title: SLC25A11 [RNCMPT01165]

description:
A403_2_N.txt
channel 2


title: RAN [RNCMPT01126]

status: Public on Mar 31 2023

type: RNA

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
A383_2_N.txt
channel 1

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on a microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 8.0.

data_processing: Experimental data is contained in a matrix where rows correspond to microarray probes and columns are the normalized intensities of the Cy3- or Cy5-labeled RNA from the GST-RBP pulldown assay. For the data processing, first, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation, calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: For the raw data files, the "N" in the headers  (linked below as a supplementary file) stands for "Normalized". The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the "N" (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

molecule: total RNA

organism: synthetic construct

source_name: Pulldown RNA labeled with Cy3

label_protocol: Purified RBP-specific pulldown RNA are labeled with Cy3 or Cy5 according to the manufacturer's recommended protocol (Kreatech, Cat# EA-021).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purified by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown


title: MAPRE1 [RNCMPT01125]

description:
A383_2_N.txt
channel 2

source_name: Pulldown RNA labeled with Cy5


title: TBCA [RNCMPT01121]

description:
A382_2_N.txt
channel 2


title: MRPL27 [RNCMPT01122]

description:
A382_2_N.txt
channel 1


title: RPS10 [RNCMPT01119]

description:
A381_2_N.txt
channel 2


title: RPS28 [RNCMPT01118]

description:
A380_2_N.txt
channel 1


title: TMSB4X [RNCMPT01120]

description:
A381_2_N.txt
channel 1


title: SEC61B [RNCMPT01116]

description:
A379_2_N.txt
channel 1


title: RPL28 [RNCMPT01115]

description:
A379_2_N.txt
channel 2


title: DUSP14 [RNCMPT01112]

description:
A377_2_N.txt
channel 1


title: UBE2N [RNCMPT01113]

description:
A378_2_N.txt
channel 2


title: RPS25 [RNCMPT01111]

description:
A377_2_N.txt
channel 2


title: RPL30 [RNCMPT01114]

description:
A378_2_N.txt
channel 1


title: EIF5A [RNCMPT01109]

description:
A376_2_N.txt
channel 2


title: WBSCR22 [RNCMPT01108]

description:
A375_2_N.txt
channel 1


title: SNRPD3 [RNCMPT01106]

description:
A374_2_N.txt
channel 1


title: RPL23 [RNCMPT01105]

description:
A374_2_N.txt
channel 2


title: RPS16 [RNCMPT01104]

description:
A373_2_N.txt
channel 1


title: HSPE1 [RNCMPT01107]

description:
A375_2_N.txt
channel 2


title: RPP25L [RNCMPT01103]

description:
A373_2_N.txt
channel 2


title: NHP2 [RNCMPT01102]

description:
A372_2_N.txt
channel 1


title: FAM103A1 [RNCMPT01094]

description:
A369_2_N.txt
channel 1


title: EIF1B [RNCMPT01097]

description:
A371_2_N.txt
channel 2


title: RPL19 [RNCMPT01098]

description:
A371_2_N.txt
channel 1


title: NOL7 [RNCMPT01096]

description:
A370_2_N.txt
channel 1


title: RPS15A [RNCMPT01095]

description:
A370_2_N.txt
channel 2


title: FCF1 [RNCMPT01092]

description:
A368_2_N.txt
channel 1


title: CSTB [RNCMPT01090]

description:
A367_2_N.txt
channel 1


title: COA6 [RNCMPT01088]

description:
A366_2_N.txt
channel 1


title: WIBG [RNCMPT01087]

description:
A366_2_N.txt
channel 2


title: TSFM [RNCMPT01086]

description:
A365_2_N.txt
channel 1


title: RPS4X [RNCMPT01089]

description:
A367_2_N.txt
channel 2


title: RPL35 [RNCMPT01117]

description:
A380_2_N.txt
channel 2


title: MAGOH2 [RNCMPT01085]

description:
A365_2_N.txt
channel 2


title: RPS14 [RNCMPT01110]

description:
A376_2_N.txt
channel 1


title: RPL11 [RNCMPT01084]

description:
A364_2_N.txt
channel 1


title: CCDC124 [RNCMPT01081]

description:
A363_2_N.txt
channel 2


title: MRPS23 [RNCMPT01082]

description:
A363_2_N.txt
channel 1


title: ABT1 [RNCMPT01083]

description:
A364_2_N.txt
channel 2


title: IMP3 [RNCMPT01080]

description:
A362_2_N.txt
channel 1


title: RPL10A [RNCMPT01079]

description:
A362_2_N.txt
channel 2


title: LSM2 [RNCMPT01078]

description:
A361_2_N.txt
channel 1


title: RPS23 [RNCMPT01101]

description:
A372_2_N.txt
channel 2


title: RPS3A [RNCMPT01076]

description:
A360_2_N.txt
channel 1


title: YWHAZ [RNCMPT01075]

description:
A360_2_N.txt
channel 2


title: PEF1 [RNCMPT01077]

description:
A361_2_N.txt
channel 2


title: RPS18 [RNCMPT01072]

description:
A358_2_N.txt
channel 1


title: MRPL40 [RNCMPT01073]

description:
A359_2_N.txt
channel 2


title: NHP2L1 [RNCMPT01071]

description:
A358_2_N.txt
channel 2


title: CCDC59 [RNCMPT01093]

description:
A369_2_N.txt
channel 2


title: SERBP1 [RNCMPT01002]

description:
A344_2_N.txt
channel 1


title: CNBP [RNCMPT00978]

description:
A332_2_N.txt
channel 1


title: NOP16 [RNCMPT01091]

description:
A368_2_N.txt
channel 2


title: LGALS1 [RNCMPT01074]

description:
A359_2_N.txt
channel 1


title: CNBP [RNCMPT00977]

description:
A332_2_N.txt
channel 2


title: PEG10 [RNCMPT00972]

description:
A329_2_N.txt
channel 1


title: PEG10 [RNCMPT00971]

description:
A329_2_N.txt
channel 2


title: CNBP [RNCMPT00979]

description:
A333_2_N.txt
channel 2


title: IFIT2 [RNCMPT00969]

description:
A328_2_N.txt
channel 2


title: ZRANB2 [RNCMPT00965]

description:
A326_2_N.txt
channel 2


title: ZRANB2 [RNCMPT00966]

description:
A326_2_N.txt
channel 1


title: NUDT21 [RNCMPT00964]

description:
A325_2_N.txt
channel 1


title: NUDT21 [RNCMPT00963]

description:
A325_2_N.txt
channel 2


title: CCDC86 [RNCMPT00898]

description:
A297_2_N.txt
channel 2


title: BTF3 [RNCMPT00902]

description:
A299_2_N.txt
channel 2


title: CNBP [RNCMPT00955]

description:
A169_2_D_Redo.txt
channel 2


title: LUC7L2 [RNCMPT00893]

description:
A295_2_N.txt
channel 1


title: LUC7L2 [RNCMPT00660]

description:
A178_2_D.txt
channel 2


title: GNL3 [RNCMPT00892]

description:
A294_2_N.txt
channel 2


title: C1orf131 [RNCMPT00659]

description:
A178_2_D.txt
channel 1


title: EIF3L [RNCMPT00662]

description:
A179_2_D.txt
channel 2


title: BTF3 [RNCMPT00650]

description:
A173_2_D.txt
channel 2


title: CSTF1 [RNCMPT00651]

description:
A174_2_D.txt
channel 1


title: MTPAP [RNCMPT00647]

description:
A172_2_D.txt
channel 1


title: NOP58 [RNCMPT00646]

description:
A171_2_D.txt
channel 2


title: EIF2S2 [RNCMPT00658]

description:
A177_2_D.txt
channel 2


title: CNBP [RNCMPT00641]

description:
A169_2_D.txt
channel 1


title: SF3A3 [RNCMPT00640]

description:
A168_2_D.txt
channel 2


title: STRAP [RNCMPT00631]

description:
A164_2_D.txt
channel 1


title: RPS19BP1 [RNCMPT00624]

description:
A160_2_D.txt
channel 2


title: GNL3 [RNCMPT00643]

description:
A170_2_D.txt
channel 1


title: LUC7L3 [RNCMPT00639]

description:
A168_2_D.txt
channel 1


title: EIF3D [RNCMPT00638]

description:
A167_2_D.txt
channel 2


title: SERBP1 [RNCMPT00625]

description:
A161_2_D.txt
channel 1


title: MRPS24 [RNCMPT00621]

description:
A159_2_D.txt
channel 1


title: CANX [RNCMPT00899]

description:
A298_2_N.txt
channel 1


title: NOP56 [RNCMPT00897]

description:
A297_2_N.txt
channel 1


title: CANX [RNCMPT00619]

description:
A158_2_D.txt
channel 1


title: RNMTL1 [RNCMPT00616]

description:
A156_2_D.txt
channel 2


title: NOP56 [RNCMPT00614]

description:
A155_2_D.txt
channel 2


title: DAP3 [RNCMPT00895]

description:
A296_2_N.txt
channel 1


title: YTHDF2 [RNCMPT00609]

description:
A153_2_D.txt
channel 1


title: MMTAG2 [RNCMPT00606]

description:
A151_2_D.txt
channel 2


title: NGDN [RNCMPT00607]

description:
A152_2_D.txt
channel 1


title: RRP1 [RNCMPT00601]

description:
A149_2_D.txt
channel 1


title: PRPF31 [RNCMPT00603]

description:
A150_2_D.txt
channel 1


title: EEF1A1 [RNCMPT00599]

description:
A148_2_D.txt
channel 1


title: TRMT10C [RNCMPT00600]

description:
A148_2_D.txt
channel 2


title: PUS1 [RNCMPT00629]

description:
A163_2_D.txt
channel 1


title: IFIT2 [RNCMPT00592]

description:
A144_2_D.txt
channel 2


title: API5 [RNCMPT00597]

description:
A147_2_D.txt
channel 1


title: DIMT1 [RNCMPT00622]

description:
A159_2_D.txt
channel 2


title: DAP3 [RNCMPT00595]

description:
A146_2_D.txt
channel 1


title: PEG10 [RNCMPT00560]

description:
A127_2_N.txt
channel 2


title: DEK [RNCMPT00406]

description:
A51_2_D.txt
channel 2


title: BZW1 [RNCMPT00557]

description:
A126_2_N.txt
channel 1


title: DUSP11 [RNCMPT00558]

