title: Brain neural stem cell, psicor

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
Using Perl scripts to process the Raw Data to ensure the quality of the data for further analysis.The filtering standards are as follows:1) Delete reads contaminated by the adapter. (Reads containing more than 5 adapter-polluted bases were considered as adapter contamination readings and would be filtered out;2) Eliminate low-quality reading. Low-quality Reads (phred quality value less than 19) accounted for more than 15% of the total base number.3) Remove reads with more than 5% of the number of N bases.
The genome index was built with Bowtie2 v2.2.3 and the Clean Data was mapped to the reference genome using TopHat v2.0.12.
Using the Integrative Genomics Viewer (IGV) to view mapping results through a Heatmap, histogram, scatter plot, or other stytles.
The Reads Count of each gene in each sample were calculated by HTSeq v0.6.0, and then FPKM (Fragments per Kilobase per Million Mapped Fragments) was calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Brain neural stem cell

extract_protocol:
Total RNA was collected with the RNA microextraction kit. A sequencing library was constructed with 2ug total RNA.
RNA libraries sequencing  were performed with standard Illumina protocols.

value: Brain neural stem cell

value: ICR

tag: developmental stage


title: SP+_1_B

status: Public on Jan 27 2023

type: SRA

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

country: USA

institute: NYU Langone

library_source: transcriptomic

data_processing:
Read trimming: Sequencing adaptors were removed using Trimmomatic (version 0.39), which was also used to trim low quality bases at the 5’ end of reads (using parameters TRAILING:20 and SLIDINGWINDOW:5:20). Reads with a minimum length of 30 bases were retained.
Alignment: STAR (version 2.7.5a)
Read counting on gene-level: HTSeq (version 0.11.2); Read counting on exon level: scripts provided as part of R package DEXSeq (Anders et al. 2012).
Each sample was sequenced five times. We used PCA to verify the absence of a sequencing lane effect, after which we merged all five fastq files of each sample and repeated alignment and read counting based on the merged fastq files.
Gene-level filtering: Raw counts were filtered to keep only genes with at least three counts per million in at least three samples and genes encoded in mitochondrial DNA were removed. We removed three samples that were outliers in PCA (C_V_6, C_SP+_2 and C_SP+_3). Exon-level filtering: As a first filtering step, we only kept exons from genes that were analyzed in the gene-level analysis and removed exons that could not be unambiguously assigned to only one gene. For the second filtering step, after normalization (see below), we removed 20% of exons with the lowest normalized counts. Finally, we removed exons that are shared across all transcript isoforms of their gene, or that are present in a gene that has only one annotated transcript isoform. As for the gene-level analysis, we removed three outlier samples (C_V_6, C_SP+_2 and C_SP+_3).
Gene-level normalization: counts per million were calculated in edgeR, using TMM normalization. Exon-level normalization: exons were normalized as recommended in Soneson et al. 2016.
Batch effect correction: to correct for high immune gene expression in a random subset of samples, Combat-seq was applied to both gene and exon counts.
Assembly: dm6 version r6.24 for gene-level alignment; BDGP6.32 for exon-level alignment
Supplementary files format and content: Matrix table with raw gene-level and exon-level read counts. Both gene and exon read counts were corrected for batch effects using ComBat-seq.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were maintained on yeast/glucose food at 25⁰C on a 12h light/dark cycle (lights on at 8 AM)

extract_protocol:
Flash frozen flies were vortexed to dislodge heads. Heads were collected in Trizol. RNA was extracted and DNA was removed using the Directzol RNA microprep kit (Zymo).
Poly(A)-selected, stranded libraries were made using the NEBnext Ultra II Directional RNA library prep kit and the Poly(A) mRNA magnetic isolation module (New England Biolabs, MA).

treatment_protocol: Females were mated to a wildtype of Sex Peptide null male within a 3 hour window in the morning (8 AM - 11 AM) and were frozen at their designated time point after mating. Virgin females were frozen in parallel.

