title: RRBS data from noncancer spleen tissue [GTEX-X585-1826-SM-L36VR]


title: SCAR_438_stranded_input_K4me3_T3_r2

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

description: EdU-labelled genomic DNA

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

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 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.

tag: cell line

tag: strain

tag: genotype


title: RRBS data from noncancer prostate tissue [GTEX-WZTO-0926-SM-L36WF]

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: prostate

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: prostate


title: RRBS data from noncancer heart tissue [GTEX-U8XE-0926-SM-L36ZY]

source_name: heart

value: heart


title: A_strain_10427_2_B

city: Rehovot

first: Alexander

last: Maman

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_2_B

library_source: transcriptomic

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

molecule: polyA RNA

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).
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

tag: cell type

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

tag: treatment

value: SPO medium

tag: time


title: RRBS data from noncancer blood vessel tissue [GTEX-U3ZH-0426-SM-L371U]

source_name: blood vessel

value: blood vessel


title: SCAR_438_stranded_input_K4me3_T0_r2

description: EdU-labelled genomic DNA


title: A_strain_10427_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_2_A


title: RRBS data from noncancer cervix uteri tissue [GTEX-TSE9-2726-SM-L372Q]

source_name: cervix uteri

value: cervix uteri


title: RRBS data from noncancer blood vessel tissue [GTEX-T5JC-0326-SM-L3748]


title: A_strain_10427_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_0_B


title: SCAR_410_stranded_input_K4me3_T8_r2

description: EdU-labelled genomic DNA

value: wildtype


title: RRBS data from noncancer pituitary tissue [GTEX-T2IS-3126-SM-L36WL]

source_name: pituitary

value: pituitary


title: A_strain_10427_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10427_0_A


title: SCAR_410_stranded_input_K4me3_T3_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-T5JC-0526-SM-L36YB]

source_name: adipose tissue

value: adipose tissue


title: RRBS data from noncancer muscle tissue [GTEX-T5JW-1826-SM-L36ZD]

source_name: muscle

value: muscle


title: RRBS data from noncancer bladder tissue [GTEX-S4UY-0926-SM-L36WZ]

source_name: bladder

value: bladder


title: SCAR_410_stranded_input_K4me3_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_438_stranded_input_K4me3_T8_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adrenal gland tissue [GTEX-1BAJH-2626-SM-L36Y6]

source_name: adrenal gland

value: adrenal gland


title: A_strain_10296_8_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_8_B

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: RRBS data from noncancer adipose tissue [GTEX-1C4CL-0426-SM-L36YW]


title: RRBS data from noncancer vagina tissue [GTEX-183WM-2126-SM-L36Z7]

source_name: vagina

value: vagina


title: A_strain_10296_8_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_8_A


title: SCAR_442_stranded_input_K27ac_T3_r2

description: EdU-labelled genomic DNA


title: A_strain_10296_6_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_6_A


title: RRBS data from noncancer ovary tissue [GTEX-183WM-1926-SM-L36VX]

source_name: ovary

value: ovary


title: A_strain_10296_6_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_6_B


title: RRBS data from noncancer blood vessel tissue [GTEX-S33H-2426-SM-L36XU]


title: RRBS data from noncancer breast tissue [GTEX-17MF6-0326-SM-L36Z1]

source_name: breast

value: breast


title: SCAR_442_stranded_input_K27ac_T1_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer esophagus tissue [GTEX-15SHU-1626-SM-L372P]

source_name: esophagus

value: esophagus


title: SCAR_442_stranded_input_K27ac_T0_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer ovary tissue [GTEX-15ER7-2326-SM-L36WC]


title: A_strain_10296_4_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_4_B


title: RRBS data from noncancer spleen tissue [GTEX-15ER7-1526-SM-L36VK]

source_name: spleen

value: spleen


title: SCAR_439_stranded_input_K27ac_T8_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer small intestine tissue [GTEX-15DZA-0826-SM-L36XP]

source_name: small intestine

value: small intestine


title: RRBS data from noncancer blood vessel tissue [GTEX-15ER7-1426-SM-L3714]


title: SCAR_439_stranded_input_K27ac_T3_r2

description: EdU-labelled genomic DNA


title: A_strain_10296_4_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_4_A


title: RRBS data from noncancer adipose tissue [GTEX-15DYW-1526-SM-L36YT]


title: RRBS data from noncancer esophagus tissue [GTEX-15DCD-1726-SM-L372F]


title: A_strain_10296_2_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_2_B


title: SCAR_442_stranded_input_K27ac_T8_r2

description: EdU-labelled genomic DNA


title: A_strain_10296_2_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_2_A


title: RRBS data from noncancer spleen tissue [GTEX-14PK6-0526-SM-L36WS]


title: RRBS data from noncancer blood vessel tissue [GTEX-14PJM-1026-SM-L36ZW]


title: SCAR_439_stranded_input_K27ac_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_K27ac_T8_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer heart tissue [GTEX-148VJ-1426-SM-L36ZI]

value: heart


title: A_strain_10296_0_A

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_0_A

value: SPO medium


title: SCAR_439_stranded_input_K27ac_T1_r2

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_K27ac_T3_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer heart tissue [GTEX-14JG1-0826-SM-L36ZF]


title: RRBS data from noncancer blood vessel tissue [GTEX-14C39-0126-SM-L3747]

value: blood vessel


title: RRBS data from noncancer heart tissue [GTEX-148VJ-1526-SM-L371V]


title: SCAR_410_stranded_input_K27ac_T1_r2

description: EdU-labelled genomic DNA


title: RRBS data from noncancer blood vessel tissue [GTEX-148VJ-0426-SM-L36Z3]


title: A_strain_10296_0_B

description: 672_AMlib8_M6aMutants_MeiosisTimepoints_A_strain_10296_0_B


title: RRBS data from noncancer kidney tissue [GTEX-13OW6-1826-SM-L36ZO]

source_name: kidney

value: kidney


title: osnat10-1 RNC-mRNA rep1

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

country: China

institute: Hunan university

description: RNC-mRNA replicate 1

data_processing:
Reads were mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
samtools mpileup to identity nucleotide at each position.
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: Mutation matrix was generated by samtools mpileup, p value was from Proportion Test. Bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.
Library strategy: RNC-seq

molecule: total RNA

organism: Oryza sativa

source_name: Seedlings

growth_protocol: Arabidopsis seedlings were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC. Oryza sativa L. ssp. japonica cultivar Nipponbare plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 mmol m-2 s -1.

extract_protocol:
For acRIP-seq, seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody. For ac4C-seq, mRNA was purified by oligodT beads. 3 ug of mRNA was used for the construction of sequencing libraries.
For RNC-seq, Arabidopsis seedlings were homogenized in liquid nitrogen and lysed in in 1 ml pre-chilled ribosome buffer (20 mM HEPES[pH 7.44ºC], 15 mM MgCl2, 200 mM KCl, 100 mg/ml cycloheximide, 2 mM dithiothreitol) with 1% Triton X-100 for 30 minutes at 4ºC. Cell lysate was centrifuged at 17,000 g for 5 minutes and supernatant was taken. The supernatants were transferred to 12.5 ml sucrose buffer (30% sucrose in ribosome buffer). After centrifuging at 185,000g for 5 hours at 4ºC, the pellet was suspended in cold ribosome buffer to get RNC.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.   ac4C-seq libraries were prepared using NEBNext UltraTM Ⅱ Directional RNA Library Prep Kit for Illumina (NEB, E7760S) following manufacturer's protocols.

treatment_protocol: mRNA was treated with either NaCNBH3 (100 mM in H2O + 100 mM HCl) or ‘mock’ buffer (H2O + 100 mM HCl) at 20ºC for 20 min.

value: Seedlings


title: osnat10-1 RNC-mRNA rep2

description: RNC-mRNA replicate 2


title: RRBS data from noncancer adrenal gland tissue [GTEX-13OW6-1726-SM-L36YC]


title: RRBS data from noncancer muscle tissue [GTEX-13OVJ-0226-SM-L36ZA]


title: RRBS data from noncancer skin tissue [GTEX-13OVJ-0826-SM-L36YI]

source_name: skin

value: skin


title: osnat10-1 mRNA rep2

description: mRNA replicate 2

data_processing:
Reads were mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
samtools mpileup to identity nucleotide at each position.
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: Mutation matrix was generated by samtools mpileup, p value was from Proportion Test. Bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.


