title: RRBS data from noncancer esophagus gast junc tissue [GTEX-17EVQ-1726-SM-L36SM]

source_name: esophagus gast junc

value: esophagus gast junc


title: ChIP_442_H3K27me3_rescue_exp_r3

status: Public on Jun 15 2023

type: SRA

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

library_source: genomic

data_processing:
Files were processed using the ENCODE ChIP-seq pipeline version 1.3.6: adapters and low quality reads were filtered with cutadapt version 2.5 and mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7) and bam files converted to tagAlign files
Narrow (H3K4me3, H3K27ac and SUZ12) peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 and either the "optimal overlap" (H3K4me3, H3K27ac) set or the "IDR optimal" (SUZ12) from the encode pipleine was used. Broad peaks (H3K27me3 and H3K9me3) were called using danpos2 regions with default parameters, to obtain a reproducible set of peaks for each clone, peaks were called on pooled replicates and only peaks overlapped by at least 50% bps of peaks in at least 2 out of 3 replicates were kept.
Assembly: mm10
Supplementary files format and content: Bed files of ChIP-seq reproducible peak sets called with macs2 for narrow peaks (H3K4me3, H3K27ac, SUZ12) or danpos2 regions for broad peaks (H3K27me3, H3K9me3)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol:
Native ChIP: Cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Native Drosophila chromatin was spiked in and mononucleosomal fragments were immunoprecipitated, followed by library preparation and sequencing. Crosslinked ChIP: Cells were crosslinked with formaldehyde for 10 min and collected by scraping. Nuclei were isolated and chromatin was solubilized using a Covaris sonicator. Crosslinked Drosophila chromatin was spiked in.
Libraries were prepared using standard Illumina protocols (KAPA Hyper Prep kit).

treatment_protocol: Samples were untreated.

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: genotype

tag: strain

tag: antibody


title: ChIP_588_H3K27me3_rescue_exp_r2

value: wildtype


title: RRBS data from noncancer blood vessel tissue [GTEX-15RJ7-0526-SM-L36SW]

city: Los Angeles

first: Shuo

last: Li

state: CA

address: 630 Charles E Young Dr S

country: USA

institute: UCLA

data_processing:
We removed the UMI sequence and trimmed the raw sequencing reads. Our custom adapters contain an 8 bp random UMI and a 5 bp fixed sequence at the beginnings of both forward and reverse reads. These sequences are removed before adapter trimming (and written into the read name). Then Trimgalore [4] was used to trim the default Illumina adapters from the sequencing reads (using the options --three_prime_clip_R1 15 --three_prime_clip_R2 13 --clip_R2 2 --length 15 --phred33). Then, we performed sequence alignment, deduplication, and methylation calling. We first used Bismark [5] to align the trimmed reads to the reference genome hg19 [6] (GRCh37 (GCA 000001405.1)). Then Umi-Grinder [7] was used to remove PCR duplicates based on the UMI labels (now in the read names), allowing 4 mismatches in the total 16 bp UMI. Bismark methylation extractor was then used to call methylation in the mapped, deduplicated reads. The methylation levels were then reformated in the bed format (.bed.gz files). We utilized wgbstools to extract fragment-level methylation information from the deduplicated reads. The fragment-level methylation information was stored in pat format (.pat.gz and .pat.gz.csi files).
Assembly: hg19
Supplementary files format and content: The .bed.gz files contained the methylation levels of all CpGs covered in the RRBS data.
Supplementary files format and content: The .pat.gz and .pat.gz.csi files contained the fragment-level methylation information of all fragments in the RRBS data.

organism: Homo sapiens

source_name: blood vessel

extract_protocol:
DNA was isolated from tissue using the Qiagen Gentra Puregene method  (QIAGEN) following the manufacturers specifications.
The RRBS libraries of the genomic DNA from the 521 tissue samples were constructed following the standard RRBS protocol. 100-200 ng of intact genomic DNA in the volume of 21.5 ul was used as input material. Restriction digestion was done with 2.5 ul 10xCutSmart buffer and 1 ul MspI (NEB) for 18 h at 37 oC and 20 min at 65 oC. 0.5 ul 10xCutSmart buffer, 0.3 ul dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 ul Klenow (exo-, 5U/ul, NEB) and 2.6 ul RT-PCR water, 0.6 ul 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30 oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 ul 10xThermoFisher HC T4 ligase buffer, 0.4 ul 100 mM ATP (ThermoFisher), 0.2 ul 50 mM DTT, 1 ul ThermoFisher HC T4 DNA ligase (30 Weiss Unit/ul), 30 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 ul RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 ul of universal and index primer each) and 25 ul KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98 oC for 45 s, 9 cycles of 98 oC for 15 s, 60 oC for 30 s and 72 oC for 30 s, followed by a final extension at 72 oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 ul EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.

tag: tissue

value: blood vessel


title: ChIP_410_H3K27me3_rescue_exp_r2

description: 410_H3K27me3_ChIP_pr_R1.rescue.reproducible_peaks.broadPeak.bed.gz


title: RRBS data from noncancer esophagus tissue [GTEX-15SHU-1526-SM-L36TA]

source_name: esophagus

value: esophagus


title: ChIP_588_H3K27me3_rescue_exp_r1


title: RRBS data from noncancer ovary tissue [GTEX-15UF6-2026-SM-L36RA]

source_name: ovary

value: ovary


title: RRBS data from noncancer adipose tissue [GTEX-15ER7-1026-SM-L36U2]

source_name: adipose tissue

value: adipose tissue


title: ChIP_442_H3K27me3_rescue_exp_r2


title: ChIP_442_H3K27me3_rescue_exp_r1


title: ChIP_410_H3K27me3_rescue_exp_r3


title: RRBS data from noncancer adrenal gland tissue [GTEX-15ER7-1126-SM-L36SG]

source_name: adrenal gland

value: adrenal gland


title: ChIP_410_H3K27me3_rescue_exp_r1


title: Cpa3Cre/+, immunized, challenge day 5, rep3

city: Heidelberg

first: Robin

last: Thiele

address: Im Neuenheimer Feld 280

department: Immunology

country: Germany

institute: German Cancer Research Center

library_source: transcriptomic

data_processing:
reads were aligned via STAR aligner (default settings, v.2.5.2b)
and counted via FeatureCount (default settings, stranded library, subread/1.5.1)
Assembly: mm10 (Mus_musculus_GRCm38_102)
Supplementary files format and content: text delimeted file includes raw counts for each sample

molecule: total RNA

source_name: intestine

extract_protocol:
Total RNA was isolated from whole Jejunum (fat and Peyer's plaques removed) according to the instructions of the PureLink RNA Mini kit (Invitrogen)
RNA libraries for RNA-seq were prepared using TruSew Stranded RNA Kit (Illumina) following manufacturer's protocols.

value: intestine

tag: Sex

value: f

tag: treatment

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on days 20-24

tag: time

value: day 5


title: Cpa3Cre/+, immunized, challenge day 5, rep2


title: RRBS data from noncancer kidney tissue [GTEX-15DYW-2026-SM-L36R7]

source_name: kidney

value: kidney


title: Cpa3Cre/+, immunized, challenge day 5, rep1


title: Cpa3Cre/+, immunized, challenge day 3, rep1

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on days 20-22

value: day 3


title: RRBS data from noncancer adipose tissue [GTEX-15SHU-2326-SM-L36T3]


title: RRBS data from noncancer pancreas tissue [GTEX-14PJM-2126-SM-L36RH]

source_name: pancreas

value: pancreas


title: ChIP_588_H3K27me3_rescue_exp_r3


title: Cpa3Cre/+, immunized, challenge day 3, rep2

value: m


title: Cpa3Cre/+, immunized, challenge day 1, rep2

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on day 20

value: day 1


title: Cpa3Cre/+, immunized, challenge day 1, rep1


title: RRBS data from noncancer small intestine tissue [GTEX-14C39-1826-SM-L36RN]

source_name: small intestine

value: small intestine


title: RRBS data from noncancer pituitary tissue [GTEX-14E7W-3126-SM-L36SB]

source_name: pituitary

value: pituitary


title: RRBS data from noncancer pituitary tissue [GTEX-148VJ-2926-SM-L36RV]


title: RRBS data from noncancer prostate tissue [GTEX-14ABY-0726-SM-L36TG]

source_name: prostate

value: prostate


title: Cpa3Cre/+, immunized, rep2

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14

value: day 0


title: RRBS data from noncancer pituitary tissue [GTEX-15ER7-3226-SM-L36RZ]


title: RRBS data from noncancer kidney tissue [GTEX-145MN-0326-SM-L36RL]


title: RRBS data from noncancer thyroid tissue [GTEX-148VJ-0726-SM-L36RO]

source_name: thyroid

value: thyroid


title: Cpa3Cre/+, immunized, rep1

value: intestine


title: Cpa3+/+, immunized, challenge day 3, rep2

value: f


title: RRBS data from noncancer breast tissue [GTEX-145MF-2226-SM-L36SS]

source_name: breast

value: breast


title: RRBS data from noncancer pituitary tissue [GTEX-13OVJ-2626-SM-L36TP]


title: RRBS data from noncancer salivary gland tissue [GTEX-13OVL-2926-SM-L36RU]

source_name: salivary gland

value: salivary gland


title: Cpa3+/+, immunized, challenge day 5, rep1

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on days 20-24

value: day 5


title: Cpa3+/+, immunized, challenge day 3, rep1

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on days 20-22

value: day 3


title: RRBS data from noncancer kidney tissue [GTEX-13112-2126-SM-L36S6]

value: kidney


title: RRBS data from noncancer pancreas tissue [GTEX-14C39-1026-SM-L36R8]

value: pancreas


title: RRBS data from noncancer ovary tissue [GTEX-12ZZX-2026-SM-L36S7]

value: ovary


title: Cpa3+/+, immunized, challenge day 1, rep1

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on day 20

value: day 1


title: RRBS data from noncancer esophagus tissue [GTEX-12ZZX-1326-SM-L36TM]

value: esophagus


title: Cpa3+/+, immunized, rep2

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14


title: Cpa3+/+, immunized, rep1

value: day 0


title: RRBS data from noncancer spleen tissue [GTEX-12WSN-0126-SM-L36R9]

source_name: spleen

value: spleen


title: Cpa3Cre/+, naive, rep2

value: intestine

value: m

value: untreated

value: naive


title: Cpa3+/+, immunized, challenge day 5, rep2

value: f

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on days 20-24


title: Cpa3Cre/+, naive, rep1


title: Cpa3+/+, naive, rep1


title: RRBS data from noncancer pituitary tissue [GTEX-11ZUS-3026-SM-L36RE]

value: pituitary


title: RRBS data from noncancer salivary gland tissue [GTEX-131XH-2626-SM-L36TE]

value: salivary gland


title: RRBS data from noncancer skin tissue [GTEX-12126-0826-SM-L36TS]

source_name: skin

value: skin


title: K562, siYTHDC1 KD, RBFOX2 KD, r2, mRNA-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0)
Assembly: hg38
Supplementary files format and content: text files include read counts for each Sample

