title: shSETD1A E2(+)

city: Incheon

first: Kwang Won

last: Jeong

address: 191 Hambakmoe-ro, Yeonsu-gu

department: College of Pharmacy

country: South Korea

institute: Gachon University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using TopHat v2.0.12(with bowtie v2.2.3) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks from Trapnell, et al. 2012, Nature Biotechnology, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA sample preparation protocols.

treatment_protocol: SETD1A was knocked down using Lentiviral shRNA system

tag: cell line

value: breast


title: B6_F_3

status: Public on Oct 24 2018

type: SRA

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: NIEHS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw data was filtered to retain only read pairs with average base quality score of at least 20 for each read.
Reads were mapped against mm9 reference genome with Bismark v0.7.8 (parameters: -X 10000 --non_bs_mm -n 2 -l 50 -e 70 --chunkmbs 1024), using Bowtie v0.12.8 as the underlying alignment tool.
All mapped hits from the same library were combined then deduplicated with the Bismark deduplication script (deduplicate_bismark_alignment_output.pl; from Bismark v0.7.8).
Mapped reads were separated by source strand (plus or minus).
Redudant mapped bases from ovlerapping mapped reads in a read pair were trimmed to avoid bias in quantification of methylation status.  The first 4 and last 1 base from each mate2 read were also clipped due to observed positional methylation bias.
Alignments for multiple libraries from a given animal were combined with MergeSamFiles.jar from the Picard suite (v1.110).
Genomic cytosines were considered validated if at least 75% of mapped bases at the N, N+1, and N+2 positions from both the C67BL/6N and C3H/HeN mice were consistent with the expected reference (mm9) context.  Each genomic cytosine was then categorized by context (CpG, CHG, CHH) and status (validated or unvalidated).  Further analysis was limited to only validated CpG sites.
Percent methylation at each validated CpG sites was calculated as methylated cytosine bases / total cytosine bases, summed over both genomic strands.
Inheritance of methylation status was assessed based on read pairs overlapping both a CpG of interest and a SNV that distinguishes between the local C67BL/6N and C3H/HeN genomes; approximately 2.8M such SNVs were catalogued.
Genome_build: mm9
Supplementary_files_format_and_content: Percent methylation at each validated CpG; format = bigWig.
Supplementary_files_format_and_content: Total methylated and unmethylated cytosine counts per validated CpG (summed over both genomic strands) per animal; format = tab-delimited text.
Supplementary_files_format_and_content: Genomic coordinate and alleles of SNVs in the local C67BL/6N and C3H/HeN genomes; format = tab-delimited text.

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: Animals were maintained in climate controlled rooms (18-26C; 35-65% humidity) on a 12:12hr light:dark cycle in polycarbonate cages with irradiated, heat treated hardwood bedding (Teklad, Indianapolis, IN).  Cotton fiber nestlets (Ancare Corp., Bellmore, NY) were supplied to mice for environmental enrichment.  NIH 31 (Harlan Teklad, Indianapolis, IN) was provided ad libitum.  Reverse osmosis treated water from sterilized bottles with stainless steel sipper tubes was provided ad libitum to all animals and changed weekly.

extract_protocol:
Frozen liver tissues were quickly pulverized with BioPulverizer (Bio Spec Products Inc.) on dry ice. DNA was extracted with Allprep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's protocol. DNA was further purified by phenol-chloroform extraction followed by ethanol precipitation.
DNA (1 µg) was spiked with 1ng unmethylated lambda DNA (Promega), fragmented using a Covaris E210 (intensity 5, duty cycle 10%, cycles per burst 200; average size  300 bp), end-repaired, A-tailed, and adapter-ligated using Truseq DNA sample prep kit (Illumina) according to the manufacturer's protocol. Adapter-ligated DNA was size selected on a Pippin Prep (Sage Science; 1.5% agarose cassette; targeted DNA size 430bp +/- 120bp). After cleaning up DNA with AMPure XP beads, bisulfite conversion was performed using EpiTect Bisulfite kit (Qiagen) with the following thermal cycles, 95°C 5 minutes, 60°C 25 minutes, 95°C 5 minutes, 60°C 85 minutes, 95°C 5 minutes, 60°C 175 minutes, 95°C 5 minutes, 60°C 180 minutes. After cleaning up DNA with AMPure XP beads DNA was eluted in 17.5 ul.  Two 4 ul aliquots of bisulfite converted DNA were amplified with PfuTurbo Cx Hotstart DNA Polymerase with following thermal cycles, 95°C 5 minutes, 98°C 30 seconds, 12 cycles of (98°C 10 seconds, 65°C 30 seconds, 72°C 30 seconds), 72°C 5 minutes. The two amplification reactions were pooled, cleaned with AMpure XP beads, and stored at -20°C until use.

tag: strain

tag: Sex

value: female

tag: replicate animal


title: B6_M_2

value: male


title: B6_M_1


title: B6_M_3


title: Adult-Male1-WTTS

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using the aligner Bowtie2 version 2.2.3 with setting"bowtie2 -L 25 -N 0 -i S,1,1.15 --no-unal". The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites.
Genome_build: Xenopus_tropicalis_v9.1

molecule: total RNA

organism: Xenopus tropicalis

source_name: Whole body

extract_protocol:
Total RNA was harvested using Trizol reagent.
WTTS libraries were constructed based on our protocols. The WTTS method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, Size selection and PCR amplication.

tag: tissue

value: Whole body

tag: developmental stage

value: Adult


title: B6_F_2


title: Adult-Male2-WTTS


title: Adult-Female1-WTTS


title: B6_F_1


title: shNS E2(-)

organism: Homo sapiens

source_name: breast cancer cells_shNS_no_estrogen


title: shNS E2(+)

source_name: breast cancer cells_shNS_with_estrogen


title: ChIP-seq_H3K9me3_D4_shCtrl_rep2

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
For ChIP-seq single-end reads were mapped to the Mus musculus mm9 reference genome using bowtie1; unique matches with no more than 2 mismatches in the best alignment stratum were kept.
Following the ENCODE guidelines, mapped reads were deduplicated with the Picar toolkit v1.94, blacklisted regions removed with bedtools v2.19.1 and the degree of IP fragment clustering determined with phantompeakqualtools v2.0. Peak calling was performed with MACS2  with default parameters for regular peak calling and using the INPUT library for the estimation of the significance of peak enrichment. Consistency of peak calling among biological replicates and the final set of peaks per condition were determined using the Irreproducible Discovery Rate (IDR) approach.
genome build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq, ATAC-seq and RNA-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: quantile normalization for the ChIP-seq and ATAC-seq datasets and DESeq2 size normalization for the RNA-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition
Supplementary_files_format_and_content: RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt: File with summarized counts (not normalized) for all the RNA-seq samples

source_name: mouse embryonic fibroblast cells E13.5

extract_protocol:
For ChIP-Seq: 10min formaldehyde fixation followed by sonication (histone marks) or Mnase digestion (transcription factors). Immunoprecipitation was performed using ChIP-IT kit (#53040, Active Motif) following manufacturer's protocol. Experiments were done in duplicates.
Libraries prepared using Microplex library Preparation kit v2 (C05010014, Diagenode) following manufacturer's protocol (V2 02.15). Libraries were size-selected (200-400bp) and clenaed-up using Agencourt AMPure XP beads (#A63881, Beckman).

tag: cell type

value: MEF expressing OKSM for 4 days

tag: passages

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)

tag: genotype

value: shCtrl


title: shSETD1A E2(-)


title: Huh7_BS

status: Public on Oct 23 2018

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
bisulfite treated mRNA
Human Hepatocellular Carcinoma

data_processing:
Raw  reads for each sample were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end reads were mapped against human (hg19) or mouse (mm10) reference genome by Bismark.
The methylated sites were called by Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/).
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: supplementary file includes the methylated sites

source_name: normal human Huh7 cells - bisulfite-treated mRNAs

extract_protocol:
mRNAs of of human and mouse cell lines were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA)

value: Hepatocellular Carcinoma


title: MRC-5_BS

description:
bisulfite treated mRNA
Human Fetal Lung Fibroblast

source_name: normal human MRC-5 cells - bisulfite-treated mRNAs

value: Fetal Lung Fibroblast


title: HCT116_BS

description:
bisulfite treated mRNA
Human Colon Cancer

source_name: normal human HCT116 cells - bisulfite-treated mRNAs

value: Colon Cancer


title: SNB19

description: Transcriptome of normal SNB19 cells

data_processing:
Reads were aligned to the hg19 or mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3
Genome_build: hg19
Supplementary_files_format_and_content: txt format with read counts

source_name: Human SNB19 cells

extract_protocol:
RNA was isolated from siCTRL and siNSUN2 HeLa cells and 3T3-L1 cells, mutiple human other cell lines, mouse other cell lines and tissues using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 or HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: normal human SNB19 cells

value: carcinoma brain


title: ChIP-seq_INPUT_ES_rep1

source_name: mouse embryonic stem cells

value: ES

value: wild type


title: 293T_BS

description:
bisulfite treated mRNA
Human Embryonic Kidney

source_name: normal human 293T cells - bisulfite-treated mRNAs

value: Embryonic Kidney


title: HCT116

description: Transcriptome of normal HCT116 cells

source_name: Human HCT116 cells

value: normal human HCT116 cells

value: carcinoma large intestine


title: Huh7

description: Transcriptome of normal Huh7 cells

source_name: Human Huh7 cells

value: normal human Huh7 cells

value: carcinoma liver


title: 293T

description: Transcriptome of normal 293T cells

source_name: Human 293T cells

value: normal human 293T cells

value: kidney


title: siNSUN2_HeLa_rep2BS

description: mRNA m5C profiles in NSUN2 deficient HeLa cells rep2

data_processing:
Raw Reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end RNA-BisSeq reads were mapped against human (hg19) reference genome by Bismark (version 0.13.0). The m5C sites calling was performed using Bismark (version 0.13.0).
Genome_build: hg19
Supplementary_files_format_and_content: txt format. Information of m5C positions and modified gene types (hg19).