title: RRBS data from noncancer testis tissue [GTEX-13OVH-0726-SM-L36YQ]

source_name: testis

value: testis


title: SCAR_410_stranded_input_K27ac_T0_r2

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells

value: wildtype


title: SCAR_442_stranded_input_K27ac_T8_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer pancreas tissue [GTEX-13FLV-0626-SM-L3739]

source_name: pancreas

value: pancreas


title: RRBS data from noncancer vagina tissue [GTEX-12ZZX-1926-SM-L36YP]


title: RRBS data from noncancer pituitary tissue [GTEX-12ZZX-3026-SM-L36W6]

source_name: pituitary

value: pituitary


title: SCAR_442_stranded_input_K27ac_T3_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer nerve tissue [GTEX-12ZZX-0426-SM-L36ZM]

source_name: nerve

value: nerve


title: osnat10-1 mRNA rep1

description: mRNA replicate 1


title: Kitaake RNC-mRNA rep2

description: RNC-mRNA replicate 2

value: Kitaake


title: SCAR_442_stranded_input_K27ac_T1_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer esophagus tissue [GTEX-12WSD-1826-SM-L36XT]


title: Kitaake RNC-mRNA rep1

description: RNC-mRNA replicate 1


title: RRBS data from noncancer skin tissue [GTEX-12WSD-0626-SM-L36YN]


title: RRBS data from noncancer esophagus tissue [GTEX-11ZUS-0926-SM-L371B]


title: Kitaake mRNA rep2

description: mRNA replicate 2


title: RRBS data from noncancer prostate tissue [GTEX-11TUW-2126-SM-L36VF]

source_name: prostate

value: prostate


title: SCAR_442_stranded_input_K27ac_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_439_stranded_input_K27ac_T8_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer adipose tissue [GTEX-11P82-0326-SM-L371L]

source_name: adipose tissue

value: adipose tissue


title: Kitaake mRNA rep1

description: mRNA replicate 1


title: RRBS data from noncancer small intestine tissue [GTEX-11P82-0826-SM-L36WV]


title: SCAR_439_stranded_input_K27ac_T3_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer salivary gland tissue [GTEX-11P81-2026-SM-L36V6]

source_name: salivary gland

value: salivary gland


title: SCAR_439_stranded_input_K27ac_T1_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer skin tissue [GTEX-11EQ9-2426-SM-L371P]


title: Control, Day15

extract_protocol:
For acRIP-seq, seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody. For ac4C-seq, mRNA was purified by oligodT beads. 3 ug of mRNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.   ac4C-seq libraries were prepared using NEBNext UltraTM Ⅱ Directional RNA Library Prep Kit for Illumina (NEB, E7760S) following manufacturer's protocols.
acRIP-seq and ac4C-seq

tag: cultivar

value: Nipponbare

value: control

value: 20 min


title: SCAR_439_stranded_input_K27ac_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_K27ac_T8_r1

description: EdU-labelled genomic DNA


title: RRBS data from noncancer esophagus tissue [GTEX-11EQ9-0826-SM-L372R]

value: esophagus


title: RRBS data from noncancer esophagus tissue [GTEX-11DYG-1326-SM-L373A]


title: ZNF92_ChIPseq

city: Lausanne

first: Jonas

last: de Tribolet-Hardy

address: Bâtiment SV 0405

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads).
Reads with mapping quality lower than 10,  from the UCSC blacklist, or from a greylist derived from TI using GreyListChIP Bioconductor package were removed from the analysis.
Peaks were called using MACS v2.2.4 with default parameters except “--keep-dup all” and -q 0.01
Assembly: hg19
Supplementary files format and content: bedfile obtained for MACS

source_name: transduced HEK293T cell line

growth_protocol: Human embryonic kidney-derived 293T cells  were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Chromatin was prepared by resuspending 3x107 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follow: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
Total inputs and chromatin immunoprecipitated samples were prepared for libraries using 10 ng of material. After end-repair and A-tailing, Illumina IDT indexes were ligated to the samples. Aliquots were tested in qPCR to determine the optimal number of PCR cycles needed to amplify each library without reaching saturation. Libraries were amplified with, size-selected using Ampure XP beads (Beckman Coulter), and always quality-checked on a Bioanalyzer DNA high sensitivity chip (Agilent) and quantified with a Qubit dsDNA HS assay kit (Qubit 2.0 Fluorometer, Invitrogen)

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/mL) for 7 days and induced using doxycyclin (1 ug / mL) for a few days before fixation with formaldehyde (1% for 10 min).

value: transduced HEK293T cell line

value: Human embryonic kidney

tag: chip antibody

value: Anti-HA :clone 16B12, Covance


title: ZNF92_ChIPseq_TI


title: RRBS data from noncancer skin tissue [GTEX-113JC-2326-SM-L36YH]

value: skin


title: RRBS data from noncancer kidney tissue [GTEX-11GS4-2326-SM-L3721]

value: kidney


title: RRBS data from noncancer vagina tissue [GTEX-113JC-1926-SM-L36ZH]

source_name: vagina

value: vagina


title: SCAR_410_stranded_input_K27ac_T3_r1

description: EdU-labelled genomic DNA

value: wildtype


title: ZNF878_ChIPseq


title: RRBS data from noncancer breast tissue [GTEX-12WSM-1726-SM-L36YO]

source_name: breast

value: breast


title: RRBS data from noncancer adipose tissue [GTEX-111FC-0226-SM-L3735]


title: RRBS data from noncancer small intestine tissue [GTEX-11DXX-1626-SM-L36WE]

value: small intestine


title: HepG2 cells, Control, 48 h

city: Jinju

first: Sang Eun

last: Ha

address: 501 Jinju-daero

department: Life Science and College of Veterinary Medicine

country: South Korea

institute: Gyeongsang National University

data_processing:
Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA)
KAPA library quantification kit (Kapa Biosystems, MA, USA)
Sequencing was progressed as paired-end (2×151bp) using Illumina NovaSeq6000 (Illumina, CA, USA)
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8
Gene expression estimation was performed by RSEM v.1.3.1 [3] considering the direction of the reads which are corresponding to the library protocol using option “strandedness”.
Assembly: Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options (refer to “Alignment” of “Help” section in the html report) with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Supplementary files format and content: Tab-delimited text files include FPKM and TPM values for each sample

growth_protocol: HepG2 hepatocellular carcinoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin/100 μg/ml streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37˚C

extract_protocol:
RNA was harvested using Trizol (Ambion). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA quantification kit according to the manufacturer’s library quantification protocol.

treatment_protocol: HepG2 cells were treated with 100 μM of Scutellareun for 48 h at 37˚C of 5% CO2

value: Hepatocellular carcinoma cells


title: HepG2 cells, Test, 48 h

value: Scutellatein


title: NaCNBH3 treated, Day15

value: Seedlings


title: NB4, RBFOX2 KD, r2, mRNA-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

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

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 acute promyelocytic leukemia cell line

value: RBFOX2 KD


title: SCAR_410_stranded_input_K27ac_T1_r1

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_K27ac_T0_r1

description: EdU-labelled genomic DNA


title: ZNF813_ChIPseq


title: NB4, Control, r2, mRNA-seq

value: Control


title: NB4, RBFOX2 KD, r1, mRNA-seq


title: NB4, Control, r1, mRNA-seq


title: ZNF747_ChIPseq


title: SCAR_442_H3K27ac_T3_r2

description: EdU-labelled genomic DNA


title: SCAR_442_H3K27ac_T8_r2

description: EdU-labelled genomic DNA


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

value: Human immortalized myelogenous leukemia cell line


title: ZNF746_ChIPseq


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


title: SCAR_442_H3K27ac_T1_r2

description: EdU-labelled genomic DNA


title: K562, Control, r2, mRNA-seq


title: K562, Control, r1, mRNA-seq


title: K562, siMETTL3 KD, RBFOX2, r2, CLIP-seq

data_processing:
Low quality reads were filtered using ‘fastq_quality_filter’, and adapter were clipped using ‘fastx_clipper’, then adapter-free were collapsed to remove PCR duplicates by using ‘fastx_collapser’ and finally reads longer than 15 nt were retained for further analysis (http://hannonlab.cshl.edu/fastx_toolkit/). Reads from rRNA were removed.
The preprocessed reads were mapped to hg38 using bowtie with ‘-v 3 -m 10 -k 1 –best –strata’ parameters.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CLIP-seq

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.

extract_protocol:
Cells were then harvested by centrifugation, lysed, and treated wiht 4 U/mL RNase I and 4 U/mL Turbo DNase at 37 °C for 5 min. Next, the cell lysate was cleared by centrifugation at 15000 g, 4 °C for 15 min, and kept on ice for the subsequent immunoprecipitation (IP). RBFOX2 antibodies were pre-conjugated to Protein A/G Magnetic Beads by incubation at room temperature for 45 min. The cell lysate was then added to the pre-conjugated beads and incubated at 4 °C overnight. RBFOX2-bound RNAs were end-repaired with T4 PNK, released by proteinase K treatment, and recovered.
Libraries were prepared using NEBNext Small RNA Library Prep Set.

treatment_protocol: K562 cells were crosslinked twice on ice with UV irradiation (254 nm) at 150 mJ/cm2.