molecule: polyA RNA

growth_protocol: K562 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 2nM L-glutamine and antibiotics in cellular incubator with 5% CO2 at 37°C. NB4 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% HEPES and antibiotics in cellular incubator with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher Scientific). Poly A RNA was isolated using Dynabeads mRNA DIRECT™ kit (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human immortalized myelogenous leukemia cell line

value: siYTHDC1 KD, RBFOX2 KD


title: K562, siYTHDC1 KD, RBFOX2 KD, r1, mRNA-seq


title: K562, siYTHDC1 KD, Control, r2, mRNA-seq

value: siYTHDC1 KD, Control


title: RRBS data from noncancer small intestine tissue [GTEX-11XUK-1426-SM-L36R4]

value: small intestine


title: Cpa3+/+, immunized, challenge day 1, rep3

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. Water + 20% egg white + 8% sugar) on day 20

value: day 1


title: RRBS data from noncancer uterus tissue [GTEX-12ZZX-2126-SM-L36RI]

source_name: uterus

value: uterus


title: K562, siYTHDC1 KD, Control, r1, mRNA-seq


title: K562, siControl, RBFOX2 KD, r2, mRNA-seq

value: siControl, RBFOX2 KD


title: RRBS data from noncancer ovary tissue [GTEX-11VI4-1026-SM-L36RC]

value: ovary


title: Cpa3+/+, immunized, challenge day 1, rep2

value: intestine


title: RRBS data from noncancer salivary gland tissue [GTEX-11TUW-2426-SM-L36R5]


title: RRBS data from noncancer thyroid tissue [GTEX-12WSE-1226-SM-L36RB]

value: thyroid


title: K562, siControl, Control, r2, mRNA-seq

value: siControl, Control


title: Cpa3+/+, naive, rep3

value: m

value: untreated

value: naive


title: RRBS data from noncancer adipose tissue [GTEX-11P7K-0826-SM-L36T9]

value: adipose tissue


title: K562, siControl, RBFOX2 KD, r1, mRNA-seq


title: K562, siControl, Control, r1, mRNA-seq


title: RRBS data from noncancer spleen tissue [GTEX-11P81-1326-SM-L36TX]

value: spleen


title: Cpa3+/+, naive, rep2

value: f


title: RRBS data from noncancer pancreas tissue [GTEX-11GSP-0426-SM-L36TQ]

value: pancreas


title: RRBS data from noncancer uterus tissue [GTEX-12WSD-2826-SM-L36S4]


title: RRBS data from noncancer blood vessel tissue [GTEX-12C56-0226-SM-L36TJ]

source_name: blood vessel

value: blood vessel


title: RRBS data from noncancer testis tissue [GTEX-11EQ9-1926-SM-L36RF]

source_name: testis

value: testis


title: NB4, RBFOX2 OE, RBFOX2, r1, b8, ChIP-seq

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were mapped to human genome using bowtie2 (version 2.4.1) in default mode: search for the multiple alignments, report the best one.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde. ChIP was preformed with the iDeal ChIP-seq kit for Histone marks (Diagenode) or the the iDeal ChIP-seq kit for Transcription Factors (Diagenode)
Library preparation was performed with KAPA HyperPrep Kit for NGS DNA Library Prep (Roche) according to the manufacturer’s protocols.

value: Human acute promyelocytic leukemia cell line

value: RBFOX2 OE

tag: chip antibody

value: Rabbit polyclonal anti-RBFOX2; Proteintech; Cat#12498-1-AP


title: RRBS data from noncancer small intestine tissue [GTEX-11VI4-1626-SM-L36SC]

value: small intestine


title: RRBS data from noncancer esophagus tissue [GTEX-11EQ9-0926-SM-L36TI]

source_name: esophagus

value: esophagus


title: 600_AMlib6_IP_wildtype__rep1

city: Rehovot

first: Alexander

last: Maman

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: WT

data_processing:
Internal barcode demultiplexing with inhouse pythong script according to Read2 position 4-10 (raw data supplied here is after this step)
alignment using STAR/2.5.3a  with added options of -(--bamRemoveDuplicatesType UniqueIdentical , --outSAMtype BAM SortedByCoordinate ,--alignIntronMax 500 , --alignEndsType Local)
reads to gene alloacation and coverage summary using txtools/0.0.7.4
m6A levels quantified using in house R-script(see paper)
Assembly: SK1, NCBI37/mm9
Supplementary files format and content: rds files of reads alloction created using txtools, contatining. Chr-chromosom, gencoor-genomic coordinates, strand - strand , gene - gene name, txcoor- transcript coordinates, refSeq - annotated nucleotide at this position, cov - total coverage at this position, start_5p-5p reads starting at this position,end_3p-reads ending at this location
Library strategy: m6A-seq2

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD (1.0% (w/v) yeast extract, 2.0% (w/v) peptone, 2.0% (w/v) glucose, and supplemented with uracil (2.5 mg/l) and adenine (1.25 mg/l)). To induce meiosis a standard protocol for sporulation was followed as described previously {Varier, 2022 #262} . In short, cells were grown until saturation for 24h in YPD, then grown in pre-sporulation medium BYTA (1.0% (w/v) yeast extract, 2.0% (w/v) bacto tryptone, 1.0% (w/v) potassium acetate, 50 mM potassium phthalate) for about 16 h, and shifted to sporulation medium (SPO) (0.3% (w/v) potassium acetate and 0.02% (w/v) raffinose)). All experiments were performed at 30°C in a shaker incubator at 300 rpm

extract_protocol:
RNA extraction was performed from yeast pellets using Acid Phenol:Chloroform pH 4.5 and Tris-EDTA-SDS (TES) buffer (0.01 M Tris-HCl pH 7.5, 0.01 M EDTA, 0.5% w/v SDS). Samples were further treated with rDNase (cat no 740.963, Macherey-Nagel) and column purified (cat no 740.948, Macherey-Nagel).
m6A levels were determined by m6A-seq2, as previously described {Dierks, 2021 #308; Schwartz, 2013 #4}.Briefly, RNA was poly-A selected twice using Dynabeads mRNA DIRECT kit, and fragmented to ~150 bp fragments. 3’ RNA barcode adaptors were then ligated (see Table S6), and all samples were pooled for m6A-IP-based enrichment. 90% of the mRNA material was subjected to two rounds of immunoprecipitation using two distinct anti-m6A antibodies, as follows: The RNA was first incubated for four hours with protein G beads (invitrogen) coupled to a Synaptic Systems poly-clonal m6A antibody (cat. 7945). Next, it was incubated overnight with protein A beads (invitrogen) coupled to a Cell Signaling poly-clonal m6A antibody (cat. D9D9W). RNA from input and IP libraries were reverse transcribed and PCR amplified as previously described  {Dierks, 2021 #308}. cDNA libraries were quantified using Qubit RNA HS kit (Life technologies) and Tapestation High Sensitivity D1000 ScreenTape (Agilent Technologies), pooled with a ratio of ⅓ Input to ⅔ IP samples, and sequenced.

treatment_protocol: For Auxin depleted experiments- To enable efficient depletion of mini-AID strains (Slz1, Vir1, Pab1 and Npl3), 1 mM of indole-3-acetic acid (IAA) and 50 µM of CuSO4 were added 2 hours after cells were shifted to SPO and samples collected at 4 hours in SPO.  As a control, the same volume of dimethyl sulphoxide (DMSO) was added to the yeast culture.

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG

value: SPO


title: 600_AMlib6_IP_untagged_pCUP_OsTIR_+DMSO_ctrl_rep2

description: untagged1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his:p550, MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his:p550


title: NB4, RBFOX2 OE, Input, r1, b8, ChIP-seq


title: RRBS data from noncancer ovary tissue [GTEX-11EMC-1726-SM-L36TF]

source_name: ovary

value: ovary


title: K562, WT, METTL3, r2, b7, ChIP-seq

value: Human immortalized myelogenous leukemia cell line

value: WT

value: Rabbit monoclonal anti-METTL3; Abcam; Cat#ab195352


title: RRBS data from noncancer breast tissue [GTEX-11EMC-2026-SM-L36R1]

value: breast


title: RRBS data from noncancer ovary tissue [GTEX-11EM3-1726-SM-L36RR]


title: RRBS data from noncancer pituitary tissue [GTEX-113JC-2826-SM-L36S3]

value: pituitary


title: 600_AMlib6_IP_untagged_pCUP_OsTIR_+DMSO_ctrl_rep1

description: untagged1+DMSO rep1


title: 600_AMlib6_IP_untagged_pCUP_OsTIR_+CuSO4+Auxinrep2

description: untagged1+Auxin rep2


title: K562, WT, METTL3, r1, b7, ChIP-seq


title: K562, WT, METTL14, r2, b6, ChIP-seq

value: Rabbit polyclonal anti-METTL14; Sigma-Aldrich; Cat#HPA038002


title: RRBS data from noncancer prostate tissue [GTEX-111FC-2026-SM-L36SI]

value: prostate


title: RRBS data from noncancer testis tissue [GTEX-ZYT6-2726-SM-L36QD]

value: testis


title: RRBS data from noncancer testis tissue [GTEX-ZUA1-2726-SM-L36NH]


title: K562, WT, METTL14, r1, b6, ChIP-seq


title: RRBS data from noncancer spleen tissue [GTEX-11P7K-0426-SM-L36SJ]

value: spleen


title: 600_AMlib6_IP_Slz1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: SLZ1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Slz1-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Slz1-MiniAID::KAN his:p550


title: 600_AMlib6_IP_untagged_pCUP_OsTIR_+CuSO4+Auxinrep1

description: untagged1+Auxin rep1


title: RRBS data from noncancer adrenal gland tissue [GTEX-ZUA1-1926-SM-L36QH]

source_name: adrenal gland

value: adrenal gland


title: RRBS data from noncancer salivary gland tissue [GTEX-ZP4G-1926-SM-L36PY]

value: salivary gland


title: RRBS data from noncancer kidney tissue [GTEX-ZC5H-1726-SM-L36NL]

value: kidney


title: K562, WT, Input, r2, b6, ChIP-seq


title: 600_AMlib6_IP_Slz1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: SLZ1+DMSO rep1


title: RRBS data from noncancer salivary gland tissue [GTEX-ZA64-1726-SM-L36QU]


title: RRBS data from noncancer testis tissue [GTEX-Z93S-1726-SM-L36OQ]


title: K562, WT, Input, r1, b6, ChIP-seq


title: 600_AMlib6_IP_Slz1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: SLZ1+Auxin rep2


title: RRBS data from noncancer small intestine tissue [GTEX-Y111-2226-SM-L36NJ]

value: small intestine


title: RRBS data from noncancer skin tissue [GTEX-Y111-0626-SM-L36Q9]

value: skin


title: RRBS data from noncancer adrenal gland tissue [GTEX-11EM3-0326-SM-L36TH]


title: K562, siYTHDC1 KD, RBM15, r2, b5, ChIP-seq

value: siYTHDC1 KD

value: Rabbit polyclonal anti-RBM15; Proteintech; Cat#10587-1-AP


title: 600_AMlib6_IP_Slz1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: SLZ1+Auxin rep1

