 Sigma-Aldrich), and polar bodies were removed by sequential digestion in 0.5% protease type XIV (C9891 Sigma-Aldrich) and hypotonic treatment in 1% sodium citrate (31404-15 Nacalai Tesque). Cumulus cells were removed by capillary washing in PBS and zygotes were cultured in EmbryoMax KSOM Medium (1X) w/ 1/2 Amino Acids (Merck Millipore) at 37˚C and 5% CO2. Two-cell embryos were harvested within 2 hours after completion of the first mitotic division for WGBS and at 24 hpf for RNA-seq. Polar bodies of 2-cell embryos for WGBS were also removed. Blastocysts were harvested at 120 hpf for WGBS. For ULI-ChIP-seq, zona pellucida of FGOs was removed by acid Tyrode’s solution, followed by neutralization in M2 medium (Sigma-Aldrich) before fresh frozen in liquid nitrogen

value: fully grown oocytes

value: wildtype


title: ChIP-seq H3K9me2 WT FGO rep2

value: anti-H3K9me2 (abcam ab1220)


title: Irf5-KO MDP rep1


title: ChIPseq-MEF_abGR_DEX

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control
ChIP- and ATAC-seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
RNA-seq alignment was performed by TopHat (2.0.8) with tophat -G annotation.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 --librarytype fr-firststrand bowtie2_annotation/prefix read1.fastq read2.fastq
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over control, 4x fold enrichment over local background, and >75 tags per site. In addition, untreated GR ChIP sample was used to further filter out noise from GR samples using default parameters on getDifferentialPeaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: Wild-type MEF cells, Dex-treated, GR ChIP

growth_protocol: Mouse adenocarcinoma and MEF cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit.
Libraries were prepared for sequencing using standard Illumina protocols.
For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.

treatment_protocol: Mouse adenocarcinoma and MEF cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq and ATAC-seq, and for 2 h in RNA-seq, prior extraction.

tag: cell line

value: MEF

value: mouse embryonic fibroblasts

tag: stably expressing

value: Dexamethasone

tag: concentration

tag: time

value: 1 h

value: GR-cocktail (Santa Cruz Biotechnology, sc-1004, lot # C1116; ABR, PA1-511A, lot # 019-147; Thermo Fisher Scientific, BuGR2, lot # PI200288)


title: ChIPseq-MEF-GRKO-GFP-GRwt_abGFP_DEX_rep2

source_name: MEF-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, GFP ChIP

value: MEF-KOGR

value: wild-type GFP-GR


title: ChIPseq-MEF-GRKO_abGFP_DEX_rep1

source_name: MEF-KOGR cells, Dex-treated, GFP ChIP


title: ChIPseq-MEF-GRKO-GFP-GRtetra_abGFP_DEX_rep1

source_name: MEF-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, GFP ChIP

value: P481R GFP-GRtetra


title: ChIPseq-MEF-GRKO-GFP-GRtetra_abGFP_NT_rep2

source_name: MEF-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, GFP ChIP

value: no treatment


title: ChIPseq-MEF-GRKO-GFP-GRtetra_abGFP_NT_rep1


title: ChIPseq-MEF-GRKO-GFP-GRtetra_abGFP_DEX_rep2


title: ChIPseq-MEF-GRKO_abGFP_DEX_rep2


title: ChIPseq-MEF-GRKO-GFP-GRwt_abGFP_DEX_rep1


title: ChIPseq-GRKO_input

source_name: 3617-KOGR cells, ChIP input

value: mouse adenocarcinoma


title: ChIPseq-GRKO-GFP-GRtetra_abH3K27ac_DEX_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, H3K27ac ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abGFP_DEX_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, GFP ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abSMARCA4_NT_rep1

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, SMARCA4 ChIP

value: SMARCA4 (BRG1, Epitomics, EPNCIR11A, made in collaboration with Epitomics, PMID:24317492)


title: ChIPseq-GRKO-GFP-GRtetra_abH3K4me1_NT_rep1

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, H3K4me1 ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abH3K27ac_NT_rep1

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, H3K27ac ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abGFP_NT_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, GFP ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abH3K27ac_DEX_rep1


title: ChIPseq-GRKO-GFP-GRtetra_abH3K4me1_NT_rep2


title: ChIPseq-GRKO-GFP-GRtetra_abGFP_NT_rep1


title: ChIP-seq H3K9me2 WT FGO rep1

tag: developmental stage


title: ChIPseq-GRKO-GFP-GRwt_abSMARCA4_DEX_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, SMARCA4 ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K4me1_DEX_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, H3K4me1 ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K4me1_DEX_rep1


title: ChIPseq-GRKO-GFP-GRwt_abSMARCA4_NT_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, SMARCA4 ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abSMARCA4_DEX_rep1

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, SMARCA4 ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K4me1_NT_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, H3K4me1 ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K4me1_NT_rep1


title: ChIPseq-GRKO-GFP-GRtetra_abH3K4me1_DEX_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, H3K4me1 ChIP


title: ChIPseq-GRKO-GFP-GRtetra_abH3K4me1_DEX_rep1


title: ChIPseq-GRKO-GFP-GRtetra_abH3K27ac_NT_rep2


title: ChIPseq-GRKO-GFP-GRtetra_abGFP_DEX_rep1


title: ChIPseq-GRKO-GFP-GRwt_abH3K27ac_DEX_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, H3K27ac ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K27ac_NT_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, H3K27ac ChIP


title: ChIPseq-GRKO-GFP-GRwt_abGFP_DEX_rep3

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, GFP ChIP


title: ChIPseq-GRKO-GFP-GRwt_abGR_DEX_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, GR ChIP