value: siMETTL3 KD

value: UV 254 nm crosslink

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


title: K562, siMETTL3 KD, RBFOX2, r1, CLIP-seq


title: SCAR_442_H3K27ac_T0_r2

description: EdU-labelled genomic DNA


title: K562, siMETTL3 KD, Input, r2, CLIP-seq


title: ZNF852_ChIPseq

value: transduced HEK293T cell line

value: Human embryonic kidney

value: Anti-HA :clone 16B12, Covance


title: ZNF732_ChIPseq_TI


title: K562, siMETTL3 KD, Input, r1, CLIP-seq


title: ZNF732_ChIPseq


title: K562, siControl, RBFOX2, r1, CLIP-seq

value: siControl


title: ZNF723_ChIPseq


title: SCAR_439_H3K27ac_T3_r2

description: EdU-labelled genomic DNA


title: SCAR_439_H3K27ac_T1_r2

description: EdU-labelled genomic DNA


title: K562, siControl, Input, r1, CLIP-seq


title: SCAR_439_H3K27ac_T0_r2

description: EdU-labelled genomic DNA


title: K562, siControl, RBFOX2, r2, CLIP-seq


title: SCAR_410_H3K27ac_T8_r2

description: EdU-labelled genomic DNA

value: wildtype


title: Rectum, nonresponder post Vedo treatment 27R_Rectum mRNA

city: La Jolla

first: Eunice

last: Choi

address: 9500 Gilman Dr

institute: University of California, San Diego

description: 10x genomics

data_processing:
Raw sequencing data were processed using the CellRanger pipeline (10x Genomics)
Samples were further processed using Seurat v4.1.1 (14). Low quality (e.g., dead) cells and potential doublets were filtered with the following parameters: <200 features, >10% mitochondrial features, >2500 features.
ADT and RNA assays were normalized using the standard Seurat workflow of ‘NormalizeData’,‘FindVariableFeatures’, and ‘ScaleData’, and ‘RunPCA’.
Cell types were assigned using SingleR v.1.4.1 (15) and verified with canonical protein markers.
Assembly: hg38
Supplementary files format and content: annotated and processed seurat object
Library strategy: CITE-seq

source_name: Rectum

extract_protocol:
Four intestinal biopsies were obtained with endoscopic biopsy forceps from the ileum and rectum and collected in separate conical tubes with Hank’s buffered saline solution (HBSS, Corning). Intestinal biopsies were transferred into freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI, 50%(v/v) FBS) and stored at -80°C. Biopsies were recovered, incubated in HBSS on a shaker, then incubated twice in HBSS + 5 mM dithiothreitol (DTT, Thermo Fisher Scientific) for 10 minutes on a rocker at 37°C, followed by a final HBSS wash. Intestinal biopsies were mechanically dissociated, then placed into a conical tube containing 10 mL of digestion mixture [complete RPMI + 1.5 mg/mL Collagenase type VIII (Sigma-Aldrich) + 50 µg/mL DNase I (Roche)]. The biopsies were digested in a shaking incubator (225 rpm) for 20 minutes at 37°C. The reaction was stopped with phosphatebuffered saline (PBS) pre-cooled to 4°C, filtered, and resuspended in fresh complete RPMI. Samples were incubated with BD Pharmingen Human BD Fc Block for 10 minutes to block non-specific binding of the Fc receptor as described in the manufacturer's protocol. The 55-plex BD AbSeq antibody cocktail was generated using 2.6 uL of each antibody and brought to volume with BD buffer. Concurrently, samples were stained with anti-human CD45 and a live/dead stain, and incubated for 60 minutes on ice. CD45 + immune cells were sorted on a FACSAria2 and collected in complete RPMI media with 10% FBS. Blood was collected in BD Vacutainer CPT tube and centrifuged at 400 x g for 25 minutes. The buffy coat layer was removed, washed, and counted. Cells were resuspended in freezing buffer (10%(v/v) Dimethylsulfoxide (DMSO, Sigma Aldrich), 40%(v/v) complete RPMI [RPMI (Corning) +10%(v/v) fetal bovine serum (FBS, Life Technologies) +100 U/mL penicillin/100 µg/mL streptomycin (Life Technologies)], 50%(v/v) FBS), placed into a freezing container (Mr. Frosty), and stored at -80°C. Cells were recovered, washed, filtered, and labeled with anti-human CD45 (2D1) (Biolegend) for sorting. CD45 + immune cells were sorted on a FACSAria2 (BD Biosciences).
Cells were washed and resuspended in phosphate-buffered saline (PBS) + 0.04%(w/v) bovine serum albumin (UltraPure BSA, Thermo Fisher Scientific) per the manufacturer’s guidelines. Single-cell libraries were prepared according to the protocol for 10x Genomics for Single Cell 3’ Gene Expression. Approximately 20,000 sorted CD45 + cells resuspended at a final concentration of 4,000 cells/uL were loaded and partitioned into Gel Bead-in-EMulsions (GEMs). The 10x Genomics cDNA generation protocol was modified to include the BD AbSeq PCR1 primer. After PCR amplification, the fractions containing the AbSeq oligos were processed through a separate library construction workflow. This AbSeq protocol generates libraries directly after cDNA amplification, eliminating intermediate steps as described in the 10x Genomics protocol. The quality of the sample fragments was determined by the High Sensitivity D5000 and D1000 ScreenTape assay (Agilent Technologies). The scRNA and protein libraries were pooled at equimolar amounts for a final 10nM concentration and sequenced on a NovaSeq 6000 S4 flow cell (Illumina).

tag: group

value: nonresponder

value: Rectum

tag: age

tag: gender

value: Male

tag: assay

value: mRNA


title: Rectum, nonresponder post Vedo treatment 27R_Rectum ADT

description: 10x genomics

value: ADT


title: PBMC, nonresponder post Vedo treatment 27P_PBMC ADT

description: 10x genomics

source_name: PBMC

value: PBMC


title: ZNF718_ChIPseq


title: ZNF735_ChIPseq


title: ZNF705E_ChIPseq


title: SCAR_410_H3K27ac_T3_r2

description: EdU-labelled genomic DNA


title: ZNF71_ChIPseq


title: PBMC, nonresponder post Vedo treatment 27P_PBMC mRNA

description: 10x genomics


title: ZNF705D_ChIPseq


title: SCAR_439_H3K27ac_T8_r2

description: EdU-labelled genomic DNA


title: Rectum, nonresponder post Vedo treatment 26R_Rectum mRNA

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 26R_Rectum ADT

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 26P_PBMC ADT

description: 10x genomics


title: SCAR_410_H3K27ac_T0_r2

description: EdU-labelled genomic DNA


title: PBMC, nonresponder post Vedo treatment 26P_PBMC mRNA

description: 10x genomics


title: K562, siControl, Input, r2, CLIP-seq


title: SCAR_410_H3K27ac_T1_r2

description: EdU-labelled genomic DNA


title: ZNF705A_ChIPseq


title: ZNF705A_ChIPseq_TI


title: Rectum, nonresponder post Vedo treatment 25R_Rectum ADT

description: 10x genomics

value: Female


title: ZNF700_ChIPseq


title: SCAR_442_H3K27ac_T3_r1

description: EdU-labelled genomic DNA


title: Rectum, nonresponder post Vedo treatment 25R_Rectum mRNA

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 25P_PBMC mRNA

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 25P_PBMC ADT

description: 10x genomics


title: Rectum, responder post Vedo treatment 24R_Rectum ADT

description: 10x genomics

value: responder


title: Rectum, responder post Vedo treatment 24R_Rectum mRNA

description: 10x genomics


title: PBMC, responder post Vedo treatment 24P_PBMC ADT

description: 10x genomics


title: SCAR_442_H3K27ac_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_442_H3K27ac_T8_r1

description: EdU-labelled genomic DNA


title: SCAR_442_H3K27ac_T1_r1

description: EdU-labelled genomic DNA


title: Rectum, responder post Vedo treatment 23R_Rectum ADT

description: 10x genomics


title: Rectum, responder post Vedo treatment 23R_Rectum mRNA

description: 10x genomics


title: ZNF689_ChIPseq


title: ZNF679_ChIPseq


title: PBMC, responder post Vedo treatment 23P_PBMC ADT

description: 10x genomics


title: PBMC, responder post Vedo treatment 24P_PBMC mRNA

description: 10x genomics


title: SCAR_439_H3K27ac_T8_r1

description: EdU-labelled genomic DNA


title: PBMC, responder post Vedo treatment 23P_PBMC mRNA

description: 10x genomics


title: ZNF677_ChIPseq


title: Rectum, responder post Vedo treatment 22R_Rectum mRNA

description: 10x genomics


title: SCAR_439_H3K27ac_T3_r1

description: EdU-labelled genomic DNA


title: Rectum, responder post Vedo treatment 22R_Rectum ADT

description: 10x genomics


title: PBMC, responder post Vedo treatment 22P_PBMC ADT

description: 10x genomics


title: SCAR_439_H3K27ac_T1_r1

description: EdU-labelled genomic DNA


title: ZNF66_ChIPseq


title: PBMC, responder post Vedo treatment 22P_PBMC mRNA

description: 10x genomics


title: ZNF699_ChIPseq


title: SCAR_439_H3K27ac_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_410_H3K27ac_T8_r1

description: EdU-labelled genomic DNA


title: Rectum, nonresponder post Vedo treatment 21R_Rectum ADT

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 21R_Rectum mRNA

description: 10x genomics


title: ZNF625_ChIPseq


title: ZNF624_ChIPseq


title: SCAR_410_H3K27ac_T3_r1

description: EdU-labelled genomic DNA


title: ZNF600_ChIPseq_TI


title: PBMC, nonresponder post Vedo treatment 21P_PBMC ADT

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 21P_PBMC mRNA

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 20R_Rectum ADT

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 20R_Rectum mRNA

description: 10x genomics


title: ZNF600_ChIPseq


title: ZNF599_ChIPseq


title: SCAR_410_H3K27ac_T0_r1

description: EdU-labelled genomic DNA


title: PBMC, nonresponder post Vedo treatment 20P_PBMC mRNA

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 19R_Rectum mRNA

description: 10x genomics


title: Rectum, nonresponder post Vedo treatment 19R_Rectum ADT

description: 10x genomics


title: ChIP_442_SUZ12_input_r3

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
peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 (narrow peaks, H3K4me3 and H3K27ac) or --nomodel --broad -p 0.01 –-broad-cutoff 0.1 (broad peaks, H3K27me3, H3K9me3 and SUZ12)
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq peak bed files called with macs2, narrow peaks (H3K4me3, H3K27ac) and broad peaks (H3K27me3, H3K9me3)