value: SPO


title: RRBS data from noncancer skin tissue [GTEX-XQ3S-1426-SM-L36PL]


title: K562, siYTHDC1 KD, RBFOX2, r2, b5, ChIP-seq

value: Human immortalized myelogenous leukemia cell line

value: Rabbit polyclonal anti-RBFOX2; Proteintech; Cat#12498-1-AP


title: 600_AMlib6_IP_Pab1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: PAB1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Pab1-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Pab1-MiniAID::KAN his:p550


title: RRBS data from noncancer nerve tissue [GTEX-WZTO-1026-SM-L36QL]

source_name: nerve

value: nerve


title: RRBS data from noncancer esophagus musc tissue [GTEX-WZTO-1526-SM-L36OZ]

source_name: esophagus musc

value: esophagus musc


title: RRBS data from noncancer esophagus gast junc tissue [GTEX-WZTO-1726-SM-L36Q4]

source_name: esophagus gast junc

value: esophagus gast junc


title: K562, siYTHDC1 KD, RBFOX2, r1, b5, ChIP-seq


title: 600_AMlib6_IP_Pab1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: PAB1+DMSO rep1


title: 600_AMlib6_IP_Pab1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: PAB1+Auxin rep2


title: K562, siYTHDC1 KD, Input, r2, b5, ChIP-seq


title: RRBS data from noncancer skin tissue [GTEX-WZTO-0126-SM-L36P8]


title: RRBS data from noncancer muscle tissue [GTEX-WZTO-0826-SM-L36OB]

source_name: muscle

value: muscle


title: RRBS data from noncancer breast tissue [GTEX-U3ZN-1926-SM-L36QA]

value: breast


title: RRBS data from noncancer heart tissue [GTEX-VJWN-1026-SM-L36OJ]

source_name: heart

value: heart


title: 600_AMlib6_IP_Npl3_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: NPL3+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550


title: 600_AMlib6_IP_Pab1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: PAB1+Auxin rep1


title: RRBS data from noncancer skin tissue [GTEX-T5JC-0426-SM-L36QR]


title: RRBS data from noncancer fallopian tube tissue [GTEX-SE5C-0926-SM-L36PH]

source_name: fallopian tube

value: fallopian tube


title: K562, siRBM15 KD, RBFOX2, r2, b5, ChIP-seq

value: siRBM15 KD


title: K562, siYTHDC1 KD, RBM15, r1, b5, ChIP-seq


title: RRBS data from noncancer cervix uteri tissue [GTEX-S4UY-1426-SM-L36O9]

source_name: cervix uteri

value: cervix uteri


title: RRBS data from noncancer cervix uteri tissue [GTEX-S341-1126-SM-L36O8]


title: RRBS data from noncancer cervix uteri tissue [GTEX-TML8-0726-SM-L36Q7]


title: 600_AMlib6_IP_Npl3_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: NPL3+DMSO rep1


title: RRBS data from noncancer bladder tissue [GTEX-S4Q7-0926-SM-L36QE]

source_name: bladder

value: bladder


title: RRBS data from noncancer fallopian tube tissue [GTEX-S341-0826-SM-L36P3]


title: K562, siRBM15 KD, Input, r2, b5, ChIP-seq


title: K562, siRBM15 KD, RBFOX2, r1, b5, ChIP-seq


title: RRBS data from noncancer prostate tissue [GTEX-S33H-1826-SM-L36QQ]

source_name: prostate

value: prostate


title: RRBS data from noncancer adrenal gland tissue [GTEX-S33H-1326-SM-L36O6]

value: adrenal gland


title: 600_AMlib6_IP_ime4::URA__rep1

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3

value: SPO


title: K562, siRBM15 KD, Input, r1, b5, ChIP-seq

value: Human immortalized myelogenous leukemia cell line


title: RRBS data from noncancer fallopian tube tissue [GTEX-S32W-1326-SM-L36Q3]


title: RRBS data from noncancer testis tissue [GTEX-RWSA-2426-SM-L36QK]

value: testis


title: K562, siMETTL3 KD, RBFOX2, r2, b5, ChIP-seq

value: siMETTL3 KD

value: Rabbit polyclonal anti-RBFOX2; Proteintech; Cat#12498-1-AP


title: K562, siYTHDC1 KD, Input, r1, b5, ChIP-seq

value: siYTHDC1 KD


title: RRBS data from noncancer fallopian tube tissue [GTEX-OHPK-2326-SM-L36QV]


title: RRBS data from noncancer salivary gland tissue [GTEX-17MFQ-1626-SM-L36QN]

source_name: salivary gland

value: salivary gland


title: 600_AMlib6_IP_dyn2::NAT_clone2_rep2

description: dyn2delta B rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT


title: 600_AMlib6_IP_dyn2::NAT_clone2_rep1

description: dyn2delta B rep1


title: RRBS data from noncancer thyroid tissue [GTEX-RWSA-0826-SM-L36OU]

source_name: thyroid

value: thyroid


title: RRBS data from noncancer pancreas tissue [GTEX-17MF6-1426-SM-L36Q1]

source_name: pancreas

value: pancreas


title: 600_AMlib6_IP_Npl3_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: NPL3+Auxin rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550


title: K562, siMETTL3 KD, Input, r2, b5, ChIP-seq


title: K562, siMETTL3 KD, Input, r1, b5, ChIP-seq


title: RRBS data from noncancer vagina tissue [GTEX-15SHU-2926-SM-L36PK]

source_name: vagina

value: vagina


title: RRBS data from noncancer esophagus tissue [GTEX-17EVQ-1926-SM-L36OF]

value: esophagus


title: K562, siControl, RBM15, r2, b5, ChIP-seq

value: siControl

value: Rabbit polyclonal anti-RBM15; Proteintech; Cat#10587-1-AP


title: RRBS data from noncancer skin tissue [GTEX-16YQH-0126-SM-L36OO]

source_name: skin

value: skin


title: RRBS data from noncancer uterus tissue [GTEX-15ER7-2426-SM-L36N9]

source_name: uterus

value: uterus


title: 600_AMlib6_IP_dyn2::NAT_clone1_rep1

description: dyn2delta A rep1

value: SPO


title: 600_AMlib6_IP_dyn2::NAT_clone1_rep2

description: dyn2delta A rep2


title: RRBS data from noncancer esophagus tissue [GTEX-15ER7-2126-SM-L36NC]

source_name: esophagus


title: 600_AMlib6_IP_Npl3_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: NPL3+Auxin rep1


title: RRBS data from noncancer spleen tissue [GTEX-15DYW-1426-SM-L36OA]

source_name: spleen

value: spleen


title: 600_AMlib6_IP_966__rep

description: 966 m6A negative control

value: MATa ho::LYS2,lys2, ndt80::LEU2 ime4::HIS3, MATalpha lys2,ho::LYS2 ndt80::LEU2 ime4::HIS3


title: RRBS data from noncancer skin tissue [GTEX-14JG1-1526-SM-L36OD]


title: RRBS data from noncancer thyroid tissue [GTEX-14E7W-0926-SM-L36QT]


title: 600_AMlib6_IP_841__rep

description: 841 m6A positive control

value: MATa ho::LYS2,lys2, ndt80::LEU2, MATalpha lys2,ho::LYS2, ndt80::LEU2


title: K562, siControl, RBFOX2, r1, b5, ChIP-seq

value: Human immortalized myelogenous leukemia cell line

value: Rabbit polyclonal anti-RBFOX2; Proteintech; Cat#12498-1-AP


title: K562, siControl, RBM15, r1, b5, ChIP-seq


title: K562, siControl, RBFOX2, r2, b5, ChIP-seq


title: 600_AMlib6_Input_wildtype__rep1

description: WT

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: RRBS data from noncancer vagina tissue [GTEX-14BMU-1926-SM-L36NB]


title: RRBS data from noncancer testis tissue [GTEX-14E7W-0726-SM-L36QY]

source_name: testis

value: testis


title: K562, siMETTL3 KD, RBFOX2, r1, b5, ChIP-seq

value: siMETTL3 KD


title: RRBS data from noncancer esophagus tissue [GTEX-148VJ-1026-SM-L36PJ]


title: RRBS data from noncancer spleen tissue [GTEX-14BMU-0426-SM-L36OL]


title: K562, siControl, Input, r2, b5, ChIP-seq


title: 600_AMlib6_Input_untagged_pCUP_OsTIR_+DMSO_ctrl_rep2

description: untagged1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his:p550, MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his:p550


title: 600_AMlib6_Input_untagged_pCUP_OsTIR_+DMSO_ctrl_rep1

description: untagged1+DMSO rep1


title: RRBS data from noncancer adrenal gland tissue [GTEX-147F4-2526-SM-L36NY]

source_name: adrenal gland

value: adrenal gland


title: RRBS data from noncancer pancreas tissue [GTEX-13SLX-1326-SM-L36QX]

value: pancreas


title: K562, siControl, Input, r1, b5, ChIP-seq


title: 600_AMlib6_Input_untagged_pCUP_OsTIR_+CuSO4+Auxinrep2

description: untagged1+Auxin rep2


title: RRBS data from noncancer adrenal gland tissue [GTEX-13OW7-2726-SM-L36ND]


title: 600_AMlib6_Input_untagged_pCUP_OsTIR_+CuSO4+Auxinrep1

description: untagged1+Auxin rep1


title: RRBS data from noncancer salivary gland tissue [GTEX-13OVK-1826-SM-L36PF]

value: salivary gland


title: RRBS data from noncancer skin tissue [GTEX-13OVJ-0126-SM-L36O5]


title: NB4, RBFOX2 KD, IP, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0).
Mapped reads were separated by strands with samtools (version 1.9) and m6A peaks on each strand were called using MACS (version 2)
Significant peaks with q < 0.01 identified by MACS2 were considered.
Assembly: hg38
Supplementary files format and content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 for each sample.
Library strategy: MeRIP-Seq

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% HEPES and antibiotics in cellular incubator with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher). Ribosome RNA was depleted by RiboMinus™ Eukaryote Kit (ThermoFisher).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 (Takara) following the manufacturer's instructions.

treatment_protocol: Chromatin fraction was extracted before RNA isolation.