tag: timepoint

tag: tissue

value: head

tag: treatment

value: mated to wildtype male

tag: genotype

value: Canton-S


title: Brain neural stem cell, sh1

country: China

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

value: KO


title: TotalRNAseq_A498_Day0_Rep2

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
ChIP-seq reads were trimmed with Trim Galore to remove adapter sequences and aligned to the hg38 genome using bwa (bwa mem) . Duplicate reads were removed from aligned reads using Picard MarkDuplicates. Reproducible histone peaks (broad peaks for H3K36me3, H3K27me3 & narrow peaks for H3K4me3, H3K9me3, H3K27ac) were identified by using MACS2 followed by IDR identification and filtering using idr-threshold < 0.05.
The reads from total RNA-seq libraries were trimmed for adapter sequences and aligned to the hg38 genome using HISAT2 with proper capture of RNA strand orientation. The bam files were normalized into CPM bedgraph files using deeptools "bamCoverage" command.
Assembly: hg38
Supplementary files format and content: Total RNAseq are processed and presented as CPM normalized bedgraph files. For ChIP-seq, MACS2-identified peaks are presented as bed files.

organism: Homo sapiens

source_name: kidney cancer cell line

growth_protocol: 786-O (ATCC Cat# CRL-1932, RRID:CVCL_1051) was cultured in RPMI 1640 medium (Corning). A-498 (ATCC Cat# HTB-44, RRID:CVCL_1056), A-704 (ATCC Cat# HTB-45, RRID:CVCL_1065) were cultured in EMEM medium (ATCC), and ACHN (ATCC Cat# CRL-1611, RRID:CVCL_1067). Caki-1 (ATCC Cat# HTB-46, RRID:CVCL_0234) and Caki-2(ATCC Cat# HTB-47, RRID:CVCL_0235) were cultured in McCoy's 5A Medium (Millipore Sigma). All media were supplemented with 10% heat-inactivated FBS (Corning) and 1% Penicillin-Streptomycin (Genesee Scientific).

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) followed by on-column DNase I digestion according to the manufacturer’s protocol. Genomic DNAs were purified using phenol–chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat# 08098140702). ChIP assays were performed following the native ChIP protocol. ChIP assays were performed following the native ChIP protocol (Ohtani et al., 2018) with minor modifications.
Total RNA-seq 786-O EV/KO Rep1 were sequenced 75 bp single end.  Total RNA-seq 786-O EV/KO Rep2 and other kidney cancer cell line total RNA-seq libraries were sequenced 50 bp paired-end. All ChIP-seq libraries were sequenced 50 bp paired-end.

treatment_protocol: Cells were seeded in 10 cm dishes and treated with 300 nM DAC for 24 hrs and harvested days after treatment as labeled.

tag: cell line

value: WT


title: TotalRNAseq_A498_Day0_Rep1


title: SP+_0.5_B


title: VSG_liver4

city: Duarte

first: Zhipeng

last: Fang

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
FastQC (v0.10.1) quality control
STAR (v2.6.0.a) genome mapping, default setting
featureCounts (v2.0.3)
Assembly: mm10
Supplementary files format and content: The processed counts.txt file is a tab-delimited table which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.

source_name: Liver samples after the VSG operation on HFD-fed male mouse

growth_protocol: 6-8-week-old mice with HFD feeding for 10 weeks

extract_protocol: Approximately 40mg liver tissue per sample was used for total RNA extraction and construction of strand-specific RNA-seq library

treatment_protocol: VSG or Sham operation, then fed with HFD for additional 12 weeks.