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.


title: ZNF597_ChIPseq


title: ZNF597_ChIPseq_TI


title: ZNF587B_ChIPseq


title: PBMC, responder post Vedo treatment 18P_PBMC ADT

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 19P_PBMC ADT

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 19P_PBMC mRNA

description: 10x genomics


title: PBMC, responder post Vedo treatment 18P_PBMC mRNA

description: 10x genomics


title: ChIP_410_SUZ12_input_r3


title: Rectum, responder post Vedo treatment 17R_Rectum ADT

description: 10x genomics


title: ChIP_442_SUZ12_input_r2


title: Rectum, responder post Vedo treatment 17R_Rectum mRNA

description: 10x genomics


title: ZNF57_ChIPseq_TI


title: PBMC, responder post Vedo treatment 17P_PBMC ADT

description: 10x genomics


title: SCAR_410_H3K27ac_T1_r1

description: EdU-labelled genomic DNA


title: ZNF57_ChIPseq


title: ChIP_439_SUZ12_input_r2


title: PBMC, responder post Vedo treatment 17P_PBMC mRNA

description: 10x genomics


title: PBMC, nonresponder post Vedo treatment 20P_PBMC ADT

description: 10x genomics


title: Rectum, responder post Vedo treatment 16R_Rectum mRNA

description: 10x genomics


title: Rectum, responder post Vedo treatment 16R_Rectum ADT

description: 10x genomics


title: ChIP_410_SUZ12_input_r2


title: PBMC, responder post Vedo treatment 16P_PBMC ADT

description: 10x genomics


title: PBMC, responder post Vedo treatment 16P_PBMC mRNA

description: 10x genomics


title: ChIP_442_SUZ12_input_r1


title: ChIP_439_SUZ12_input_r3


title: Rectum, responder post Vedo treatment 15R_Rectum mRNA

description: 10x genomics


title: Rectum, responder post Vedo treatment 15R_Rectum ADT

description: 10x genomics


title: ZNF556_ChIPseq_TI


title: PBMC, responder post Vedo treatment 15P_PBMC ADT

description: 10x genomics


title: ChIP_439_SUZ12_input_r1


title: ChIP_410_SUZ12_input_r1


title: ZNF556_ChIPseq


title: PBMC, responder post Vedo treatment 15P_PBMC mRNA

description: 10x genomics


title: PBMC, responder post Vedo treatment 14P_PBMC ADT

description: 10x genomics


title: PBMC, responder post Vedo treatment 14P_PBMC mRNA

description: 10x genomics


title: Rectum, responder post Vedo treatment 14R_Rectum mRNA

description: 10x genomics


title: ChIP_439_SUZ12_r3

description: 439_SUZ12_ChIP_pr_R1.idr_peaks.narrowPeak.bed.gz

tag: antibody


title: ZNF554_ChIPseq


title: Rectum, responder post Vedo treatment 14R_Rectum ADT

description: 10x genomics


title: ZNF560_ChIPseq


title: ZNF559_ChIPseq


title: ChIP_410_SUZ12_r3

description: 410_SUZ12_ChIP_pr_R1.idr_peaks.narrowPeak.bed.gz


title: PBMC fresh cells technical replicate 1

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

description:
A2
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 (file 10X Genomics refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Filtered feature files from CellRanger. Each tar archive contains three files with the count matrix, barcodes file and features file.

source_name: Blood

extract_protocol:
Twelve ml (2 tubes by donor) of fresh blood was collected in EDTA anticoagulant. PBMCs were isolated using HISTOPAQUE-1077 (Sigma Aldrich; cat\# 10771-6X100ML). After centrifugation (285 rcf x g for 5 min at room temperature without the brake), PBMCs remained at the plasma-HISTOPAQUE-1077 interface and were carefully transferred to a new tube. PBMCs were washed two or three times with 3x volume 1X PBS (cat\# 10010023 Gibco) followed by a centrifugation (285 rcf x g for 5 min at room temperature without the brake). A visual check was done after each centrifugation to look if platelets remain.
PBMCs were counted with a Malassez counting chamber, dead cells rate and cellular debris were checked. The cells were centrifuged at 285 rcf x g for 5 min at room temperature without the brake. The supernatant was removed, and the cell pellet was resuspended in 1 mL 1X PBS (cat\# 10010023 Gibco) containing 0.04\% filtered Bovine Serum Albumin (BSA, 50 mg/ml cat\#AM2616, ThermoFischer Scientific). Resuspended cells were centrifuged at 285 rcf x g for 5 min at room temperature. The supernatant was removed delicately and the cell pellet was resuspended in 1 mL 1X PBS containing 0.04\% filtered BSA. For the frozen cells, PBMCs were thawed and resuspended according to the manufacturer’s protocol (Fresh Frozen Human Peripherical Blood Mononuclear Cells for Single Cell RNA sequencing  CG00039 revD, 10X Genomics). In the end, the cells are also resuspended in 1 ml 1X PBS containing 0.04\% filtered BSA. Cells were again counted with a Malassez counting chamber. According the manufacturer's protocol, we need to have for the next step a concentration between 700,000 and 1,200,000 cells par ml. The volume was adapted if needed to reach this range of concentration.

value: Blood

tag: cell subtype

value: PBMC fresh cells


title: ChIP_442_SUZ12_r2

description: 442_SUZ12_ChIP_pr_R1.idr_peaks.narrowPeak.bed.gz


title: PBMC fresh cells technical replicate 2

description:
B2
10X Genomics


title: PBMC frozen cells technical replicate 2

description:
B3
10X Genomics

value: PBMC frozen cells


title: ZNF510_ChIPseq


title: ZNF493_ChIPseq


title: PBMC stimulated witth LPS (4 hours) replicate 1

description:
G1
10X Genomics

value: PBMC stimulated witth LPS (4 hours)


title: PBMC frozen cells technical replicate 1

description:
A3
10X Genomics


title: ZNF500_ChIPseq

value: transduced HEK293T cell line


title: ZNF490_ChIPseq

value: Human embryonic kidney


title: ChIP_439_SUZ12_r2


title: testis_12-14GW_CBD-THC_EH3345

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Gévezé, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the homo sapiens reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,484 genes detected.

source_name: Fetal testis

growth_protocol: The fetal testes were cut into explants of 1mm3 and placed in cell culture inserts put in 24-well companion culture plates . On each insert, 3 or 4 testicular explants were placed and cultivated in 350µl of phenol red-free medium 199 supplemented with 50µg/mL gentamicin, 2,5µg/mL Fungizone and 0,1 IU/mL of human chorionic gonadotropin. The cultures were incubated at 37°C for 96h in a humidified atmosphere of 95% air and 5% CO2. Explants were cultured in 199 medium supplemented with hCG for the first 24 h of culture (D0) without any drug. After D0, the explants were exposed to treatments for 3 days by adding CBD and/or THC at concentrations of 10-5M, 10-6M or 10-7M to the medium, or to dimethylsulfoxyde (DMSO, Sigma-Aldrich) and/or ethanol, the solvents of CBD and THC, respectively.

extract_protocol:
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.
3'Bulk RNA Barcoding and sequencing (BRB-seq)

value: XY

tag: exposure

value: CBD-THC

tag: developmental stage

tag: age (pcw)

tag: outlier

value: no


title: testis_12-14GW_CBD-THC_EH3412

treatment_protocol: Explants were cultured in 199 medium supplemented with hCG for the first 24 h of culture (D0) without any drug. After D0, the explants were exposed to treatments for 3 days by adding CBD and/or THC at concentrations of 10-5M, 10-6M or 10-7M to the medium, or to dimethylsulfoxyde (DMSO, Sigma-Aldrich) and/or ethanol, the solvents of CBD and THC, respectively.