description:
A126_2_N.txt
channel 2


title: LLPH [RNCMPT00559]

description:
A127_2_N.txt
channel 1


title: MRPS31 [RNCMPT00408]

description:
A52_2_D.txt
channel 2


title: DUSP11 [RNCMPT00407]

description:
A52_2_D.txt
channel 1


title: BRIX1 [RNCMPT00405]

description:
A51_2_D.txt
channel 1


title: CCDC86 [RNCMPT00617]

description:
A157_2_D.txt
channel 1


title: UTP11 [RNCMPT00400]

description:
A48_2_D.txt
channel 2


title: PEG10 [RNCMPT00404]

description:
A50_2_D.txt
channel 2


title: TRUB2 [RNCMPT00398]

description:
A47_2_D.txt
channel 2


title: RPF2 [RNCMPT00402]

description:
A49_2_D.txt
channel 2


title: NPM3 [RNCMPT00612]

description:
A154_2_D.txt
channel 2


title: ZRANB2 [RNCMPT00397]

description:
A47_2_D.txt
channel 1


title: IFIT2 [RNCMPT00970]

description:
A328_2_N.txt
channel 1


title: ANXA2 [RNCMPT00395]

description:
A46_2_D.txt
channel 1


title: NPM1 [RNCMPT00387]

description:
A42_2_D.txt
channel 1


title: PPIB [RNCMPT00391]

description:
A44_2_D.txt
channel 1


title: RPUSD4 [RNCMPT00389]

description:
A43_2_D.txt
channel 1


title: MRPL45 [RNCMPT00393]

description:
A45_2_D.txt
channel 1


title: SUB1 [RNCMPT00561]

description:
A128_2_N.txt
channel 1


title: PPIA [RNCMPT00381]

description:
A39_2_D.txt
channel 1


title: UTP3 [RNCMPT00385]

description:
A41_2_D.txt
channel 1


title: TXN [RNCMPT00377]

description:
A37_2_D.txt
channel 1


title: HIST1H1C [RNCMPT00375]

description:
A36_2_D.txt
channel 1


title: SUB1 [RNCMPT00369]

description:
A33_2_D.txt
channel 1


title: EDF1 [RNCMPT00367]

description:
A32_2_D.txt
channel 1


title: APOBEC3C [RNCMPT00379]

description:
A38_2_D.txt
channel 1


title: SARNP [RNCMPT00361]

description:
A29_2_D.txt
channel 1


title: PHF5A [RNCMPT00365]

description:
A31_2_D.txt
channel 1


title: LLPH [RNCMPT00371]

description:
A34_2_D.txt
channel 1


title: EZR [RNCMPT00348]

description:
A21_2_D.txt
channel 2


title: LYAR [RNCMPT00355]

description:
A25_2_D.txt
channel 2


title: BZW1 [RNCMPT00356]

description:
A26_2_D.txt
channel 1


title: RPS27A [RNCMPT00363]

description:
A30_2_D.txt
channel 1


title: EBNA1BP2 [RNCMPT00332]

description:
A15_2_N.txt
channel 2


title: EBNA1BP2 [RNCMPT00322]

description:
A15_2_D.txt
channel 2


title: MDH2 [RNCMPT00320]

description:
A14_2_D.txt
channel 2


title: ILF2 [RNCMPT00297]

description:
A3_2.txt
channel 1


title: NUDT21 [RNCMPT00296]

description:
A2_2.txt
channel 2


title: PRDX1 [RNCMPT00294]

description:
A1_2.txt
channel 2


title: H1F0 [RNCMPT00383]

description:
A40_2_D.txt
channel 1


title: Human6_H3

status: Public on Mar 17 2023

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Briefly, Illumina sequencing reads (~6 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
CUT&Tag analysis was performed as outlined in Zheng et al, following the protocols.io tutorial (https://dx.doi.org/10.17504/protocols.io.bjk2kkye).The qualities of the FASTQs were checked by running FASTQC/0.11.9.The reads were aligned with bowtie/2-2.4.2 using the end-to-end option.
Sam output files were then filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM (reads per kilobase per million mapped reads) normalized bigWig files. H3 was subtracted from H3K27me3  with bigwigCompare function of deepTools/3.5.0.
Genome_build: hg38, K-12
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

molecule: genomic DNA

organism: Homo sapiens

source_name: human liver

extract_protocol:
Cut&Tag was performed following guidelines in the CUT&Tag@home v.1 protocol by Henikoff et al (Henikoff et al., 2020). Briefly, nuclei were isolated from ~20mg frozen human liver tissue using Minute Detergent-free Nuclei Isolation Kit (Invent Biotechnologies). The nuclei were permeabilized with 0.1% Triton X-100 and their integrity and number was checked under a microscope using a hemocytometer. ~10,000 nuclei per sample were bound to Concanavalin A beads (Bangs Laboratories). The bead-bound nuclei were incubated with primary antibody (1 h at room temperature), secondary antibody (0.5 h at room temperature) and home-made pA-Tn5 transposome (1 h at room temperature). Targeted tagmentation was then performed by addition of buffer containing MgCl2 for 1 h at 37°C. The tagmented DNA was washed with a TAPS-EDTA wash buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA) to remove excess salt and Mg2+ ions followed by targeted release with 0.1% SDS and neutralization of SDS by Triton X-100.
The released DNA was amplified using dual-indexing primers following a PCR protocol that biases amplification of short DNA fragments. The excess primers were removed by a 1.3X SPRI bead purification (Beckman Coulter). Library quality and quantity was confirmed on a BioAnalyzer (Agilent) DNA HS chip. Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (New England Biolabs).

treatment_protocol: Old as treated group

tag: tissue

value: liver

tag: chip antibody

tag: group

value: old


title: Human8_H3

value: young


title: MDH2 [RNCMPT00330]

description:
A14_2_N.txt
channel 2


title: Human5_H3


title: SYF2 [RNCMPT00354]

description:
A25_2_D.txt
channel 1


title: Human3_H3K27me3

value: H3K27me3 (Cell signaling technology, 9733S,Lot 16


title: Human4_H3K27me3


title: Human7_H3K27me3


title: Human8_H3K27me3


title: Human4_H3


title: Human6_H3K27me3


title: Human2_H3K27me3


title: Human5_H3K27me3


title: Y_0_rep2

data_processing:
Library strategy: DNA-Seq
Illumina sequencing reads (~54 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with cutadapt/3.0 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option to the GRCm38/mm10 genome assembly
Sam output files were then filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM (reads per kilobase per million mapped reads) normalized bigWig files. Input reads were subtracted from the different salt fractions and pellet with bigwigCompare.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

organism: Mus musculus

source_name: mouse liver

extract_protocol:
Nuclei was released from frozen tissue by douncing in TM2 buffer (10 mM Tris HCl, pH 7.4, 2 mM MgCl2 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF), pelleted by centrifugation and washed once to remove debris. The washed pellet was resuspended in TM2 buffer with 1 mM CaCl2 and 12000U of MNase (New England Biolabs), incubated at 23°C for 15 minutes and the reactions stopped by addition of 0.5 mM EGTA. Approximately 30% was saved for analysis (“0”) and the rest was pelleted by centrifugation. The supernatant was removed and saved as “Supernatant” fraction after clearing. The nuclei were washed once with TM2 buffer and then resuspended in 70 µl Triton buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 2 mM EGTA, 0.1% Triton X-100 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF) and evenly divided. The first aliquot was saved as “Input” while the second was used for sequential salt extraction by using Triton buffer with either 67.5, 150, 250 or 350 mM NaCl. Each extraction was done by incubating the resuspended pellet at 4°C for 2 hours. After each extraction, the nuclei were pelleted by centrifugation and the supernatant saved as “67.5”, “150”, “250” or “350” mM fraction. Finally, the remainder pellet which corresponds to ~5–10% of chromatin, was resuspended in 35 µl of TNE buffer (10 mM Tris–HCl pH 7.4, 200 mM NaCl, 1 mM EDTA supplemented with 1X Halt protease and phosphatase inhibitor) and labeled as “Pellet” fraction. DNA was purified from each of these fractions using DNA clean and concentrator columns (Zymo Research).
Purified DNA (~10 ng) was used to make libraries using the NEBNext Ultra II kit (New England Biolabs).

tag: strain

tag: salt concentration


title: Y_pellet_rep2

value: pellet


title: Y_Input_rep2

value: Input


title: Human1_H3K27me3


title: HMGB2 [RNCMPT00373]

description:
A35_2_D.txt
channel 1


title: Y_350_rep2


title: SSBP1 [RNCMPT00295]

description:
A2_2.txt
channel 1


title: MRM1 [RNCMPT00357]

description:
A26_2_D.txt
channel 2


title: Human3_H3


title: Human2_H3


title: Human7_H3


title: Y_250_rep2


title: Y_150_rep2


title: Human1_H3


title: Y_67_rep2


title: O_pellet_rep1


title: O_0_rep1


title: O_350_rep1


title: O_150_rep1


title: Y3_kidney_Input

data_processing:
Illumina sequencing reads (~50 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option separately to the GRCm38/mm10 and GRCh38/hg38 genome assemblies.
Sam output files were then filtered to keep alignments with a minimum mapping quality of 10 using samtools/1.9 and PCR duplicates removed with picard/2.23.7. Sambamba/0.7.1 was used to keep only uniquely aligned reads. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. H3 and input reads were subtracted from H3K27me3 and IgG respectively with bigwigCompare.
Peaks were called using peakranger/1.18 with the bcp option using H3 and input as background for H3K27me3 and IgG respectively from the same animal
Genome_build: mm10, hg38
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

source_name: mouse kidney

extract_protocol:
Crude nuclei preparations were made from ~100 mg frozen tissue by douncing in nuclei preparation buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP-40, 0.01% digitonin and 1 mM BSA, supplemented with protease inhibitors and 1 mM sodium butyrate). After centrifugation, the nuclei pellet was crosslinked with 1% formaldehyde in 2 ml PBS by constant rotation at room temperature for 10 min followed by quenching with 125 mM glycine and two PBS washes. The nuclei were lysed with nuclei lysis buffer (10 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium-deoxycholate, 0.5% N-lauroylsarcosine supplemented with protease inhibitors and 1mM sodium butyrate) and sheared to <500bp using a Covaris S220 Ultrasonicator. An aliquot of the sheared chromatin sample was removed to check sonication success and to quantify the amount of chromatin. The immunoprecipitation, wash and elution steps were performed as reported previously (Sen et al., 2019) except ~4% HeLa chromatin was spiked in to 2 µg mouse chromatin prior to immunoprecipitation (only for liver samples).
DNA (~5 ng) was used to prepare libraries with the NEBNext Ultra II library preparation kit with unique dual index primers (New England Biolabs). The library quality and quantity were verified by BioAnalyzer DNA 1000 (Agilent) run and qPCR with NEBNext Library Quant kit (New England Biolabs) respectively.