value: liver

value: VSG


title: Sham_liver2

source_name: Liver samples after the sham operation on HFD-fed male mouse

value: sham


title: TotalRNAseq_CAKI1_Day25_Rep2

value: 300nM DAC


title: TotalRNAseq_CAKI1_Day0_Rep2


title: Sham_liver3


title: VSG_liver5


title: Sham_liver1


title: SP+_12_A


title: SP+_24_A


title: NC_Input

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

institute: Peking University

description:
NC H3K27ac Input
Illumina Prep Kit libraries

library_source: genomic

data_processing:
Paired-end sequencing reads were mapped to the human genome hg19 with boH3K56ie2 (V 2.2.3)  (Langmead and Salzberg, 2012) after cut adapotr wiht cutadapt (V 2.7) (Martin, 2011) (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGA).
In order to obtain the accurate mapping reads, discordantly, duplicate and multi-mapping reads were discarded, and the filtered reads were converted into bigwig files using bamCoverage (V 3.3.1) from deepTools (Ramirez et al., 2014) and visualization using Integrative Genomics Viewer (IGV V2.8.9) (Robinson et al., 2011). In order to detect the accurate binding site, the filtered reads were used to call peaks with MACS2 (V 2.2.7.1) (Zhang et al., 2008) for the two replicates separately, and only the repeatable peaks were used. The peak overlap analysis was performed using the findOverlapsOfPeaks function of the ChIPpeakAnno (V 3.18.2) (Zhu et al., 2010).
In order to visualize the signal change of ChIP-Seq at the specific regions, computeMatrix (V 3.3.1) and plotProfile (V 3.3.1) from deepTools (Ramirez et al., 2014) to profile the average ChIP-Seq signal and in order to describe the changes of ChIP-Seq in these regions more clearly, we also used boxplot to quantify the ChIP-Seq signal in these regions.
And to identify the changes of H3K27ac signal at the super enhancer regions after Nabhb treatment, DiffBind (V 2.12.0) (Ross-Innes et al., 2012) was used for differential analysis with FDR<0.05 and foldchange>log(2) as cutoff.
Assembly: hg19
Supplementary files format and content: bigwig file contain the genome-wide binding profile of each protein

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: 1.  Plasmids  pcDNA4-H3-K56TAG (C-terminal myc-His-tag) was transfected into the relative PylRS stable cell line of HEK293T and supplemented with 0.2 mM Kcr/Kbhb. After growing for 6 h, the cells were changed into DMEM with 1mM Kcr/Kbhb. The cells were cultured for additional 36 hours to express the corresponding H3 protein. For cells harboring H3K56, pcDNA4-H3K56-H3 (C-terminal myc-His-tag) was transfected and growing for the same time. 2. HEK293T cells were grown in DMEM culture medium supplemented with 10% fetal bovine serum. Metabolites mimics,  Nabhb 20 mM was added when cells arriving at 60% confluency. The cells were then harvested after growing to 100%.

extract_protocol:
For crosslinking, the cells suspension was treated with formaldehyde at a final concentration of 1% (H3K56/vol) and incubated for 10 min at room temperature, followed by quenching with 0.125 M glycine for 5 min at room temperature. After pelleted through 1,000 g for 5 min at 4 °C, the harvested cells were washed twice with ice cold PBS, aliquoted to 20 million aliquots per 1.5 ml Eppendorf tube, and stored at -80 °C or directly for chromatin immunoprecipitation. 20 million crosslinked cells were lysed gently with 0.6 ml of ice-cold NP-40 lysis buffer (10 mM Tris·HCl, pH 7.5, 150 mM NaCl and 0.05% Nonidet P-40) on ice for 7 min. The cell lysates were then transferred on top of 1.25 ml sucrose cushion (24% sucrose (H3K56/vol) in NP-40 lysis buffer), centrifuged at 20,000 g, 10 min at 4 °C to discard the supernatant of cytoplasmic fraction. After washing once with 1ml PBS/1 mM EDTA, the chromatin pellet was resuspended in sonication buffer (20 mM Tris HCl, pH 8.0 ,150 mM NaCl, 2 mM EDTA, pH 8.0,0.1% SDS,1% Triton X-100) with 5 mM CaCl2. The suspension was treated with 400 U Micrococcal Nuclease and incubated at 37 °C for 15 min with 700 rpm shaking. The digestion was stopped by adding 20 μl 0.5 M EDTA and 40 μl 0.5 M EGTA and mixed thoroughly to inactivate MNase. The MNase digested chromatin were divided into 100 μl per tube and sonicated by the Bioruptor system (Diagenode, Bioruptor Plus) twice with high energy, at 30 s ON, 60 s OFF for 10 cycles. After centrifuged twice at 20,000 g, 10 min at 4 °C, 20 μl supernatant were sampled as input, and the rest supernatant was transferred into 2 new DNase free tube (600 μl/tube).   1 μg of myc-tag, H3K4me3, H3K27ac, GLYR1, BRD4, MED1 or Pol II antibody, was added for each ChIP reaction, respectively. After incubated overnight at 4 °C with low-speed rotation, the reaction mixture was treated with pre-washed 30 μl protein A/G magnetic beads by sonication buffer and incubated for another 4 h. The beads-antibody-protein complexes were washed through magnetic frame three times with sonication buffer, twice with high-salt wash buffer (20 mM Tris·HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), twice with LiCl wash buffer (10 mM Tris HCl, pH 8.0,250 mM LiCl, 1 mM EDTA, 1% NP-40), three times with TE buffer (1 mM EDTA, 10 mM Tris HCl, pH 8.0). Washed bead-antibody-protein complexes were resuspended in 300 μl elution buffer (50 mM Tris HCl, pH 8.0,10 mM EDTA,1% SDS). In parallel, 250 μl elution buffer, and 5 μl 10% SDS were added to 50 μl of each input sample. In order to digest the proteins and reverse the crosslinking, 3 μl of Proteinase K solution (Invitrogen, 20 mg/ml) was added to the input samples and bead-antibody-protein complexes eluate, incubated overnight at 65 °C while shaking on the thermomixer, and the protease K was further inactivated at 80 °C for 20 min. The DNA was purified using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (pH8.0), precipitated using ethanol, and redissolved in DEPC water.
Libraries from the purified ChIP-ed DNA were prepared using NEB Next Ultra II DNA library prep kit according to the manufacturer-supplied protocol, the 200~400 bp length amplified DNA were size selected using the SPRIselect double side size selection kit (Beckman Coulter), analyzed with Qubit assays and Fragment Analyzer, and finally sequenced on the HiSeq Xten PE150 sequencing platform (Novogene, Beijing).