title: ZNF551_ChIPseq

tag: cell line

tag: genotype

value: Anti-HA :clone 16B12, Covance


title: testis_12-14GW_CBD-THC_EH4115


title: testis_12-14GW_CBD-THC_EH3234


title: ChIP_442_SUZ12_r3

tag: strain


title: ChIP_442_SUZ12_r1


title: ZNF471_ChIPseq

tag: cell type


title: testis_12-14GW_CBD-THC_EH4075


title: testis_12-14GW_CBD-THC_EH3351


title: ChIP_410_SUZ12_r1

value: wildtype


title: ChIP_442_K27ac_input_r2


title: PBMC resting cells replicate 1

description:
D1
10X Genomics

tag: tissue

value: PBMC resting cells


title: ChIP_439_K27ac_input_r2


title: ZNF415_ChIPseq


title: testis_12-14GW_CBD-THC_EH4109


title: testis_12-14GW_CBD-THC_EH4114


title: testis_10-12GW_CBD-THC_EH4105


title: ChIP_410_SUZ12_r2


title: ZNF394_ChIPseq


title: testis_10-12GW_CBD-THC_EH4155


title: ChIP_421_K27ac_input_r2


title: testis_10-12GW_CBD-THC_EH4112


title: testis_10-12GW_CBD-THC_EH4138

value: yes


title: testis_10-12GW_CBD-THC_EH4111


title: ChIP_410_K27ac_input_r2


title: ChIP_439_SUZ12_r1


title: ZNF41_ChIPseq


title: ChIP_442_K27ac_input_r1


title: testis_10-12GW_CBD-THC_EH3417


title: testis_12-14GW_CBD-THC_EH3265


title: testis_12-14GW_CBD-THC_EH4168


title: testis_10-12GW_CBD-THC_EH4147


title: testis_10-12GW_CBD-THC_EH4080


title: ZNF420_ChIPseq


title: ZNF286A_ChIPseq


title: ZNF256_ChIPseq_TI


title: ZNF37A_ChIPseq


title: testis_12-14GW_THC_EH3412

value: THC


title: testis_10-12GW_CBD-THC_EH4142


title: testis_12-14GW_THC_EH3345


title: ChIP_439_K27ac_input_r1


title: testis_10-12GW_CBD-THC_EH4072


title: ChIP_421_K27ac_input_r1


title: testis_12-14GW_THC_EH4075


title: testis_12-14GW_THC_EH3366


title: ZNF316_ChIPseq


title: ZNF256_ChIPseq


title: testis_12-14GW_THC_EH3351


title: testis_12-14GW_THC_EH4168


title: ZNF250_ChIPseq


title: ChIP_442_H3K27ac_r2


title: ChIP_439_H3K27ac_r2


title: ZNF230_ChIPseq


title: testis_12-14GW_THC_EH4109


title: testis_10-12GW_THC_EH4080


title: ZNF234_ChIPseq


title: testis_12-14GW_THC_EH4114


title: ZNF233_ChIPseq


title: testis_12-14GW_THC_EH4115


title: ChIP_421_H3K27ac_r2


title: testis_10-12GW_THC_EH4105


title: ZNF227_ChIPseq


title: ChIP_410_H3K27ac_r2

description: 410_H3K27ac_ChIP_pr_R1.original.reproducible_peaks.narrowPeak.bed.gz


title: testis_10-12GW_THC_EH4174


title: testis_10-12GW_THC_EH4072


title: ZNF20_ChIPseq


title: testis_10-12GW_THC_EH4138


title: ChIP_410_K27ac_input_r1


title: ZNF215_ChIPseq


title: testis_10-12GW_THC_EH3413


title: testis_10-12GW_THC_EH4155


title: ChIP_442_H3K27ac_r1


title: testis_10-12GW_THC_EH4142


title: ChIP_439_H3K27ac_r1


title: testis_10-12GW_THC_EH4111


title: ZNF177_ChIPseq


title: testis_12-14GW_CBD_EH4115

value: CBD


title: ChIP_421_H3K27ac_r1


title: RNA_421_r2

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: tab separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts mm10 repeat ids)

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 manufacturers protocol.


title: testis_12-14GW_THC_EH3265


title: testis_12-14GW_CBD_EH3366


title: testis_10-12GW_THC_EH4147


title: testis_12-14GW_CBD_EH3345


title: testis_12-14GW_CBD_EH3412


title: ZNF155_ChIPseq


title: ZNF175_ChIPseq


title: ChIP_410_H3K27ac_r1


title: ZNF138_ChIPseq


title: testis_12-14GW_CBD_EH3351


title: RNA_421_r1


title: testis_12-14GW_CBD_EH3265


title: ZNF14_ChIPseq


title: testis_10-12GW_CBD_EH4105


title: RNA_419_r2


title: testis_12-14GW_CBD_EH4168


title: testis_12-14GW_CBD_EH4109


title: RNA_419_r1


title: testis_12-14GW_CBD_EH4114


title: RNA_418_r2


title: testis_10-12GW_CBD_EH4072


title: testis_12-14GW_CBD_EH4075


title: ZNF112_ChIPseq


title: RNA_418_r1


title: ZNF136_ChIPseq


title: ZKSCAN1_ChIPseq


title: RNA_417_r1


title: testis_10-12GW_CBD_EH4111


title: ZFP92_ChIPseq


title: testis_10-12GW_CBD_EH4112


title: testis_10-12GW_CBD_EH4026


title: RNA_443_r2


title: Batch_07_ChIPseq_TI

value: mixed total input


title: ZFP92_ChIPseq_TI


title: testis_10-12GW_CBD_EH4174


title: RNA_443_r1


title: testis_10-12GW_CBD_EH4142


title: testis_10-12GW_CBD_EH4155


title: RNA_417_r2


title: testis_10-12GW_CBD_EH4138


title: Batch_05_ChIPseq_TI


title: testis_10-12GW_CBD_EH3840


title: testis_12-14GW_Ctrl_EtOH_EH3412

value: EtOH


title: testis_12-14GW_Ctrl_EtOH_EH3345


title: Batch_06_ChIPseq_TI


title: testis_12-14GW_Ctrl_EtOH_EH4075


title: testis_12-14GW_Ctrl_EtOH_EH4115


title: testis_12-14GW_Ctrl_EtOH_EH3366


title: RNA_510_r2


title: Batch_04_ChIPseq_TI


title: testis_12-14GW_Ctrl_EtOH_EH3351


title: RNA_510_r1


title: Batch_03_ChIPseq_TI


title: testis_12-14GW_Ctrl_EtOH_EH3265


title: RNA_509_r2


title: testis_12-14GW_Ctrl_EtOH_EH4168


title: testis_12-14GW_Ctrl_EtOH_EH4114


title: Batch_02_ChIPseq_TI


title: testis_12-14GW_Ctrl_EtOH_EH4109


title: testis_10-12GW_Ctrl_EtOH_EH4080


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM12239Bu

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

institute: University of Geneva

data_processing:
Software to map the reads to the UCSC hg19 human reference genome: TopHat 1049v.2.0.11
Software to estimate the read counts for each gene: HTSeq v0.6p1 1052
Genome_build: hg19
Supplementary_files_format_and_content: Table of raw gene counts for each gene (rows) and each sample (columns)

growth_protocol: At the start of the experiment, the cell lines were thawed and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (HyClone, South Logan, UT, USA) and 1% Penicillin-Streptomycin (Gibco) and incubated at 37°C, 5% CO2-humidified atmosphere according to manufacturer’s recommendations.

extract_protocol:
Total RNA was isolated using the using PureLink RNA Mini kit (Invitrogen, Thermo Scientific, Wilmington, DE, USA).
Sequencing libraries were prepared from total RNA using the stranded Illumina TruSeq RNA-seq protocol with polyA enrichment. Sequencing libraries were prepared from 0.5 or 1 μg total RNA using the TruSeq stranded mRNA reagents (Illumina HiSeq 2000 library preparation kit with millions of reads [100PE]).
The samples were sequenced on a HiSeq 4000 (Illumina) with 100 bp single-end reads.

treatment_protocol: The LCLs were incubated for 48h with and without 100 µM busulfan (Sigma-Aldrich, Germany) and 1% dimethylsulfoxide (DMSO; Sigma-Aldrich, Germany).

tag: sample type


title: RNA_508_r2


title: RNA_509_r1


title: AC115220_ChIPseq

tag: chip antibody


title: testis_10-12GW_Ctrl_EtOH_EH4072


title: RNA_508_r1


title: testis_10-12GW_Ctrl_EtOH_EH3413


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM12239


title: RNA_507_r2


title: testis_10-12GW_Ctrl_EtOH_EH4174


title: testis_10-12GW_Ctrl_EtOH_EH4155


title: testis_10-12GW_Ctrl_EtOH_EH4142


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM12057Bu


title: RNA_507_r1


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM12057


title: RNA_506_r2


title: testis_10-12GW_Ctrl_EtOH_EH4105


title: RNA_506_r1


title: testis_10-12GW_Ctrl_EtOH_EH4111


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH3412

value: DMSO-EtOH


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH3345


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM7056


title: testis_10-12GW_Ctrl_EtOH_EH4147


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM12489Bu


title: RNA_503_r2


title: testis_10-12GW_Ctrl_EtOH_EH4138


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM12489


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH3234


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH4115


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH4168


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH3351


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH4075


title: RNA_410_r5


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH4109


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH3265


title: RNA_410_r4


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM12546Bu


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM12546


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM7056Bu


title: testis_12-14GW_Ctrl_DMSO-EtOH_EH4114


title: immortalized non-malignant lymphoblastoid cell lines incubated with busulfan GM12762Bu


title: RNA_439_r6


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4105


title: immortalized non-malignant lymphoblastoid cell lines incubated without busulfan GM12762


title: RNA_439_r4


title: RNA_439_r5


title: RNA_503_r1


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4142


title: Arabidopsis RNC-mRNA rep2

description:
RNC-mRNA replicate 2
Translation_efficiency_RNC-mRNA-seq.xlsx

library_source: other

data_processing:
library strategy: RNC-seq
library strategy: RNC-seq
Reads were mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
samtools mpileup to identity nucleotide at each position.
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: Mutation matrix was generated by samtools mpileup, p value was from Proportion Test. Bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.