molecule: polyA RNA

source_name: Human HeLa cells

extract_protocol:
mRNAs of siNSUN2 HeLa cell were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: HeLa

tag: transfection

value: carcinoma cervical


title: siNSUN2_HeLa_rep1BS

description: mRNA m5C profiles in NSUN2 deficient HeLa cells rep1

extract_protocol:
mRNAs of siNSUN2 HeLa cells were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.


title: siCTRL_HeLa_rep2BS

description: mRNA m5C profiles in normal  HeLa cells rep2

extract_protocol:
mRNAs of siCTRL HeLa cells were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: siCTRL


title: siCTRL_HeLa_rep1BS

description: mRNA m5C profiles in normal  HeLa cells rep1

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R.
Raw Reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end RNA-BisSeq reads were mapped against human (hg19) reference genome by Bismark (version 0.13.0). The m5C sites calling was performed using Bismark (version 0.13.0).
Genome_build: hg19
Supplementary_files_format_and_content: txt format. Information of m5C positions and modified gene types (hg19).


title: siNSUN2_HeLa_rep2

description: Transcriptome of NSUN2 deficient HeLa cells rep2

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R. Raw RNA seq reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic.
Filtered paired-end reads were mapped against hg19 genome using TopHat v2.0.9. Reads counts of all genes were computed using HTSeq v0.5.3p9.
Genome_build: hg19
Supplementary_files_format_and_content: txt format. Read counts for each gene.

extract_protocol: RNA was isolated from siNSUN2 HeLa cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Adult-Female2-WTTS

value: Whole body

value: Adult


title: M-1_BS

description:
bisulfite treated mRNA
Mouse Collecting Tubular Epithelial

source_name: normal mouse M-1 cells - bisulfite-treated mRNAs

value: Collecting Tubular Epithelial


title: M-1

description: Transcriptome of normal M-1 cells

data_processing:
Reads were aligned to the hg19 or mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3
Genome_build: mm10
Supplementary_files_format_and_content: txt format with read counts

source_name: Mouse M-1 cells

value: normal mouse M-1 cells


title: SNB19_BS

description:
bisulfite treated mRNA
Human Glioma

source_name: normal human SNB19 cells - bisulfite-treated mRNAs

value: Glioma


title: siNSUN2_HeLa_rep1

description: Transcriptome of NSUN2 deficient HeLa cells rep1


title: siCTRL_HeLa_rep1

description: Transcriptome of normal  HeLa cells rep1

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R. Raw RNA seq reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic.
Filtered paired-end reads were mapped against hg19 genome using TopHat v2.0.9. Reads counts of all genes were computed using HTSeq v0.5.3p9.
Genome_build: hg19
Supplementary_files_format_and_content: txt, read counts for each gene

extract_protocol: RNA was isolated from siCTRL HeLa cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: U14_BS

description:
bisulfite treated mRNA
Mouse Uterine Cervix Cancer

source_name: normal mouse U14 cells - bisulfite-treated mRNAs

value: Uterine Cervix Cancer


title: siCTRL_HeLa_rep2

description: Transcriptome of normal  HeLa cells rep2


title: U14

description: Transcriptome of normal U14 cellls

source_name: Mouse U14 cells

value: normal mouse U14 cells


title: Thymus_8w_BS

description: mRNA m5C profiles in 8-week-old mouse thymus

data_processing:
Raw Reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end RNA-BisSeq reads were mapped against mouse (mm10) reference genome by Bismark (version 0.13.0). The m5C sites calling was performed using Bismark (version 0.13.0).
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Information of m5C positions and modified gene types (mm10).

source_name: 8-week-old Mouse thymus

extract_protocol:
mRNAs of 8-week-old mouse thymus were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

tag: gender

value: male

tag: age

value: 8 weeks

value: thymus


title: Small-intestine_8w_BS

description: mRNA m5C profiles in 8-week-old mouse small intestine

source_name: 8-week-old Mouse small intestine

extract_protocol:
mRNAs of 8-week-old mouse small intestine were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: small intestine


title: MRC-5

description: Transcriptome of normal MRC-5 cells

source_name: Human MRC-5 cells

value: normal human MRC-5 cells

value: lung


title: Spleen_8w_BS

description: mRNA m5C profiles in 8-week-old mouse spleen

source_name: 8-week-old Mouse spleen

extract_protocol:
mRNAs of 8-week-old mouse spleen were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: spleen


title: Large-intestine_8w_BS

description: mRNA m5C profiles in 8-week-old mouse large intestine

source_name: 8-week-old Mouse large intestine

extract_protocol:
mRNAs of 8-week-old mouse large intestine were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: large intestine


title: Kidney_8w_BS

description: mRNA m5C profiles in 8-week-old mouse kidney

source_name: 8-week-old Mouse kidney

extract_protocol:
mRNAs of 8-week-old mouse kidney were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: kidney


title: Muscle_8w_BS

description: mRNA m5C profiles in 8-week-old mouse muscle

source_name: 8-week-old Mouse muscle

extract_protocol:
mRNAs of 8-week-old mouse muscle were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: muscle


title: Lung_8w_BS

description: mRNA m5C profiles in 8-week-old mouse lung

source_name: 8-week-old Mouse lung

extract_protocol:
mRNAs of 8-week-old mouse lung were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.


title: Liver_8w_BS

description: mRNA m5C profiles in 8-week-old mouse liver

source_name: 8-week-old Mouse liver

extract_protocol:
mRNAs of 8-week-old mouse liver were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: liver


title: Brain_8w_BS

description: mRNA m5C profiles in 8-week-old mouse brain

source_name: 8-week-old Mouse brain

extract_protocol:
mRNAs of 8-week-old mouse brain were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: brain


title: Cerebellum_8w_BS

description: mRNA m5C profiles in 8-week-old mouse cerebellum

source_name: 8-week-old Mouse cerebellum

extract_protocol:
mRNAs of 8-week-old mouse cerebellum were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: cerebellum


title: siNSUN2_3T3-L1_rep2BS

description: mRNA m5C profiles in NSUN2 deficient 3T3-L1 cells rep2

source_name: Mouse 3T3-L1 cells

extract_protocol:
mRNAs of siNSUN2 3T3-L1 were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: adipose tissue


title: Testis_4w_BS

description: mRNA m5C profiles in 4-week-old mouse testis

source_name: 4-week-old Mouse testis

extract_protocol:
mRNAs of 4-week-old mouse testis were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: 4 weeks

value: testis


title: siCTRL_3T3-L1_rep2BS

description: mRNA m5C profiles in normal 3T3-L1 cells rep2

extract_protocol:
mRNAs of siCTRL 3T3-L1 cell were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: siCTRL


title: Heart_8w_BS

description: mRNA m5C profiles in 8-week-old mouse heart

source_name: 8-week-old Mouse heart

extract_protocol:
mRNAs of 8-week-old mouse heart were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

value: male

value: heart


title: siCTRL_3T3-L1_rep1BS

description: mRNA m5C profiles in normal  3T3-L1 cells rep1

extract_protocol:
mRNAs of siCTRL 3T3-L1 were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.


title: Spleen_8w

description: Transcriptome of 8-week-old Mouse spleen

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R. Raw RNA seq reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic.
Filtered paired-end reads were mapped against mouse genome (mm10) using TopHat v2.0.9. Reads counts of all genes were computed using HTSeq v0.5.3p9.
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Read counts for each gene.