value: kidney


title: O_Input_rep1


title: O_67_rep1


title: O4_kidney_Input


title: Y1_kidney_Input


title: Y4_kidney_Input


title: Y2_kidney_Input


title: O2_kidney_Input


title: O1_kidney_Input


title: Y4_kidney_H3


title: Y2_kidney_H3


title: O_250_rep1


title: O4_kidney_H3


title: Y3_kidney_H3


title: Y1_kidney_H3


title: Y4_kidney_H3K27me3


title: Y1_kidney_H3K27me3


title: Y2_kidney_H3K27me3


title: O4_kidney_H3K27me3


title: O3_kidney_H3


title: O1_kidney_H3


title: Y_liver_IgG


title: Y2_liver_Input_1


title: O1_kidney_H3K27me3


title: O3_liver_Input_1


title: O2_kidney_H3


title: O_liver_IgG


title: O3_kidney_H3K27me3


title: Y3_liver_H3_1


title: Y2_liver_H3_1


title: O1_liver_Input_1


title: Y3_liver_Input_1


title: Y1_liver_H3_1


title: O2_kidney_H3K27me3


title: Y1_liver_Input_1


title: Y3_kidney_H3K27me3


title: O1_liver_H3_1


title: SF3A3 [RNCMPT00900]

description:
A298_2_N.txt
channel 2


title: Y1_liver_H3K27me3_1


title: Y2_liver_H3K27me3_1


title: O3_liver_H3K27me3_1


title: O2_liver_H3K27me3_1


title: O1_liver_H3K27me3_1


title: O3_kidney_Input


title: O2_liver_Input_1


title: AD4_Control

status: Public on Mar 03 2023

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

description:
counts.txt
annotation.txt
embeddings.txt

library_source: transcriptomic

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix, cell annotations and UMAP embeddings

molecule: polyA RNA

source_name: retinal organoids

growth_protocol: adaped protocol based on Kuwahara et al., 2015

extract_protocol:
Retinal organoids (day 200) were dissociated to single cells using the Neurosphere Dissociation kit (P) (Miltenyi Biotech) according to the manufacturer’s protocol
Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)

treatment_protocol: drug exposure for 24 hours (Sildenafil for 7 days)

value: retinal organoids

tag: treatment

value: PBS


title: WGBS32 [repeat WGBS04]

status: Public on Feb 20 2023

city: Geraardsbergen

first: An

last: Vanden Broeck

address: Gaverstraat 4

country: Belgium

institute: Research Institute for Nature and Forest

description: Bisulfite-treated genomic DNA

data_processing:
Quality trimming, trim_galore --paired --cores <threads> -o trimmed_data <read_1> <read_2>
Mapping with Bismark, bismark --parallel <threads> --score_min L,0,-0.4 -o bismark_mapping --genome genome --temp_dir bismark_temp  -1 <trimmed_read_1> -2 <trimmed_read_2>
Deduplication with Bismark, deduplicate_bismark --output_dir bismark_dedup <mapped_sample.bam>
Methylaton Extraction with Bismark, bismark_methylation_extractor --multicore <threads> --comprehensive --report --gzip --output bismark_methylation <mapped_sample_dedup.bam>
Bedgraph with Bismark, bismark2bedGraph --scaffolds --buffer_size 12G --CX --dir bismark_methylation -o <out_name> <bismark_dedup.txt>
Assembly: Populus_trichocarpa.Pop_tri_v3 (dna.primary.assembly)
Supplementary files format and content: Bismark coverage files for the three contexts (CpG, CHG, CHH)

organism: Populus nigra

source_name: Populus nigra cv. Italica

growth_protocol: vegetative propagated by hardwood cuttings (one-year-old twigs) in an open greenhouse

extract_protocol:
Total genomic DNA was extracted from fresh leaves with the Qiagen Plant DNA kit (Hilden, Germany). The integrity of the DNA was assessed on 1.5% agarose gels, and DNA quantification was performed with Quant-iT™ PicoGreen® dsDNA Assay Kit (Thermo Fisher Scientific, Massachusetts, USA) using a Synergy HT plate reader (BioTek, Vermont, USA).
Up to 250 ng of DNA was fragmented to 300 bp with a Covaris S2 sonicator prior to whole-genome library preparation (NEBNExt Ultra II kit), ligation of methylated adaptors and size selection on 2% E-gels (400-550 bp). Bisulfite conversion was performed using the EZ DNA methylation gold kit (Zymo Research), followed by an enrichment PCR of 12 cycli. Paired-end 100-bp sequencing of the library fragments was performed on an Illumina Novaseq S2 sequencer, generating on average 83,886,466 ± 14,181,156 reads (mean ± SD) and an average read depth of approximately 17x.

treatment_protocol: planted in sttandard potting soil

value: leaf

tag: cultivar

value: Italica

tag: sampling date

tag: location ortet

value: Spain


title: WGBS31 [pool 15]

description: Bisulfite-treated genomic DNA

value: NL


title: O2_liver_H3_1


title: O3_liver_H3_1


title: WGBS27 [pool 11]

description: Bisulfite-treated genomic DNA

value: ITS


title: WGBS30 [repeat WGBS25]

description: Bisulfite-treated genomic DNA

value: BEA


title: WGBS24 [pool 08]

description: Bisulfite-treated genomic DNA

value: FRL


title: WGBS23 [pool 07]

description: Bisulfite-treated genomic DNA

value: UKD


title: WGBS25 [pool 09]

description: Bisulfite-treated genomic DNA


title: WGBS29 [pool 13]

description: Bisulfite-treated genomic DNA

value: SILB


title: WGBS26 [pool 10]

description: Bisulfite-treated genomic DNA

value: FRA


title: WGBS22 [pool 06]

description: Bisulfite-treated genomic DNA

value: SILA


title: WGBS21 [pool 05]

description: Bisulfite-treated genomic DNA

value: HRZ


title: WGBS20 [pool 04]

description: Bisulfite-treated genomic DNA

value: GEB


title: WGBS17 [pool 01]

description: Bisulfite-treated genomic DNA

value: CZP


title: WGBS16 [UKD2_F2_02_June2018]

description: Bisulfite-treated genomic DNA

source_name: Populus nigra cv. ‘Italica‘ Duroi

value: 'Italica' Duroi

value: UK

tag: geographic coordinates ortet's location


title: WGBS18 [pool 02]

description: Bisulfite-treated genomic DNA

value: BGS


title: Y3_liver_H3K27me3_1

value: liver

value: young


title: WGBS15 [ITS3_F2_02_June2018]

description: Bisulfite-treated genomic DNA

value: leaf

value: Italy


title: WGBS14 [HUN4_F2_June2018]

description: Bisulfite-treated genomic DNA

value: Hungary


title: WGBS11 [SPC1_F2_01_June2018]

description: Bisulfite-treated genomic DNA

value: Spain


title: WGBS13 [SPC1_F2_03_June2018]

description: Bisulfite-treated genomic DNA


title: WGBS10 [ITS3_F2_01_June2018]

description: Bisulfite-treated genomic DNA


title: WGBS09 [SPC1_F2_02_June2018]

description: Bisulfite-treated genomic DNA


title: WGBS28 [pool 12]

description: Bisulfite-treated genomic DNA

value: Italica

value: GEH


title: WGBS08 [UKD2_F1_July2017]

description: Bisulfite-treated genomic DNA


title: WGBS12 [UKD2_F2_01_June2018]

description: Bisulfite-treated genomic DNA


title: WGBS05 [HUN4_F1_July2017]

description: Bisulfite-treated genomic DNA


title: WGBS07 [SPC1_F1_July2017]

description: Bisulfite-treated genomic DNA


title: WGBS03 [UKD2_F1_March2017]

description: Bisulfite-treated genomic DNA


title: WGBS04 [SPC1_F1_March2017]

description: Bisulfite-treated genomic DNA


title: WGBS02 [ITS3_F1_March2017]

description: Bisulfite-treated genomic DNA


title: WGBS06 [ITS3_F1_July2017]

description: Bisulfite-treated genomic DNA


title: WGBS01 [HUN4_F1_March2017]

description: Bisulfite-treated genomic DNA


title: N324301, scRNAseq

status: Public on Feb 18 2023

city: Changsha

first: Zhou

last: Tailai

address: Xiangya street, Changsha,

country: China

institute: Central South University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We used CellRanger, a data processing software provided by 10X Genomics, to preprocess the single cell sequencing data in the fastq format.
hese data were compared to the human reference genome GRCh38 for cell and UMI counting to generate a gene expression matrix that contained a total of 32,851 cells and 23,428 genes. Moreover, we removed the possible doublets or low-quality cell populations following the cell cluster-based doublets removal method (for example, we excluded the low-quality cell groups in T cells). The Seurat package was then used to read the cell-gene expressing matrix. In addition, we set the filtering criteria as follows: cells with nFeature_RNA > 200, nFeature_RNA < 2500, percent.Mt < 20 were included in further analysis. In addition, we excluded genes that were not expressed in at least 10 cells, as well as mitochondrial and ribosomal genes. This led to the inclusion of a total of 18,869 cells and 18,672 genes for further bioinformatics analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human bladder tissue

extract_protocol:
The fresh human bladder tissue was immediately placed in GEXSCOPE® tissue preservation solution (Singleron) after sampling. After this, the sample was removed from the preservation solution and cleaned in PBS (Hyclone, CAT.No.SA30256.01) for a total of 3 times, cut into smaller pieces, and placed in a centrifuge tube with 2 mL GEXSCOPE® tissue dissociation solution (Singleron). The centrifuge tube was then placed at room temperature and shook for 15 minutes (180 rpm). After tissue dissociation, we added PBSA (containing 0.4%BSA) and filtered the cell suspension using a 400um sterile cell filter. Next, we centrifuged the filtered cell suspension (3000rpm, 5min, 4℃), poured the supernatant and added PBS for resuspension. A total of 2 ml of GEXSCOPETM erythrocyte lyser (Singleron) were added for 5 minutes, after which we added an equal volume of PBSA to terminate the reaction, centrifuged the cell suspension again, and added PBSA to clean and resuspend the cell precipitation. Finally, we used trypan blue standing to evaluate the cell activity under the microscope.
The bladder samples were diluted to 1x10^5 cells/mL, and the single-cell transcriptome library was prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits V3.1 (10x Genomics). According to Reagent Kits User Guide, we used the Chromium instrument for cell lysis and mRNA capture, then obtained cDNA solution by reverse transcription to construct the sequencing library. The amplified cDNA was used to construct the Illumina sequencing library. DNA sequencing was performed using an Illumina Novaseq 6000 sequencer.