molecule: other

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
For acRIP-seq, seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody. For ac4C-seq, mRNA was purified by oligodT beads. 3 ug of mRNA was used for the construction of sequencing libraries.
For RNC-seq, Arabidopsis seedlings were homogenized in liquid nitrogen and lysed in in 1 ml pre-chilled ribosome buffer (20 mM HEPES[pH 7.44], 15 mM MgCl2, 200 mM KCl, 100 mg/ml cycloheximide, 2 mM dithiothreitol) with 1% Triton X-100 for 30 minutes at 4ºC. Cell lysate was centrifuged at 17,000 g for 5 minutes and supernatant was taken. The supernatants were transferred to 12.5 ml sucrose buffer (30% sucrose in ribosome buffer). After centrifuging at 185,000g for 5 hours at 4ºC, the pellet was suspended in cold ribosome buffer to get RNC.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.   ac4C-seq libraries were prepared using NEBNext UltraTM Ⅱ Directional RNA Library Prep Kit for Illumina (NEB, E7760S) following manufacturer's protocols.

value: Seedlings

tag: molecule subtype

value: RNC-mRNA


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4111


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4155


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4072


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4112


title: RNA_438_r3


title: RNA_438_r2


title: Arabidopsis RNC-mRNA rep1

description:
RNC-mRNA replicate 1
Translation_efficiency_RNC-mRNA-seq.xlsx


title: Arabidopsis mRNA rep2

description:
mRNA replicate 2
Translation_efficiency_RNC-mRNA-seq.xlsx

data_processing:
library strategy: RNC-seq
Reads were mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
samtools mpileup to identity nucleotide at each position.
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: Mutation matrix was generated by samtools mpileup, p value was from Proportion Test. Bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4147


title: testis_12-14GW_Ctrl_DMSO_EH3345

value: DMSO


title: RNA_438_r1


title: Arabidopsis mRNA rep1

description:
mRNA replicate 1
Translation_efficiency_RNC-mRNA-seq.xlsx


title: testis_12-14GW_Ctrl_DMSO_EH3412


title: RNA_410_r3


title: testis_12-14GW_Ctrl_DMSO_EH4115


title: testis_12-14GW_Ctrl_DMSO_EH4075


title: NaCNBH3 treated, Day10

tag: cultivar

tag: treatment

tag: time

value: 20 min


title: testis_12-14GW_Ctrl_DMSO_EH3366

tag: gender


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4080


title: Control, Day10

value: control


title: RNA_410_r2


title: testis_12-14GW_Ctrl_DMSO_EH3351

value: XY


title: RNA_410_r1


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH4138


title: testis_12-14GW_Ctrl_DMSO_EH4168


title: testis_12-14GW_Ctrl_DMSO_EH4114


title: RNA_442_r3


title: testis_12-14GW_Ctrl_DMSO_EH4109


title: testis_10-12GW_Ctrl_DMSO_EH4105


title: M20_2_IP

city: Chongqing

first: Libangxi

last: Liu

address: 183 Xinqiao Main Street Shapingba, Chongqing 400037, People’s  Republic of China

institute: Department of Orthopedics Xinqiao Hospital, Army Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: Nucleus pulposus

extract_protocol:
MeRIP-seq and RNA-seq were conducted by LC-Bio Technologies (Hangzhou, China). Briefly, TRIzol (Invitrogen, USA) was used to extract total RNA from NP tissues. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, USA) and confirmed by electrophoresis with denaturing agarose gel. Dynabeads Oligo (dT) 25-61005 (Thermo Fisher, USA) and Magnesium RNA Fragmentation Module (NEB, USA) were used to purify and fragment Poly (A) RNA. Then the cleaved RNA fragments were incubated with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer to perform m6A RNA immunoprecipitation. Both input samples without immunoprecipitation and the m6A IP samples were used to construct libraries for MeRIP-seq.
MeRIP

value: Nucleus pulposus


title: M20_1_IP


title: M20_3_IP


title: testis_10-12GW_Ctrl_DMSO_EH4026

value: no


title: testis_10-12GW_Ctrl_DMSO_EH4072


title: testis_10-12GW_Ctrl_DMSO_EH4155


title: RNA_442_r2


title: RNA_439_r3


title: M10_3_IP


title: testis_12-14GW_Ctrl_DMSO_EH3265


title: RNA_442_r1


title: testis_10-12GW_Ctrl_DMSO-EtOH_EH3417


title: testis_10-12GW_Ctrl_DMSO_EH4174


title: M10_2_IP


title: RNA_439_r2


title: testis_10-12GW_Ctrl_DMSO_EH4142


title: M10_1_IP


title: testis_10-12GW_Ctrl_DMSO_EH4111


title: testis_10-12GW_Ctrl_DMSO_EH4138


title: testis_10-12GW_Ctrl_DMSO_EH4112


title: testis_10-12GW_Ctrl_DMSO_EH3840


title: M2_3_IP


title: RNA_439_r1


title: RNA_504_r3


title: M2_2_IP


title: RNA_504_r2


title: 23_S23

city: Aurora

first: Rebecca

middle: E

last: Schweppe

state: Colorado

department: Endocrinology

institute: The University of Colorado Anschutz Medical Campus

data_processing:
Paired-end 150 bp-long sequences were aligned to the hg38 human reference genome using STAR RNA-seq aligner (PMID: 23104886)
Transcript counts were estimated with the help of htseq-count script from HTSeq 0.11.1 (PMID: 25260700)
Supplementary files format and content: Gene-level expression was calculated by summing FPKM (fragments per kilobase million) values for gene transcripts

source_name: CUTC60 48 hour ulixertinib

growth_protocol: CUTC5 and CUTC60 cells were grown in RPMI supplemented with 5% fetal bovine serum (FBS) and maintained in 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
paired end 150 cycle 2x150, 50 million paire end reads
Poly A Selected Total RNA Lib
Universial PlusTM mRNA-seq library preparation kit

treatment_protocol: Cells were treated with DMSO, 100 nM dabrafenib, or 1 uM ulixertinib for 48 hours

value: anaplastic thyroid cancer

value: ulixertinib

value: 48 hours


title: 24_S24

source_name: CUTC60 48 hour dabrafenib + ulixertinib

value: dabrafenib+ulixertinib


title: 22_S22

source_name: CUTC60 48 hour dabrafenib

value: dabrafenib


title: RNA_504_r1

source_name: Embryonic stem cells

value: wildtype


title: 21_S21

source_name: CUTC60 48 hour DMSO


title: M20_3_input


title: 19_S19


title: 20_S20


title: 16_S16


title: 17_S17


title: 18_S18


title: M20_2_input


title: 14_S14


title: 13_S13


title: 15_S15


title: M20_1_input


title: M10_3_input


title: SCAR_438_stranded_input_T8_K4me3_r1

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:
After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase under native conditions. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
OTHER

treatment_protocol: Cells were incubated in EdU media (f.c. 10 um)  for 15 min and then either collected (T0) or cultured for indicated maturation intervals (T3; T8) in media without EdU before collection.


title: SCAR_439_stranded_input_T8_K4me3_r1

description: EdU-labelled genomic DNA


title: SCAR_439_stranded_input_T3_K4me3_r1

description: EdU-labelled genomic DNA


title: M10_2_input


title: SCAR_439_stranded_input_T0_K4me3_r1

description: EdU-labelled genomic DNA


title: 12_S12

source_name: CUTC5 48 hour dabrafenib + ulixertinib

value: papillary thyroid cancer


title: 11_S11

source_name: CUTC5 48 hour ulixertinib


title: SCAR_438_stranded_input_T3_K4me3_r1

description: EdU-labelled genomic DNA


title: 10_S10

source_name: CUTC5 48 hour dabrafenib


title: 9_S9

source_name: CUTC5 48 hour DMSO


title: SCAR_438_stranded_input_T0_K4me3_r1

description: EdU-labelled genomic DNA


title: M10_1_input


title: M2_1_IP


title: M2_3_input


title: 7_S7


title: 5_S5


title: SCAR_410_stranded_input_T8_K4me3_r1

description: EdU-labelled genomic DNA


title: 6_S6


title: M2_1_input


title: 4_S4


title: SCAR_410_stranded_input_T3_K4me3_r1

description: EdU-labelled genomic DNA


title: 3_S3


title: 2_S2


title: K562, Input, untreated, SAC-seq

description:
Non-ribosomal chromatin-associated RNA
RBFOX2-Input-untreated-r1-S7_caRNA-SAC_K562

data_processing:
Raw reads containing adapter sequence were clipped by using Cutadapt v2.10
Unique molecular identifiers (UMIs) were used for accurate detection and removal of PCR duplicates by using ‘clumpify.sh’ from BBMAP tools
The preprocessed reads were then aligned to human genome and transcriptome (hg38) using STAR v2.7.3a with parameters according to the ENCODE long RNA-seq processing pipeline with parameter '--outFilterMismatchNoverReadLmax 0.06'
After mapping, mutation calling was performed using VarScan v2.3.9 subcommand ‘somatic’ in two pair-wise comparisons.
Assembly: hg38
Supplementary files format and content: m6A sites

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 37C.