title: ChIPseq-GRKO-GFP-GRwt_abH3K27ac_NT_rep1


title: ChIPseq-GRKO-GFP-GRwt_abGR_NT_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, GR ChIP


title: ChIPseq-GRKO-GFP-GRwt_abGR_NT_rep2


title: ChIPseq-GRKO-GFP-GRwt_abGFP_NT_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, GFP ChIP


title: ChIPseq-GRKO-GFP-GRwt_abGFP_NT_rep2


title: ChIPseq-GRKO_abGR_DEX_rep2

source_name: 3617-KOGR cells, Dex-treated, GR ChIP


title: ChIPseq-GRKO-GFP-GRwt_abGFP_DEX_rep1


title: ChIPseq-GRKO_abGFP_DEX_rep1

source_name: 3617-KOGR cells, Dex-treated, GFP ChIP


title: ChIPseq-GRKO_abGFP_NT_rep2

source_name: 3617-KOGR cells, non-treated, GFP ChIP


title: ChIPseq-GRKO_abGFP_NT_rep1


title: ChIPseq-GRKO-GFP-GRwt_abH3K27ac_DEX_rep2


title: 12434_PCW10_H3K27ac

city: Berkeley

first: Axel

last: Visel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: Chromatin IP against H3K27ac

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline)
Genome_build: hg38
Supplementary_files_format_and_content: *replicated.broadPeak, peaks called by MACS2 with a q-value <= 0.05

source_name: fetal heart, H3K27ac ChIP

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen left ventricle tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp.  Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated  with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2500 or 4000.

tag: tissue

value: heart

tag: disease

tag: antibody

value: anti-H3K27ac (Active motif, 39133)


title: 12522_PCW10_H3K27ac

description: Chromatin IP against H3K27ac


title: ChIPseq-GRKO-GFP-GRwt_abGR_DEX_rep1

tag: cell type


title: 12569_PCW10_H3K27ac

description: Chromatin IP against H3K27ac


title: 11963_CS22_H3K27ac

description: Chromatin IP against H3K27ac

source_name: embryonic heart, H3K27ac ChIP


title: LV1532_explant_H3K27ac

description: Chromatin IP against H3K27ac

source_name: adult left ventricle, H3K27ac ChIP

value: left ventricle

value: adult

value: idiopathic dilated cardiomyopathy (DCM)


title: LV1535_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1433_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1437_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1371_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: ChIPseq-GRKO_abGR_DEX_rep1


title: LV1392_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1342_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: ChIPseq-GRKO_abGFP_DEX_rep2


title: LV1304_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1264_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1072_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1300_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: ChIPseq-GRKO_abGR_NT_rep2

source_name: 3617-KOGR cells, non-treated, GR ChIP


title: LV1223_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1033_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: ChIPseq-GRKO_abGR_NT_rep1


title: LV1028_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1290_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1558_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1262_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1009_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1275_explant_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1471_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1452_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1400_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1356_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1248_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1215_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1273_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1277_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1202_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1226_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1259_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1183_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: LV1294_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: Right_FACS.4T1_6185

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the mm10 reference version using HISAT.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.

source_name: FACS-isolated 4T1-Luc2-RFP cells from MIND tumors (mammary glands)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen Germantown, MD, USA)
The RNA-Seq libraries were created using TruSeq RNA Sample Prep kit (Illumina San Diego, CA, USA)

tag: strain

value: balb/c


title: Right_FACS.4T1_6184

value: FACS-isolated 4T1-Luc2-RFP cells from MIND tumors (mammary glands)


title: SampleChr1768_T47D_SGK1___MD___CLEAN_NORM.bedgraph

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: cell buffer concentration: 0.2% IGEPAL

data_processing:
Starting from fastq files containing ATAC-seq paired-end reads, sequencing adaptors were removed using Trimmomatic.
Trimmed reads were mapped to the hg19 human genome using Bowtie2 allowing at most 1 seed mismatch and keeping only uniquely aligned reads.
Duplicates were removed using Picard.
For peak-calling the read start sites were adjusted (reads aligning to the +/- strand were offset by +4bp/-5bp, respectively) to represent the center of the transposon binding-event.
Peak calling was performed using MACS2 with a permissive P-value threshold (-p 1e-2).
Genome_build: hg19 human genome
Supplementary_files_format_and_content: bedgraph.tdf

source_name: Breast Cancer Cell

growth_protocol: T47D cells were maintained in RPMI 1640 with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
50,000 T47D cells were dissociated with acutase treatment and lysed with double the concentration of IGEPAL for successful library preparation.
ATAC-seq libraries were prepared using Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: 50,000 T47D control cells or SGK1 S422D overexrpressed cells

tag: passages

value: SGK1 S422D overexrpressed


title: SampleChr1767_T47D_plenti___MD___CLEAN_NORM

description: cell buffer concentration: 0.2% IGEPAL

value: control


title: NonInjected_4T1_6186

source_name: cultured 4T1-Luc2-RFP cells

value: cultured 4T1-Luc2-RFP cells


title: SPLGC_GFPGL71

city: Gothenburg

first: Mats

last: Bemark

address: PO Box 435

department: Departement of microbiology and immunity

institute: University of Gothenburg

data_processing:
Paired fastq files were imported into CLC workbench 11.0.1 using standard procedures.
The sequence data was aligned to the mouse genome using default settings in CLC workbench to create gene expression (GE) tracks
Genome_build: Mouse genome GRCm38
Supplementary_files_format_and_content: The gene expression data was exported to .csv files and RNASeq quality reports were exported for each alignment from CLC workbench.