tag: antibody


title: SP+_8_A


title: PsA_BacDrop

city: Cambridge

first: Peijun

last: Ma

state: MA

address: 415 Main Street

department: Infectious Disease and Microbiome program

institute: The Broad Institute of MIT and Harvard

description: PsA

data_processing:
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Cell barcodes were extracted using UMI-Tools package installed in Python-3.6
Alignment was using BWA
FeatureCounts was used to assign reads to gene, count transcripts and generate counts tables.
Counts matrix from BacDrop experiments were generated using UMI-Tools
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Counts matrix

organism: Pseudomonas aeruginosa

source_name: A P. aeruginosa pathogenic isolate

growth_protocol: 37ºC, regular laboratory condition

extract_protocol: Trizol RNA extraction for Bulk RNAseq data

value: untreated

tag: method

value: BacDrop

tag: accession no.


title: TotalRNAseq_CAKI1_Day25_Rep1


title: H3K56bhb_rep2

description: Illumina Prep Kit libraries

data_processing:
To improve the ratio of reads mapping, fastq files of paired-end sequencing were removed adaptors and low-quality reads with Cutadapt (V 2.7) (Martin, 2011).
The remaining high-quality reads were then mapped to the mouse genome hg19 with bowtie2. To obtain the accurate mapping reads, discordantly, duplicate and multi-mapping reads were removed from the aligned bam files.
The final bam files were used to identification peaks with MACS2 (V 2.7), and the peaks reproducible (IDR <= 0.05) in two replicates were used for downstream analysis. And differential peaks were identified with DiffBind (V 2.12.0) (Ross-Innes et al., 2012) using FDR<0.05 as cutoff.
Assembly: hg19
Supplementary files format and content: bigwig file contain the genome-wide chromatin accessibility information

extract_protocol:
50,000 cells were resuspended in 50 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin, and incubated on ice for 3 minutes. After centrifuging at 500 rcf for 5 min at 4 °C, the lysis was washed out with 1 ml cold ATAC-RSB containing 0.1% Tween-20. Cell pellet was resuspended in 50 ml of transposition mixture (25 ml 2x TD buffer, 2.5 ml transposase (100nM final), 16.5 ml PBS, 0.5 ml 1% digitonin, 0.5 ml 10% Tween-20, 5 ml H2O) and incubated at 37°C for 30 minutes at 1000 rpm.
Libraries from the purified DNA were prepared using Vazyme TruePrepTM DNA Library Prep Kit V2 for Illumina® according to the manufacturer-supplied protocol, the 200~700 bp length amplified DNA were size selected using the SPRIselect double side size selection kit (Beckman Coulter), analyzed with Qubit assays and Fragment Analyzer, and finally sequenced on the HiSeq Xten PE150 sequencing platform (Novogene, Beijing).