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher). Ribosome RNA was depleted by RiboMinus™ Eukaryote Kit (ThermoFisher).
RBFOX2-bound RNA was enriched by protein pulldown, and RNA was extracted with TRIzol reagent (ThermoFisher).
Libraries were prepared by adaptor ligation and PCR.

treatment_protocol: Chromatin fraction was extracted before RNA isolation.

tag: rna treatment

value: Human derived hepatoma cell line

value: WT

tag: antibody


title: K562, RBFOX2 IP, untreated, SAC-seq

description:
Non-ribosomal chromatin-associated RNA
RBFOX2-IP-untreated-r1-S8_caRNA-SAC_K562

value: anti-His RBFOX2 (ThermoFisher Cat# 10104D)


title: 1_S1


title: SCAR_439_stranded_input_T3_K27me3_r1

description: EdU-labelled genomic DNA


title: SCAR_439_stranded_input_T8_K27me3_r1

description: EdU-labelled genomic DNA


title: K562, Input, MjDim1 treated, SAC-seq

description:
Non-ribosomal chromatin-associated RNA
RBFOX2-Input-treated-r1-S3_caRNA-SAC_K562

value: recombinant MjDim1 enzyme


title: SCAR_439_stranded_input_T0_K27me3_r1

description: EdU-labelled genomic DNA


title: K562, RBFOX2 IP, MjDim1 treated, SAC-seq

description:
Non-ribosomal chromatin-associated RNA
RBFOX2-IP-treated-r1-S4_caRNA-SAC_K562


title: K562, 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) with ‘--rna-strandness RF’ parameters.
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.

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in cellular incubator with 5% CO2 at 37C. K562 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 2nM L-glutamine and antibiotics in cellular incubator with 5% CO2 at 37C.

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.

value: Human immortalized myelogenous leukemia cell line

value: RBFOX2 knockdown

tag: m6a merip_antibody

value: EpiMark N6-Methyladenosine Enrichment Kit


title: 8_S8


title: K562, RBFOX2 KD, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, Control, IP, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

value: Control


title: M2_2_input

value: Nucleus pulposus


title: K562, Control, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: SCAR_438_stranded_input_T3_K27me3_r1

description: EdU-labelled genomic DNA


title: SCAR_438_stranded_input_T8_K27me3_r1

description: EdU-labelled genomic DNA


title: K562, RBFOX2 KD, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, RBFOX2 KD, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, Control, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, Control, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: SCAR_438_stranded_input_T0_K27me3_r1

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_T0_K4me3_r1

description: EdU-labelled genomic DNA


title: Atrx-DMSO_1

city: Houston

first: Prit Benny

last: Malgulwar

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

institute: U.T. M.D. ANDERSON CANCER CENTER

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis, followed by alignment to mouse mm9 genome using RNASTAR (version 2.7.8a)
Raw transcript counts were generated using HTseq-count tool (version 0.9.1), followed by Principal Component Analysis (PCA).
Differentially expressed genes (DEGs) were calculated using DESeq2 (version 2.11.40.7) and were later subjected to Gene Set Enrichment Analysis (GSEA) analysis using a desktop version of the analysis tool
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary cell line

growth_protocol: Neuroprogenitor Cells were grown in NeuroCult Basal Medium containing NeuroCult Proliferation Supplement, 20 ng/ml EGF, 10 ng/ml basic FGF, 2 μg/ml heparin (Stemcell Technologies), 50 units/ml penicillin, and 50 μg/ml streptomycin (Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA extraction using Qiagen RNeasy Plus kit
RNA libraries for RNA-seq were prepared using Truseq library preparation kits (Illumina)  following manufacturer's protocols.

treatment_protocol: Atrx- mNPCs were treated with Sirt2 inhibitor (AGK2: 1uM) or DMSO vehicle for 48 hours

value: Primary cell line

value: Neuroepithelial progenitor cell

value: DMSO


title: Atrx-DMSO_2

value: 48 hours


title: Atrx-AGK2_1


title: Atrx-AGK2_3


title: Atrx-DMSO_3


title: Atrx-AGK2_2


title: K562, IP, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: SCAR_410_stranded_input_T8_K27me3_r1

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_T3_K27me3_r1

description: EdU-labelled genomic DNA


title: SCAR_410_stranded_input_T0_K27me3_r1

description: EdU-labelled genomic DNA


title: HepG2, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: HepG2, IP, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: E14

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

description: 10X Genomics V2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software using mm10 reference genome.
Cell Ranger output files were processed to create loom files required for RNA velocity analysis
Assembly: mm10
Supplementary files format and content: loom files

source_name: Skin

extract_protocol:
Single-cell suspension from whole skin collected at E14.5, E17.5, P5 WT mice were processed and prepared for 10X Genomics 3' Gene Expression kit (v2)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Mixed

value: Skin

tag: age


title: WT-ASN3-4h

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg19) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (v19) .
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: T cell

growth_protocol: The naïve CD8 T cells were activated using plate bound anti CD3 and anti CD28 and cultured for 4, 24 and 72h

extract_protocol:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Nationwide Children's hospital.

treatment_protocol: Cells were cultured in complete or asparagine restriction medium

value: LN,Spleen

value: CD8 T cells

tag: Sex

value: male

value: 8-12 weeks

value: Wild Type

tag: agent

tag: time point


title: HepG2, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

tag: cell line

value: Human derived hepatoma cell line

tag: genotype

value: WT


title: E17

description: 10X Genomics V2

tag: cell type

tag: tissue

tag: strain


title: HepG2, Input, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: WT-ASN2-4h


title: P5

description: 10X Genomics V2


title: SCAR_439_H3K4me3_T3_r2

description: EdU-labelled genomic DNA


title: SCAR_439_H3K4me3_T8_r2

description: EdU-labelled genomic DNA


title: K562, Control, IP, r2, KAS-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
Library strategy: KAS-Seq

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher). Azide containing RNA was labeled with DBCO-biotin and captured with Dynabeads™ MyOne™ Streptavidin C1 (ThermoFisher)
Libraries were prepared using Accel-NGS Methyl-seq DNA library kit (Swift)

treatment_protocol: K562 cells were treated with N3-kethoxal before collection.

value: Human immortalized myelogenous leukemia cell line

tag: ip method

value: N3-kethoxal biotin IP


title: SCAR_439_H3K4me3_T0_r2

description: EdU-labelled genomic DNA


title: WT-cnl3-4h


title: K562, Control, Input, r1, KAS-seq

description: RBFOX2-shCtrl-Ctrl-Input-r1-K1.27_KAS_K562

value: Control


title: SCAR_438_H3K4me3_T8_r2

description: EdU-labelled genomic DNA


title: K562, IP, r1, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA

value: EpiMark N6-Methyladenosine Enrichment Kit


title: WT-cnl2-4h


title: K562, RBFOX2 KD, IP, r1, KAS-seq

value: RBFOX2 knockdown


title: SCAR_438_H3K4me3_T3_r2

description: EdU-labelled genomic DNA


title: WT-cnl1-4h


title: K562, Input, r2, MeRIP-seq

description: Non-ribosomal chromatin-associated RNA


title: K562, siYTHDC1 KD, Input, r2, b4, 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.
Peaks were called using HOMER mode in histone (for histone modification ChIP-seq) or factor (for hranscriptional factor ChIP-seq) with default parameters.
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: siYTHDC1 knockdown

tag: chip antibody


title: WT-ASN3-24h


title: K562, siControl, Input, r2, b4, ChIP-seq

value: siControl


title: WT-ASN1-4h


title: K562, siControl, Input, r1, b4, ChIP-seq


title: WT-ASN2-24h


title: K562, Control, IP, r1, KAS-seq


title: K562, siYTHDC1 KD, SUZ12, r2, b4, ChIP-seq

value: Rabbit monoclonal anti-SUZ12 (Cat#3737, Cell Signaling Technology)


title: SCAR_410_H3K4me3_T3_r2

description: EdU-labelled genomic DNA

value: wildtype


title: K562, Control, Input, r2, KAS-seq

description: RBFOX2-shCtrl-Ctrl-Input-r2-K2.28_KAS_K562


title: K562, siYTHDC1 KD, SUZ12, r1, b4, ChIP-seq


title: K562, RBFOX2 KD, Input, r2, KAS-seq


title: K562, siYTHDC1 KD, EZH2, r1, b4, ChIP-seq

value: Rabbit polyclonal anti-EZH2 (Cat# #5246, Cell Signaling Technology)


title: WT-cnl2-24h

value: LN,Spleen


title: WT-ASN1-24h

value: CD8 T cells


title: WT-cnl3-24h

value: male


title: K562, siControl, SUZ12, r1, b4, ChIP-seq


title: K562, siControl, EZH2, r2, b4, ChIP-seq


title: K562, siYTHDC1 KD, Input, r1, b4, ChIP-seq


title: SCAR_439_H3K4me3_T8_r1

description: EdU-labelled genomic DNA


title: SCAR_438_H3K4me3_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_410_H3K4me3_T8_r2

description: EdU-labelled genomic DNA


title: K562, RBFOX2 KD, Input, r2, b4, ChIP-seq


title: K562, siControl, EZH2, r1, b4, ChIP-seq


title: K562, siControl, SUZ12, r2, b4, ChIP-seq


title: WT-ASN3-72h

value: 8-12 weeks


title: SCAR_410_H3K4me3_T0_r2

description: EdU-labelled genomic DNA


title: K562, RBFOX2 KD, IP, r2, KAS-seq


title: K562, siYTHDC1 KD, EZH2, r2, b4, ChIP-seq


title: K562, RBFOX2 KD, Input, r1, b4, ChIP-seq


title: WT-ASN2-72h

value: Wild Type


title: K562, Control, Input, r2, b4, ChIP-seq


title: SCAR_438_H3K4me3_T8_r1

description: EdU-labelled genomic DNA


title: Mycelium of mutant delta POX01387, rep3

city: Nanning

first: Shuai

last: Zhao

state: Guangxi

address: 100 Daxue Road

institute: Guangxi University

description: Mycelium of 1 gram mutant delta POX01387 were cultured in 2% Avicel liquid medium for 24 hours, rep3

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000, and the genes information used have been uploaded to the previous GSE80076.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Fresh spores of the delta Ku70 and mutant delta POX01387 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 5 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 spores per milliliter. The inoculated MMM containing glucose (1.0% w/v) with a final concentration of 1 × 10e6 spore/mL was pre-grown for 24 h at 28°C. The mycelia (~ 1.0 g) were collected and then transferred into fresh 100 mL liquid MMM containing Avicel for 24 h.