source_name: Sorted GFP+GL7+ Spleen B cells

extract_protocol:
Cells were sorted using a BD FACSAria III, spun down, disolved in RLT buffer and frozen. After thawing, total RNA was prepared using Qiagen RNAEasy Micro kits.
RNA was shiped to BGI Sequncing on dry ice and libraries were prepared by amplification using a SMARTer kit there

tag: organ

value: Spleen

tag: gl7 expression


title: SPLGC_GFPGL73


title: LV1160_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: SPL_Naive2

source_name: Sorted GL7- Spleen B cells


title: LV1325_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: SPLGC_GL71

source_name: Sorted GL7+ Spleen B cells


title: LV1200_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: SPL_Naive3


title: LV1121_donor_H3K27ac

description: Chromatin IP against H3K27ac


title: PPGC_GFP3

source_name: Sorted GFP+ PP B cells

value: Peyer's patch


title: SPL_Naive1


title: PPGC_GFP1


title: PP_Naive3

source_name: Sorted GL7- PP B cells


title: Right_FACS.4T1_6181


title: PP_Naive1


title: NonInjected_4T1_6180


title: PPGC_GL71

source_name: Sorted GL7+ PP B cells


title: PPGC_GL73


title: PPGC_GL7GFP1

source_name: Sorted GFP+GL7+ PP B cells


title: RNAseq-GRKO-GFP-GRtetra_NT_rep5

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, RNA

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit. Libraries were prepared for sequencing using standard Illumina protocols.For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.
transcriptomic

tag: chip antibody


title: Prx1_Cre_LTHSC-1

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

description: Cells from Prx1-Cre recipient mice

data_processing:
Illumina Converter was used to convert bcl files to obtain raw fastq files
Raw fastq files were trimmed with Trim Galore! version 0.4.4 with parameters --fastq_args "--nogroup --noextract"
Trimmed reads were aligned using STAR version 2.5.3a with parameters --genomeDir --readFilesIn --outFileNamePrefix --outReadsUnmapped Fastx --runThreadN --outSAMtype BAM SortedByCoordinate --outSAMattributes ALL --readFilesCommand gunzip -c --outSAMattrRGline
HTSeq-count version 0.9.1 created the raw count files from the STAR aligned files with paramters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.18.1 was used for differential expression
Genome_build: Gencode GRCm38 p4 Release 11
Supplementary_files_format_and_content: tab delimited text file containing raw counts from HTSeq-count

source_name: Leukemic stem cells (LTHSC)

growth_protocol: Leukemic long-term hematopoietic stem cells were FACS sorted from various Cre-transgenic primary mice based using conventional cell surface markers.

extract_protocol:
Sequencing libraries were prepared with the SMARTer Ultra Low Input RNA Kit for Sequencing (v4, TaKaRa Clontech, catalog no. 634891) and Nextera XT DNA Library Preparation Kit (96 samples, Illumina, cat no. FC-131-1096).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: CML

value: Bone marrow


title: Tek_Cre_LTHSC-4

description: Cells from Tek-Cre recipient mice


title: Prx1_Cre_LTHSC-4

description: Cells from Prx1-Cre recipient mice


title: RNAseq-GRKO-GFP-GRtetra_NT_rep4

value: P481R GFP-GRtetra

tag: treatment

value: no treatment


title: Tek_Cre_LTHSC-3

description: Cells from Tek-Cre recipient mice


title: Tek_Cre_LTHSC-2

description: Cells from Tek-Cre recipient mice


title: No_Cre_LTHSC-3

description: Cells from No Cre recipient mice


title: Tek_Cre_LTHSC-1

description: Cells from Tek-Cre recipient mice


title: No_Cre_LTHSC-1

description: Cells from No Cre recipient mice


title: No_Cre_LTHSC-4

description: Cells from No Cre recipient mice


title: Prx1_Cre_LTHSC-2

description: Cells from Prx1-Cre recipient mice


title: KO-ribosome profiling replicate 2

city: Beijing, China

first: Huamin

last: Wang

address: Three N0. 5 dongdan street, Dongcheng District, Beijing

department: Department of Immunology

country: China

institute: Peking Union Medical College, Chinese Academy of Medical Sciences,

description: 80S monosome protected RNA

data_processing:
Library strategy: Ribosome profiling
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
The sequencing data obtained from ribosome profiling (portion II) were denoted as ribosome-protected fragments and that from RNA input (portion I) as mRNA input. Translation efficiency was defined as the ratio of ribosome-protected fragments and mRNA input, which reflected the relative occupancy of 80S ribosome per mRNA species.
Genome_build: mm10
Supplementary_files_format_and_content: excel document includes RPKM values of each sample and caculated translation efficiency

source_name: dendritic cells

growth_protocol: Bone marrow (BM) from 6 week’s C57 BL/6 mice were cultured in RPMI-1640 medium (PAA laboratories) supplemented with 10% FBS (fetal bovine serum) (Gibco), recombinant mouse GM-CSF (granulocyte-macrophage colony-stimulating factor) (10ng/ml) (R&D) and IL-4 (1ng/ml) (R&D). After 3d, non-adherent cells were gently removed and the remaining cells were further cultured with fresh medium containing GM-CSF and IL-4. On the fifth day, loosely adherent cells were subjected to positive selection with magnetic beads coated with anti-mouse CD11c and were defined as immature DC (imDC). The CD11c+imDC were stimulated with LPS (100 ng/ml) for 24 h and were defined as mature DC (maDC).