treatment_protocol: groH3K56h protocol:  1.  Plasmids  pcDNA4-H3-K56TAG (C-terminal myc-His-tag) was transfected into the relative PylRS stable cell line of HEK293T and supplemented with 0.2 mM Kcr/Kbhb. After growing for 6 h, the cells were changed into DMEM with 1mM Kcr/Kbhb. The cells were cultured for additional 36 hours to express the corresponding H3 protein. For cells harboring H3K56, pcDNA4-H3K56-H3 (C-terminal myc-His-tag) was transfected and growing for the same time. 2. HEK293T cells were grown in DMEM culture medium supplemented with 10% fetal bovine serum. Metabolites mimics,  Nabhb 20 mM was added when cells arriving at 60% confluency. The cells were then harvested after growing to 100%.

tag: histone


title: SP+_6_A


title: Nabhb_Input

description:
Nabhb H3K27ac Input
Illumina Prep Kit libraries

treatment_protocol: 1.  Plasmids  pcDNA4-H3-K56TAG (C-terminal myc-His-tag) was transfected into the relative PylRS stable cell line of HEK293T and supplemented with 0.2 mM Kcr/Kbhb. After growing for 6 h, the cells were changed into DMEM with 1mM Kcr/Kbhb. The cells were cultured for additional 36 hours to express the corresponding H3 protein. For cells harboring H3K56, pcDNA4-H3K56-H3 (C-terminal myc-His-tag) was transfected and growing for the same time. 2. HEK293T cells were grown in DMEM culture medium supplemented with 10% fetal bovine serum. Metabolites mimics,  Nabhb 20 mM was added when cells arriving at 60% confluency. The cells were then harvested after growing to 100%.


title: TotalRNAseq_CAKI1_Day12_Rep1


title: VSG_liver6


title: H3K56bhb_rep1

description: Illumina Prep Kit libraries


title: H3K56_rep1

description: Illumina Prep Kit libraries


title: TotalRNAseq_CAKI1_Day0_Rep1


title: TotalRNAseq_CAKI1_Day12_Rep2


title: TotalRNAseq_ACHN_Day22_Rep2

value: ACHN


title: H3K56bhb

description: Illumina Prep Kit libraries

data_processing:
The paired-end sequencing Hi-C data were aligned to hg19 using HiC-PRO (v2.9.0) (Servant et al., 2015). The process is briefly described as follows: reads were aligned to hg19 using the bowtie2 '-very-sensitive' option,
and in order to filter out the available reads, self-cycle, dangling, dumped reads and duplicated reads due to PCR amplification are removed, and the final interaction files were generated using the available reads. In order to compare the chromatin interaction between diffrent conditons,
Hi-C allValidPairs files were sampled to the equal amout with subsample, and the interaction pairs less than 10kb were removed. Finally, the sampled allValidPairs files were converted into .hic files with the script hicpro2juicebox.sh from HiC-PRO.
Assembly: hg19
Supplementary files format and content: hic file contain the genome-wide chromatin interaction information

extract_protocol:
For crosslinking, the cells suspension was treated with formaldehyde at a final concentration of 1% (H3K56/vol) and incubated for 10 min at room temperature, followed by quenching with 0.125 M glycine for 5 min at room temperature. After pelleted through 1,000 g for 5 min at 4 °C, the harvested cells were washed twice with ice cold PBS, aliquoted to 20 million aliquots per 1.5 ml Eppendorf tube, and stored at -80 °C for further delivery to Novogene Com., Beijing for Hi-C library generation.
Hi-C library generation was conducted by Novogene Com., Beijing.

treatment_protocol: groH3K56h protocol:  1.  Plasmids  pcDNA4-H3-K56TAG (C-terminal myc-His-tag) was transfected into the relative PylRS stable cell line of HEK293T and supplemented with 0.2 mM Kbhb. After growing for 6 h, the cells were changed into DMEM with 1mM Kbhb. The cells were cultured for additional 36 hours to express the corresponding H3 protein. For cells harboring H3K56, pcDNA4-H3K56-H3 (C-terminal myc-His-tag) was transfected and growing for the same time. 2. HEK293T cells were grown in DMEM culture medium supplemented with 10% fetal bovine serum.