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
After the enriched and purified mRNA was fragmented, N6 random primers were used for reverse transcription, and then another strand of cDNA was synthesized. The end of the synthesized double stranded DNA was flattened and phosphorylated at the 5 'end. The 3' end formed a sticky end protruding "A", and then connected with a bubbly junction protruding "T" at the 3' end. The ligation products were amplified by PCR with specific primers. PCR products were heat denatured into single strand, and then cyclized with a bridge primer to obtain a single strand circular DNA library. Finally, BGISEQ-500 platform was used for sequencing.

value: mutant delta POX01387

value: Mycelium


title: K562, Control, Input, r1, b4, ChIP-seq

value: Human immortalized myelogenous leukemia cell line


title: SCAR_438_H3K4me3_T3_r1

city: Copenhagen

first: Anja

last: Groth

institute: Novo Nordisk Foundation Center for Protein Research

description: EdU-labelled genomic DNA


title: WT-ASN1-72h


title: SCAR_439_H3K4me3_T3_r1

description: EdU-labelled genomic DNA


title: K562, RBFOX2 KD, Input, r1, KAS-seq


title: Mycelium of mutant delta POX01387, rep2

description: Mycelium of 1 gram mutant delta POX01387 were cultured in 2% Avicel liquid medium for 24 hours, rep2


title: K562, RBFOX2 KD, RBM15, r2, b4, ChIP-seq

value: Rabbit polyclonal anti-RBM15 (Cat#10587-1-AP, Proteintech)


title: SCAR_438_H3K4me3_T0_r1

description: EdU-labelled genomic DNA


title: Mycelium of mutant delta POX01387, rep1

description: Mycelium of 1 gram mutant delta POX01387 were cultured in 2% Avicel liquid medium for 24 hours, rep1


title: WT-cnl3-72h


title: WT-cnl1-24h


title: SCAR_439_H3K4me3_T0_r1

description: EdU-labelled genomic DNA


title: K562, RBFOX2 KD, RBM15, r1, b4, ChIP-seq


title: WT-cnl2-72h


title: SCAR_410_H3K4me3_T8_r1

description: EdU-labelled genomic DNA


title: K562, Control, RBM15, r2, b4, ChIP-seq

value: Control


title: SCAR_410_H3K4me3_T3_r1

description: EdU-labelled genomic DNA


title: Mycelium of mutant delta ku70, rep3

description: Mycelium of 1 gram mutant delta ku70 were cultured in 2% Avicel liquid medium for 24 hours, rep3

value: mutant delta ku70


title: WT-cnl1-72h


title: Mycelium of mutant delta ku70, rep2

description: Mycelium of 1 gram mutant delta ku70 were cultured in 2% Avicel liquid medium for 24 hours, rep2


title: SCAR_410_H3K4me3_T0_r1

description: EdU-labelled genomic DNA


title: K562, Control, RBM15, r1, b4, ChIP-seq


title: K562, Control, YTHDC1, r2, b4, ChIP-seq

value: Rabbit polyclonal anti-YTHDC1 (Cat# ab122340, Abcam)


title: SCAR_439_H3K27me3_T8_r2

description: EdU-labelled genomic DNA


title: K562, Control, YTHDC1, r1, b4, ChIP-seq


title: Mycelium of mutant delta ku70, rep1

description: Mycelium of 1 gram mutant delta ku70 were cultured in 2% Avicel liquid medium for 24 hours, rep1


title: K562, RBFOX2 KD, Input, r2, b3, ChIP-seq

value: RBFOX2 knockdown


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 4 hours T

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with various carbon sources including 1% (w/v) AV, WB, MC, HEV and Glu, respectively, and incubated in a shaker at 180 rpm and 28°C for 4‒48 h, and basic medium without carbon source (NC) was used for a control.

extract_protocol: Total RNA were extracted using TRIzol RNA Kit

tag: treatment

value: 1% wheat bran liquid medium for 4 hours


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 4 hours S


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 4 hours F


title: K562, RBFOX2 KD, Input, r1, b3, ChIP-seq


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 4 hours T

value: 1% Avicel liquid medium for 4 hours


title: TNBC cancer 3

type: RNA

city: Seoul

first: Yesol

last: Kim

address: Cheongpa-ro 47-gil 100, Yongsan-gu

institute: Sookmyung Women's University

hyb_protocol: The labeled RNA samples were dried in a Vacuum Concentrator for one hour. Once samples are completely dried, they were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. Arrays were hybridized in 45 µl of the mixture, and then rotated at 20 rpm for 20 h at 55°C. Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System

scan_protocol: Agilent Gene expression were scanned on a Agilent Technologies G4900DA SureScanner using 3 µm resolution

data_processing: Data were acquired using Agilent Feature Extraction software version 11.0.1.1

source_name: TNBC cancer tissue 3

label_protocol: 100 ng total RNA was dephosphorylated(PO4) at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour

extract_protocol: Total RNA from human tissue was isolated using TRIzol (Life Technologies) following the manufacturer's protocol.

value: female

tag: disease subtype

value: TNBC

value: TNBC cancer tissue


title: TNBC cancer 2

source_name: TNBC cancer tissue 2

tag: gender


title: K562, Control, Input, r2, b3, ChIP-seq


title: TNBC cancer 1

source_name: TNBC cancer tissue 1


title: TNBC adjacent normal 3

source_name: TNBC adjacent normal tissue 3

value: normal

value: TNBC adjacent normal tissue


title: SCAR_438_H3K27me3_T8_r2

address: Blegdamsvej 3B

description: EdU-labelled genomic DNA


title: SCAR_438_H3K27me3_T3_r2

description: EdU-labelled genomic DNA


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 4 hours S


title: SCAR_438_H3K27me3_T0_r2

description: EdU-labelled genomic DNA


title: K562, Control, Input, r1, b3, ChIP-seq


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 4 hours F


title: TNBC adjacent normal 2

source_name: TNBC adjacent normal tissue 2


title: K562, RBFOX2 KD, H3K27me3, r2, b3, ChIP-seq

value: Rabbit anti-H3K27me3 (Cat#9733, Cell Signaling Technology)


title: SCAR_410_H3K27me3_T8_r2

description: EdU-labelled genomic DNA

value: wildtype


title: TNBC adjacent normal 1

source_name: TNBC adjacent normal tissue 1


title: SCAR_439_H3K27me3_T3_r2

description: EdU-labelled genomic DNA


title: luminal B cancer 2

source_name: luminal B cancer tissue 2

value: Luminal B

value: luminal B cancer tissue


title: K562, RBFOX2 KD, H3K27me3, r1, b3, ChIP-seq

value: Human immortalized myelogenous leukemia cell line


title: SCAR_439_H3K27me3_T0_r2

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells


title: luminal B cancer 1

source_name: luminal B cancer tissue 1


title: SCAR_410_H3K27me3_T3_r2

description: EdU-labelled genomic DNA


title: 9_hd_LATSkd_1

city: Boston

first: Steen

last: Hansen

state: MA

address: Enders Building, Room 1016

department: GI Division

institute: Boston Children's Hospital

description:
all_counts_LATSkd.csv
LATS_kd3.expected_count

data_processing:
Sequence reads were filtered with SOAPnuke software to remove read with adapters, unknown bases, and low-quality reads.
Genome mapping of filtered reads to reference genome GRCh38 was performed using HISAT2 and Bowtie2 software.
Raw data of RNA-seq were normalized and processed using R package DEseq2
Assembly: GRCh38
Supplementary files format and content: all_counts_LATSkd.csv include raw count values for all the samples

source_name: cell line

growth_protocol: H661 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen) (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was subjected to Oligo dT selection for enrichment of mRNA followed by reverse transcription and second strand synthesis.

treatment_protocol: 1x10^6 cells were plated in a 6-well plate and cultured for 1 week to reach saturation density

value: cell line

value: p190A expression with LATS1/2 knockdown

value: culture to saturation density


title: 8_hd_LATSkd_1

description:
all_counts_LATSkd.csv
LATS_kd2.expected_count


title: SCAR_410_H3K27me3_T0_r2

description: EdU-labelled genomic DNA


title: K562, Control, H3K27me3, r2, b3, ChIP-seq

value: Control


title: 7_hd_LATSkd_1

description:
all_counts_LATSkd.csv
LATS_kd1.expected_count


title: luminal B adjacent normal 2

source_name: luminal B adjacent normal tissue 2

value: luminal B adjacent normal tissue


title: SCAR_439_H3K27me3_T8_r1

description: EdU-labelled genomic DNA


title: K562, Control, H3K27me3, r1, b3, ChIP-seq


title: luminal B adjacent normal 1

source_name: luminal B adjacent normal tissue 1


title: 6_hd_p190A_1

description:
all_counts_LATSkd.csv
p190A_3.expected_count

value: wild-type p190A expression