tag: disease state

value: cystitis glandularis

tag: cell type

value: Epithelial cells

value: Normal bladder tissue of CG

value: Human bladder tissue

tag: age


title: N202801, scRNAseq

description: 10x Genomics


title: C310501, scRNAseq

description: 10x Genomics

value: Inflammatory bladder tissue of CG


title: N310501, scRNAseq

description: 10x Genomics


title: HDaa-cd14_S46_L001

status: Public on Feb 15 2023

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: PCR amplicon

data_processing:
Paired-end Bulk ATAC-seq reads were quality trimmed using Trimmomatic.
trimmed reads were aligned to human genome (hg19) using BWA
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized within the cinaR package.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized Counts for Consensus Peak Set for CD14 Monocytes
Supplementary_files_format_and_content: Normalized Counts for Consensus Peak Set for HSPC (CD34).

source_name: PBMC

extract_protocol: As previously described in Corces, M.R. et al. 2017, PMID: 28846090

value: CD14 Monocytes

tag: age (in years)

tag: Sex

value: Female

tag: clinical status

value: Healthy


title: HDy-cd14_S44_L001

description: PCR amplicon

value: Male


title: jcov94-cd14_S20_L001

description: PCR amplicon


title: C194901, scRNAseq

description: 10x Genomics


title: C223101, scRNAseq

description: 10x Genomics


title: HDab-cd14_S45_L001

description: PCR amplicon


title: C324301, scRNAseq

description: 10x Genomics


title: WGBS19 [pool 03]

description: Bisulfite-treated genomic DNA

value: HUN


title: jcov79-cd34_S16_L001

description: PCR amplicon

value: HSPC


title: jcov79-cd14_S6_L001

description: PCR amplicon


title: jcov78-cd34_S15_L001

description: PCR amplicon


title: jcov78-cd14_S5_L001

description: PCR amplicon


title: jcov77-cd14_S4_L001

description: PCR amplicon


title: jcov77-cd34_S14_L001

description: PCR amplicon


title: jcov67-cd14_S28_L002

description: PCR amplicon


title: jcov53-cd34_S41_L001

description: PCR amplicon


title: jcov51-cd34_S12_L002

description: PCR amplicon


title: jcov53-cd14_S19_L001

description: PCR amplicon


title: jcov51-cd14_S27_L002

description: PCR amplicon


title: jcov49-cd34_S11_L002

description: PCR amplicon


title: C202801, scRNAseq

description: 10x Genomics


title: jcov49-cd14_S26_L002

description: PCR amplicon


title: jcov46-cd14_S25_L002

description: PCR amplicon


title: jcov40-cd14_S24_L002

description: PCR amplicon


title: jcov35-cd34_S8_L002

description: PCR amplicon


title: jcov26-cd34_S29_L002

description: PCR amplicon


title: jcov26-cd14_S21_L002

description: PCR amplicon


title: jcov35-cd14_S23_L002

description: PCR amplicon


title: jcov85-cd14_S29_L002

description: PCR amplicon

value: nonCoV


title: jcov20-cd14_S20_L002

description: PCR amplicon


title: jcov18-cd14_S21_L002

description: PCR amplicon


title: jcov108-cd34_S17_L001

description: PCR amplicon


title: jcov19-cd14_S19_L002

description: PCR amplicon


title: jcov106-cd14_S15_L001

description: PCR amplicon


title: jcov103-cd14_S13_L001

description: PCR amplicon


title: jcov104-cd14_S14_L001

description: PCR amplicon


title: HDw-cd34_S33_L001

description: PCR amplicon


title: HDt-cd34_S9_L001

description: PCR amplicon


title: HDs-cd34_S31_L001

description: PCR amplicon


title: HDr-cd14_S7_L001

description: PCR amplicon


title: HDq-cd34_S6_L001

description: PCR amplicon


title: HDg-cd14_S17_L002

description: PCR amplicon


title: RTCB [RNCMPT00293]

description:
A1_2.txt
channel 1

tag: protocol

value: GST-tagged RNA-binding protein pulldown


title: HDp-cd14_S5_L001

description: PCR amplicon

tag: tissue


title: HDe-cd14_S3_L001

description: PCR amplicon


title: P047

status: Public on Feb 10 2023

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale. Genes with an absolute read count < 5 in at least three samples were removed
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated files with raw gene counts and CPM-log2 normalized values respectively for each gene in each sample
Supplementary_files_format_and_content: Comma seperated file with metadata,

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads

value: Ectocervix

tag: subjectid

value: female


title: P038


title: P049


title: P032


title: P037


title: P023


title: P009


title: P028


title: P010


title: P011


title: P013


title: BM6

status: Public on Jan 17 2023

city: St. Louis

first: Ravi

last: Vij

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
BM6

data_processing:
Single cell RNA sequence data was de-multiplexed to FASTQ, aligned to the human reference genome (GRCh38), and transposed into gene-by-cell UMI count matrices using the proprietary software tool Cell Ranger (v3.0.0) from 10x Genomics.
Seurat v3.0.0 [11] was used for all subsequent analysis. First, all data underwent quality filtering (as recommended by Seurat) to remove barcodes with: too few total transcript counts (< 300); too few genes expressed (< 200) or too few UMIs (< 1,000), indicating possible debris;  too many genes expressed (> 50,000) and too many UMIs (> 10,000), indicating the presence of multiplet; or too high proportion of mitochondrial gene expression over the total transcript counts (> 20%), indicating a dying cell. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA", "percent.mito"), return.only.var.genes = F).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).

source_name: Donor BMMC, aspirate, scRNAseq

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were isolated using Ficoll-Paque purification and cryopreserved in a 1:10 mixture of dimethyl sulfoxide and fetal bovine serum. Upon thawing in 37⁰C water baths, whole BMMCs from WashU cohort 1 were loaded onto the 10X Genomics Chromium Controller using 10x Genomics Chromium Single Cell 3’v2 Library Kits. BMMCs aliquots from WashU Cohort 2, MMRF, and healthy donors were centrifuged upon thawing at 300G for 5 min to pellet cells. All supernatant was removed. To prepare cells for the Miltenyi Dead Cell Removal Kit, cells were resuspended in 100 uL of  beads and incubated at room temperature for 15 minutes. Cells were then run through the DepeleS selection using the autoMACS®Pro Separator. The negative fraction (live cells) were pelleted by centrifugation at 450G for 5 minutes. Cells were finally resuspended in ice cold phosphate buffer saline (PBS) and 0.5% BSA and loaded onto the 10x Genomics Chromium Controller. WashU Cohort 2 and healthy donor samples were loaded using 10x Genomics Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.2. MMRF cohort samples were loaded using 10x Genomics Chromium Controller and using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.3.
Using the 10x Genomics Chromium Single Cell and Chromium instrument, approximately 16,500 to 20,000 cells were partitioned into nanoliter droplets to achieve single cell resolution for a maximum of 10,000 individual cells per sample. The resulting cDNA was tagged with a common 16nt cell barcode and 10nt Unique Molecular Identifier during reverse transcription. Full length cDNA from poly-A mRNA transcripts was enzymatically fragmented and size selected for ~400bp cDNA amplicons optimal for library construction (10x Genomics). The concentration of the 10x single cell library was determined through qPCR (Kapa Biosystems) or automated electrophoresis (Agilent TapeStation) to produce cluster counts appropriate for the HiSeq 4000 or NovaSeq 6000 platform (Illumina). 26x98bp sequence data were generated targeting between 25K-50K read pairs/cell, which provided digital gene expression profiles for each individual cell.

value: BMMC

value: Bone Marrow


title: P007


title: Akata 12h treated replicate 2

status: Public on Jan 06 2023

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
Library strategy: PRO-Seq
Data was aligned to reference genome using Danko lab PRO-Seq pipeline, available here: https://github.com/Danko-Lab/utils/tree/master/proseq
Reference genome contained Hg38, Dm3 and appropriate EBV genomes (KC207814.1/KC207813.1).
BigWig files can views on IGV genome browser: www.broadinstitute.org/igv/
Genome_build: hg38 and Dm3
Supplementary_files_format_and_content: bigWig

source_name: Akata cells

growth_protocol: EBV positive Burkitt’s lymphoma cell line Mutu I and Akata were maintained in RPMI 1640 containing 12% FBS and antibiotics (penicillin and streptomycin). Drosophila melanogaster S2 (ATCC) cells were grown in Schneider’s medium (Lonza) containing 10% foetal bovine serum (FBS) and maintained at 23C.

extract_protocol:
Nuclei were isolated and nuclear run-on performed with biotinylated nucleotides. Biotinylated RNA transcripts were isolated using streptavidin coated magnetic beads.
Constructed as detailed in Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq). Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Mutu I cells were treated with NaB (1 mM) and TPA (20 ng/ml) for 0, 1, 4, or 12 hrs, and Akata cells were treated with 10 mg/ml of goat anti-human IgG (Sigma I1886) for 0, 1, 4, or 12 hrs.

tag: cell line

value: Akata

value: EBV+ Burkitt's lymphoma cell line

value: anti-IgG treated (12h)


title: HDs-cd14_S8_L001

description: PCR amplicon


title: Akata 12h treated replicate 3


title: Akata 1h treated replicate 3

value: anti-IgG treated (1h)


title: P060


title: Akata 12h treated replicate 1


title: Akata 1h treated replicate 2


title: Akata 4h treated replicate 1

value: anti-IgG treated (4h)


title: Akata Latent replicate 3

value: Untreated


title: Akata Latent replicate 2


title: Akata Latent replicate 1


title: Mutu-I 12h treated replicate 2

source_name: Mutu-I cells

value: Mutu-I

value: NaB/TPA treated (12h)


title: Mutu-I 12h treated replicate 1


title: Mutu-I 4h treated replicate 3

value: NaB/TPA treated (4h)


title: Mutu-I 1h treated replicate 2

value: NaB/TPA treated (1h)


title: Mutu-I 4h treated replicate 2


title: Mutu-I 1h treated replicate 1


title: Mutu-I 4h treated replicate 1


title: Mutu-I Latent replicate 3


title: Akata 4h treated replicate 2


title: R_DDX23_2

status: Public on Dec 16 2022

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

data_processing:
base calling analysis using the standard Illumina pipeline and sample de-multiplexing according to index read data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
peaks were called using MACS2 with the following setting: macs2 callpeak -t -c -f BAM -g 2.7e+9 -n --outdir macs2
Assembly: hg19
Supplementary files format and content: bed files were genereated using bedtools by overlaping the peaks of two replicates
Supplementary files format and content: wig files were generated using deeptools