extract_protocol: RNA was isolated from 8 weeks spleen using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: 8 weeks


title: Thymus_8w

description: Transcriptome of 8-week-old Mouse thymus

extract_protocol: RNA was isolated from 8 weeks thymus using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: thymus


title: Large-intestine_8w

description: Transcriptome of 8-week-old Mouse large intestine

extract_protocol: RNA was isolated from 8 weeks large intestine using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Small-intestine_8w

description: Transcriptome of 8-week-old Mouse small intestine

extract_protocol: RNA was isolated from 8 weeks small intestine using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: small intestine


title: Heart_8w

description: Transcriptome of 8-week-old Mouse heart

extract_protocol: RNA was isolated from 8 weeks heart using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Lung_8w

description: Transcriptome of 8-week-old Mouse lung

extract_protocol: RNA was isolated from 8 weeks lung using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: lung


title: Muscle_8w

description: Transcriptome of 8-week-old Mouse muscle

extract_protocol: RNA was isolated from 8 weeks muscle using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Cerebellum_8w

description: Transcriptome of 8-week-old Mouse cerebellum

extract_protocol: RNA was isolated from 8 weeks cerebellum using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Liver_8w

description: Transcriptome of  8-week-old Mouse liver

extract_protocol: RNA was isolated from 8 weeks liver using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Kidney_8w

description: Transcriptome of 8-week-old Mouse kidney

extract_protocol: RNA was isolated from 8 weeks kidney using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Testis_8w

description: Transcriptome of 8-week-old Mouse testis

source_name: 8-week-old Mouse tesits

extract_protocol: RNA was isolated from 8 weeks testis using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Brain_8w

description: Transcriptome of 8-week-old Mouse brain

extract_protocol: RNA was isolated from 8 weeks brain using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Testis_4w

description: Transcriptome of 4-week-old Mouse testis

extract_protocol: RNA was isolated from 4 weeks testis using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Testis_8w_BS

description: mRNA m5C profiles in 8-week-old mouse testis

source_name: 8-week-old Mouse testis

extract_protocol:
mRNAs of 8-week-old mouse testis were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.


title: siCTRL_3T3L-1_rep2

description: Transcriptome of normal 3T3-L1 cells rep2

extract_protocol: RNA was isolated from siCTRL 3T3-L1 cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: siCTRL_3T3-L1_rep1

description: Transcriptome of normal  3T3-L1 cells rep1


title: siNSUN2_3T3-L1_rep1

description: Transcriptome of NSUN2 deficient 3T3-L1 cells rep1

extract_protocol: RNA was isolated from siNSUN2 3T3-L1 cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: ALYREF-IP_rep1BS

description:
bisulfite treated ALYREF-IP-mRNA
Human HeLa cells

source_name: ALYREF-IP human HeLa cells - bisulfite-treated mRNAs

extract_protocol:
mRNAs of of human and mouse cell lines were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA)

value: HeLa

value: Carcinoma cervical


title: siNSUN2_3T3L-1_rep2

description: Transcriptome of NSUN2 deficient 3T3-L1 cells rep2


title: siNSUN2_3T3-L1_rep1BS

description: mRNA m5C profiles in NSUN2 deficient 3T3-L1 cells rep1

extract_protocol:
mRNAs of siNSUN2 3T3-L1 cell were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.


title: Testis_3w

description: Transcriptome of 3-week-old Mouse testis

source_name: 3-week-old Mouse testis

extract_protocol: RNA was isolated from 3 weeks testis using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: 3 weeks


title: Control shRNA [ChIP]

city: Guangzhou

first: Shidong

last: Lv

state: State...

address: 1838 Guangzhou North Ave.

institute: Nanfang Hospital

data_processing:
The data was filtered and removed low quality reads, N reads and adaptor sequences.
ChIP-seq reads were aligned to the hg19 genome assembly using SOAP2 (Version: 2.21t)
The alignment results were used for peaks calling by SICER.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using SICER

source_name: PC-3 cell line

growth_protocol: Human prostate cancer cells PC-3 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
We performed H3K4me1 ChIP using a Pierce Agarose ChIP Kit.PC-3 cells were fixed with 1% formaldehyde, lysed and digested by micrococcal nuclease leading to a DNA size range from 100-500bp. 4 ul of H3K4me1 antibody was added to the precleared sample and incubated overnight at 4 °C. The complexes were purified using ChIP Grade Protein A/G Plus Agarose followed by elution from the beads and reverse cross-linking. DNA was purified by DNA Clean-Up Column.
CHIP product was quantified by BioAnalyzer 2100 and Qubit fluorimeter. Then performed DNA-end repair and ligation of methylated sequencing adaptor. Then DNA was amplified by PCR and selected size at 100-300bp. Finally, prepared libraries were sequenced by BGISEQ-500.

treatment_protocol: PC-3 cells (3×105/well) were seeded in 6-well plates and transfected with shRNA expressing lentivirus for 1 week

value: PC-3 cell line

value: KMT2D normal

value: Prostate cancer cell line

tag: antibody

value: H3K4me1 (Abcam, ab8895)


title: Control shRNA

data_processing:
Data Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads
Reads Mapping performed by Bowtie2 to map clean reads to reference gene and use  HISAT to reference genome.
Gene quantified by FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA for RNA sequencing (RNA-seq) was isolated from PC-3 cells transfected with shRNA expressing lentivirus for 1 week. After extracting from cells, total RNA was quantified and integrity measured by BioAnalyzer 2100. Oligo (dT) magnetic beads were used to select mRNA with polyA tail and the target RNA was obtained after purification.
Fragmented the target RNA and reversed transcription to double-strand cDNA (dscDNA) by N6 random primer. Then End repair was performed. The dscDNA was ligated with adaptor and amplified by PCR. Denatured the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

tag: tag

value: Perform sequence after transfection with Control shRNA for 7 days

value: Prostate cancer cell

tag: gentoype


title: KMT2D shRNA [ChIP]

value: KMT2D deficiency


title: Fibroblasts2

status: Public on Oct 22 2018

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

data_processing:
Reads were de-multiplexed and converted to FASTQ files using bcl2fastq (version 2.17) software from Illumina by the ServiceXS sequencing facility  (Genome Analysis Facility, Leiden, The Netherlands).
Reads were trimmed for adapter sequences using Trimmomatic v0.30. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12.
FASTQ files were mapped to the hg19/GCh37 reference human genome (iGenomes); Bowtie2 (version 2.1.0) and TopHat2 (version 2.0.14) software was used for read alignment
Read counts per transcript were determined using HTSeq software (version 0.6.1)
Normalized read counts per transcript were calculated using DESeq2 (version 1.16.1) within the R environment (version 3.4.0)
Fragments Per Kilobase Million (FPKM) values were calculated using gene length and library size.
Genome_build: hg19/GCh37
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized expression values and FPKM values for each sample

source_name: fibroblasts

extract_protocol:
Samples were harvested in Trizol and stored in the -80C untill RNA isolation. total RNA was isolated using the miRNAeasy mini kit according the the producers instructions. For further details consult the methods section in the manuscript
Library preparation was performed by the Service XS sequencing facility (Genome Analysis Facility, Leiden, The Netherlands) using standard Illumina protocols.

tag: time in culture

value: Passage 2-5

tag: growth protocol

value: Fibroblasts were kept in culture in medium containing 10% Fetal Bovine serum in DMEM-GlutaMAX, passaged with trypsin

tag: donor date of birth


title: Fibroblasts5


title: Fibroblasts1


title: iPSC6

source_name: iPSC

tag: repprogramming method

value: Lentiviral transfection

value: iPSC's were kept in feeder free condition prior to sample collection according to what is described in the manuscript


title: KMT2D shRNA1

value: Perform sequence after transfection with KMT2D shRNA for 7 days


title: iPSC2


title: ALYREF-IP_rep2BS

data_processing:
Raw  reads for each sample were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end reads were mapped against human (hg19) or mouse (mm10) reference genome by Bismark.
The methylated sites were called by Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/).
Genome_build: hg19
Supplementary_files_format_and_content: supplementary file includes the methylated sites

tag: cell line


title: oMG3.52

source_name: oMG microglia

value: 52 days in culture

tag: derived from

value: iPSC3 line

value: organoids were grown and microglia were isolated as described in the manuscript methods section


title: pMG16-137

source_name: ex vivo adult microglia

value: Samples were obtained through the Netherlands Brain bank and microglia isolation was performed according to what's is described in the methods section of the manuscript

tag: donor age


title: pMG17-005


title: oMG5.38

value: 38 days in culture

value: iPSC5 line


title: KMT2D shRNA2

tag: cell type


title: iPSC1


title: oMG1.52

value: iPSC1 line


title: iPSC3


title: oMG3.38


title: oMG1.38


title: oMG5.52


title: WT Rep3

city: Porto

first: Jorge

last: Pinheiro

state: Porto

address: Rua Alfredo Allen, 208

department: Host Interaction and Response

country: Portugal

institute: IBMC-Institute for Molecular and Cell Biology, i3S-Institute for Research and Innovation in Health

data_processing:
Basecalling, trimming of adapter sequences and filtering and removal of poor signal reads was done using the Ion Torrent Suite version 4.4.
Reads were aligned to L. monocytogenes EGD-e genome using the aligner TopHat2.
The tools Cufflinks and Cuffdiff were utilized to calculate transcript abundance as FPKM.
Genome_build: Listeria monocytogenes EGD-e RefSeq: GCF_000196035.1, GenBank: GCA_000196035.1, assembly ASM19603v1
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values

organism: Listeria monocytogenes EGD-e

source_name: Listeria monocytogenes

growth_protocol: Bateria were grown in BHI broth at 37 ºC with agitation until the exponential phase (OD600= 1).