value: Human acute promyelocytic leukemia cell line

value: RBFOX2 KD

tag: m6a merip_antibody

value: EpiMark N6-Methyladenosine Enrichment Kit


title: NB4, RBFOX2 KD, IP, r3, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: RRBS data from noncancer pancreas tissue [GTEX-13FTX-1226-SM-L36OG]


title: 600_AMlib6_Input_Slz1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: SLZ1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Slz1-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Slz1-MiniAID::KAN his:p550


title: RRBS data from noncancer thyroid tissue [GTEX-13OVJ-0626-SM-L36NW]

value: thyroid


title: RRBS data from noncancer uterus tissue [GTEX-1313W-2826-SM-L36PP]

value: uterus


title: NB4, RBFOX2 KD, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: 600_AMlib6_Input_Slz1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: SLZ1+DMSO rep1

value: SPO


title: NB4, RBFOX2 KD, Input, r3, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: RRBS data from noncancer pancreas tissue [GTEX-13O1R-1826-SM-L36PE]


title: RRBS data from noncancer skin tissue [GTEX-12ZZX-2426-SM-L36QW]

value: skin


title: RRBS data from noncancer ovary tissue [GTEX-1313W-2726-SM-L36NE]

source_name: ovary

value: ovary


title: NB4, RBFOX2 KD, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: RRBS data from noncancer spleen tissue [GTEX-12WSK-0126-SM-L36OW]

value: spleen


title: 600_AMlib6_Input_Slz1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: SLZ1+Auxin rep2


title: RRBS data from noncancer pancreas tissue [GTEX-12WSD-1626-SM-L36OY]


title: RRBS data from noncancer testis tissue [GTEX-11ZUS-2726-SM-L36OK]


title: NB4, RBFOX2 KD, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: 600_AMlib6_Input_Slz1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: SLZ1+Auxin rep1


title: RRBS data from noncancer prostate tissue [GTEX-11ZUS-2126-SM-L36NS]

value: prostate


title: 600_AMlib6_Input_Pab1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: PAB1+DMSO rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Pab1-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Pab1-MiniAID::KAN his:p550


title: RRBS data from noncancer uterus tissue [GTEX-11ZTS-2326-SM-L36QS]


title: 600_AMlib6_Input_Pab1_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: PAB1+DMSO rep1


title: RRBS data from noncancer testis tissue [GTEX-11P82-1526-SM-L36NM]

value: testis


title: NB4, Control, IP, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

value: Control


title: RRBS data from noncancer uterus tissue [GTEX-11P81-1626-SM-L36OS]


title: RRBS data from noncancer salivary gland tissue [GTEX-11EQ9-2026-SM-L36NO]


title: NB4, Control, IP, r3, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: 600_AMlib6_Input_Pab1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: PAB1+Auxin rep2


title: RRBS data from noncancer thyroid tissue [GTEX-11EQ9-0626-SM-L36PZ]


title: RRBS data from noncancer ovary tissue [GTEX-11GSP-0226-SM-L36OR]


title: RRBS data from noncancer adrenal gland tissue [GTEX-11DXY-1626-SM-L36Q6]

value: adrenal gland


title: 600_AMlib6_Input_Pab1_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: PAB1+Auxin rep1


title: RRBS data from noncancer pancreas tissue [GTEX-11EQ9-1026-SM-L36PX]

value: pancreas


title: 600_AMlib6_Input_Npl3_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep1

description: NPL3+DMSO rep1

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG Npl3-MiniAID::KAN his:p550


title: NB4, Control, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

value: Human acute promyelocytic leukemia cell line


title: NB4, Control, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: NB4, Control, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: RRBS data from noncancer uterus tissue [GTEX-113JC-2226-SM-L36OI]


title: 600_AMlib6_Input_Npl3_v5_miniAID_pCUP_OsTIR_+DMSO_ctrl_rep2

description: NPL3+DMSO rep2


title: 600_AMlib6_Input_Npl3_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep2

description: NPL3+Auxin rep2


title: RRBS data from noncancer thyroid tissue [GTEX-111FC-1026-SM-L36N8]


title: RRBS data from noncancer liver tissue [GTEX-ZYT6-0626-SM-L36OT]

source_name: liver

value: liver


title: RRBS data from noncancer spleen tissue [GTEX-111FC-1326-SM-L36PD]


title: RRBS data from noncancer small intestine tissue [GTEX-111YS-1426-SM-L36OH]

source_name: small intestine

value: small intestine


title: RRBS data from noncancer testis tissue [GTEX-111FC-1926-SM-L36PB]


title: 600_AMlib6_Input_Npl3_v5_miniAID_pCUP_OsTIR_+CuSO4+Auxinrep1

description: NPL3+Auxin rep1


title: Ag+Te challenge - BT3

city: Calgary

first: Raymond

last: Turner

address: 447-Biological Sciences Building, 2500 University Dr. NW

country: Canada

institute: University of Calgary

data_processing:
For quantification of gene expression, RNA-seq reads were mapped using salmon v1.9.0 against the P. aeruginosa ATCC 27853 transcripts downloaded from NCBI RefSeq (GCF_001618925.1).
After mapping, salmon “quant” files were used to generate a gene-level expression matrix with tximport v1.22.0.
The expression matrix was finally used for the analysis of differentially expressed genes with DESeq2 v1.34.0 by setting the p-values cut-off for multiple testing adjustment to 0.01.
Genes were selected as differentially expressed based on an FDR (Benjamini-Hochberg correction, false discovery rate) of < 0.05 and |log2 fold-change| > 1.0.
Assembly: P. aeruginosa ATCC 27853 from NCBI RefSeq (GCF_001618925.1)
Supplementary files format and content: tab-delimited text file (counts.txt) includes gene-level raw counts of all the samples

organism: Pseudomonas aeruginosa

source_name: Mid-log phase culture exposed to silver nitrate at 0.125 mM potassium tellurite at 0.25 mM for two hours

growth_protocol: Pseudomonas aeruginosa ATCC 27853 were cultured in 3mL of SWF and were incubated at 37 ºC for ~ 2 h in a shaker incubator (150 rpm) to reach the OD600 of 0.08.

extract_protocol:
1ml of samples were centrifuged at 3,500 X g for 10 min to pellet the cells. The cell density here was 1.5 X 108CFU/ml bacteria. Zirconia beads were used for cell lysis for at least 2 min using a bead beater instrument. The total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit (Invitrogen, USA) according to the manufacturer's recommendations.
To ensure that the DNA was completely removed, residual DNA was removed with DNase (Sigma-Aldrich Inc, St Louis, MO, USA) to get a pure RNA sample. Libraries were prepared using the New England Biolabs NEBNext rRNA depletion bacteria kit and NEBNext Ultra II Directional RNA library prep kit for Illumina, according to the manufacturer's instructions.

treatment_protocol: Cultures were treated with inhibitory concentrations of metal antibacterials along with the control group (treated with PBS instead), and incubated at 37 ºC for 2 h in a shaker incubator (150 rpm).

value: WT

value: Ag+Te challenge

value: bacterial cell


title: Ag+Te challenge - BT2


title: RRBS data from noncancer stom tissue [GTEX-ZVT3-2126-SM-L36QF]

source_name: stom

value: stom


title: RRBS data from noncancer colon tissue [GTEX-ZAB4-2426-SM-L3713]

source_name: colon

value: colon


title: 600_AMlib6_Input_dyn2::NAT_clone2_rep2

description: dyn2delta B rep2

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT

value: SPO


title: Ag+Te challenge - BT1


title: NB4, Control, Input, r3, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: RRBS data from noncancer small intestine tissue [GTEX-1192X-2526-SM-L36PQ]


title: RRBS data from noncancer liver tissue [GTEX-YFC4-1526-SM-L36P4]


title: RRBS data from noncancer lung tissue [GTEX-YFC4-1126-SM-L3766]

source_name: lung

value: lung


title: 600_AMlib6_Input_dyn2::NAT_clone2_rep1

description: dyn2delta B rep1


title: 600_AMlib6_Input_ime4::URA__rep1

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3


title: RRBS data from noncancer lung tissue [GTEX-Y111-1026-SM-L36RM]


title: RRBS data from noncancer stom tissue [GTEX-WZTO-2126-SM-L36X8]


title: Te challenge - BT3

source_name: Mid-log phase culture exposed to potassium tellurite at 0.25 mM for two hours

value: Te challenge


title: Te challenge - BT2


title: RRBS data from noncancer lung tissue [GTEX-WZTO-0426-SM-L36WD]


title: Te challenge - BT1


title: 600_AMlib6_Input_dyn2::NAT_clone1_rep2

description: dyn2delta A rep2


title: 600_AMlib6_Input_dyn2::NAT_clone1_rep1

description: dyn2delta A rep1


title: RRBS data from noncancer lung tissue [GTEX-RWSA-1126-SM-L375O]


title: 600_AMlib6_Input_966__rep

description: 966 m6A negative control

value: MATa ho::LYS2,lys2, ndt80::LEU2 ime4::HIS3, MATalpha lys2,ho::LYS2 ndt80::LEU2 ime4::HIS3


title: RRBS data from noncancer stom tissue [GTEX-T5JC-1926-SM-L36O4]


title: RRBS data from noncancer lung tissue [GTEX-RNOR-0726-SM-L36SP]


title: RRBS data from noncancer liver tissue [GTEX-O5YT-0826-SM-L374D]


title: RRBS data from noncancer colon tissue [GTEX-1BAJH-2326-SM-L36TR]


title: 600_AMlib6_Input_841__rep

description: 841 m6A positive control

value: MATa ho::LYS2,lys2, ndt80::LEU2, MATalpha lys2,ho::LYS2, ndt80::LEU2


title: Ag challenge - BT1

source_name: Mid-log phase culture exposed to silver nitrate at 0.125 mM for two hours

value: Ag challenge


title: RRBS data from noncancer stom tissue [GTEX-1A8G6-1426-SM-L36S9]


title: RRBS data from noncancer colon tissue [GTEX-183WM-2526-SM-L3723]


title: Ag challenge - BT2


title: RRBS data from noncancer stom tissue [GTEX-18A7A-2726-SM-L36PN]


title: PBS control - BT3

source_name: Mid-log phase culture treated with PBS instead of metal exposure

value: PBS control


title: RRBS data from noncancer stom tissue [GTEX-17MF6-2126-SM-L373R]


title: RRBS data from noncancer colon tissue [GTEX-17MF6-2426-SM-L375G]


title: B_strain_9307_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_6_D

data_processing:
Internal barcode demultiplexing with inhouse pythong script according to Read2 position1-6 (raw data supplied here is after this step and only includes Read1 data)
alignment of R1 only using STAR/2.5.3a  with added options of (--outSAMtype BAM Unsorted, --alignIntronMax 500 ,--alignEndsType Local , --outBAMsortingBinsN 300 , --limitBAMsortRAM 1254135158)
deduplication using UMI-tools 1.0.1
reads to 3' gene ends (attached Ensinck_TableS7_Transcript3End.BED) allocation  and coverage summary using txtools/0.0.7.4
m6A levels quantified using in house R-script(see paper)
Samples with more than two standard deviations below the mean mapped reads per sample, or with low gene coverage (below 5000 genes mapped) were not included in the analysis (this excluded 3 samples)
Assembly: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary files format and content: data table of un-normalized gene read counts for each sample according to title collumn

extract_protocol:
RNA extraction was performed from yeast pellets using Acid Phenol:Chloroform pH 4.5 and Tris-EDTA-SDS (TES) buffer (0.01 M Tris-HCl pH 7.5, 0.01 M EDTA, 0.5% w/v SDS). Samples were further treated with rDNase (cat no 740.963, Macherey-Nagel) and column purified (cat no 740.948, Macherey-Nagel).
RNA levels were quantified by sequencing 3’ RNA ends as previously described {Chapal, 2019 #326}. Briefly, RNA was reverse transcribed using oligo dT primers coupled with internal barcodes (Table S6). RNA-DNA hybrids were then pooled and tagmented using Tn5, adding adaptors to their 5’ end, followed by PCR amplification of the fragments, inserting Illumina barcodes and adaptors. A total of four biological replicates were sequenced for each mutant-timepoint combination, two of each were processed in each of two pools.
RNA-tagmentationSeq