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
Briefly, 2×107 cells were cross-linked by adding formaldehyde dropwise directly to the media for a final concentration of 1% and rotating gently at room temperature for 10 min. The reaction was quenched by adding 2.5 M glycine to the media for a final concentration of 125 mM and incubated with shaking for 5 min at room temperature. After washing with 1× PBS three times, the cells were resuspended in PBS. After centrifugation, the cell pellet was resuspended in RIPA buffer (50 mM Tris–HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS and protease inhibitor cocktail) at 4 °C for 30 min with rotation. Chromatin was sheared using a Covaris S220 sonicator at 4°C for 10 min with a peak incident power of 140, a duty cycle of 10%, and 200 cycles per burst. After centrifugation at 16,000g for 15 min, the supernatant was incubated with pre-blocked anti-FLAG M2 affinity gel (Sigma) on a rotator at 4°C overnight. After washing, DNA was eluted from the beads with 120 µL 100 mM NaHCO3 and 1% SDS at 68 °C for 2 h. Cross-links were subsequently reversed by adding 4.8 µL of 5 M NaCl and 2 µL RNase A (10 mg/mL) and incubated with shaking at 65°C overnight. After reverse cross-links, proteins in the resulting DNA samples were removed with 2 µL proteinase K (20 mg/mL) and incubated while shaking at 60°C for 2 h. Finally, the DNA was purified using Cycle Pure Kit (omega). Purified DNA was quantified and verified on an Agilent 2100 Bioanalyzer.
The library was then constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a HiSeq4000 system (Illumina).

value: HEK293T cells

value: Human embryonic kidney

tag: genotype

tag: antibody

value: Polk


title: Akata 1h treated replicate 1

tag: treatment


title: R_WT_2

value: WT


title: R_POLK_1

value: POLK-/-


title: R_POLK_2


title: R_WT_1


title: R_DDX23_Control_1


title: R_DDX23_Control_2


title: R_POLK_Control_2


title: POLK_2

description: Tandem affinity tag was introduced to the C-terminus of endogenous Pol η


title: R_WT_Control_1


title: R_WT_Control_2


title: Mutu-I 12h treated replicate 3


title: POLK_1

value: Tandem affinity tag was introduced to the C-terminus of endogenous Pol


title: Control_2


title: R_POLK_Control_1


title: Control_1


title: Ring1bKO-G1

status: Public on Dec 02 2022

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

data_processing:
For CaptureC, paired-end reads were aligned to mm10 and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Capture-C

growth_protocol: FUCCI-Ring1bfl/fl mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco) and hygromycin B (InvivoGen) as described previously (Asenjo et al, 2020)

extract_protocol:
Chromatin extraction and fixation was carried out from 2x106 cells from G1 and G2-sorted FUCCI-Ring1bfl/fl and FUCCI-Ring1b-/- cells. Cells were resuspended in 1.86 ml of complete medium and fixed with formaldehyde (1.89%) and incubated for 10 minutes on a rotating wheel at room temperature. The fixation reaction was stopped by adding cold glycine (final concentration 150 mM). Fixated cells were centrifuged (5 min 1000 rpm 4°C) and washed 1x with cold PBS. After centrifugation, cells were resuspended in cold lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% NP-40, 1x protease inhibitors (Roche)) and incubated for 20 min on ice. Subsequently, the pellet was centrifuged (5 min, 1800 rpm, 4°C) and resuspended in 200 μl of lysis buffer. Next steps were carry out as described previously in (Dimitrova et al., 2021)
2-4 µg DNA from each sample were adaptor-ligated and indexed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). The libraries were amplified with 7 PCR cycles using Herculase II Fusion Polymerase kit (Agilent). Libraries hybridisation was performed as described previously (Dimitrova et al., 2021)

treatment_protocol: Treatment with 800 nM 4-hydroxytamoxifen (Tmx, Sigma) for 48 hours and collected for downstream analyses 24 hours later (72 hours total). 4-thiouridine labelling during 1 hour 37ºC. Cell-cycle sorting using an Aria Fusion cell sorter.

tag: cell-type

value: Mouse embryonic stem cells

tag: strain

value: Derived from male blastocysts in (Endoh et al 2008)

tag: developmental stage


title: Neocortical lesion, HME, 4688

status: Public on Nov 17 2022

city: La Jolla

first: Changuk

last: Chung

address: 9500 Gilman Dr

institute: UCSD

description:
HME_4688
mRNA

data_processing:
Fastq files from single-nucleus libraries were processed through Cell Ranger (v6.0.2) analysis pipeline with –include-introns option and hg19 reference genome. Pooled library was demultiplexed and singlets were taken by demuxlet (v1.0). Seurat (v4.0.5) package was used to handle single nuclei data objects. Nuclei passed a control filter (number of genes > 500, number of reads >1000, percentage of mitochondrial gene < 10%) was used for downstream analysis. Protein coding genes were used for further downstream analysis. Data were normalized and scaled with the most variable 3000 features using the ‘SCTransform’ functions. Dimensionality reduction by PCA and UMAP embedding was performed using runPCA and runUMAP functions. Clustering was performed by FindNeighbors and FindClusters functions. Cell type identification was performed using known cell type markers expressed in the brain including excitatory (RORB, CUX2, SATB2), inhibitory neuron (GAD1, GAD2), astrocyte (SLC1A2, SLC1A3), oligodendrocyte (MOBP, PLP1), immature oligodendrocyte (BCAS1), oligodendrocyte precursor cell (PDGFRA), microglia (PTPRC), and endothelial cell markers (CLDN5, ID1) as well as using positive markers found by FindAllMarkers function with 3000 most variable features in scaled data. DEG analysis was performed by ‘FindMarkers’ function in Seurat v4.0 with all genes available in the assay.
Assembly: hg19
Supplementary files format and content: Tab-separated barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary files format and content: Comma-separated metadata.csv file.

source_name: Neocortical lesion

extract_protocol:
A fresh-frozen brain tissue (~50 mg) was placed into a glass dounce homogenizer containing 1 ml cold lysis buffer (0.05% (v/v) NP-40, 10 mM Tris (pH 7.4), 3 mM MgCl2, 10 mM NaCl) and dounce 10 times with a loose pestle and following 10 times with a tight pestle. The homogenate was incubated for 10 min in RT. 9 ml of wash buffer (1% BSA in 1X PBS) was added to the homogenate and filtered by a 30 um cell strainer. The strained homogenate was spun down in 500 g to remove the supernatant. The pellet was resuspended with 5 ml of wash buffer. Straining and spinning down steps were performed once more, and the pellet was resuspended into 500 ul of wash buffer. 10 ul of nuclei resuspension was mixed with counting solution (0.02% Tween 20, 0.1ug/ml DAPI, 1% BSA in 1X PBS) and nuclei density was measured by manual nuclei counting using DAPI signal. The resuspension was diluted by wash buffer to make the desired concentration (800~1000 nuclei/ul). Maximum 2 samples were pooled together targeting 10000 nuclei per reaction.
Gel beads emulsion (GEM) generation, cDNA, and sequencing library constructions were performed in accordance with instructions in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1). A library pool was sequenced with 800 million read pairs using NovaSeq 6000.

value: Neocortical lesion

tag: disease

value: Hemimegalencephaly


title: Neocortical lesion, HME, 6593

description:
HME_6593
mRNA


title: Neocortex, Neurotypical, 8352_8353

description:
CTRL_8352_8353
mRNA

source_name: Neocortex

value: Neocortex

value: Neurotypical


title: Neocortical lesion, FCD, 4512

description:
FCD_4512
mRNA

value: Focal cortical dysplasia


title: Mutu-I Latent replicate 2

value: Mutu-I

value: EBV+ Burkitt's lymphoma cell line

value: Untreated


title: Mutu-I Latent replicate 1


title: Neocortical lesion, TSC, 4259

description:
TSC_4259
mRNA

value: Tuberous sclerosis complex


title: R_DDX23_1

value: HEK293T cells


title: Neocortical lesion, TSC, 4258

description:
TSC_4258
mRNA


title: Regulatory small RNA RevI-H2i2-zuc GLKD

status: Public on Sep 30 2022

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

country: France

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

data_processing: Adapters were trimmed and size selection was performed to retain only 18-29 nucleotide reads.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Argonaute-bound sRNAs were isolated with the TRApR kit according to Grentzinger et al. (2020)
gel-free protocol without size selection - Library preparation using QIAseq-miRNA kit

value: ovaries

value: RevI-H2i2- nos-Gal4- expressed dsRNA-Zuc BDSC_35227

tag: time

value: 3-6 day old female


title: Healthy5_snATAC-seq

status: Public on Sep 18 2022

first: Yoshiharu

last: Muto

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

data_processing:
Fastq files was processed with CellrangerATAC 1.2.0 by "count" function with refdata-cellranger-atac-GRCh38-1.2.0
Supplementary_files_format_and_content: Filtered barcode-peak matrix and fragment file
Supplementary_files_format_and_content: metadata_ATAC.csv: Metadata for each barcode in the processed snATAC-seq dataset.
Genome_build: GRCh38

source_name: Human Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)

tag: gender

value: Female

tag: race

value: NHW

tag: egfr

tag: global glomerulosclerosis

tag: ifta

value: kidney


title: Healthy4_snATAC-seq

tag: age

value: Male


title: Healthy3_snATAC-seq

tag: tissue


title: ADPKD6_snATAC-seq

data_processing:
Fastq files was processed with CellrangerATAC 1.2.0 by "count" function with GRCh38
Supplementary_files_format_and_content: Filtered barcode-peak matrix and fragment file
Supplementary_files_format_and_content: metadata_ATAC.csv: Metadata for each barcode in the processed snATAC-seq dataset.
Genome_build: GRCh38

source_name: Human ADPKD Kidney cortical cup

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)


title: ADPKD7_snATAC-seq


title: Akata 4h treated replicate 3

value: Akata

tag: cell type

value: anti-IgG treated (4h)


title: Healthy2_snATAC-seq

value: HIS


title: Healthy1_snATAC-seq


title: ADPKD4_snATAC-seq


title: ADPKD7_snRNA-seq

data_processing:
Fastq files was counted with cellranger v6.0.0 with --include-introns argument using GRCh38.
Supplementary_files_format_and_content: Filtered and raw barcode-feaure matrix
Supplementary_files_format_and_content: metadata_RNA.csv: Metadata for each barcode in the processed snRNA-seq dataset.
Supplementary_files_format_and_content: count_RNA.rds: Count matrix for snRNA-seq data analysis (ambient RNA corrected with SoupX).
Supplementary_files_format_and_content: count_ATAC.rds: Count matrix for snATAC-seq data.
Genome_build: GRCh38