extract_protocol:
Total RNAs were extracted by the phenol-chlorophorm method and enriched for mRNAs before sequencing.
Sequencing of mRNAs was performed using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) and quality control for RNA fragmentation and library construction was assessed by Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and 2200 TapeStation (Agilent) analyses. Template preparation was achieved with an Ion Chef system (Thermo Fisher Scientific) and sample sequencing was done in triplicates with an Ion Proton System (Thermo Fisher Scientific).

tag: strain

value: Wild Type

tag: growth phase

value: Exponential (OD600= 1)

tag: growth conditions

value: 37 ºC, BHI broth


title: WT Rep1


title: Ck2

city: Wuhan

first: Jianyong

last: An

state: Hubei Province

address: Shizi shan Street, Hongshan District

institute: Huazhong Agricultural Univeristy

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files
Data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps:  1. Remove reads with adaptor sequences.  2. Remove reads in which the percentage of unknown bases (N) is greater than 10%.  3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2[Li et al., 2009]. No more than 2 mismatches were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads). The RPKM method is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression level. Therefore, the RPKM values can be directly used for comparing the difference of gene expression among samples. If there is more than one transcript for a gene, the longest one is used to calculate its expression level and coverage.
Genome_build: Citrus sinensis genome (http://citrus.hzau.edu.cn/) 2013 Verison 2.0
Supplementary_files_format_and_content: RPKM represent the expression of genes.

organism: Citrus trifoliata

source_name: root

growth_protocol: Poncirus trifoliata (L.) Raf seeds were surface-sterilized by washing in 1M NaOH for 15 min and in 2% sodium hypochlorite for 20 min, followed by rinsing with distilled water. The seeds were placed in dish and covered with sterilized gauze for one week in the dark (28°C), and then sown in autoclaved vermiculite in greenhouse. The seedlings were transplanted into sterile quartz sand with eight plants per pots (18cm×18cm). For mycorrhizal experiments, seedlings were inoculated with 50g of mycorrhizal inoculum containing ~3000 Glomus versiforme (BGC NM03C, Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences) spores per pots. Plants were watered twice a week with 250 ml half-strength Hoagland solution containing 20 μM phosphorus concentration.

extract_protocol:
Total RNA was extracted using TRIzol® (Invitrogen, USA) reagent according to the on-line manuals (http://tools.lifetechnologies.com/content/sfs/manuals/trizol_reagent.pdf). TURBO DNAase reagent kit (Ambion, USA) was used to remove DNA contamination.
Total RNA from 6 samples (three biological replicates of mycorrhizal and non-mycorrhizal samples) were used for RNA-seq via an Illumina HiSeqTM2000 at the Beijing Genomics Institute (Shenzhen). Firstly, total RNA from each sample was used to enrich mRNA using the oligo (dT) magnetic beads, then the mRNA was interrupted and used for the synthesis of the double-strand cDNA (Mortazavi et al., 2008). The double-strand cDNA was purified, washed in EB buffer for end repair, added with single nucleotide A (Adenine) and ligated with sequencing adaptors. The fragments obtained were used for PCR amplification, followed by library construction and sequencing. The Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used for checking the quality and quantity of the library.

tag: tissue

value: root

tag: protocol

value: Roots were not inoculated with arbuscular mycorrhizal fungi.


title: Gv3

value: Roots were conlonized with arbuscular mycorrhizal fungi Glomus versiforme.


title: Gv2


title: Gv1


title: Ck1


title: Ck3


title: Mut Rep2

source_name: Listeria monocytogenes DmouR

value: mouR deletion mutant


title: testis / opossum

status: Public on Oct 21 2018

city: Cambridge

first: Jenny

last: Chen

address: 16 Divinity Ave

institute: Harvard

data_processing:
RSEM v1.2.12 was used to align reads to the transcriptome of each species and to quantify transcripts per million (TPM) of each gene using default parameters.
Genome_build: oryCun2, canFam3, musFur1, dasNov3, monDom5
Supplementary_files_format_and_content: RSEM results in txt format

organism: Monodelphis domestica

source_name: testis

extract_protocol: 10ug total RNA was poly-A selected twice using Dynabeads mRNA Purification Kit (Invitrogen, 610.06). Resulting mRNA was DNase treated (Ambion AM1907) and then fragmented using heat. First strand cDNA synthesis was performed using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, 11917-010), supplementing in SuperScript III Reverse Transcriptase (Invitrogen, 18080-093), incorporating SUPERase*In (Ambion, AM2694), and Actinomycin D (USB, 10415). First strand cDNA was cleaned using 1.8x RNAClean XP SPRI beads (Beckman Coulter, A64987). Second-Strand Synthesis was performed replacing dTTP with dUTP, and the resulting double-stranded cDNA was cleaned using a MinElute PCR Purification Kit (Qiagen, 28004). Illumina libraries were constructed by repairing the ends of the cDNA, ligating adapters, and cleaning/size-selecting with 0.7x SPRI. Illumina libraries were treated with USER to excise dUTP, and amplified via PCR using Fusion Master mix with GC buffer (NEB, F532S). Samples were sequenced on HiSeq 2000 machines, to a minimum depth of 35 million reads.

value: testis


title: Mut Rep1


title: WT Rep2


title: Mut Rep3


title: testis / dog

organism: Canis lupus familiaris


title: lung / opossum

source_name: lung

value: lung


title: skeletal muscle / dog

source_name: skeletal muscle

value: skeletal muscle


title: lung / dog


title: skeletal muscle / opossum


title: liver / dog

source_name: liver

value: liver


title: liver / opossum


title: kidney / opossum

source_name: kidney

value: kidney


title: kidney / dog


title: heart / dog

source_name: heart

value: heart


title: brain / dog

source_name: brain

value: brain


title: heart / opossum


title: skeletal muscle / ferret

organism: Mustela putorius furo


title: lung / rabbit

organism: Oryctolagus cuniculus


title: liver / ferret


title: liver / rabbit


title: testis / ferret


title: liver / armadillo

organism: Dasypus novemcinctus


title: lung / ferret


title: lung / armadillo


title: heart / armadillo


title: skeletal muscle / armadillo


title: heart / rabbit


title: kidney / armadillo


title: brain / opossum


title: kidney / ferret


title: testis / rabbit


title: ARhi3

status: Public on Oct 20 2018

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using Bowtie2 v2.1.0 to hg19. Data were conversed and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 4x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: hg19
Supplementary_files_format_and_content: raw data count

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) biological replication_003

extract_protocol:
RNA was isolated using Trizol Reagent according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

value: LNCaP


title: ARhi1

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) biological replication_001


title: ARhiAPPshRNA3

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) together with APPshRNA #11043_biological replication_003


title: ARhiAPPshRNA1

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) together with APPshRNA #11043_biological replication_001


title: PcDNA3APPShRNA3

source_name: LNCaP pcDNA3.1 stably transduced with APPshRNA #11043 biological replication_003


title: brain / ferret


title: skeletal muscle / rabbit


title: ARhi2

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) biological replication_002


title: pMG17-003

source_name: ex vivo adult microglia

value: Samples were obtained through the Netherlands Brain bank and microglia isolation was performed according to what's is described in the methods section of the manuscript


title: PcDNA3APPShRNA2

source_name: LNCaP pcDNA3.1 stably transduced with APPshRNA #11043 biological replication_002


title: kidney / rabbit


title: brain / rabbit


title: heart / ferret


title: PcDNA2

source_name: LNCaP prostate cancer cells stably transduced with pcDNA3.1 empty vector biological replication_002


title: PcDNA1

source_name: LNCaP prostate cancer cells stably transduced with pcDNA3.1 empty vector biological replication_001


title: ARhiAPPshRNA2

source_name: LNCaP prostate cancer cells stably transduced with full-length wild-type androgen receptor (AR) together with APPshRNA #11043_biological replication_002


title: PcDNA33

source_name: LNCaP prostate cancer cells stably transduced with pcDNA3.1 empty vector biological replication_003


title: PcDNA3APPShRNA1

source_name: LNCaP pcDNA3.1 stably transduced with APPshRNA #11043 biological replication_001


title: M truncatula w/o TAP, HD, rep2

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: Mt 4.0
Supplementary_files_format_and_content: csv, raw abundances

organism: Medicago truncatula

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: no specific treatment was applied (no TAP treatment was applied prior to the library preparation)