title: SP+_3_A


title: H3K56ac_rep3

data_processing:
In order to optimize the mapping ratio, paired-end sequencing reads were trimed with Cutadapt (V 2.7) (Martin, 2011) (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT), and STAR (2.7.3a) (Dobin et al., 2013) was used to mapping paired-end sequencing reads to the human genome hg19.
In order to obtain accurate mapping reads, duplicate, discordantly and multi-mapping reads were discarded. In order to obtain the expression of each gene, featureCounts (V 2.0.1） (Liao et al., 2014) was used to calculate the reads counts of each gene with the annotaton file from ENCODE (Frankish et al., 2019).
And to find the differential genes in different condition, DESeq2 (V 1.24.0) (Love et al., 2014) was used to perform differential analysis with FDR<0.05 foldchange>1.5 as cutoff. For effectively display the results of differential analysis, volcano plot and MA plot were used in this study.
Assembly: hg19

extract_protocol:
Cells were lysed in Trizol reagent and extracted RNA according to the manufacture’s protocol
With the confirmation of the concentration and integrity of the total RNA, they were delivered for poly-A RNA library generation by Novogene Com., Beijing.

treatment_protocol: groH3K56h protocol: 1. Plasmids pcDNA4-H3-K56TAG (C-terminal myc-His-tag) was transfected into the relative PylRS stable cell line of HEK293T and supplemented with 0.2 mM Kcr/Kbhb. After growing for 6 h, the cells were changed into DMEM with 1mM Kcr/Kbhb. The cells were cultured for additional 36 hours to express the corresponding H3 protein. For cells harboring H3K56, pcDNA4-H3K56-H3 (C-terminal myc-His-tag) was transfected and growing for the same time. 2. HEK293T cells were grown in DMEM culture medium supplemented with 10% fetal bovine serum. Metabolites mimics, Nabhb 20 mM was added when cells arriving at 60% confluency. The cells were then harvested after growing to 100%.


title: H3K56

description: Illumina Prep Kit libraries


title: H3K56ac_rep2


title: SP+_2_A


title: TotalRNAseq_ACHN_Day14_Rep2


title: TotalRNAseq_ACHN_Day5_Rep2


title: H3K56_Pol II_rep2

description:
WT-H3(H3K56) Pol II
Illumina Prep Kit libraries

data_processing:
Paired-end sequencing reads were mapped to the human genome hg19 with boH3K56ie2 (V 2.2.3)  (Langmead and Salzberg, 2012) after cut adapotr wiht cutadapt (V 2.7) (Martin, 2011) (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGA).
In order to obtain the accurate mapping reads, discordantly, duplicate and multi-mapping reads were discarded, and the filtered reads were converted into bigwig files using bamCoverage (V 3.3.1) from deepTools (Ramirez et al., 2014) and visualization using Integrative Genomics Viewer (IGV V2.8.9) (Robinson et al., 2011). In order to detect the accurate binding site, the filtered reads were used to call peaks with MACS2 (V 2.2.7.1) (Zhang et al., 2008) for the two replicates separately, and only the repeatable peaks were used. The peak overlap analysis was performed using the findOverlapsOfPeaks function of the ChIPpeakAnno (V 3.18.2) (Zhu et al., 2010).
In order to visualize the signal change of ChIP-Seq at the specific regions, computeMatrix (V 3.3.1) and plotProfile (V 3.3.1) from deepTools (Ramirez et al., 2014) to profile the average ChIP-Seq signal and in order to describe the changes of ChIP-Seq in these regions more clearly, we also used boxplot to quantify the ChIP-Seq signal in these regions.
And to identify the changes of H3K27ac signal at the super enhancer regions after Nabhb treatment, DiffBind (V 2.12.0) (Ross-Innes et al., 2012) was used for differential analysis with FDR<0.05 and foldchange>log(2) as cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file contain the genome-wide binding profile of each protein