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snRNA-seq library(3' ver3 kit)


title: ADPKD5_snATAC-seq


title: ADPKD1_snATAC-seq


title: ADPKD6_snRNA-seq


title: ADPKD8_snRNA-seq


title: ADPKD5_snRNA-seq


title: ADPKD4_snRNA-seq


title: ADPKD3_snATAC-seq


title: Healthy4_snRNA-seq

source_name: Human control Kidney cortex


title: ADPKD2_snRNA-seq


title: Healthy5_snRNA-seq


title: ADPKD3_snRNA-seq


title: Healthy2_snRNA-seq


title: ADPKD1_snRNA-seq


title: 40y_snATAC

status: Public on Oct 31 2022

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
genomic DNA
same donor as RL2124

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
cellranger-atac mkfastq with Cellranger-ATAC v1.2 to generate fastq files as input for count pipeline.
cellranger-atac count with Cellranger-ATAC v1.2 to generate BED-like tabular file with contains frgaments captured by the assay and barcode information in single cell output tables.
Genome_build: hg19
Supplementary_files_format_and_content: For snRNA-seq data: feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known-good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files. For snATAC, a BED-like tabular fragment file with each line representing a unique ATAC-seq fragment captured by the assay,  an index for the fragments file as well as a singlecell file containing cell barcodes, QC information and ATAC signal.

source_name: prefrontal cortex, BA9

extract_protocol:
Per sample, 50 mg of frozen brain tissue was lysed and nuclei extracted. Nuclei were then either enriched by DAPI-positive FANS for single cell gene expression library generation or cleaned with a sucrose gradient centrifugation for single cell ATAC library generation.
10X Genomics 3' Single Cell Gene Expression v2/v3 , 10X Genomics Single Cell ATAC
snRNA-seq, snATAC-seq

value: brain


title: Healthy3_snRNA-seq


title: Healthy1_snRNA-seq


title: HeLa, Active Motif 20ug H3K9me3

status: Public on Sep 03 2022

city: Grand Rapids

first: Ariana

last: Kupai

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description:
9AMhiparams.in
input is inputDMSO from GSE207783

data_processing:
Final processed data obtained from sans spike-in quantitative ChIP-seq (siQ-ChIP) pipeline. Full codes at github via github.com/BradleyDickson/siQ-ChIP
IP and input data were aligned to genome, quantitative scale was computed from sample masses, fragment lengths, etc, and the siQ-scaled process track is alpha * IP/input
Peaks were called in each 20ug IP dataset and compared to the same genomic region in the 2.5ug IP for the same antibody. Processing code is in frechet.f90 on https://github.com/BradleyDickson/siQ-ChIP.
Assembly: hg38
Supplementary files format and content: bigwig files are quantitative siQ-ChIP tracks
Supplementary files format and content: peak files: The format of that data is as follows: peak_number chr start end frechet 1.0 response area_numerator area_denominator max_numerator max_denominator left right where 'left' and 'right' are the location of the maximum for that interval

source_name: cervical

growth_protocol: DMEM, 10% FBS, 1% penicillin-streptomycin, grown in 37°C with 5% CO2

extract_protocol:
Cells were fixed with 0.75% formaldehyde for 5 minutes. Cells were quenched with 750mM Tris for 5 minutes. After cell lysis, chromatin was fragmented using micrococcal nuclease (worthington).
Library preparation was done using KAPA HyperPrep Kit (Roche, KK8504) with 4 uL of Illumina adapters (IDT, UDI) and sequenced on Illumina NextSeq 500 with a Mid-Output (paired-end 75 bp reads) flow cell. Input libraries had between 83-102M reads, and each IP library had 27-46M reads that passed QC, with 88% of the bases having quality scores >= 30.

value: cervical

tag: cell line

value: HeLa

tag: chip antibody

value: Active Motif H3K9me3 #39161 lot:30220003


title: ADPKD8_snATAC-seq


title: HeLa, Diagenode 2.5ug H3K27ac

description:
DIloparams.in
input is inputDMSO from GSE207783


title: ADPKD2_snATAC-seq


title: HeLa, Diagenode 20ug H3K27ac

description:
DIhiparams.in
input is inputDMSO from GSE207783


title: HeLa, Active Motif 2.5ug H3K27ac

description:
AMloparams.in
input is inputDMSO from GSE207783

value: Active Motif H3K27ac #39133 lot:06921014


title: HeLa, Active Motif 20ug H3K27ac

description:
AMhiparams.in
input is inputDMSO from GSE207783


title: HeLa, CST 20ug H3K9me3

description:
9CSThiparams.in
input is inputDMSO from GSE207783

value: CST#13969S H3K9me3 lot:5


title: 11_30_L042617-NO-IL15_S18

status: Public on Aug 03 2022

city: Indianapolis

first: Yuan

last: Liu

state: IN

address: 410 W. 10th Street

institute: Indiana University

data_processing: The raw RNA-seq cleaned with Trim Galore, and then aligned to the corresponding reference genome using HISAT2. Subsequently, we mapped captured these RNA-seq reads mapping on to the regions of genes by SAMtools and calculated the read counts per gene using Stringtie. Then we and used TPM to normalize the gene expression.

source_name: adipose

growth_protocol: Adipogenic differentiation of human preadipocytes was induced with a differentiation media (Zenbio,Inc) consisting insulin, dexamethasone and isobutylmethylxanthine (IBMX) and pioglitazone supplemented with 10% FBS. After 3 days, the media was changed to adipocyte maintenance media (Zenbio, Inc) containing only insulin, dexamethasone in DMEM/F12 supplemented with 10% FBS (Fetal bovine serum). The cells were then left to differentiate for another 11–12 days with medium changed every other day.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Once terminally differentiated at day 14, human adipocytes were treated with vehicle or 250 ng/ml of recombinant human IL15 protein (Peprotech) in triplicate for 5 days.

value: adipose

value: human primary adipocytes

tag: genotype

value: WT

value: Vehicle

value: Day 5


title: 11_30_L042617-YES-IL15_S15

tag: treatment

value: Day 0


title: 11_30_LM050709B-YES-IL15_S9


title: 11_30_L052011-YES-IL15_S19


title: 11_30_L052011-NO-IL15_S2


title: 11_30_LM080414A-NO-IL15_S13


title: 11_30_L062016-YES-IL15_S12


title: 11_16_LM050709B-YES-IL15_S9


title: 11_30_LM050709B-NO-IL15_S6


title: BC8-Stroma-M1

status: Public on Aug 22 2022

city: Singapore

first: Kanaga

last: Sabapathy

state: --None--

address: 11 Hospital Crescent

department: Division of Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

hyb_protocol: Hybridization was performed according to standard protocols.

scan_protocol: Scanning was performed according to standard protocols.

data_processing: The R package affy was used for data processing. The rma function (Robust Multiarray Average) was used for quantile normalization and background correction.

label: biotin

source_name: Tumor adjacent normal tissue

label_protocol: Labeling was performed according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted using TRIzol reagent according to manufacturer’s instructions and homogenized using QIAGEN TissueLyser II. Extracted RNA was treated with DNase and purified on a RNeasy column. RNA quality and quantity were analyzed on a ND-1000 NanoDrop spectrophotometer and reverse transcribed using Superscript II (Invitrogen), before running on the human Clariom™ S Assay (ThermoFisher Scientific).

treatment_protocol: Free-hand dissection using sterile scalpel blades was performed on mastectomy specimens to obtain five samples per tumor from different regions, as well as from non-pathological regions around the tumor to obtain peri-tumoral stromal samples. Tissues within 1 cm macroscopic distance from the visible tumor were avoided to ensure only non-pathological breast tissue is collected. Within each distance zone (Zone 1: 1-3 cm, Zone 2: 3-5 cm, Zone 3: 5-7 cm), tissue was collected in four radial directions with an approximate size of 0.5 x 0.5 x 0.5 cm.

value: Stroma

tag: patient id

tag: patient age

tag: ethnicity

value: Chinese

tag: region

value: M

tag: distance zone from tumor edge

tag: molecular subtype

value: Normal

tag: stromal cluster


title: 11_30_L092815A-YES-IL15_S10

tag: time


title: HeLa, Active Motif 2.5ug H3K9me3

description:
9AMloparams.in
input is inputDMSO from GSE207783


title: 11_30_L062016-NO-IL15_S7


title: 11_30_L092815A-NO-IL15_S16


title: 11_16_L042617-YES-IL15_S15


title: BC8-Tum-S

source_name: Breast Tumor

value: Tumor

value: S

value: Basal


title: BC8-Stroma-L1

value: L


title: 11_16_LM050709B-NO-IL15_S6


title: BC8-Tum-M


title: BC8-Tum-C

value: C


title: BC8-Tum-Inf

value: Inf


title: 11_16_L062016-YES-IL15_S12


title: 11_16_LM080414A-YES-IL15_S21


title: 11_16_L062016-NO-IL15_S7


title: 11_16_LM080414A-NO-IL15_S13


title: 11_16_L042617-NO-IL15_S18


title: 11_30_LM080414A-YES-IL15_S21


title: 11_16_L052011-YES-IL15_S19


title: 11_16_L092815A-YES-IL15_S10


title: BC8-Stroma-S1


title: TCM0

status: Public on Jun 01 2022

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB/KU Leuven

data_processing:
sequenced reads were then mapped to the mouse genome (mm10 build GRCm38.p6) using the Cell Ranger software (10x Genomics)
raw UMI count matrices for each individual sample were first imported using Seurat, and then converted for further processing with Monocle
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cell barcodes, gene identifiers, and UMI count values for each cell and gene in each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: intravenous (iv) injections of control media or tumor conditioned media for 3 weeks