tag: adapters

value: HD


title: M truncatula w/o TAP, IL, rep1

value: standard


title: Sturgeon_NF36_RiboZero

city: Woods Hole

first: Esther

middle: Jane

last: Pearl

state: MA

address: 7 MBL Street

department: National Xenopus Resource

institute: Marine Biological Laboratory

data_processing:
Casava version 1.8.2 was used for base calling
samples were adapter/quality trimmed using Trimmomatic
Ribosomal reads were removed and remaining high quality paired reads were aligned to reference set using Bowtie, using default parameters except setting k_min_coverage=2 to minimize noise
RSEM package was used to determine abundance estimates for all transcripts, transcripts with little read support were filtered out
Genome_build: de-novo assembly (fasta file provided by Leonid Peshkin)
Supplementary_files_format_and_content: stu_merged.counts (showing TPM counts)

organism: Acipenser sturio

source_name: whole embryo

growth_protocol: embryos were raised in 0.1 X MMR

extract_protocol:
total RNA was extracted using TRIzol
libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 14 cycles of PCR amplification

treatment_protocol: embryos were harvested and RNA extracted from fresh tissue

value: Bester hybrid Sturgeon - Beluga (Huso huso) x Sterlet (Acipenser ruthenus)

tag: developmental stage


title: Sturgeon_NF35_RiboZero


title: Sturgeon_NF15_RiboZero


title: Sturgeon_NF29_RiboZero


title: Sturgeon_NF18_RiboZero


title: Sturgeon_NF23_RiboZero


title: Sturgeon_NF24_RiboZero


title: Sturgeon_NF13_RiboZero


title: Sturgeon_NF26_RiboZero


title: Sturgeon_NF12_RiboZero


title: Sturgeon_NF32_RiboZero


title: Sturgeon_NF16_RiboZero


title: Sturgeon_NF19_RiboZero


title: Sturgeon_NF12_5_RiboZero


title: Sturgeon_NF11_RiboZero


title: Sturgeon_NF13_5_RiboZero


title: Sturgeon_NF22_RiboZero


title: Sturgeon_NF10_5_RiboZero


title: M truncatula w/o TAP, IL, rep2


title: Sturgeon_NF8_RiboZero


title: Sturgeon_NF4_RiboZero


title: Sturgeon_NF0_RiboZero


title: Sturgeon_NF9_RiboZero


title: Sturgeon_NF10_RiboZero


title: Sturgeon_NF20_RiboZero


title: S Lycopersicum w TAP, IL, rep2

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v 3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum lycopersicum

treatment_protocol: the RNA was TAP treated prior to library construction

tag: adapter


title: yidC1 mutant

status: Public on Oct 19 2018

city: Columbus

first: Sara

middle: R

last: Palmer

state: Ohio

address: 305 West 12th Avenue

department: College of Dentistry

institute: The Ohio State University

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina, to Streptococcus mutans UA159 genome
Step 5: SortSAM-coordinate
Step 6: BAM-to-SAM
Step 7: htseq-count
Step 8: DeGust-EdgeR was used for differential expression analysis
Genome_build: NC_004350.2
Supplementary_files_format_and_content: CVS file with read counts and DE expression analysis from DeGust EdgeR

organism: Streptococcus mutans

source_name: Bacterial batch culture

growth_protocol: Bacterial cells were grown in BHI medium, and bacterial cultures were grown staticly without agitation in 5% CO2 incubator at 37°C to mid-exponential phase.

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy kit (Qiagen). Ribosomal RNAs were removed using the MICROExpress bacteriala mRNA enrichment kit (Ambion Life Technologies).
cDNA libraries were made from the enriched mRNA sample using the NEBNext Ultra Diractional RNA library prep kit for Illumina and NEBNext multiplex oligonucleotides for Illumina (New England Biolabs).  Single-ended short reads were obtained from a set of cDNA libraries.

tag: parental strain

tag: media

value: BHI


title: S Lycopersicum w TAP, HD, rep1

data_processing:
Raw fastq 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), using the parameter values specified in the yaml files provided as supplementary material to the published paper (Plasschaert et al.). 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 indrop.py custom pipeline are given in the yaml files. Libraries called ""not_included_in_study_*"" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing."
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, see Supplementary Files 1-3 of the manuscript for details). The reference transcriptome was built using annotations from ENSEMBL (GRCm38 and GRCh37 for mouse and human, respectively). 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. Resulting raw count files are provided and called  *.counts.tsv.gz.
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%. For human sample, M = 25%, and  N = 1500,1500, 2000, and 1500 for donors 1-3 and the lentiviral transduction experiment, respectively. In mouse data, cell with strong immune gene expression were also excluded from this study. Counts were normalized as described in methods, and combined into three normalized filtered matrices (genes x cells ): filtered_normalized_counts_mouse.tsv.gz, filtered_normalized_counts_human.tsv.gz, and filtered_normalized_counts_human_viral_transduction.tsv.gz)
genome build: hg19 and mm10
The *.counts.tsv.gz files include raw unique molecular identifier (UMI)-filtered counts for all cell barcodes (prior to filtering). The file filtered_normalized_counts_*.tsv.gz contains filtered normalized counts. The file meta_raw_counts_*.tsv.gz contains meta information for each cell prior to filtering, including raw count file name, cell barcode, and the  index of the cell in the filtered normalized count matrix ('nan' for cells that were filtered out). The file meta_filtered_counts_*.tsv.gz contains meta information about filtered counts, such as library id, mouse id, raw count file name, barcode, and x and y coordinates used for 2-dimensional data representations.


title: UA159


title: EV_VitD3_S41

last: Nolte-'t Hoen

address: Yalelaan 2

department: Biochemistry & Cell Biology

institute: Utrecht University

description:
EV_VitD3_23_S41
EV_VitD3_23_S41

data_processing:
All data was processed as paired-end reads (150bp). Reads were clipped to 100bp with cutadapt (v 1.8) to remove low quality reads. Sequences with a minimal length of 17 bp after adapter trimming were retained to ensure high quality reads (cutadapt -q 30 -u -51 -U -51 -n1 --minimum-length 17 -a AGATCGGAAGAGCACACGTCTGAAC -A GATCGTCGGACTGTAGAACTCTGAA).
Reads were mapped to the mouse genome mm10 using gsnap (v2014-12-23; gsnap --novelsplicing 1 --npaths 3 --format sam)
Count tables were prepared using Htseq (v 0.6.1p1; htseq-count --minaqual 0 --format bam --order pos --stranded yes). For miRNA count tables miRbase v20 annotation was used. Gene annotation for snoRNA, snRNA, miscRNA were retrieved from Biomart (Ensembl 84). tRNA and rRNA chromosomal positions were retrieved from the UCSC mm10 repeat mask track.
Genome_build: mouse mm10
Supplementary_files_format_and_content: .xls file contains counts for all libraries as prepared by htseq (see data processing step)

source_name: EV derived from BMDC + VitD3

growth_protocol: Bone marrow derived dendritic cells were grown from primary mouse bone marrow according to Lutz et al 1999 J. Immunol. Methods in GM-CSF containing medium. Extracellular vesicles were purified by differential centrifugation and sucrose density gradient centrifugation according to van der Vlist et al. Nature Protocols 2012

extract_protocol:
RNA was isolated using the miRNeasy Micro kit (Qiagen) + small RNA enrichment protocol. Isolated RNA was treated with Ambion Turbo DNAse, ribosomal RNA was depleted using RiboZero Gold kit (Human/Mouse/Rat) (Illumina) before library preparation
Libraries were prepared with NebNext small RNA kit for Illumina with the following adaptations: 3' adapter ligation overnight at 16C, PCR amplification with Kapa HiFi Readymix 2x PCR mastermix for 15 cycles.

treatment_protocol: Cells were treated for 12 days with 10 nM VitD3, or treated for 24h with LPS before extracellular vesicle production

value: bone marrow-derived dendritic cell (BMDC)

tag: treated with

value: 10 nM VitD3 for 12 days

tag: rna extracted from

value: extracellular vesicles (EV)

tag: molecule subtype

value: small RNA

tag: replicate number

tag: index

tag: sequencing run


title: S Lycopersicum w TAP, HD, rep2


title: EV_VitD3_S12

description:
EV_VitD3_S12
H7YMWBBXX_S12_EV_VitD3_NEBi_19_GTGAAAA

tag: cell type


title: EV_LPS_S11

description:
EV_LPS_S11
H7YMWBBXX_S11_EV_LPS_NEBi_18_GTCCGCA

source_name: EV derived from BMDC + LPS

value: LPS for 24hrs


title: EV_LPS_S40

description:
EV_LPS_22_S40
EV_LPS_22_S40


title: EV_LPS_S14

description:
EV_LPS_S14
H7YMWBBXX_S14_EV_LPS_NEBi_21_GTTTCGA


title: EV_control_S39

description:
EV_control_21_S39
EV_control_21_S39

source_name: EV derived from BMDC

value: none (untreated control)