extract_protocol:
RNA was concentrated by ethanol precipitation and finally dissolved in 10 μl of RNase-free water. The input RNA was first purified by TRIzol and the input mRNA was then separated by Dynabeads mRNA Purification Kit (Invitrogen). The resulting mRNA was concentrated by ethanol precipitation and dissolved in 10μl of RNase-free water. The mRNA was fragmented by RNA fragmentation kit (Ambion).
The library of ribosome protected RNA was prepared accoring to NEBNext® Multiplex Small RNA Library Prep Set for Illumina®, while the input library was prepared according to NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: Microbeads anti-CD11c were cocultured with BMDC from Mettl3 WT or Mettl3 KO mice at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated and stimulated for 24hours with LPS(100ng/ml). Before collection, cycloheximide (CHX) was added to the media at 100 mg/ml for 7 min. The media was removed, and the cells were collected with 5ml cold PBS with CHX (100mg/ml). The cell suspension was spun at 600g for 5 min and the cell pellet was washed once by 1ml PBS-CHX. 1ml lysis buffer (10mM Tris, pH 7.4, 150mM KCl, 5mM MgCl2, 100mg/ml CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40U/ml Recombinant RNase Inhibitor (RRI)) was added to suspend the cells and then kept on ice for 15 min with occasional pipetting and rotating. After centrifugation at 15,000g for 15 min, 8μl DNase RQ1 (Promega) was added to the lysate. The lysate was then split by the ratio of 1:5 (Portion I/Portion II). 3μl RRI was added to Portion I, 80μl MNase buffer and 3.5μl MNase (7,000 gelunits, BioLabs) was added to Portion II. Both portions were kept at room temperature for 15 min, and then 8μl RRI was added to Portion II to stop the reaction. Portion I was saved and mixed with 500μl TRIzol to purify input mRNA. Portion II was used for ribosome profiling. 15/45%w/v sucrose gradient was prepared in a lysis buffer without Triton-X-100. Portion II was loaded onto the sucrose gradient and centrifuged at 4°C for 3.5h at 41000 r.p.m. (Beckman, rotor SW41). The sample was then fractioned and analyzed by Gradient Station (BioCamp) equipped with UV monitor (BioRad) and fraction collector. The fractions corresponding to 80S monosome (not 40S or 60S) were collected, combined, and mixed with an equal volume of TRIzol to purify the RNA. The RNA pellet was dissolved in 15μl water, mixed with 15μl TBE-urea loading buffer (Invitrogen), and separated on a 10% TBE-urea gel. A 21-nt and a 42-nt ssRNA oligo were used as size markers, and the gel band between 21nt and 42nt was cut. The RNA of gel was extracted using Poly-gel RNA extraction kit (Promega).

value: Bone marrow derived mature dendritic cells

tag: genotype


title: No_Cre_LTHSC-2

description: Cells from No Cre recipient mice


title: RNAseq-GRKO-GFP-GRwt_NT_rep3

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, RNA

tag: cell line

value: mouse adenocarcinoma

value: wild-type GFP-GR


title: RNA-seq FGO cKO rep1

source_name: fully grown oocytes

value: fully grown oocytes

value: G9a conditional KO


title: RNA-seq FGO cKO rep2


title: WT-ribosome profiling replicate 2

description: 80S monosome protected RNA

value: wild type


title: RNA-seq FGO control rep2


title: PBAT GO cKO rep2

source_name: growing oocytes

value: growing oocytes


title: PBAT blastocyst mat-KO rep2

source_name: blastocysts

value: blastocysts

value: G9a maternal KO


title: PBAT GO cKO rep1


title: PBAT GO control rep1

value: control


title: RNA-seq 2cell mat-KO rep1

source_name: 2-cell embryos

value: C57BL/6 (maternal), JF1 (paternal)

value: 2-cell embryos


title: PPGC_GL7GFP3

value: Peyer's patch


title: Prx1_Cre_LTHSC-3

description: Cells from Prx1-Cre recipient mice

value: CML


title: RNAseq-GRKO-GFP-GRwt_NT_rep4

tag: stably expressing


title: PBAT blastocyst mat-KO rep1


title: RNAseq-GRKO_DEX_rep3

source_name: 3617-KOGR cells, Dex-treated, RNA

value: Dexamethasone

tag: concentration

value: 2 h


title: RNAseq-GRKO_NT_rep2

source_name: 3617-KOGR cells, non-treated, RNA

value: no treatment

tag: time


title: RNAseq-GRKO_DEX_rep2


title: RNAseq-GRKO_DEX_rep1


title: PBAT blastocyst control rep2

tag: developmental stage


title: RNAseq-GRKO_NT_rep1


title: RNAseq-parental_DEX_rep3

source_name: 3617 parental cells, Dex-treated, RNA

value: Parental


title: RNAseq-parental_DEX_rep1

value: mouse adenocarcinoma


title: PBAT GO control rep2


title: RNAseq-GRKO-GFP-GRtetra_NT_rep2

value: P481R GFP-GRtetra


title: RNAseq-GRKO-GFP-GRtetra_DEX_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, RNA


title: RNAseq-GRKO-GFP-GRtetra_NT_rep3


title: Ma-Input-replicate2

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
the longest isoform was used if multiple isoforms was detected. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates in order to eliminate the interference from intron in peak calling. To call m6A peaks, the longest isoform of each mouse gene was scanned using a 100-bp sliding window with 10-bp steps. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package.
The window was called as positive if FDR<1% and log2(enrichment score)≥1 in both two replicates. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median read count of the IP sample in all 100-bp windows on the current mRNA (b), read count of the input sample in the current peak/ window (c), and median read count of the input sample in all 100-bp windows on the current mRNA (d), the enrichment score of each window was calculated as (a)×(d)/(b)×(c).
Genome_build: mm10
Supplementary_files_format_and_content: excel documents include m6A peak identified in imDC, maDC and DCreg