tag: strain

value: BALB/c

tag: Sex

value: female

value: lung

value: 9-10 weeks-old

value: Tumor conditioned media iv injections


title: 66IC4: Treated IC20 patient-derived organoid rep4

status: Public on Apr 08 2022

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using bowtie2 with default parameters
htseq software was used to estimate the raw gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Genome_build: hg38
Supplementary_files_format_and_content: txt files are generated from htseq and DESeq2 results using R

source_name: Treated IC20 patient-derived organoid

growth_protocol: Starting material was freshly isolated  organoid cells, which were trypsinized and disrupted to obtain single cells.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

tag: patient-derived organoid

tag: origin

value: colorectal tumor

tag: phenotype

value: treated 5-FU+Iri IC20

value: organoid


title: 66IC2: Treated IC20 patient-derived organoid rep2

tag: cell type


title: 66IC3: Treated IC20 patient-derived organoid rep3


title: BC8-Stroma-S2

tag: tissue

value: Stroma

value: Chinese


title: 66CT3: Untreated patient-derived organoid rep3

source_name: Untreated patient-derived organoid


title: 66IC1: Treated IC20 patient-derived organoid rep1


title: CM0

tag: age

value: Control media iv injections


title: 66CT2: Untreated patient-derived organoid rep2

value: untreated


title: 5301: Treated IC30 patient-derived organoid rep1

tag: treatment

value: treated 5-FU+Iri IC30


title: 5302: Treated IC30 patient-derived organoid rep2


title: p53 ChIP-seq from treated IC20 patient-derived organoid replicate 1

description: No use of DSP crosslink

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the hg38 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

source_name: Patient-derived organoid

extract_protocol:
Cells were crosslinked with 0.5% formaldehyde and lysated. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Starting material was freshly isolated  organoid cells, which were trypsinized and disrupted to obtain single cells.

tag: chip antibody

value: p53, abcam ab1101


title: Input from treated IC20 patient-derived organoid

description: No use of DSP crosslink


title: p53 ChIP-seq from treated IC20 patient-derived organoid replicate 2

description: No use of DSP crosslink


title: 5201: Treated IC20 patient-derived organoid rep1


title: 5202: Treated IC20 patient-derived organoid rep2


title: 5CT1: Untreated patient-derived organoid rep1

source_name: Untreated patient-derived organoid rep1


title: 66CT1: Untreated patient-derived organoid rep1


title: 5CT2: Untreated patient-derived organoid rep2

source_name: Untreated patient-derived organoid rep2


title: 11_16_L052011-NO-IL15_S2

value: adipose

tag: cell line

value: human primary adipocytes

tag: genotype

value: WT

value: Vehicle

value: Day 5


title: 11_16_L092815A-NO-IL15_S16

value: Day 0


title: 66CT4: Untreated patient-derived organoid rep4


title: H1703_R_rep2

status: Public on Nov 23 2021

city: Gliwice

first: Alexander

middle: Jorge

last: Cortez

state: Silesia

address: Wybrzeze Armii Krajowej 15

department: Department of Biostatistics and Bioinformatics

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

data_processing:
Sequenced reads were trimmed for adaptor sequences with Cutadapt
Quantification was performed using the Salmon tool against reference genome GRCh38 (hg38)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (tab delimited file)

source_name: non-small cell lung cancer

growth_protocol: NCI-H1581 cells were routinely maintained in DMEM/F12, NCI-H1703 were maintained in RPMI 1640 medium. All culture media contained 10% of FBS and penicillin/streptomycin (100 U/ml/ 100 μg/ml). Cells were grown at 37°C in a humidified atmosphere of 5% CO2. All culture media and corresponding supplements were purchased from Merck KGaA (Darmstadt, Germany) or Biowest (Riverside, MO, USA). For RNA-seq experiment, NCI-H1581 and NCI-H1703 cells (sensitive and resistant cell line variants) were seeded onto 6 cm-diameter dishes. The next day, the medium was replaced with a fresh medium, and after 24 h, cells were harvested. This procedure was repeated to obtain a second replicate.

extract_protocol:
Total RNA was extracted from the cells using RNeasy Plus Mini Kit, Qiagen (Hilden, Germany) with simultaneous DNase I digestion, according to the manufacturer’s instructions. RNA purity and concentration were estimated with Nanodrop ND-2000 spectrophotometer, Thermo Fisher Scientific (Waltham, MA, USA). RNA quality was assessed using the 2100 Bioanalyzer with the RNA 6000 Nano Kit, Agilent Technologies (Santa Clara, CA, USA). All the samples had RNA integrity number (RIN) above 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To develop resistance to the FGFR inhibitor CPL304110, NCI-H1581 and NCI-H1703 cell lines were exposed to increasing concentrations of CPL304110 (starting from 50 nM). Cells were maintained in a medium containing the inhibitor, which was replaced every three days. When growth kinetics of treated cells were similar to wild-type cells, the concentration of CPL304110 was increased until a final concentration of 2.5 μM for NCI-H1581 and 5 μM for NCI-H1703 was achieved. After 4-6 months of such culture, resistant cells were established and termed NCI-H1581R and NCI-H1703R.

value: non-small cell lung cancer

tag: variant

value: resistant


title: H1581_R_rep2


title: H1703_R_rep1


title: H1703_S_rep2

value: sensitive


title: H1703_S_rep1


title: H1581_R_rep1


title: H1581_S_rep2


title: ESC O4f/- CreER 36h 4OHT RNA rep1

status: Public on Jun 17 2021

city: Edinburgh

first: Lawrence

middle: E

last: Bates

address: Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh

data_processing:
Adapters were trimmed and low quality sequences removed using TrimGalore v0.1.4, then aligned to mm10 using TopHat2 v2.1.0 with parameters --read-mismatch 1 --max-multihits 1
Gene-wise counts were generated using featureCounts v1.5.1 based on annotation from Ensembl GRCm38.86 release.
Normalization was performed using NOISeq: low count genes were excluded using CPM filtering with a cutoff of 1 CPM before TMM normalization was performed.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw gene counts for each sample
Supplementary_files_format_and_content: csv file containing TMM normalized counts for each gene for all samples

source_name: Embryonic stem cells

growth_protocol: Cells were grown in N2B27 supplemented with 1μM PD03, 3μM Chiron and 1x mLIF, passaged as required using accutase onto tissue-culture plastic precoated in 0.1% gelatin in PBS. ZHBT ESCs were maintained with 1μg/ml doxycylin to prevent expression of wild-type Oct4.

extract_protocol:
RNA was extracted using a Qiagen Rneasy mini kit with on-column DNA digest.
Depletion of ribosomal RNA was performed on 2-5 μg of total RNA using the Ribo-Zero rRNA Removal Kitand libraries were produced from 10-100ng of ribosomal-depleted RNA using NextFlex Rapid Directional RNA-seq Kit

treatment_protocol: Cells were treated with 500nM 4OHTor 500μM IAA as described.

value: Mixed 129SV C57BL/6

value: Embryonic stem cells

value: Treated with 4OHT for 36hr

value: Oct4Fl/-; CAG CreER


title: ZHBT O4AID 0h RNA

value: Untreated

value: Oct4-/-; TetOFF Oct4; CAG Oct4AID; CAG Tir1


title: ESC O4f/- CreER 24h 4OHT RNA rep1

value: Treated with 4OHT for 24hr


title: ZHBT O4AID 10h IAA RNA

value: Treated with IAA for 10hr


title: ESC O4f/- CreER 18h 4OHT RNA rep2

value: Treated with 4OHT for 18hr


title: ZHBT O4AID 6h IAA RNA

value: Treated with IAA for 6hr


title: ESC O4f/- CreER 36h 4OHT RNA rep2


title: ESC O4f/- CreER 18h 4OHT RNA rep1


title: ESC O4f/- CreER 12h 4OHT RNA rep2

value: Treated with 4OHT for 12hr


title: ZHBT O4AID 1.5h IAA RNA

value: Treated with IAA for 1.5hr


title: ZHBT O4AID 24h IAA RNA

value: Treated with IAA for 24hr


title: ESC O4f/- CreER 12h 4OHT RNA rep1


title: H1581_S_rep1


title: ESC O4f/- CreER 24h 4OHT RNA rep2


title: ESC O4f/- CreER 0h RNA rep2


title: ZHBT-O4AID 1.5h IAA Nanog rep1

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2 v2.3.4.3.
Reads were deduplicated, then normalized enrichment tracks were generated using MACS2 callpeak function with the --SPMR flag.
For analysis of signal intensity, peaks were called from pooled uninduced samples using MACS2 callpeak. Signal was normalized using deepTools2 bamCoverage and blacklisted regions from the ENCODE project consortium were excluded.
Peaks with an RPKM < 0.9 in both uninduced and induced samples were considered to be background and excluded from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: csv text files with RPKM values for each sample
Supplementary_files_format_and_content: csv text file with intensity values for pooled samples, with Oct4 proximity, and classification as enhancer-, promoter-, and/or repressed chromatin associated.
Supplementary_files_format_and_content: bedGraph files

extract_protocol:
Nuclei were prepared from fixed cells, then sonicated. Protein-DNA complexes were immunoprecipitated with specified antibodies
Sequencing libraries were prepared using the ThruPLEX DNA-Seq Kit

treatment_protocol: Cells were treated with 500μM IAA as described.