title: EV_cont_S13

description:
EV_cont_S13
H7YMWBBXX_S13_EV_cont_NEBi_20_GTGGCCA


title: cell_VitD3_S38

description:
cell_VitD3_20_S38
cell_VitD3_20_S38

source_name: BMDC VitD3 treated

value: cells


title: cell_LPS_S5

description:
cell_LPS_S5
H7YMWBBXX_S5_cell_LPS_NEBi_12_CTTGTAA

source_name: BMDC LPS treated


title: cell_LPS_S8

description:
cell_LPS_S8
H7YMWBBXX_S8_cell_LPS_NEBi_15_ATGTCAA


title: cell_VitD3_S6

description:
cell_VitD3_S6
H7YMWBBXX_S6_cell_VitD3_NEBi_13_AGTCAAA


title: EV_VitD3_S15

description:
EV_VitD3_S15
H7YMWBBXX_S15_EV_VitD3_NEBi_22_CGTACGA


title: cell_VitD3_S9

description:
cell_VitD3_S9
H7YMWBBXX_S9_cell_VitD3_NEBi_16_CCGTCCA


title: cell_control_S4

description:
cell_control_S4
H7YMWBBXX_S4_cell_control_NEBi_11_GGCTACA

source_name: BMDC


title: S Lycopersicum w TAP, IL, rep1


title: CaSki-NANOG-siGFP

status: Public on Oct 18 2018

city: Seoul

first: Kwon-Ho

last: Song

address: 73 Inchon-ro, Sungbuk-gu

institute: Korea University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer, bbmap), then mapped to hg19 whole genome using Tophat2
FPKM extraction and nomalization were performed using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CaSki-NANOG-siGFP

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Prep Kit standard protocols.

tag: cell line

value: CaSki

value: epidermoid cervical carcinoma

tag: overexpression

value: pMSCV/FLAG-NANOG

tag: sirna

value: siGFP


title: cell_control_S7

description:
cell_control_S7
H7YMWBBXX_S7_cell_control_NEBi_14_AGTTCCA


title: yidC2 mutant


title: EV_cont_S10

description:
EV_cont_S10
H7YMWBBXX_S10_EV_cont_NEBi_17_GTAGAGA


title: CaSki-no-siGFP

source_name: CaSki-no-siGFP

value: pMSCV empty vector


title: CaSki-NANOG-siHDAC1


title: TetO-YAP TEAD4

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Adapter trimming with skewer (https://github.com/kendomaniac/docker4seq, skewer function, min.length=40)
mapping with BWA (https://github.com/kendomaniac/docker4seq, bwa function, mm10 UCSC mouse assembly)
peack calling woth MACS  (TEAD4 - parameters: macs.min.mfold=10, macs.max.mfold=30, macs.pval=1e-20  and YAP - parameters: macs.min.mfold=10, macs.max.mfold=30, macs.pval=1e-5) or SICER (H3K27 acetilation - prameters: sicer.wsize=600, sicer.gsize=200, sicer.fdr=0.10)  (https://github.com/kendomaniac/docker4seq, chipseq function)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: liver

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of average 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Immunoprecipitated complexes were recovered on Protein-A/G agarose beads (Pierce) and, after extensive washes, DNA was recovered by reverse crosslinking and purification using QIAquick PCR purification kit (QIAGEN).
Libraries for ChIP-sequencing were generated by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and barcoded added using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB) according to manufacturer’s recommendation.

treatment_protocol: Tetracycline-inducible YAPS127A expression mice were previously described (Camargo et al., 2007). AAV8-TBG-Cre were obtained by University of Pennsylvania Vector Core. 1x10^11 pfu of AAV viruses are injected retro-orbitally. For TetOYAP overexpression, 3 days after AAV-Cre delivery, mice were administered doxycycline (1 mg/ml) ad libitum in their water.

tag: genotype/variation

value: Tetracycline-inducible YAPS127A

tag: sample type

value: strain described in Camargo et al Curr Biol. 2007 Dec 4;17(23):2054-60

tag: antibody

value: anti-TEAD4 (Abcam ab58310)


title: TetO-YAP YAP

value: anti-YAP (Cell Signaling 14074)


title: R3_14dpi

city: Barcelona

first: Josep

middle: V.

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

description: non-exercised, cryoinjured

data_processing:
Sequencing was performed at GenomeScan B.V. (Netherlands), using an ISO/IEC 17025 accredited RNA-seq pipeline for the Illumina NextSeq 500 platform
Alignment against Zebrafish genome was done using TopHat 2.1.0 with default parameters for single reads.
Read counts were extracted with HTSeq 0.6.0 for stranded single reads with Q>10
Gene counts normalization and differential expression was evaluated using the R package DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: Differencial expression profile (single TSV file)

organism: Danio rerio

source_name: Heart ventricle

extract_protocol:
Hearts were dissected, placed in sterile PBS to remove the atrium or bulbus arteriosus and the remaining ventricle was subsequently flash frozen in liquid nitrogen and stored at -80ºC. Total RNA from three or four ventricles was isolated and homogenized in 150 µl of QIAzolLysis Reagent. Pooled samples were processed with the miRNeasy MicroKit (Qiagen). The miRNeasy Micro Kit DNAse treatment was included for RNA-seq analysis to remove genomic DNA, following the manufacturer's specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols (NebNext Ultra)
RNA-Seq (poly-A capture)

tag: origin

value: pool 3 ventricles

tag: developmental stage

value: adults

value: wild-type


title: R2_14dpi

description: non-exercised, cryoinjured


title: S4_14dpi

description: exercised, cryoinjured

value: pool 4 ventricles


title: R4_14dpi

description: non-exercised, cryoinjured


title: cell_LPS_S37

description:
cell_LPS_19_S37
cell_LPS_19_S37

value: bone marrow-derived dendritic cell (BMDC)

value: small RNA


title: cell_control_S36

description:
cell_control_18_S36
cell_control_18_S36

value: none (untreated control)


title: S1_14dpi

description: exercised, cryoinjured


title: SHAM3_14dpi

description: non-exercised, sham-operated


title: SHAM4_14dpi

description: non-exercised, sham-operated


title: SHAM1_14dpi

description: non-exercised, sham-operated


title: R4_7dpi

description: non-exercised, cryoinjured


title: SHAM2_14dpi

description: non-exercised, sham-operated


title: R2_7dpi

description: non-exercised, cryoinjured


title: S2_7dpi

description: exercised, cryoinjured


title: R1_7dpi

description: non-exercised, cryoinjured


title: S4_7dpi

description: exercised, cryoinjured


title: TetO-YAP Input


title: SHAM4_7dpi

description: non-exercised, sham-operated


title: S3_7dpi

description: exercised, cryoinjured


title: S2_14dpi

description: exercised, cryoinjured


title: SHAM2_7dpi

description: non-exercised, sham-operated


title: Ctrl-siRNA-8170

status: Public on Oct 17 2018

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Multiplexed fastq reads were pooled for each sample
Pooled reads were aligned to GRCh38 reference genome using HISAT2 (2.0.5) aligner
Aligned SAM filere were converted to BAM using samtools V 0.1.19-96b5f2294a
Gene counts were computed from BAM files using HTSeq Counts
Genome_build: GRCh38_V24
Supplementary_files_format_and_content: Text files with gene expression values (read counts)

source_name: HEK293 cells

growth_protocol: HEK293 cells were cultured in DMEM (Fisher MT10013CV) medium supplemented with 10% FBS at 37°C in 5% CO2.

extract_protocol:
RNA extraction Kit "Aurum Total RNA Fatty and Fibrous Tissue Kit "
Illumina TruSeq Stranded mRNA library preparation protocol (p/n 15031047, rev. E)

treatment_protocol: siRNAs

tag: passages

value: ON-TARGET plus Non-targeting siRNA #3, D-001810-03-20


title: S3_14dpi

description: exercised, cryoinjured


title: Ctrl-siRNA-8171


title: Cherp-siRNA-8179

value: SMARTpool:ON-TARGETplus CHERP siRNA, L-016176-02-0005


title: Cherp-siRNA-8180


title: Cherp-siRNA-8178


title: Rbm17-siRNA-8163

value: SMARTpool:ON-TARGETplus RBM17 siRNA L-005158-01-0005


title: Rbm17-siRNA-8162


title: U2Surp-siRNA-8176

value: SMARTpool:ON-TARGETplus U2SURP siRNA, L-023607-02-0005


title: U2Surp-siRNA-8175


title: R1_14dpi

description: non-exercised, cryoinjured


title: Rbm17-siRNA-8164


title: Fetal duodenum derived epithelial enterosphere 15 weeks gestational age

city: Boston

first: Stefania

last: Senger

address: 114, 16th st. Charlestown, Navy Yard

department: Pediatrics

institute: Massachusetts General Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to the human genome (build hg19) with splice-aware aligner STAR vers-2.3.0 using hg19 Ensembl gtf version 75
To calculate RPKM expression values, sequencing reads were counted over an assembly of all putative exons for each gene and normalized by the length of the exon assembly and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for each sample are given in tab-delimited txt files.