growth_protocol: Bone marrow (BM) from 6 week’s C57 BL/6 mice were cultured in RPMI-1640 medium (PAA laboratories) supplemented with 10% FBS (fetal bovine serum) (Gibco), recombinant mouse GM-CSF (granulocyte-macrophage colony-stimulating factor) (10ng/ml) (R&D) and IL-4 (1ng/ml) (R&D). After 3d, non-adherent cells were gently removed and the remaining cells were further cultured with fresh medium containing GM-CSF and IL-4. On the fifth day, loosely adherent cells were subjected to positive selection with magnetic beads coated with anti-mouse CD11c and were defined as immature DC (imDC). The CD11c+imDC were stimulated with LPS (100 ng/ml) for 24 h and were defined as mature DC (maDC). Mature DC were co-cultured with spleen endothelial cells in RPMI-1640 supplemented with 5% FBS for 7d were defined as regulatory DC (DCreg).

extract_protocol:
Total RNA of BMDCs was isolated with Trizol regent (Invitrogen) and mRNA was enriched by Dynabeads mRNA Purification Kit (Invitrogen). Removal of ribosomal RNA was confirmed by 2200 Tape Station detection (Agilent). About 8μg mRNA was fragmented to 100-200bp in length and 1/10 volume was separated as input. The remaining fragmented RNA was mixed with dynabeads protein A (Life technology) pre-mixed with anti-m6A antibody overnight.
The library preparation was constructed according toNEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Microbeads anti-CD11c were cocultured with dendritic cells at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated and used for next experiments

value: Bone marrow derived mature dendritic cells

tag: merip antibody


title: RNAseq-GRKO-GFP-GRtetra_DEX_rep3


title: RNAseq-GRKO-GFP-GRwt_DEX_rep1

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, RNA

value: wild-type GFP-GR


title: RNAseq-GRKO-GFP-GRwt_DEX_rep2


title: RNAseq-GRKO-GFP-GRwt_NT_rep1


title: RNAseq-GRKO-GFP-GRwt_NT_rep2


title: RNAseq-GRKO-GFP-GRwt_DEX_rep3


title: Im-IP-replicate2

value: Bone marrow derived immature dendritic cells

value: m6A specific antibody (Synaptic Systems,cat 202003)


title: RNAseq-parental_DEX_rep2


title: Ma-IP-replicate2


title: RNAseq-GRKO-GFP-GRtetra_NT_rep1


title: WT-ribosome profiling input

description: polyA RNA

value: wildtype


title: KO-ribosome profiling

description: 80S monosome protected RNA


title: RNAseq-parental_NT_rep1

source_name: 3617 parental cells, non-treated, RNA


title: DCreg-IP-replicate2

value: Bone marrow derived regulatory dendritic cells


title: DCreg-Input


title: DCreg-Input-replicate2


title: RNAseq-parental_NT_rep2


title: RNAseq-GRKO-GFP-GRtetra_DEX_rep1


title: DCreg-IP


title: PBAT blastocyst control rep1

value: blastocysts

value: control


title: WT-ribosome profiling

description: 80S monosome protected RNA


title: Im-IP

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
the longest isoform was used if multiple isoforms was detected. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates in order to eliminate the interference from intron in peak calling. To call m6A peaks, the longest isoform of each mouse gene was scanned using a 100-bp sliding window with 10-bp steps. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package.
The window was called as positive if FDR<1% and log2(enrichment score)?1 in both two replicates. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median read count of the IP sample in all 100-bp windows on the current mRNA (b), read count of the input sample in the current peak/ window (c), and median read count of the input sample in all 100-bp windows on the current mRNA (d), the enrichment score of each window was calculated as (a)×(d)/(b)×(c).
genome_build: mm10
Supplementary_files_format_and_content: excel documents include m6A peak identified in imDC, maDC and DCreg

extract_protocol:
Total RNA of BMDCs was isolated with Trizol regent (Invitrogen) and mRNA was enriched by Dynabeads mRNA Purification Kit (Invitrogen). Removal of ribosomal RNA was confirmed by 2200 Tape Station detection (Agilent). About 8μg mRNA was fragmented to 100-200bp in length and 1/10 volume was separated as input. The remaining fragmented RNA was mixed with dynabeads protein A (Life technology) pre-mixed with anti-m6A antibody overnight.
The library preparation was constructed according to TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Microbeads anti-CD11c were cocultured with dendritic cells at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated and used for next experiments.


title: NonInjected_4T1_6183

source_name: cultured 4T1-Luc2-RFP cells

value: cultured 4T1-Luc2-RFP cells

value: balb/c


title: KO-ribosome profiling input

description: polyA RNA


title: U1

city: San Diego

middle: L

last: Gallo

address: 9452 Medical Center Drive

department: Dermatology

institute: UCSD

data_processing:
Isolated RNA for single experimental treatment from four independent experiments submitted to the UCSD IGM Genomics Center for analysis by a Tapestation bioanalyzer (Agilent, LA Jolla, CA). Samples with RIN values of 9.0 and above were utilized for Illumina library preparation and subsequent RNA-sequencing using a high-output run V4 platform (Illumina, San Diego, USA) with a single read 100 cycle runs. Subsequent analysis was done on Partek flow software (Partek, St. Louis, MO) using the Tophat2 aligner (version 2.0.8) quantifying to the transcriptome using the mm10_RefSeq Transcripts 16_08_01_v2. Euclidean distance and average pairwise linkage was used for hierarchal clustering.
Gene ontology (GO) enrichment analysis was performed on differentially regulated genes (≥1.5-fold) using DAVID 6.8

growth_protocol: Human dermal endothelial cells were grown to 80 percent confluence at 37 degree celcius in a humidified incubator.