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN

value: SPO medium


title: B_strain_9307_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_8_D


title: B_strain_9307_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_8_C


title: PBS control - BT2


title: PBS control - BT1


title: RRBS data from noncancer liver tissue [GTEX-17F96-1226-SM-L3767]

value: liver


title: RRBS data from noncancer lung tissue [GTEX-T5JC-0826-SM-L36WU]


title: Ag challenge - BT3

value: WT


title: RRBS data from noncancer stom tissue [GTEX-17HII-2426-SM-L36UT]


title: B_strain_9307_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_6_C


title: RRBS data from noncancer colon tissue [GTEX-17EVQ-1826-SM-L36PT]


title: RRBS data from noncancer lung tissue [GTEX-17EVQ-1526-SM-L36NU]


title: B_strain_9307_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_4_D


title: RRBS data from noncancer colon tissue [GTEX-15UF6-2726-SM-L3742]


title: B_strain_9307_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_4_C


title: RRBS data from noncancer colon tissue [GTEX-15RJE-2226-SM-L36UD]


title: leyomyoma [US0031]

type: RNA

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: gender

value: Female


title: leyomyoma [US0032]


title: RRBS data from noncancer lung tissue [GTEX-15ER7-0926-SM-L36WB]


title: RRBS data from noncancer colon tissue [GTEX-15ER7-2826-SM-L36Z5]


title: RRBS data from noncancer lung tissue [GTEX-14E7W-1326-SM-L36OP]


title: RRBS data from noncancer colon tissue [GTEX-14PK6-1726-SM-L36XI]


title: RRBS data from noncancer stom tissue [GTEX-15G19-1526-SM-L36V3]


title: RRBS data from noncancer colon tissue [GTEX-14JG6-1726-SM-L375H]


title: B_strain_9307_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_0_D


title: B_strain_9307_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_2_D


title: B_strain_9307_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_0_C


title: RRBS data from noncancer colon tissue [GTEX-14BMV-2426-SM-L36NA]


title: B_strain_9307_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_9307_2_C


title: RRBS data from noncancer colon tissue [GTEX-14E6E-1526-SM-L36RT]


title: B_strain_6505_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_8_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG slz1::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG slz1::NAT


title: RRBS data from noncancer colon tissue [GTEX-14ICL-1226-SM-L36TL]


title: RRBS data from noncancer colon tissue [GTEX-14BIN-3026-SM-L36UJ]


title: RRBS data from noncancer stom tissue [GTEX-14BMV-2226-SM-L36RX]

value: stom


title: B_strain_6505_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_8_C


title: RRBS data from noncancer colon tissue [GTEX-14C39-1926-SM-L36W5]

value: colon


title: RRBS data from noncancer colon tissue [GTEX-15SHU-2526-SM-L36QG]


title: leyomyoma [US0030]


title: leyomyoma [US0027]


title: leyomyoma [US0026]


title: leyomyoma [US0028]


title: leyomyoma [US0025]


title: RRBS data from noncancer stom tissue [GTEX-145MN-1326-SM-L36UX]


title: STUMP [US0024]


title: RRBS data from noncancer colon tissue [GTEX-145MH-2726-SM-L373J]


title: RRBS data from noncancer lung tissue [GTEX-145MH-0626-SM-L36P9]


title: B_strain_6505_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_4_D


title: RRBS data from noncancer colon tissue [GTEX-13SLW-2826-SM-L373O]


title: RRBS data from noncancer lung tissue [GTEX-13SLW-1226-SM-L371Y]


title: RRBS data from noncancer colon tissue [GTEX-13OW6-2126-SM-L36T4]


title: B_strain_6505_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_6_C


title: RRBS data from noncancer colon tissue [GTEX-139D8-2926-SM-L36UL]


title: B_strain_6505_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_2_D


title: RRBS data from noncancer colon tissue [GTEX-147GR-2726-SM-L36VO]


title: RRBS data from noncancer stom tissue [GTEX-139D8-2326-SM-L372Z]


title: RRBS data from noncancer colon tissue [GTEX-13OVJ-1826-SM-L371X]


title: RRBS data from noncancer colon tissue [GTEX-132NY-2726-SM-L374L]


title: B_strain_6505_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_6_D


title: RRBS data from noncancer liver tissue [GTEX-13OVJ-1026-SM-L36R6]


title: RRBS data from noncancer lung tissue [GTEX-132NY-1226-SM-L372I]


title: B_strain_6505_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_2_C


title: RRBS data from noncancer colon tissue [GTEX-12ZZZ-2426-SM-L371S]


title: leyomyoma [US0029]


title: RRBS data from noncancer lung tissue [GTEX-12WSE-0826-SM-L36O1]


title: B_strain_6505_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_0_C


title: ESS [US0023]


title: leyomyoma [US0021]


title: RRBS data from noncancer liver tissue [GTEX-12WSD-1426-SM-L372H]


title: Adenosarcoma [US0020]


title: leyomyoma [US0019]


title: Leiomyosarcoma [US0022]


title: B_strain_6505_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_4_C


title: Leiomyoma with bizarre nuclei [US0018]


title: RRBS data from noncancer lung tissue [GTEX-12WSD-0826-SM-L374Z]


title: ESS [US0017]


title: RRBS data from noncancer liver tissue [GTEX-11ZVC-0726-SM-L36UW]


title: B_strain_1511_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_8_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: RRBS data from noncancer lung tissue [GTEX-11ZUS-0126-SM-L36VV]


title: leyomyoma [US0015]


title: RRBS data from noncancer liver tissue [GTEX-11ZUS-2526-SM-L371K]


title: Leiomyosarcoma [US0014]


title: RRBS data from noncancer colon tissue [GTEX-11TT1-0926-SM-L36PA]


title: B_strain_1511_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_6_D


title: B_strain_1511_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_6_C


title: RRBS data from noncancer colon tissue [GTEX-11P82-1026-SM-L3744]


title: B_strain_6505_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_6505_0_D


title: RRBS data from noncancer stom tissue [GTEX-11P82-0726-SM-L3755]


title: RRBS data from noncancer colon tissue [GTEX-11P7K-1826-SM-L36ZZ]


title: leyomyoma [US0012]


title: leyomyoma [US0013]


title: B_strain_1511_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_4_D


title: RRBS data from noncancer stom tissue [GTEX-11EQ9-1226-SM-L36OE]


title: RRBS data from noncancer liver tissue [GTEX-11EQ9-0526-SM-L373L]


title: B_strain_1511_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_4_C


title: B_strain_1511_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_2_D


title: Leiomyosarcoma [US0010]


title: RRBS data from noncancer colon tissue [GTEX-11EM3-1626-SM-L371G]


title: RRBS data from noncancer stom tissue [GTEX-11EM3-1026-SM-L36VA]


title: B_strain_1511_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_8_C


title: RRBS data from noncancer liver tissue [GTEX-11TT1-1726-SM-L3712]


title: B_strain_1511_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_2_C


title: RRBS data from noncancer colon tissue [GTEX-117XS-2226-SM-L36NV]


title: Leiomyosarcoma [US0009]


title: Leiomyosarcoma [US0007]


title: B_strain_1511_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_1511_0_C


title: RRBS data from noncancer skin tissue [GTEX-ZVTK-0226-SM-L36YD]

source_name: skin

value: skin


title: RRBS data from noncancer uterus tissue [GTEX-YFC4-2826-SM-L36VD]

source_name: uterus

value: uterus


title: RRBS data from noncancer liver tissue [GTEX-11NUK-1226-SM-L36UG]


title: RRBS data from noncancer esophagus muscularis tissue [GTEX-Y111-1726-SM-L36Z4]

source_name: esophagus muscularis

value: esophagus muscularis


title: RRBS data from noncancer skin exposed tissue [GTEX-Y111-0126-SM-L36V5]

source_name: skin exposed

value: skin exposed


title: leyomyoma [US0005]


title: RRBS data from noncancer lung tissue [GTEX-11EQ9-0226-SM-L36RD]

value: lung


title: RRBS data from noncancer blood vessel tissue [GTEX-XUZC-0626-SM-L3733]

source_name: blood vessel

value: blood vessel


title: Uterine tumor resembling ovarian sex-cord tumor  [US0004]


title: RRBS data from noncancer pituitary tissue [GTEX-WZTO-3026-SM-L36W3]

source_name: pituitary

value: pituitary


title: B_strain_10734_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_6_C

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG KAR4::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG kar4::NAT


title: RRBS data from noncancer esophagus tissue [GTEX-U8XE-1326-SM-L36V2]

source_name: esophagus

value: esophagus


title: B_strain_10734_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_4_D

value: SPO medium


title: leyomyoma [US0008]


title: RRBS data from noncancer thyroid tissue [GTEX-ZVZQ-0626-SM-L36UY]

source_name: thyroid

value: thyroid


title: Adenosarcoma [US0002]


title: RRBS data from noncancer nerve tissue [GTEX-U8XE-0526-SM-L36XZ]

source_name: nerve

value: nerve


title: Cellular leiomyoma [US0003]

value: Female


title: leyomyoma [US0006]


title: B_strain_10734_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_4_C


title: Jejunum epithelial cells, Prkci flox/flox VillinCRE, rep 3 [867]

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
Raw sequence data was processed by the on-instrument Real Time Analysis software (v.2.4.11) to basecall files.
Basecall files were converted to de-multiplexed FASTQ files with the Illumina supplied scripts in the BCL2FASTQ software (v2.17).
The quality of reads was determined with the FASTQC software to evaluate per base sequence quality, duplication rates, and overrepresented k-mers.
Illumina adapters were trimmed from the ends of the reads using the Trim Galore! Package.
Reads were aligned to the mouse reference genome (mm10) with the STAR aligner (v2.5.0a).
Gene count quantification was performed using the GeneCounts function within STAR against the GENCODE vM25 mouse transcript .gtf file.
Assembly: mm10
Supplementary files format and content: Processed file is a tab delimited matrix file with the first column representing the Ensembl gene name, second column the official gene symbol, third column the chromosomal location of the gene in mm10, and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: Epithelial

growth_protocol: Animals were co-housed in regular environment and euthanized when 3 - 4 months old. All animals were genotyped by tail biopsy.

extract_protocol:
Total RNA was extracted using 1 mL TRIzol® Reagent, separation in chloroform phenol, DNAse treatment and Poly-A selection
KAPA rna HyperPrep with RiboErase HMR

treatment_protocol: Epithelial cells were harvested after euthanasia and purified by multiple cycles of washing in 0 mM glucose, 30 mM EDTA, 5 mM DTT and mild centrifugation. Mesenchymal contamination was monitored by WB using keratin/vimenting ratio.