source_name: Aborted fetus  intestine

growth_protocol: Stem cell media: DMEM/F12;FBS; NEAA; P/S; AcetylCysteine; NaPyruvate; EGF; Gastrin N2; B27; Gastrin; PGE2; L-WNR conditioned media used as 1:1 with stem cell media; A83-01; Y27623

extract_protocol:
TRIZOL® (ThermoFisher, MA) accordingly to manufacturer instruction. RNA was further purified using Direct-zol™ RNA Kits (ZYMO research, CA)
Total RNA was subjected to polyA selection, followed by NGS library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).
Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

tag: tissue

value: Aborted fetus  intestine

value: Primary cells

tag: passage


title: Adult duodenum derived epithelial enterosphere 11

source_name: Human dudenal biopsy

value: Human dudenal biopsy


title: Fetal duodenum derived epithelial enterosphere 17.5 weeks gestational age


title: Adult duodenum derived epithelial enterosphere 14


title: Adult duodenum derived epithelial enterosphere 15


title: Fetal duodenum derived epithelial enterosphere 21.5 weeks gestational age


title: SHAM3_7dpi

description: non-exercised, sham-operated


title: Fetal duodenum derived epithelial enterosphere 14 weeks gestational age


title: SHAM1_7dpi

description: non-exercised, sham-operated


title: Ctrl-siRNA-8169


title: Fetal duodenum derived epithelial enterosphere 22.5 weeks gestational age


title: Tet_RNA_WT7_R2

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
6mA peaks were called by MACS2 by comparing the pull-down reads versus input DNA. Cutoff FDR<0.01 was set to increase the reliability of 6mA candidates.
Single 6mA sites were determined by a binomial estimation with FDR<0.01 (6mA-RE-seq).
RNA-seq data were normalized together by Cufflinks and the fpkm value for each gene in each sample was calculated.
Genome_build: T_thermophila_June2014
Supplementary_files_format_and_content: fpkm, The gene identifiers in the RNA-seq processed data are according to Tetrahymena Genome Database WIKI ( http://ciliate.org/index.php/home/welcome ).

organism: Tetrahymena thermophila

source_name: SB210 WT strain

growth_protocol: Cells are cultured in proteose peptone (PP) medium (2% proteose peptone, 10 μM FeCl3 or 90 μM sequestrene (Fe-EDTA)) at 31 ºC.

extract_protocol: The genomic DNA was extracted by Quick-DNA™ Miniprep Kit (Zymo Research, Cat. No. D3024). Total RNA was extracted by Direct-zol™ RNA MiniPrep (Zymo Research, Cat. No. R2050) and further purified to mRNA by Dynabeads® mRNA Purification Kit (Thermo Fisher Scientific, Cat. No. 61006).

value: WT

tag: strain

tag: chip antibody

value: RNA sequencing library was prepared using TruSeq RNA Sample Preparation Kit v2 with standard protocol. Briefly, mRNA was poly-T selected and fragmented into  200 nucleotides, ligated with an adaptor using T4 RNA ligase, reverse transcribed into cDNA, PCR amplified to construct sequencing libraries.


title: U2Surp-siRNA-8177


title: Tet_RNA_WT6_R2


title: S1_7dpi

description: exercised, cryoinjured


title: Tet_RNA_WT6_R1


title: Tet_RNA_NP7_R1

source_name: SB210 KO strain

value: KO


title: Tet_Nuc_NP7_R1

data_processing:
Library strategy: DNA-seq
6mA peaks were called by MACS2 by comparing the pull-down reads versus input DNA. Cutoff FDR<0.01 was set to increase the reliability of 6mA candidates.
Single 6mA sites were determined by a binomial estimation with FDR<0.01 (6mA-RE-seq).
RNA-seq data were normalized together by Cufflinks and the fpkm value for each gene in each sample was calculated.
Genome_build: T_thermophila_June2014
Supplementary_files_format_and_content: bed files were generated by MACS2, which include the peak regions representing the 6mA loci and the nucleosome loci.The bed files from 6mA-RE-seq include the single-base locus of 6mA sites.Gene expression file includes the fpkm values calculated by Cufflinks.

value: DNA segments were size-selected by gel cutting from the MNase treatment of nuclei. The purified DNA was used to construct the library according to the standard Illumina DNA-seq protocol. Generally, DNA segments were end-repaired, 3'-adenylated and ligated to Illumina adaptors by using NEBNext® DNA Library Prep Kit (NEB, Cat. No. E6040S). Then DNA was amplified for 15 PCR cycles, purified by Agencourt AMPure XP (Beckman Coulter), and suspended in 16 uL of resuspension buffer to yield the sequencing library.


title: Tet_RNA_NP6_R2


title: Tet_RNA_NP6_R1


title: Tet_Nuc_NP6_R2


title: Tet_RNA_WT7_R1


title: Tet_Nuc_WGA


title: Fetal small intestine derived epithelial enterosphere 11weeks gestational age


title: Tet_Nuc_NP6_R1


title: Tet_Nuc_vitro_R2


title: Tet_Nuc_vitro_R1


title: Tet_RNA_NP7_R2


title: 19431_mWTl

city: Vienna

first: Daniel

last: Szappanos

address: Dr Bohr Gasse 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: MFPL

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using STAR 2.5.0a; reads in genes were counted with htseq-count (HTSeq version 0.6.1p1) ; differential expression analysis was performed with DESeq2 (v 1.10.1)
TPM estimation was performed with RSEM (v1.2.25)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (standard output RSEM)

growth_protocol: Macrophages were differentiated from bone marrow in DMEM (10%FBS; pen/srep) containing recombinant M-CSF (0,5ng/mL) for 8-9 days. Cells were passaged once on day 5, when induction of Cre was carried out using 4-OHT in a final concentration of 500nM. Cre mediated deletion of the target gene was performed under starvation conditions (DMEM, 2%FBS; pen/strep). After the 2 days of deletion media was replaced to complete DMEM (10%FBS;M-CSF; pen/strep)

extract_protocol:
For RNA extraction we used the NucleoSpin RNA II kit according to the manufacturer' instructions (Macherey-Nagel).
Illumina TruSeq protocol

treatment_protocol: Macrophages were infected either with Listeria monocytogenes (strain LO28) with a multiplicity of infection of 10 or with the combination of heat-killed listeria with a multiplicity of infection of 50 together with 250u/mL IFNβ.

tag: genotype

tag: background strain

value: bone marrow

value: macrophages

tag: gender

value: male


title: 19428_mWTc

tag: cell type


title: 19432_mWTc


title: 19426_mKOc


title: Tet_Nuc_NP7_R2


title: M truncatula w/o TAP, HD, rep1

source_name: leaf

tag: adapters

value: HD


title: 19423_fWTl

value: female


title: 19424_fWTc


title: Tet_DpnII_cut


title: Tet_Nuc_WT_R2


title: 19427_mWTh

source_name: male_WT_heat-killed listeria with IFN Beta


title: 19429_mKOl


title: Tet_Nuc_WT_R1


title: 19430_mKOc


title: Tet_DpnI_cut


title: Tet_CviAII_cut


title: 19420_fWTc


title: 19421_fKOl


title: Tet_chipexo_R1

data_processing:
Library strategy: ChIP-exo
6mA peaks were called by MACS2 by comparing the pull-down reads versus input DNA. Cutoff FDR<0.01 was set to increase the reliability of 6mA candidates.
Single 6mA sites were determined by a binomial estimation with FDR<0.01 (6mA-RE-seq).
RNA-seq data were normalized together by Cufflinks and the fpkm value for each gene in each sample was calculated.
Genome_build: T_thermophila_June2014
Supplementary_files_format_and_content: bed files were generated by MACS2, which include the peak regions representing the 6mA loci and the nucleosome loci.The bed files from 6mA-RE-seq include the single-base locus of 6mA sites.Gene expression file includes the fpkm values calculated by Cufflinks.

value: SYSY anti-m6A antibody

value: Fragment DNA was first immunoprecipitated according to the 6mA-IP-seq process. Then the DNA fragment was further polished by T4 DNA polymerase (NEB) and T4 PNK (NEB). Then, universal adaptor R1 was ligated to DNA catalyzed by T4 DNA ligase (NEB). Phi29 DNA polymerase (NEB) was used to repair the nick between adaptor and DNA. Lambda exonuclease and RecJf exonuclease were applied to the beads to chop off the 50 end of the antibody-DNA complex and any nonspecific bound DNA. Antibody-DNA complex was eluted by ChIP elution buffer (25 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 200 mM NaCl 0.5% SDS) at 65 C on the thermomixer and the bound DNA was isolated by adding proteinase K (Thermo Fisher) to the final concentration of 2 mg/ml and incubating at 65 C overnight. The proteinase K-treated reaction mixture was purified by phenol-chloroform extraction and ethanol precipitation. The DNA molecule was repaired to dsDNA molecule by Phi29 DNA polymerase mediated primer extension. Amplification adaptor R2 was ligated to dsDNA by T4 DNA ligase. The product was purified by AMPure beads (Agilent) and amplified by using PCR primers in TruSeq small RNA preparation kit.