extract_protocol:
RNA was extracted with Ambion total RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1000ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared with Illumina protocols according to manufacturers recommendations

treatment_protocol: Cells were treated with U1, LL-37 and co-treated with U1 and LL-37 for 24 hours.

tag: cells

value: Human Dermal Microvascular Endothelial Cells


title: LL-37


title: Im-Input


title: U1 + LL-37


title: Ma-input


title: Control Untreated

treatment_protocol: Cells were co-treated with poly IC and LL-37 for 24 hours.

value: human dermal microvascular endothelial cells

value: untreated


title: Control Untreated 2


title: poly IC + LL-37

source_name: LP1, LP2, LP3, LP4

value: poly IC and LL-37 for 24 hours


title: 11963_CS22_RNA

description: Stranded (first-strand synthesis)

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC RNA-seq pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Gene-wise counts were computed using htseq-count from the HTSeq package (PMID: 25260700; v0.9.1) with -s set to no.
Genome_build: hg38
Supplementary_files_format_and_content: *.counts.txt, HTseq quantifications

source_name: embryonic heart, total RNA

extract_protocol:
RNA was isolated from homogenized left ventricle using the TRIzol Reagent (Thermo Fisher Scientific). RNA samples were DNase-treated with the TURBO DNA-free Kit (Thermo Fisher Scientific), and then RNA quality was assessed via 2100 Bioanalyzer (Agilent) and an RNA 6000 Nano Kit (Agilent).
RNA-seq libraries were generated via the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina), according to manufacturer protocols.
RNA-seq libraries were subjected to additional purification steps to remove remaining high molecular weight products.

tag: tissue

value: heart

tag: disease


title: RNA-seq_ADAR3_active Rep3

city: Davis

first: Peter

last: Beal

address: 5469 chem annex, One Shields Ave

department: Chemistry

institute: University of California, Davis

data_processing:
Base call performed using CASAVA version 1.8
RNASeq data preprocessed using scythe version c128b19 and sickle version 7667f147e6
Preprocessed reads aligned to GRCh38 using STAR version 2.5.2b
variant call performed using Freebayes version 1.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: VCF;  variants including A-to-G variants

growth_protocol: Human glioblastoma cell line U87 was grown and maintained in DMEM (Gibco) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 100 units/ml penicillin and 100 μg/ml streptomycin in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from cells 48 h post-transfection using RNAqueous-4PCR kit.
Strand-specific and barcode indexed RNA-seq libraries were generated from 1 μg total RNA each after poly-A enrichment using the Kapa Stranded mRNA-seq kit (Kapa Biosystems, Cape Town, South Africa) following the instructions of the manufacturer.

treatment_protocol: 10e6 U87 cells were transfected with 2.5 μg hADAR3 M3 or hADAR3 M3 E434A plasmid DNA.

tag: disease state

value: glioblastoma

value: brain

tag: cell type

value: expressing active ADAR3 mutant

tag: sample type

value: new A-to-I editing introduced


title: RNA-seq_ADAR3_active Rep2


title: RNA-seq_ADAR3_active Rep1


title: RNA-seq_ADAR3_inactive Rep3

value: expressing inactive counterpart of the ADAR3 mutant


title: RNA-seq_ADAR3_inactive Rep2


title: LV1535_explant_RNA

description: Stranded (first-strand synthesis)

source_name: adult left ventricle, total RNA

value: left ventricle

value: adult

value: idiopathic dilated cardiomyopathy (DCM)


title: LV1471_donor_RNA

description: Stranded (first-strand synthesis)


title: Ma-IP

value: Bone marrow derived mature dendritic cells

tag: strain

value: m6A specific antibody (Synaptic Systems,cat 202003)


title: RNA-seq_ADAR3_inactive Rep1

value: control


title: LV1558_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1028_explant_RNA

description: Stranded (first-strand synthesis)


title: LV1294_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1325_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1215_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1452_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1264_explant_RNA

description: Stranded (first-strand synthesis)


title: LV1437_explant_RNA

description: Stranded (first-strand synthesis)


title: LV1121_donor_RNA

description: Stranded (first-strand synthesis)


title: ATACseq-GRKO-GFP-GRtetra_DEX_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, Dex-treated, ATAC

value: mouse adenocarcinoma

value: P481R GFP-GRtetra

value: Dexamethasone

value: 1 h


title: PP_Naive2

source_name: Sorted GL7- PP B cells

tag: organ

value: Peyer's patch

tag: gl7 expression


title: SPLGC_GL73

source_name: Sorted GL7+ Spleen B cells

value: Spleen


title: ATACseq-GRKO-GFP-GRtetra_DEX_rep1

tag: treatment


title: LV1273_donor_RNA

description: Stranded (first-strand synthesis)


title: RNA-seq FGO control rep1

source_name: fully grown oocytes

value: fully grown oocytes

tag: genotype


title: LV1532_explant_RNA

description: Stranded (first-strand synthesis)


title: ATACseq-GRKO-GFP-GRtetra_NT_rep2

source_name: 3617-KOGR cells, stably integrated P481R GFP-GRtetra, non-treated, ATAC

tag: cell line

value: no treatment


title: RNA-seq 2cell control rep1

value: C57BL/6 (maternal), JF1 (paternal)

value: 2-cell embryos


title: ATACseq-GRKO-GFP-GRtetra_NT_rep1

tag: stably expressing


title: ATACseq-GRKO-GFP-GRwt_DEX_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, ATAC

value: wild-type GFP-GR

tag: concentration


title: MCF7 Plenti Input

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences using TrimGalore.
Reads were aligned to human assembly hg19 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: hg19 human genome
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: Breast Cancer Cell

growth_protocol: T47D cells were maintained in RPMI 1640 with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin. MCF7 cells were maintained in DMEM/DF12 with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
Cell samples were crosslinked with 1% formaldehyde for 10 min, and quenched by glycine to a 125nM final concentration. The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the indicated antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads, library was prepared and samples were subjected to high-throughput sequencing using HiSeq 2000 platform (Illumina).
ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: 1 milion plenti (emty vector, EV) or SGK1 plenti (S422D) were subjected to ChIP-seq.