value: Epithelial

value: genetic modification

value: enterocyte

value: Prkci flox/flox Villin-CRE


title: RRBS data from noncancer blood vessel coronary tissue [GTEX-U3ZN-0426-SM-L36U5]

source_name: blood vessel coronary

value: blood vessel coronary


title: RRBS data from noncancer breast tissue [GTEX-T5JC-2126-SM-L36YE]

source_name: breast

value: breast


title: RRBS data from noncancer liver tissue [GTEX-11DXY-0526-SM-L372W]

source_name: liver

value: liver


title: RRBS data from noncancer vagina tissue [GTEX-U3ZN-0926-SM-L36UI]

source_name: vagina

value: vagina


title: B_strain_10734_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_8_D


title: B_strain_10734_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_2_D


title: B_strain_10734_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_8_C


title: RRBS data from noncancer vagina tissue [GTEX-T2IS-1926-SM-L36WT]


title: RRBS data from noncancer adrenal gland tissue [GTEX-XQ3S-1726-SM-L36XA]

source_name: adrenal gland

value: adrenal gland


title: RRBS data from noncancer bladder tissue [GTEX-SNOS-0526-SM-L36UQ]

source_name: bladder

value: bladder


title: B_strain_10734_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_6_D


title: RRBS data from noncancer cervix uteri endocervix tissue [GTEX-S341-1326-SM-L36WA]

source_name: cervix uteri endocervix

value: cervix uteri endocervix


title: Jejunum epithelial cells, Prkci flox/flox VillinCRE, rep 1 [826]


title: RRBS data from noncancer testis tissue [GTEX-WK11-0326-SM-L36WX]

source_name: testis

value: testis


title: B_strain_10734_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_2_C

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG KAR4::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG kar4::NAT


title: Jejunum epithelial cells, Prkci flox/flox, rep 3 [794]

value: Prkci flox/flox


title: RRBS data from noncancer esophagus tissue [GTEX-S33H-0826-SM-L36VM]

value: esophagus


title: RRBS data from noncancer nerve tissue [GTEX-1EWIQ-0426-SM-L36XX]

value: nerve


title: RRBS data from noncancer adipose tissue [GTEX-1BAJH-0426-SM-L36XS]

source_name: adipose tissue

value: adipose tissue


title: B_strain_10734_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_0_C

value: SPO medium


title: Jejunum epithelial cells, Prkci flox/flox VillinCRE, rep 2 [861]

value: Epithelial

value: genetic modification


title: Jejunum epithelial cells, Prkci flox/flox, rep1 [784]

value: enterocyte


title: RRBS data from noncancer heart tissue [GTEX-1E1VI-1426-SM-L36YG]

source_name: heart

value: heart


title: Jejunum epithelial cells, Prkci flox/flox, rep 2 [787]


title: B_strain_10443_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_8_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT


title: RRBS data from noncancer pituitary tissue [GTEX-16YQH-3126-SM-L36VP]

value: pituitary


title: leyomyoma [US0001]

source_name: Serum

value: Female


title: RRBS data from noncancer breast tissue [GTEX-15ER7-1626-SM-L36VY]

value: breast


title: RRBS data from noncancer vagina tissue [GTEX-15ER7-2526-SM-L36VI]

value: vagina


title: RRBS data from noncancer pancreas tissue [GTEX-15ER7-1326-SM-L36WW]

source_name: pancreas

value: pancreas


title: B_strain_10443_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_8_C


title: B_strain_10443_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_6_D


title: RRBS data from noncancer vagina tissue [GTEX-14PJM-2926-SM-L36Y8]


title: RRBS data from noncancer heart atrial tissue [GTEX-14E7W-1126-SM-L36YR]

source_name: heart atrial

value: heart atrial


title: Young, scRNAseq

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The reads were mapped to the mouse mm10 genome and analyzed using STAR: >90% reads mapped confidently to genomic regions and >50% mapped to exonic regions.
Cell Ranger 2.1.0 was employed to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. >80,000 mean reads and 900 median genes per cell were obtained.
The UMI (unique molecular identifier) counts were used to quantify the gene expression levels and the t-SNE algorithm was used for dimensionality reduction.
The Log2FoldChange was the ratio of gene expression of one cluster to that of all other cells. The p-value was calculated using the negative binomial test and the false discovery rate was determined by Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: “cloupe” files include UMI values for each sample.

source_name: bone marrow

extract_protocol:
CD133+ cells isolated from murine bone marrow by FACS (>90% viability) were used for single-cell RNA sequencing.  The cDNAs were quantified using an Agilent Bioanalyzer 2100 DNA Chip, and the library was sequenced using an Illumina Hiseq PE150 with ~10-30M raw data assigned for each cell.
A sequence library was built according to the Chromium Single Cell Instrument library protocol (49). Briefly, single-cell RNAs were barcoded and reverse-transcribed using the Chromium™ Single Cell 3’ Reagent Kits v2 (10 × Genomics), then fragmented and amplified to generate cDNAs.

value: bone marrow

tag: age


title: Ctrl, scRNAseq

description: 10x Genomics


title: Old, scRNAseq

description: 10x Genomics


title: RRBS data from noncancer kidney tissue [GTEX-14C39-2126-SM-L36VG]

source_name: kidney

value: kidney


title: RRBS data from noncancer small intestine tissue [GTEX-148VJ-2226-SM-L36V9]

source_name: small intestine

value: small intestine


title: B_strain_10443_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_6_C


title: B_strain_10443_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_4_D


title: RRBS data from noncancer skin tissue [GTEX-145MH-2826-SM-L36UO]

source_name: skin

value: skin


title: B_strain_10734_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10734_0_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG KAR4::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG kar4::NAT


title: RNA_550_r2_POLE4-KO_exp

data_processing:
Sequences were trimmed for adapters and adapting filtering for low quality reads was performed with trimmomatic (version 0.39) with default parameters. Mapping (mm10) was performed with STAR (version 2.7.1a) using GENCODE (version M24) annotations with parameters --twopassMode Basic --twopass1readsN -1 --alignSJDBoverhangMin 10 and multimapping parameters -winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for further repeats quantification
Gene level quantification was obtained from processed bam files using the featureCounts function in the Rsubread (version 2.0) R package and repeat subfamilies were quantified using the tool TEcount (version 2.1.3) ), using the provided curated repeat annotations for mm10 (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/).
Differential expression analysis of gene level and repeat subfamily level was performed with DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_Pole4_gene_and_repeat_counts.txt: Tab-separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts mm10 repeat ids).

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA.

extract_protocol:
RNA was extracted from 5*10^6 cells using RNeasy Plus Mini Kit (Qiagen) and DNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen). RNA was treated with the NEBNext rRNA Depletion kit (NEB #E6310) and strand-specific RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420).
NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420) following the manufacturer's protocol.


title: RRBS data from noncancer blood vessel tissue [GTEX-13X6J-1326-SM-L36YZ]

source_name: blood vessel

value: blood vessel


title: RRBS data from noncancer spleen tissue [GTEX-16XZY-0126-SM-L36U7]

source_name: spleen

value: spleen


title: RRBS data from noncancer blood vessel tissue [GTEX-13PLJ-0526-SM-L371C]


title: RRBS data from noncancer blood vessel tissue [GTEX-13OW8-1626-SM-L36UA]


title: B_strain_10443_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_2_D

value: SPO medium


title: RRBS data from noncancer kidney tissue [GTEX-13OVL-1826-SM-L36UB]


title: RRBS data from noncancer adipose tissue [GTEX-13OVJ-0326-SM-L36Y5]

value: adipose tissue


title: B_strain_10443_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_4_C


title: RNA_550_r1_POLE4-KO_exp


title: B_strain_10443_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_2_C


title: RNA_552_r3_POLE4-KO_exp


title: RNA_552_r2_POLE4-KO_exp


title: B_strain_10443_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_0_D


title: RRBS data from noncancer esophagus tissue [GTEX-13NYB-0826-SM-L36YS]

source_name: esophagus

value: esophagus


title: RRBS data from noncancer ovary tissue [GTEX-139D8-2426-SM-L36VW]

source_name: ovary

value: ovary


title: RNA_552_r1_POLE4-KO_exp


title: RRBS data from noncancer adipose tissue [GTEX-139D8-1626-SM-L36V1]


title: RRBS data from noncancer prostate tissue [GTEX-132NY-2826-SM-L36UM]

source_name: prostate

value: prostate


title: RRBS data from noncancer heart tissue [GTEX-131XH-0226-SM-L36YM]

value: heart


title: RRBS data from noncancer heart tissue [GTEX-1313W-1426-SM-L36YV]


title: RNA_551_r3_POLE4-KO_exp


title: RRBS data from noncancer muscle tissue [GTEX-1313W-0526-SM-L36Z6]

source_name: muscle

value: muscle


title: RRBS data from noncancer spleen tissue [GTEX-12WSD-1726-SM-L36UK]


title: RNA_551_r2_POLE4-KO_exp


title: B_strain_10443_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10443_0_C

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT


title: RNA_550_r3_POLE4-KO_exp


title: RNA_551_r1_POLE4-KO_exp


title: RRBS data from noncancer blood vessel tissue [GTEX-11UD2-0826-SM-L36ZL]


title: B_strain_10427_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_6_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG mum2::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG mum2::KAN


title: B_strain_10427_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_8_C


title: RRBS data from noncancer esophagus muscularis tissue [GTEX-11P82-0626-SM-L3715]

source_name: esophagus muscularis

value: esophagus muscularis


title: B_strain_10427_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_8_D


title: RNA_410_r3_POLE4-KO_exp

value: wildtype


title: RRBS data from noncancer heart tissue [GTEX-11TUW-1026-SM-L36UF]


title: RRBS data from noncancer esophagus gast junc tissue [GTEX-11P82-0426-SM-L36YY]

source_name: esophagus gast junc

value: esophagus gast junc


title: RNA_410_r2_POLE4-KO_exp


title: B_strain_10427_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_6_C


title: RRBS data from noncancer esophagus tissue [GTEX-11NUK-1326-SM-L36VB]


title: RRBS data from noncancer breast tissue [GTEX-13SLW-2526-SM-L36UE]

source_name: breast

value: breast


title: RRBS data from noncancer salivary gland tissue [GTEX-11WQK-2926-SM-L36U9]

source_name: salivary gland

value: salivary gland


title: RRBS data from noncancer muscle tissue [GTEX-11GSP-2726-SM-L36Y1]


title: B_strain_10427_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_4_D


title: RNA_410_r1_POLE4-KO_exp


title: RRBS data from noncancer heart tissue [GTEX-11GS4-0426-SM-L36YA]

source_name: heart


title: RRBS data from noncancer small intestine tissue [GTEX-11EQ9-1326-SM-L36VN]

value: small intestine


title: RRBS data from noncancer adipose tissue [GTEX-11EMC-2826-SM-L36Y4]

source_name: adipose tissue


title: SCAR_588_stranded_input_T0_rescue_exp_r2

description: EdU-labelled genomic DNA

data_processing:
Library strategy: SCAR-seq
adapters and low quality reads were filtered with cutadapt version 2.5
reads were mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Genome_build: mm10
Supplementary_files_format_and_content: SCAR-seq Partition scores in bigwig format

extract_protocol: Native SCAR-seq: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced. Crosslinked SCAR-seq: Cells were crosslinked with formaldehyde for 10 min. Nuclei were isolated and chromatin was solubilized using a Covaris sonicator. See methods for more details.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10, 15 or 30 min (see data S1 for details) and then either collected (T0) or cultured for indicated maturation intervals (T1; T3; T8) in media without EdU before collection.