title: 19417_fKOh

source_name: female_KO_heat-killed listeria with IFN Beta


title: 19419_fWTh

source_name: female_WT_heat-killed listeria with IFN Beta


title: 19418_fKOc


title: Tet_Input_R2

data_processing:
6mA peaks were called by MACS2 by comparing the pull-down reads versus input DNA. Cutoff FDR<0.01 was set to increase the reliability of 6mA candidates.
Single 6mA sites were determined by a binomial estimation with FDR<0.01 (6mA-RE-seq).
RNA-seq data were normalized together by Cufflinks and the fpkm value for each gene in each sample was calculated.
Genome_build: T_thermophila_June2014
Supplementary_files_format_and_content: bed files were generated by MACS2, which include the peak regions representing the 6mA loci and the nucleosome loci.The bed files from 6mA-RE-seq include the single-base locus of 6mA sites.Gene expression file includes the fpkm values calculated by Cufflinks.

value: Genomic DNA was segmented to ~250 bp by sonicator (Bioruptor, Diagenode). Then, DNA segments were end-repaired, 3'-adenylated and ligated to Illumina adaptors by using NEBNext® DNA Library Prep Kit (NEB, Cat. No. E6040S). After ChIP process, the precipitated DNA was amplified for 15  PCR cycles, purified by Agencourt AMPure XP (Beckman Coulter), and suspended in 16 uL of resuspension buffer to yield the sequencing library.


title: 19425_mKOh

source_name: male_KO_heat-killed listeria with IFN Beta


title: Tet_Input_R1


title: Tet_IP_R1


title: 19422_fKOc


title: Tet_IP_R2


title: N7

status: Public on Oct 16 2018

city: San Francisco

first: Minnie

last: Sarwal

state: CA

address: 500 Parnassus Ave

institute: UCSF

data_processing:
QC check FASTQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Aligned by STAR  (Spliced Transcripts Alignment to a Reference) 2.4.2a software with default setting
filtered backgroup with 1 per million in minimal sample size
Coverage were count and differential analysis was performed by algorithms embedded in EdgeR
summary was generated under R 3.2.1
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: TXT and count

source_name: normal

growth_protocol: clinical collection blood

extract_protocol:
Sample were prepared by using TruSeq Stranded Total RNA Library Prep Kit
Illumina Truseq Stranded, libraries were prepared according to a version of Illumina's RNA-Seq protocol, Illumina PE RNAseq

treatment_protocol: not treatment

tag: group

value: normal rejection


title: N8


title: N5


title: N6


title: N4


title: Tet_chipexo_R2


title: N3


title: N1


title: N12


title: N11


title: M3

source_name: mixed

value: mixed rejection


title: M2


title: M4


title: N10


title: H9

source_name: humoral

value: humoral rejection


title: H7


title: H5


title: H6


title: N9


title: M1


title: H4


title: Day 0, replicate 4

status: Public on Oct 25 2018

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

description:
Normal chow control
fat_D0_27

data_processing:
Basecalls were generated using CASAVA
Resulting reads (2 x 100 bp) were aligned to the mouse genome (Ensembl release 80) using STAR
Uniquely mapped reads were counted against gene annotations from Gencode (version M6) using featureCounts.
Gene expression levels were normalized using TMM and differential expression was assessed using linear modelling and the limma package (R version 3.0).
Genome_build: Ensembl release 80
Supplementary_files_format_and_content: raw counts

source_name: Day 0

extract_protocol:
RNA was isolated from epididymal fat tissue using RNeasy® Mini Kit (Qiagen) according to the manufacturer’s recommendations
Samples were prepared for RNA-seq using Illumina’s TruSeq RNA Sample Preparation Kit

tag: diet

value: Normal chow

tag: time

value: control

value: Adipose tissue


title: H8


title: N2


title: H3


title: H2


title: H10


title: H1


title: H11


title: H12


title: C9

source_name: cellular

value: cellular rejection


title: C6


title: C5


title: C4


title: C2


title: C8


title: R3_7dpi

description: non-exercised, cryoinjured

value: pool 3 ventricles

value: adults

value: wild-type


title: C13


title: C3


title: C12


title: C1


title: C10


title: C11


title: Tet1_ChIP_RNaseH1_rep1

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: HA-Tet1 ChIP from mESHA-Tet1 treated with RNAse H1, replicate 1

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina's bcl2fastq conversion software v.2.18.
The reads were aligned to the mouse reference genome (NCBIM37/mm9 build from Illumina iGenomes) using Bowtie v.2.2.8 with options ‘-q --phred33 --very-sensitive -p 4 --fr --end-to-end --maxins 1000’.
Multi-mapped and discordant reads were removed with SamTools v.1.3.1 (‘samtools view -f 2 -q 3’), and duplicated read pairs (likely PCR artefacts) were deduplicated using Picard MarkDuplicates v.2.6.0.
The filtered BAM files were converted into RPKM-normalised bigWig coverage tracks using deepTools bamCoverage v.2.4.3 and parameters ‘--smoothLength 60 --binSize 20 --normalizeUsingRPKM --outFileFormat bigwig’.
Peak calling for each ChIP sample against the respective pooled Input control was carried out with MACS v.2.1.1 and options ‘macs2 callpeak -m 5 50 -g mm --bw 200 --format BAMPE’.
Peaks overlapping abnormal genome regions as determined by the ENCODE project (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed from further analysis with BedTools v.2.25.0 (‘intersectBed -v’).
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: RPKM-normalized coverage tracks in bigWig format and blacklist-filtered MACS peaks in BED format

source_name: Mouse Embryonic Stem Cells (mESHA-Tet1)

growth_protocol: Mouse embryonic stem cells (mESHA-Tet1) were cultured in 0.1% gelatin-coated plates in DMEM 20% FCS and 0.4% leukemia inhibitory factor and 0.1 mM beta-mercaptoethanol, 100 uM of essential amino-acids and 1mM sodium  pyruvate,  5 mM L-glutamine

extract_protocol:
ChIP-Seq of endogenous HA-Tet1 in mouse embryonic stem cells (mESHA-Tet1) was performed on cells grown on 0.1% gelatin-coated plates in DMEM 20% FCS and 0.4% leukemia inhibitory factor. Cells were permeabilized for 15min in cold PBS with 0.05% Tween 20 at 4°C, washed with cold PBS  and were incubated with RNase H1 0.2 U/ul (NEB) and Nuclease S1 0.05 U/ul (Fermentas) or mock treated for 20 min at RT. The cells were then washed and crosslinked in PBS with 2mM disuccinimidyl glutarate (DSG) for 45 min. The cells were washed and crosslinked again with 0.7% formaldehyde for 15 min and quenched with 0.5 M glycine for 5 min. Finally the cells were washed with PBS, lysed and the chromatin was sonicated using Bioruptor Pico (Diagenode) for 10 cycles of 30 sec on, 30 sec off to yield 250 bp average size fragments. The sonicated chromatin was immunoprecipitated with HA antibody  (Abcam ab9111) at a ratio of 1.5 ug HA antibody per 20 ug chromatin. For Inputs, 5% of the chromatin from each replicate was collected and pooled into one Input control sample per condition. The subsequent ChIP procedures were performed as described in Arab et al. 2014 (doi:10.1016/j.molcel.2014.06.031).
ChIP-seq libraries were prepared using NuGEN Ovation Ultralow System V2 following the manufacturer’s recommendations. The libraries were profiled on a 2100 Bioanalyzer (Agilent Technologies) and quantified with a Qubit 2.0 Fluorometer (Life Technologies). The samples were pooled in equimolar ratio and sequenced on NextSeq 500 (Illumina) in paired-end mode for 42 cycles (PE42) plus 7 cycles for the index read.

tag: agent

value: RNAse H1

value: HA


title: Tet1_ChIP_RNaseH1_rep2

description: HA-Tet1 ChIP from mESHA-Tet1 treated with RNAse H1, replicate 2

tag: antibody


title: Tet1_ChIP_Mock_rep3

description: HA-Tet1 ChIP from mESHA-Tet1 mock treated, replicate 3

value: mock treated


title: Input_Mock

description: Pooled Input DNA from mESHA-Tet1 mock treated


title: Input_RNaseH1

description: Pooled Input DNA from mESHA-Tet1 treated with RNAse H1


title: Tet1_ChIP_Mock_rep1

description: HA-Tet1 ChIP from mESHA-Tet1 mock treated, replicate 1


title: Tet1_ChIP_Mock_rep2

description: HA-Tet1 ChIP from mESHA-Tet1 mock treated, replicate 2


title: Tet1_ChIP_RNaseH1_rep3

description: HA-Tet1 ChIP from mESHA-Tet1 treated with RNAse H1, replicate 3


title: C7