tag: passages

tag: chip-antibody

value: Non applicable


title: ATACseq-GRKO-GFP-GRwt_DEX_rep1

tag: time


title: LV1200_donor_RNA

description: Stranded (first-strand synthesis)

value: left ventricle

tag: developmental stage

value: adult


title: ATACseq-GRKO-GFP-GRwt_NT_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, non-treated, ATAC


title: T47D Plenti SGK1 S422D H3K4me2


title: ATACseq-GRKO-GFP-GRwt_NT_rep1


title: PPGC_GFP2

source_name: Sorted GFP+ PP B cells


title: MCF7 Plenti SGK1 S422D H3K4me2


title: T47D Plenti Input


title: MCF7 Plenti H3K4me2


title: MCF7 Plenti SGK1 S422D H3K4me1


title: 12569_PCW10_RNA

description: Stranded (first-strand synthesis)

source_name: fetal heart, total RNA

tag: tissue

value: heart


title: T47D Plenti SGK1 S422D Input


title: T47D Plenti H3K4me1


title: 12434_PCW10_RNA

description: Stranded (first-strand synthesis)

tag: disease


title: Im-Input-replicate2

source_name: dendritic cells

value: Bone marrow derived immature dendritic cells

tag: merip antibody


title: MCF7 Plenti H3K4me1


title: LV1433_explant_RNA

description: Stranded (first-strand synthesis)

value: idiopathic dilated cardiomyopathy (DCM)


title: UBC-CreERT2;Ddx5flox/flox spermatogonia VEH-treated (control) replicate 4

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Raw sequencing reads in FASTQ format were filtered and trimmed with Trimmomatic (v0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt)
Reads mapped to the complete mouse genome (GENCODE GRCm38 primary, annotation version vM15) with STAR
Gene read counting was performed with featureCounts.
Differential gene expression was performed with Degust webtool (http://degust.erc.monash.edu) using limma-voom.
Genome_build: GENCODE GRCm38 primary, annotation version vM15
Supplementary_files_format_and_content: Raw counts file was generated by featureCounts and uploaded to Degust.

source_name: Cultured undifferentiated spermatogonia

growth_protocol: Cultured undifferentiated spermatogonia were maintained in StemPro-34 media supplemented with GDNF, bFGF, EGF, insulin and other additives.

extract_protocol:
RNA was extracted using Trizol LS (Thermo Fisher Scientific) and Direct-zol RNA Miniprep kit (Zymo Research).
Libraries were generated according to the Illumina Stranded mRNA protocol using 12 cycles of amplification. Library size (~350bp) was checked using Bioanalyzer and quantified with Qubit and qPCR.

treatment_protocol: Cells were treated with 4-hydroxytamoxifen for 4 days.

value: Testis

tag: cell type

value: Cultured undifferentiated spermatogonia

value: vehicle


title: UBC-CreERT2;Ddx5flox/flox spermatogonia VEH-treated (control) replicate 3


title: LV1371_explant_RNA

description: Stranded (first-strand synthesis)


title: LV1342_explant_RNA

description: Stranded (first-strand synthesis)


title: UBC-CreERT2;Ddx5flox/flox spermatogonia TMX-treated (Ddx5 knockout) replicate 3

value: TMX-treated


title: MCF7 Plenti SGK1 S422D Input


title: T47D Plenti H3K4me2


title: UBC-CreERT2;Ddx5flox/flox spermatogonia TMX-treated (Ddx5 knockout) replicate 2


title: UBC-CreERT2;Ddx5flox/flox spermatogonia VEH-treated (control) replicate 2


title: LV1304_explant_RNA

description: Stranded (first-strand synthesis)


title: LV1300_explant_RNA

description: Stranded (first-strand synthesis)


title: UBC-CreERT2;Ddx5flox/flox spermatogonia VEH-treated (control) replicate 1

data_processing:
Raw sequencing reads in FASTQ format were filtered and trimmed with Trimmomatic (v0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt)
Reads mapped to the complete mouse genome (GENCODE GRCm38 primary, annotation version vM15) with STAR
Gene read counting was performed with featureCounts.
Differential gene expression was performed with Degust webtool (http://degust.erc.monash.edu) using limma-voom.
Genome_build: GENCODE GRCm38 primary, annotation version vM15
Supplementary_files_format_and_content: Raw counts file was generated by featureCounts and uploaded to Degust. The provided processed data file includes Geneid, Log2 fold changes for TMX/VEH, VEH/VEH (all 0), FDR, AveExpr, P value, counts and CPM for all samples.