value: Nanog (Bethyl labs A300-397A)


title: ZHBT-O4AID 1.5h IAA Nanog rep2


title: ZHBT-O4AID 1.5h IAA K27ac rep2

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2 v2.3.4.3.
Reads were deduplicated, then normalized enrichment tracks were generated using MACS2 callpeak function with the --SPMR flag.
For analysis of signal intensity, peaks were called from pooled uninduced samples using MACS2 callpeak. Peak signals were then RPKM normalized using DiffBind. Peaks with RPKM <0.5 were excluded as background.
Peaks were subset based on proximity to Oct4 peaks; Oct4 peaks were called using MACS2 callpeak on data obtained from GEO acession GSM307137.
Genome_build: mm10
Supplementary_files_format_and_content: csv text files with RPKM values for each sample
Supplementary_files_format_and_content: csv text file with intensity values for pooled samples, with Oct4 proximity
Supplementary_files_format_and_content: bedGraph files

value: H3K27ac (Abcam ab4792)


title: ZHBT-O4AID Uninduced Nanog rep1


title: ZHBT-O4AID 1.5h IAA K27ac rep3


title: ZHBT-O4AID 1.5h IAA K27ac rep1


title: ZHBT-O4AID Uninduced K27ac rep2


title: ZHBT-O4AID Uninduced Nanog rep2


title: ATAC_12h_Bioreplicate 1

status: Public on Jun 03 2021

city: Staten Island

first: Cesar

last: Arenas-Mena

state: New York

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY

data_processing:
ENCOCE-DCC atac-seq-pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) default parameters
MACS2 peak call p threshold set to 0.05.
Genome_build: Sp3.1
Supplementary_files_format_and_content: ATAC12h7_ATAC12h6_RPM_0.bw, bigwig file of the merged samples
Supplementary_files_format_and_content: ATAC_12h_TOTAL_Sep2020.pooled.pval0.05.300K.bfilt.narrowPeak_sort_merge.bed, Bed file for the peak calls of the merged samples.

organism: Strongylocentrotus purpuratus

source_name: 12 hour hatching blastula embryos

growth_protocol: 15 degrees Celsius

extract_protocol:
Density gradient nuclear prep
Nextera DNA Sample Preparation Kit (24 Samples)  (Illumina Cat # FC-121-1030) was used for library generation

value: embryo


title: ATAC_12h_Bioreplicate 2


title: PRO-seq_12h_SE_Biorep3

data_processing:
library strategy: PRO-seq
proseq2.0 default parameters https://github.com/Danko-Lab/proseq2.0
Genome_build: Sp3.1
Supplementary_files_format_and_content: 12h_PROseq_Total_Nov2020_minus3.rpm.bw and 12h_PROseq_Total_Nov2020_plus3.rpm.bw,   bigwig files for the combinned signal from all replicates
Supplementary_files_format_and_content: 12h_Sep_2020_TOTAL_B.dREG.peak.prob.bed.gz, bed file dREG predictions based on the total signal from all replicates

extract_protocol:
Density gradient nuclear prep
Chu et al., 2018. PMCID: PMC6204104


title: ZHBT-O4AID Uninduced K27ac rep3


title: PRO-seq_12h_SE_Biorep2

description: s_12h67P45_CKDL200162589-1a-45_HCJKGCCX2_L6


title: H1703_R

type: genomic

description: resistant variant of non-small cell lung cancer cell line NCI-H1703

hyb_protocol: performed acording to stardard Agillient protocol to the 60K SurePrint G3 Unrestricted CGH arrays

scan_protocol: Raw image files were quantified using Agilent Feature Extraction software (version 11.0.1.1), protocol CGH_1100_Jul11.

data_processing: Data preprocessing was conducted with Bioconductor package rCGH according to standard protocol dedicated for Agilent dual-color hybridization chips. Signals were adjusted for GC content and cy3/cy5 bias, genome profiles were segmented using the Circular Binary Segmentation algorithm, LRRs were centered using an expectation-maximization algorithm

label_protocol: labeling was performed using stardard Agillient protocol to the 60K SurePrint G3 Unrestricted CGH arrays

growth_protocol: NCI-H1581 cells were routinely maintained in DMEM/F12, NCI-H1703 were maintained in RPMI 1640 medium. All culture media contained 10% of FBS and penicillin/streptomycin (100 U/ml/ 100 μg/ml). Cells were grown at 37°C in a humidified atmosphere of 5% CO2. All culture media and corresponding supplements were purchased from Merck KGaA (Darmstadt, Germany) or Biowest (Riverside, MO, USA).

extract_protocol: DNA from the cells was isolated using GeneJET Genomic DNA Purification Kit, Thermo Fisher Scientific (Waltham, MA, USA)

value: non-small cell lung cancer

tag: gender

value: male

value: resistant

source_name: standard reference genomic DNA

value: standard reference genomic DNA


title: sample 21, healthy control 21

status: Public on Dec 14 2021

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a healthy individual

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: healthy control

tag: therapy

value: female

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: ZHBT-O4AID Uninduced K27ac rep1

tag: strain

value: Embryonic stem cells

value: Untreated

value: Oct4-/-; TetOFF Oct4; CAG Oct4AID; CAG Tir1


title: H1703_S

description: sensitive variant of non-small cell lung cancer cell line NCI-H1703

value: sensitive


title: H1581_S

description: sensitive variant of non-small cell lung cancer cell line NCI-H1581


title: H1581_R

description: resistant variant of non-small cell lung cancer cell line NCI-H1581


title: PRO-seq_12h_SE_Biorep1.2

description: s_12h6_2P_CKDL200146116-1a-17_H75NYBBXX_L1


title: sample 18, healthy control 18

tag: Sex


title: sample 17, healthy control 17


title: sample 20, healthy control 20


title: ESC O4f/- CreER 0h RNA rep1

value: Mixed 129SV C57BL/6

tag: cell type

value: Oct4Fl/-; CAG CreER


title: sample 19, healthy control 19


title: sample 16, healthy control 16


title: Input__SeaUrchin_embryos_Ext 179

description: Input

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned using bowtie version 1.0.1 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.2 with the following setting: -p 1e-5
Genome_build: Sp3.1
Supplementary_files_format_and_content: PolII_SE355_SE356_LW228_MERGED_SORTED.bw, bigwig file of the total signal of the 3 Biological replicatesreplicates.
Supplementary_files_format_and_content: CHIP_SOR_TED.bed, bed file of the macs peak calls of the total signal of the 3 biological replicates.

source_name: 20 hour hatching blastula embryos

growth_protocol: 15 degrees Celsius, How long were they grown for and when they were collected?

extract_protocol:
The sample was  dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: How were these formaldehyde treated?

tag: tissue


title: Input-corr-ChIP 644__SeaUrchin_emb_Ext 211

description: Input-corr-ChIP 644


title: Input-corr-ChIP 643__SeaUrchin_emb_Ext 210

description: Input-corr-ChIP 643


title: PRO-seq_12h_SE_Biorep1.1

description: s_12h6_2P_CKDL190141930-1a-17_H723JBBXX_L2


title: 8WG16_ab817_SeaUrchin_emb_Ext 211

description: Abcam ab817, RNA Pol II CTD repeat YSPTSPS

tag: antibody (target, vendor catalog number)

tag: matching input


title: ATAC_20h_Bioreplicate 1.techinical replicate 1

data_processing:
ENCOCE-DCC atac-seq-pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) default parameters
MACS2 peak call p threshold set to 0.05.
Genome_build: Sp3.1
Supplementary_files_format_and_content: MACS2_ATAC_20h.pooled.pval0.05.300K.bfilt.narrowPeak_sort_merge.bed , Bed file for the peak calls of the merged samples.
Supplementary_files_format_and_content: ATACve49_ve59_VE07_RPM_0.bw , bigwig file of the merged samples

extract_protocol:
Nuclear prep, Hajdu et al., 2016. PMID: 27896813
Wash nuclei once with Cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) Nextera DNA Sample Preparation Kit (24 Samples)  (Illumina Cat # FC-121-1030) was used for the transposase reaction.
Nextera DNA Sample Preparation Kit (24 Samples)  (Illumina Cat # FC-121-1030) was used for library generation


title: ATAC_20h_Bioreplicate 1.techinical replicate 2


title: ATAC_20h_Bioreplicate 2

extract_protocol:
Density gradient nuclear prep.
Wash nuclei once with Cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) Nextera DNA Sample Preparation Kit (24 Samples)  (Illumina Cat # FC-121-1030) was used for the transposase reaction.
Nextera DNA Sample Preparation Kit (24 Samples)  (Illumina Cat # FC-121-1030) was used for library generation


title: PRO-seq_20h_SE_Biorep3

data_processing:
proseq2.0 default parameters https://github.com/Danko-Lab/proseq2.0
Genome_build: Sp3.1
Supplementary_files_format_and_content: 20h_TOTAL_Sep2020_plus3.rpm.bw and 20h_TOTAL_Sep2020_minus3.rpm.bw, bigwig files for the combinned signal from all replicates
Supplementary_files_format_and_content: 20hTOTAL_sep2020.dREG.peak.prob.bed.gz, bed file dREG predictions based on the total signal from all replicates

extract_protocol:
Density gradient nuclear prep
Chu et al., 2018. PMCID: PMC6204104
PRO-seq


title: PRO-seq_20h_SE_Biorep1_Tech_1


title: PRO-seq_20h_SE_Biorep2.2


title: Glucose_rep_E2

status: Public on May 17 2021

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.38 and rRNA reads were filtered using SortmeRNA v. 2.0.
QC reads were mapped into the Xanthomonas citri pv. citri str. 306 genome using Bowtie2 algorithm.
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparison against the control (Glucose) condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the control condition (Glucose) were determined by applying p-ajusted ≤ 0.05 as the threshold.
Genome_build: Xanthomonas
Genome_build: European Nucleotide Archive ASM716v1
Genome_build: genome-build-accession GCA_000007165.1
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results

organism: Xanthomonas citri pv. citri

source_name: Bacterial culture

growth_protocol: X. citri was cultivated in LB-medium without sodium chloride (LB ON) with 100 µg/mL of ampicillin, being maintained at 30 °C and 200 rpm for 16 hours. The bacterial cultures were centrifuged and washed with XVM2m medium once, and then inoculated in the XVM2m medium containing glucose or xylooligosaccharides as sole carbohydrate source with an initial optical density at 600 nm of 0.01. Bacteria were grown with constant shaking at 200 rpm and 30 °C and were harvested when reached the mid-exponential phase.

extract_protocol:
RNA was harvested from X. citri cultures at mid-exponential phase using the Trizol/chloroform protocol.  Genomic DNA was then removed, followed by purification of the samples with the RNeasy Mini Kit (Qiagen). Then, 2-2.5 µg of RNA was used for depletion of rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria - Epicenter Biotechnologies).
The preparation of the cDNA libraries was achieved with the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol.  Libraries were sequenced on the Illumina HiSeq 2500.

tag: carbon source

value: Glucose

tag: biological replicate


title: 8WG16_ab817_SeaUrchin_emb_Ext 210


title: Glucose_rep_B0


title: Glucose_rep_C2


title: Glucose_rep_B1


title: 8WG16_ab817_SeaUrchin_embryos_Ext 179


title: PRO-seq_20h_SE_Biorep2.1


title: Glucose_rep_A1