value: Pol II


title: SP+_1_A


title: H3K56_Pol II_rep1


title: H3K56ac_rep1


title: TotalRNAseq_ACHN_Day22_Rep1


title: SP+_0.5_A


title: SP+_5_A


title: SP-_24_C

value: mated to SP null male


title: H3K56_MED1_rep2

description:
WT-H3(H3K56) MED1
Illumina Prep Kit libraries


title: H3K56_MED1_rep1


title: SP+_4_A


title: H3K56_H3K27ac_rep2

description:
WT-H3(H3K56) H3K27ac
Illumina Prep Kit libraries


title: TotalRNAseq_ACHN_Day14_Rep1


title: H3K56_rep2

description: Illumina Prep Kit libraries


title: SP-_12_C


title: H3K56_H3K27ac_rep1


title: TotalRNAseq_ACHN_Day5_Rep1


title: H3K56_BRD4_rep2

description:
WT-H3(H3K56) BRD4
Illumina Prep Kit libraries


title: SP-_8_C


title: H3K56_BRD4_rep1


title: NC_Pol II_rep2

description:
NC Pol II
Illumina Prep Kit libraries


title: TotalRNAseq_ACHN_Day0_Rep2


title: NC_MED1_rep2

description:
NC MED1
Illumina Prep Kit libraries


title: H3K56-Site-Seq_rep2

description:
WT-H3(H3K56) myc
Illumina Prep Kit libraries

value: myc


title: TotalRNAseq_ACHN_Day0_Rep1


title: SP-_6_C


title: NC_H3K27ac_rep2

description:
NC H3K27ac
Illumina Prep Kit libraries


title: H3K56-Site-Seq_rep1


title: H3K36me3_ChIP_786O_EV_Day5_Rep2

tag: chip antibody

value: H3K36me3 (Cell Signaling Technology Cat# 4909, RRID:AB_1950412)


title: H3K36me3_ChIP_786O_EV_Day0_Rep2


title: NC_Pol II_rep1

description:
NC Pol II
Illumina Prep Kit libraries


title: SP-_4_C


title: NC_MED1_rep1

description:
NC MED1
Illumina Prep Kit libraries


title: SP-_5_C


title: H3K36me3_ChIP_786O_KO_Day23_Rep1


title: NC_H3K27ac_rep1

description:
NC H3K27ac
Illumina Prep Kit libraries


title: NC_BRD4_rep2

description:
NC BRD4
Illumina Prep Kit libraries


title: NC_BRD4_rep1

description:
NC BRD4
Illumina Prep Kit libraries


title: SP-_2_C


title: H3K36me3_ChIP_786O_KO_Day5_Rep1


title: H3K36me3_ChIP_786O_KO_Day0_Rep1


title: Nabhb_Pol II_rep2

description:
Nabhb Pol II
Illumina Prep Kit libraries


title: Nabhb_H3K27ac_rep2

description:
Nabhb H3K27ac
Illumina Prep Kit libraries


title: Nabhb_MED1_rep2

description:
Nabhb MED1
Illumina Prep Kit libraries


title: H3K36me3_ChIP_786O_EV_Day5_Rep1


title: H3K36me3_ChIP_786O_EV_Day23_Rep1


title: SP-_0.5_C


title: Nabhb_BRD4_rep2

description:
Nabhb BRD4
Illumina Prep Kit libraries


title: SP-_24_B


title: Nabhb_BRD4_rep1

description:
Nabhb BRD4
Illumina Prep Kit libraries


title: Nabhb_Pol II_rep1


title: H3K36me3_ChIP_786O_EV_Day0_Rep1


title: SP-_12_B


title: H3K56cr_GLYR1_rep1

description:
H3K56cr GLYR1
Illumina Prep Kit libraries


title: H3K56cr_GLYR1_rep2


title: H3K56bhb_Pol II_rep2

description:
H3K56bhb Pol II
Illumina Prep Kit libraries


title: SP-_8_B


title: H3K9me3_ChIP_786O_KO_Day0_Rep2

value: H3K9me3 (Active Motif Cat# 39161, RRID:AB_2532132)