title: KO-ribosome profiling input replicate 2

description: polyA RNA

value: Bone marrow derived mature dendritic cells


title: T47D Plenti SGK1 S422D H3K4me1


title: WT-ribosome profiling input replicate 2

description: polyA RNA

value: wild type


title: LV1290_explant_RNA

description: Stranded (first-strand synthesis)


title: Input rep 2

data_processing:
ChIPseq reads were mapped to the iGenome UCSC mm10 genome using bowtie2 (ver 2.2.5) with end-to-end settings (--end-to-end flag)
Unmapped and poor quality reads were removed and SAM files are converted to BAM with samtools view (samtools version 1.3.1). Flags used: -F 1548 -q 30
HOMER (ver v4.8) was used for peak calling. Tag directories for both input and IP were generated using makeTagDirectory with mm10 as the genome chosen
Peak calling was carried out seperately for DDX5 ChIP-Seq rep 1 and DDX5 ChIP-Seq rep 2 with the findPeaks function with the histone flag used. Both IP and Input were passed to findPeaks. The peaks for DDX5 ChIP-Seq rep 1 and DDX5 ChIP-Seq rep 2 were merged with the mergePeaks function.
Lastly the merged DDX5 peaks were annotated with annotatePeaks.pl, using mm10 for annotation
Genome_build: iGenomes UCSC mm10
Supplementary_files_format_and_content: Tab file containing merged DDX5 peaks annotated to nearest mm10 RefSeq TSS. Columns 1-19: peak name, chr, start, end, strand, score, peak origin, Annotation, Detailed Annotation, Dist to nearest TSS, Native ID of annotation file, entrez ID, unigene ID, RefSeq ID, Ensembl ID, gene symbol, gene alias, gene description, biotype

growth_protocol: Undifferentiated spermatogonia were cultured on mitomycin-inactivated mouse embryonic fibroblast (MEF) feeder cells in StemPro-34 media (Thermo Fisher Scientific) supplemented with 10ng/ml GDNF, 10ng/ml bFGF, 20ng/ml EGF, 25μg/ml insulin and other additives as previously described (Hobbs et al., 2012).

extract_protocol:
Samples were quantified by Qubit and 20ng of DNA was used as starting amounts for all libraries. Samples were sheared by Covaris to ~200-300bp prior to library generation.
Libraries were constructed using Ovation Ultralow System V2 using Nugen protocol M01379v1, 2014. Libraries were initially quantified by Qubit and size profile determined using Bioanalyzer followed by quantification by qPCR and pooled in equimolar ratio. Upon qPCR, 200pM of a library pool was used for cluster generation with c-bot (Ilumina Protocol 15006165 v02 Jan 2016). Two lanes of Illumina HiSeq3000 (Ilumina Protocol 15066493 Rev A, February 2015) were used for 50bp single end reads.

treatment_protocol: Cross-linking of cells, chromatin digestion and chromatin immunoprecipitation were performed as per SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology #9003)

tag: chip antibody


title: DDX5 ChIP-Seq rep 2


title: 12522_PCW10_RNA

description: Stranded (first-strand synthesis)


title: LV1275_explant_RNA

description: Stranded (first-strand synthesis)


title: DDX5 ChIP-Seq rep 1


title: Input rep 1


title: LV1223_explant_RNA

description: Stranded (first-strand synthesis)


title: KO-RNA seq-rep2

description: RNA seq-rep2.xls

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: excel documents include RPKM values for each sample

extract_protocol:
Total RNA of BMDCs was isolated with Trizol regent (Invitrogen) and mRNA was enriched by Dynabeads mRNA Purification Kit (Invitrogen). Removal of ribosomal RNA was confirmed by 2200 Tape Station detection (Agilent).
The library preparation was constructed according to NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Microbeads anti-CD11c were cocultured with BMDC from Mettl3 WT or Mettl3 KO mice at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated . Before collection, the CD11c+ BMDC were stimulated for 24hours with LPS(100ng/ml).

tag: strain


title: WT-RNA seq-rep1

description: RNA seq-rep1.xls

value: wildtype


title: WT-RNA seq-rep2

description: RNA seq-rep2.xls


title: LV1033_explant_RNA

description: Stranded (first-strand synthesis)


title: WT-D3-6h lifetime

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
The degradation rate of RNA k was estimated by Log2(At/Ao)=-kt, where t is transcription inhibition time (h), At and A0 represent mRNA quantity (attomole) at time t and time 0. Two k values were calculated: time 3 h versus time 0 h, and time 6 h versus time 0 h. The final lifetime was calculated by using the average of k3h and k6h, that is t1/2=2/(k3h+k6h)
Genome_build: mm10
Supplementary_files_format_and_content: excel document containg RPKM values for each sample and the calculated lifetime

source_name: WT dendritic cells treated with Actinomycotoxin D for 6 h

extract_protocol:
Total RNA of BMDCs was isolated with Trizol regent (Invitrogen) and mRNA was enriched by Dynabeads mRNA Purification Kit (Invitrogen). Removal of ribosomal RNA was confirmed by 2200 Tape Station detection (Agilent). ERCC RNA spike-in control (Ambion) was added to each sample proportional to total RNA according to the instructions.
The library preparation was constructed according to NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Microbeads anti-CD11c were cocultured with BMDC from Mettl3 WT or Mettl3 KO mice at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated . After the CD11c+ BMDC were stimulated for 24hours with LPS(100ng/ml), cells were divided in triplicate, one for Actinomycotoxin D 6h, another for 3h and the last with no treatment.

tag: time (hours)


title: WT-D3-3h lifetime

source_name: WT dendritic cells treated with Actinomycotoxin D for 3 h


title: KO-RNA seq-rep1

description: RNA seq-rep1.xls


title: LV1400_donor_RNA

description: Stranded (first-strand synthesis)


title: KO-D2-3h lifetime

source_name: KO dendritic cells treated with Actinomycotoxin D for 3 h