title: B_strain_10427_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_2_D


title: RRBS data from noncancer blood vessel tissue [GTEX-ZYT6-1526-SM-L375F]

value: blood vessel


title: SCAR_442_stranded_input_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer nerve tissue [GTEX-111FC-0526-SM-L36U8]

source_name: nerve

value: nerve


title: SCAR_410_stranded_input_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer muscle tissue [GTEX-ZWKS-0326-SM-L375I]


title: B_strain_10427_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_2_C

value: SPO medium


title: B_strain_10427_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_0_D


title: RRBS data from noncancer pancreas tissue [GTEX-ZAB4-1726-SM-L373V]

source_name: pancreas

value: pancreas


title: RRBS data from noncancer vagina tissue [GTEX-YFC4-2926-SM-L374R]

source_name: vagina

value: vagina


title: SCAR_588_stranded_input_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer breast tissue [GTEX-YFC4-1426-SM-L373T]


title: RRBS data from noncancer adipose tissue [GTEX-Y111-0226-SM-L3746]

value: adipose tissue


title: RRBS data from noncancer heart tissue [GTEX-WZTO-1226-SM-L375T]


title: B_strain_10427_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_0_C


title: SCAR_410_stranded_input_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer heart tissue [GTEX-U3ZN-1426-SM-L375C]


title: RRBS data from noncancer adipose tissue [GTEX-TKQ1-1126-SM-L375D]


title: SCAR_442_stranded_input_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: B_strain_10427_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10427_4_C


title: B_strain_10296_8_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_8_D

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4::KAN


title: SCAR_588_H4K20me0_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer kidney tissue [GTEX-T5JC-1526-SM-L36VS]

source_name: kidney

value: kidney


title: B_strain_10296_8_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_8_C


title: RRBS data from noncancer cervix uteri tissue [GTEX-S32W-1626-SM-L3763]

source_name: cervix uteri

value: cervix uteri


title: SCAR_588_H3K27me3_T0_rescue_exp_r2

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells


title: RRBS data from noncancer bladder tissue [GTEX-SE5C-1026-SM-L3765]

source_name: bladder

value: bladder


title: B_strain_10296_6_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_6_D


title: RRBS data from noncancer cervix uteri tissue [GTEX-S32W-1526-SM-L373U]


title: SCAR_442_H4K20me0_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer esophagus tissue [GTEX-1EWIQ-1526-SM-L3743]

source_name: esophagus

value: esophagus


title: RRBS data from noncancer small intestine tissue [GTEX-1BAJH-2526-SM-L371N]

source_name: small intestine


title: RRBS data from noncancer kidney tissue [GTEX-1BAJH-1826-SM-L373Y]


title: B_strain_10296_4_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_4_D


title: SCAR_442_H3K27me3_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: B_strain_10296_4_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_4_C


title: RRBS data from noncancer blood vessel tissue [GTEX-18A7A-0526-SM-L374T]

source_name: blood vessel


title: RRBS data from noncancer blood vessel tissue [GTEX-17HII-1126-SM-L375N]


title: SCAR_410_H4K20me0_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: B_strain_10296_2_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_2_D


title: RRBS data from noncancer vagina tissue [GTEX-17F9Y-2326-SM-L374A]


title: RRBS data from noncancer blood vessel tissue [GTEX-17F9Y-1426-SM-L3764]


title: RRBS data from noncancer pituitary tissue [GTEX-17EVQ-2926-SM-L371J]

source_name: pituitary

value: pituitary


title: RRBS data from noncancer muscle tissue [GTEX-17EVQ-1226-SM-L374G]

source_name: muscle

value: muscle


title: RRBS data from noncancer blood vessel tissue [GTEX-17EVQ-1126-SM-L374U]


title: SCAR_588_H4K20me0_T0_rescue_exp_r1

description: EdU-labelled genomic DNA

value: wildtype


title: B_strain_10296_2_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_2_C


title: B_strain_10296_0_D

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_0_D


title: RRBS data from noncancer esophagus tissue [GTEX-15D1Q-1526-SM-L375P]


title: SCAR_410_H3K27me3_T0_rescue_exp_r2

description: EdU-labelled genomic DNA


title: B_strain_10296_6_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_6_C


title: RRBS data from noncancer vagina tissue [GTEX-15UF6-2126-SM-L371T]


title: B_strain_10296_0_C

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_B_strain_10296_0_C


title: A_strain_9307_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_8_B

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN


title: RRBS data from noncancer spleen tissue [GTEX-15CHQ-1226-SM-L3718]

source_name: spleen

value: spleen


title: RRBS data from noncancer ovary tissue [GTEX-14JG6-0626-SM-L36X4]

source_name: ovary

value: ovary


title: RRBS data from noncancer small intestine tissue [GTEX-14PJN-0826-SM-L371Q]

value: small intestine


title: SCAR_442_H3K27me3_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: SCAR_442_H4K20me0_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer skin tissue [GTEX-14C39-1726-SM-L375J]

source_name: skin

value: skin


title: SCAR_410_H4K20me0_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: A_strain_9307_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_6_B

value: SPO medium


title: A_strain_9307_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_8_A


title: RRBS data from noncancer adipose tissue [GTEX-14BMV-1626-SM-L375L]


title: RRBS data from noncancer pituitary tissue [GTEX-145MH-3126-SM-L372B]


title: SCAR_410_H3K27me3_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: SCAR_588_H3K27me3_T0_rescue_exp_r1

description: EdU-labelled genomic DNA


title: SCAR_552_stranded_input_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA

value: Pole4 KO


title: RRBS data from noncancer nerve tissue [GTEX-145MH-1426-SM-L375B]

value: nerve


title: A_strain_9307_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_6_A


title: A_strain_9307_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_4_B


title: RRBS data from noncancer breast tissue [GTEX-13SLX-2326-SM-L3754]

source_name: breast

value: breast


title: RRBS data from noncancer heart tissue [GTEX-13VXT-1126-SM-L374X]

source_name: heart

value: heart


title: RRBS data from noncancer nerve tissue [GTEX-13S7M-0426-SM-L375Y]

source_name: nerve


title: SCAR_410_stranded_input_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-13OW6-2426-SM-L36Y7]

source_name: adipose tissue

value: adipose tissue


title: A_strain_9307_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_2_B


title: RRBS data from noncancer testis tissue [GTEX-145MH-2326-SM-L3752]

source_name: testis

value: testis


title: RRBS data from noncancer heart tissue [GTEX-14E7W-1226-SM-L3753]


title: RRBS data from noncancer adrenal gland tissue [GTEX-132NY-2226-SM-L372O]

source_name: adrenal gland

value: adrenal gland


title: SCAR_552_stranded_input_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: SCAR_551_stranded_input_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer esophagus tissue [GTEX-13OVL-1926-SM-L374J]

value: esophagus


title: A_strain_9307_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_0_B


title: RRBS data from noncancer nerve tissue [GTEX-132NY-0526-SM-L3761]


title: RRBS data from noncancer thyroid tissue [GTEX-145MH-0426-SM-L373M]

source_name: thyroid

value: thyroid


title: A_strain_9307_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_4_A


title: A_strain_9307_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_0_A


title: SCAR_410_stranded_input_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells


title: RRBS data from noncancer heart tissue [GTEX-1212Z-0626-SM-L375X]


title: RRBS data from noncancer esophagus tissue [GTEX-12WSD-1926-SM-L375S]


title: SCAR_552_H4K20me0_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-12ZZX-0226-SM-L374M]


title: A_strain_6505_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_8_B

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG slz1::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG slz1::NAT


title: RRBS data from noncancer ovary tissue [GTEX-11ZVC-1426-SM-L36XC]


title: SCAR_552_H3K27me3_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: A_strain_6505_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_8_A


title: RRBS data from noncancer esophagus tissue [GTEX-13OVJ-1426-SM-L375A]


title: RRBS data from noncancer skin tissue [GTEX-11ZUS-2626-SM-L375V]


title: SCAR_551_H4K20me0_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer muscle tissue [GTEX-11NV4-0326-SM-L374N]

value: muscle


title: RRBS data from noncancer esophagus tissue [GTEX-11P82-0526-SM-L375U]


title: A_strain_6505_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_6_B


title: RRBS data from noncancer heart tissue [GTEX-11GSP-1226-SM-L3768]


title: RRBS data from noncancer blood vessel tissue [GTEX-11GSP-1126-SM-L375R]

value: blood vessel


title: RRBS data from noncancer skin tissue [GTEX-11GSP-2326-SM-L375E]


title: RRBS data from noncancer breast tissue [GTEX-11GS4-2126-SM-L3751]


title: A_strain_9307_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_9307_2_A

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN


title: A_strain_6505_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_6_A


title: RRBS data from noncancer esophagus tissue [GTEX-11GS4-1426-SM-L374S]


title: RRBS data from noncancer breast tissue [GTEX-11EQ9-1826-SM-L374V]


title: SCAR_551_H3K27me3_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer prostate tissue [GTEX-11EQ9-1726-SM-L373C]

source_name: prostate

value: prostate


title: SCAR_410_H4K20me0_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA

value: wildtype


title: SCAR_410_H3K27me3_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: A_strain_6505_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_4_B


title: RRBS data from noncancer spleen tissue [GTEX-11EQ9-0426-SM-L36XK]

value: spleen


title: RRBS data from noncancer adrenal gland tissue [GTEX-11EQ9-0126-SM-L372A]


title: SCAR_552_H4K20me0_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: A_strain_6505_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_4_A

value: SPO medium


title: A_strain_6505_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_2_B


title: RRBS data from noncancer salivary gland tissue [GTEX-11EMC-2526-SM-L375M]

source_name: salivary gland

value: salivary gland


title: A_strain_6505_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_2_A


title: RRBS data from noncancer uterus tissue [GTEX-11EMC-1826-SM-L36XF]

source_name: uterus

value: uterus


title: RRBS data from noncancer uterus tissue [GTEX-11EM3-1926-SM-L36XE]


title: A_strain_6505_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_0_B


title: RRBS data from noncancer pituitary tissue [GTEX-11DYG-3126-SM-L372U]

value: pituitary


title: SCAR_551_H4K20me0_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA

value: Pole4 KO


title: SCAR_551_H3K27me3_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer blood vessel tissue [GTEX-1128S-0326-SM-L3769]

source_name: blood vessel


title: RRBS data from noncancer esophagus tissue [GTEX-11DXY-1426-SM-L3762]

source_name: esophagus


title: RRBS data from noncancer kidney tissue [GTEX-ZYT6-2226-SM-L373K]

source_name: kidney

value: kidney


title: A_strain_6505_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_6505_0_A


title: RRBS data from noncancer heart tissue [GTEX-YFC4-0426-SM-L372T]

value: heart


title: A_strain_1511_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_8_A

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: RRBS data from noncancer skin tissue [GTEX-ZYT6-2326-SM-L372E]

value: skin


title: A_strain_1511_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_8_B


title: RRBS data from noncancer spleen tissue [GTEX-ZTTD-1726-SM-L36VT]

source_name: spleen


title: RRBS data from noncancer blood vessel tissue [GTEX-WZTO-1126-SM-L373F]


title: SCAR_X_442_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_410_H4K20me0_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer nerve tissue [GTEX-WHSE-1026-SM-L36ZS]

value: nerve


title: SCAR_410_H3K27me3_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: SCAR_552_H3K27me3_T0_Pole4KO_exp_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer bladder tissue [GTEX-U3ZN-1226-SM-L36XL]

source_name: bladder

value: bladder


title: SCAR_X_439_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: A_strain_1511_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_6_A


title: SCAR_X_410_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer fallopian tube tissue [GTEX-T6MO-1026-SM-L36XH]

source_name: fallopian tube

value: fallopian tube


title: A_strain_1511_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_4_B


title: RRBS data from noncancer blood vessel tissue [GTEX-U3ZN-0526-SM-L374Y]

value: blood vessel


title: SCAR_551_stranded_input_T0_Pole4KO_exp_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer cervix uteri tissue [GTEX-T5JW-0726-SM-L36UR]

source_name: cervix uteri

value: cervix uteri


title: RRBS data from noncancer uterus tissue [GTEX-T2IS-2226-SM-L36WR]


title: RRBS data from noncancer blood vessel tissue [GTEX-T5JC-0226-SM-L3717]


title: A_strain_1511_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_4_A


title: SCAR_X_442_stranded_input_SUZ12_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer ovary tissue [GTEX-T2IS-2026-SM-L36WJ]

source_name: ovary

value: ovary


title: RRBS data from noncancer esophagus tissue [GTEX-T2IS-0826-SM-L3716]

value: esophagus


title: A_strain_1511_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_2_B


title: SCAR_X_439_stranded_input_SUZ12_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_X_410_stranded_input_SUZ12_T0_r2

description: EdU-labelled genomic DNA

value: wildtype


title: RRBS data from noncancer heart tissue [GTEX-S33H-0526-SM-L372D]

source_name: heart


title: A_strain_1511_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_6_B

value: SPO medium


title: SCAR_X_439_stranded_input_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer skin tissue [GTEX-17EVQ-0126-SM-L36Z8]

source_name: skin


title: A_strain_1511_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_2_A


title: RRBS data from noncancer blood vessel tissue [GTEX-16YQH-0826-SM-L374B]


title: A_strain_1511_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_0_B


title: A_strain_1511_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_1511_0_A


title: RRBS data from noncancer breast tissue [GTEX-17EVQ-0426-SM-L373P]

source_name: breast

value: breast


title: A_strain_10734_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_8_B

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG KAR4::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG kar4::NAT


title: RRBS data from noncancer spleen tissue [GTEX-15RIF-0526-SM-L36W8]

value: spleen


title: RRBS data from noncancer nerve tissue [GTEX-17EVQ-1026-SM-L36ZQ]

source_name: nerve


title: SCAR_X_410_stranded_input_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-15DZA-0626-SM-L374F]

source_name: adipose tissue

value: adipose tissue


title: RRBS data from noncancer small intestine tissue [GTEX-14PK6-1626-SM-L36XO]

source_name: small intestine

value: small intestine


title: A_strain_10734_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_8_A


title: RRBS data from noncancer esophagus tissue [GTEX-15ER7-2226-SM-L373D]


title: SCAR_X_442_H3K27me3_T0_r2

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells


title: SCAR_X_439_H3K27me3_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adrenal gland tissue [GTEX-14JG6-0126-SM-L371W]

source_name: adrenal gland

value: adrenal gland


title: SCAR_X_410_H3K27me3_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_X_442_stranded_input_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer vagina tissue [GTEX-18A7A-2826-SM-L372M]

source_name: vagina

value: vagina


title: RRBS data from noncancer esophagus tissue [GTEX-14E7W-1926-SM-L3758]


title: SCAR_X_442_H3K27me3_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer blood vessel tissue [GTEX-14H4A-0526-SM-L374E]

source_name: blood vessel


title: A_strain_10734_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_6_A


title: A_strain_10734_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_4_B


title: RRBS data from noncancer muscle tissue [GTEX-13SLW-0326-SM-L372J]

source_name: muscle

value: muscle


title: RRBS data from noncancer heart tissue [GTEX-13SLW-0826-SM-L371M]

value: heart


title: A_strain_10734_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_4_A


title: RRBS data from noncancer ovary tissue [GTEX-13OVJ-2426-SM-L36WN]


title: SCAR_X_410_H3K27me3_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_X_442_SUZ12_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer blood vessel tissue [GTEX-13OW6-1526-SM-L374I]


title: RRBS data from noncancer kidney tissue [GTEX-13O1R-2526-SM-L372G]

source_name: kidney

value: kidney


title: RRBS data from noncancer esophagus tissue [GTEX-13OVJ-1226-SM-L371D]

source_name: esophagus


title: A_strain_10734_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_2_B


title: RRBS data from noncancer kidney tissue [GTEX-13NYB-1726-SM-L3734]


title: A_strain_10734_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_2_A


title: RRBS data from noncancer breast tissue [GTEX-13FTY-2226-SM-L36Z9]


title: A_strain_10734_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_0_B


title: RRBS data from noncancer nerve tissue [GTEX-133LE-2126-SM-L36ZN]

value: nerve


title: A_strain_10734_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_6_B


title: RRBS data from noncancer vagina tissue [GTEX-14JG6-0726-SM-L373I]


title: SCAR_X_439_SUZ12_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer skin tissue [GTEX-148VJ-0626-SM-L373X]

value: skin


title: RRBS data from noncancer adipose tissue [GTEX-13112-2726-SM-L3745]


title: RRBS data from noncancer heart tissue [GTEX-13112-0426-SM-L372N]


title: A_strain_10734_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10734_0_A


title: SCAR_X_442_SUZ12_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_X_439_H3K27me3_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer salivary gland tissue [GTEX-12WSN-2226-SM-L3741]

source_name: salivary gland

value: salivary gland


title: RRBS data from noncancer ovary tissue [GTEX-12WSD-2726-SM-L36WM]

value: ovary


title: RRBS data from noncancer adrenal gland tissue [GTEX-12WSD-2126-SM-L36Z2]


title: SCAR_X_439_SUZ12_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_X_410_SUZ12_T0_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-12584-2126-SM-L374P]


title: SCAR_439_stranded_input_K27me3_T8_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer heart tissue [GTEX-12584-0926-SM-L373B]


title: RRBS data from noncancer heart tissue [GTEX-11ZUS-0326-SM-L3756]


title: RRBS data from noncancer prostate tissue [GTEX-11WQK-2726-SM-L3728]

source_name: prostate

value: prostate


title: SCAR_X_410_SUZ12_T0_r2

description: EdU-labelled genomic DNA

value: wildtype


title: RRBS data from noncancer muscle tissue [GTEX-11TT1-2326-SM-L3722]


title: RRBS data from noncancer vagina tissue [GTEX-131YS-2426-SM-L3729]


title: A_strain_10443_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_4_A

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG dyn2::NAT

value: SPO medium


title: SCAR_439_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer breast tissue [GTEX-11P82-1326-SM-L36ZB]

value: breast


title: SCAR_438_stranded_input_K27me3_T8_r2

description: EdU-labelled genomic DNA


title: A_strain_10443_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_8_B


title: RRBS data from noncancer esophagus tissue [GTEX-11P81-1026-SM-L3737]

value: esophagus


title: RRBS data from noncancer prostate tissue [GTEX-11P82-1126-SM-L36YX]


title: RRBS data from noncancer salivary gland tissue [GTEX-11NV4-1926-SM-L36V8]


title: SCAR_438_stranded_input_K27me3_T3_r2

description: EdU-labelled genomic DNA


title: A_strain_10443_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_8_A


title: RRBS data from noncancer small intestine tissue [GTEX-11I78-1126-SM-L36WY]


title: A_strain_10443_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_6_B


title: RRBS data from noncancer blood vessel tissue [GTEX-12126-0726-SM-L36ZJ]

value: blood vessel


title: RRBS data from noncancer vagina tissue [GTEX-11GSP-2226-SM-L373E]


title: RRBS data from noncancer esophagus tissue [GTEX-11EQ9-0726-SM-L3711]


title: SCAR_410_stranded_input_K27me3_T8_r2

description: EdU-labelled genomic DNA


title: A_strain_10443_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_0_B


title: RRBS data from noncancer pituitary tissue [GTEX-11EMC-3126-SM-L36Y3]

source_name: pituitary

value: pituitary


title: SCAR_439_stranded_input_K27me3_T3_r2

description: EdU-labelled genomic DNA


title: SCAR_438_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: A_strain_10443_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_6_A


title: RRBS data from noncancer esophagus tissue [GTEX-11TUW-1226-SM-L373Z]


title: A_strain_10443_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_4_B


title: RRBS data from noncancer testis tissue [GTEX-117XS-2026-SM-L3731]

source_name: testis

value: testis


title: RRBS data from noncancer small intestine tissue [GTEX-1122O-1326-SM-L36XG]

value: small intestine


title: SCAR_410_stranded_input_K27me3_T3_r2

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_K27me3_T0_r2

description: EdU-labelled genomic DNA


title: A_strain_10443_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_2_B


title: A_strain_10427_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_8_A

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG mum2::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG mum2::KAN


title: RRBS data from noncancer esophagus tissue [GTEX-ZYT6-1126-SM-L36YK]


title: A_strain_10427_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_8_B


title: SCAR_439_stranded_input_K4me3_T8_r2

description: EdU-labelled genomic DNA


title: A_strain_10427_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_6_B


title: A_strain_10443_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_2_A


title: RRBS data from noncancer nerve tissue [GTEX-ZYT6-1426-SM-L36ZK]


title: RRBS data from noncancer spleen tissue [GTEX-111CU-0426-SM-L36WP]

source_name: spleen

value: spleen


title: SCAR_439_stranded_input_K4me3_T3_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer prostate tissue [GTEX-XQ3S-2526-SM-L36VQ]


title: RRBS data from noncancer esophagus tissue [GTEX-Y111-1826-SM-L371R]


title: RRBS data from noncancer adipose tissue [GTEX-XQ3S-2426-SM-L36ZV]

value: adipose tissue


title: A_strain_10427_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_6_A


title: RRBS data from noncancer heart tissue [GTEX-XPT6-0126-SM-L36ZX]

source_name: heart

value: heart


title: A_strain_10443_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10443_0_A


title: SCAR_439_stranded_input_K4me3_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer nerve tissue [GTEX-Y111-0526-SM-L36YF]

value: nerve


title: A_strain_10427_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_4_A


title: RRBS data from noncancer pituitary tissue [GTEX-11DXY-3026-SM-L36X3]


title: A_strain_10427_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_4_B


title: RRBS data from noncancer testis tissue [GTEX-WZTO-0326-SM-L36X9]