title: H3K9me3_ChIP_786O_KO_Day23_Rep2


title: SP-_6_B

value: head


title: H3K9me3_ChIP_786O_KO_Day5_Rep2


title: H3K56bhb-Site-Seq_rep1

description:
H3K56bhb myc
Illumina Prep Kit libraries


title: SP-_5_B


title: H3K56bhb_MED1_rep2

description:
H3K56bhb MED1
Illumina Prep Kit libraries


title: SP-_3_C


title: H3K56bhb-Site-Seq_rep2


title: H3K56bhb_Pol II_rep1


title: Nabhb_MED1_rep1

description:
Nabhb MED1
Illumina Prep Kit libraries


title: H3K56bhb_MED1_rep1


title: Nabhb_H3K27ac_rep1


title: H3K9me3_ChIP_786O_EV_Day23_Rep2


title: SP-_1_C


title: H3K56bhb_BRD4_rep1

description:
H3K56bhb BRD4
Illumina Prep Kit libraries


title: SP-_3_B


title: H3K56bhb_H3K27ac_rep1

description:
H3K56bhb H3K27ac
Illumina Prep Kit libraries


title: H3K56cr_rep2

description: transcriptomic

data_processing:
In order to optimize the mapping ratio, paired-end sequencing reads were trimed with Cutadapt (V 2.7) (Martin, 2011) (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT), and STAR (2.7.3a) (Dobin et al., 2013) was used to mapping paired-end sequencing reads to the human genome hg19.
In order to obtain accurate mapping reads, duplicate, discordantly and multi-mapping reads were discarded. In order to obtain the expression of each gene, featureCounts (V 2.0.1） (Liao et al., 2014) was used to calculate the reads counts of each gene with the annotaton file from ENCODE (Frankish et al., 2019).
And to find the differential genes in different condition, DESeq2 (V 1.24.0) (Love et al., 2014) was used to perform differential analysis with FDR<0.05 foldchange>1.5 as cutoff. For effectively display the results of differential analysis, volcano plot and MA plot were used in this study.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq rawcount, TPM count and DESeq2 results

tag: sample type


title: H3K56bhb_BRD4_rep2


title: SP-_2_B


title: SP-_4_B


title: H3K9me3_ChIP_786O_EV_Day5_Rep2


title: H3K56cr_rep3

description: transcriptomic


title: H3K9me3_ChIP_786O_EV_Day0_Rep2


title: H3K9me3_ChIP_786O_KO_Day23_Rep1


title: H3K56_rep3

description: transcriptomic


title: H3K56cr_rep1

description: transcriptomic


title: H3K56bhb_H3K27ac_rep2


title: SP-_1_B


title: H3K56_rep1

description: transcriptomic


title: H3K9me3_ChIP_786O_KO_Day5_Rep1


title: SP-_0.5_B


title: NC_rep3

description: transcriptomic

value: NC


title: SP-_24_A

value: Canton-S


title: H3K9me3_ChIP_786O_KO_Day0_Rep1


title: SP-_12_A


title: H3K9me3_ChIP_786O_EV_Day23_Rep1


title: Nabhb_rep3

description: transcriptomic

value: Nabhb


title: H3K9me3_ChIP_786O_EV_Day5_Rep1

value: WT


title: NC_rep2

description: transcriptomic


title: NC_rep1

description: transcriptomic


title: SP-_8_A


title: Nabhb_rep2

description: transcriptomic


title: H3K56bhb_rep3

description: transcriptomic


title: H3K56_rep2

description: transcriptomic


title: H3K27ac_ChIP_786O_KO_Day23_Rep2

value: H3K27ac (Active Motif Cat# 39685, RRID:AB_2793305)


title: H3K9me3_ChIP_786O_EV_Day0_Rep1


title: H3K56bhb_rep1

description: transcriptomic


title: SP-_5_A


title: SP-_6_A


title: H3K56bhb_rep2

description: transcriptomic


title: H3K27ac_ChIP_786O_KO_Day5_Rep2


title: Nabhb_rep1

description: transcriptomic


title: SP-_4_A


title: 12_T4_10nM

city: Paris

first: Evelyne

last: Duvernois-Berthet

address: 43 rue Cuvier

department: AVIV

country: France

institute: Museum national d'Histoire naturelle

data_processing:
Raw reads were first cleaned by removing PCR bias conserving one copy per cluster of duplicated reads (python script).
Then, reads were trimmed for the first 11 and last 1 nucleotides (fastx-trimmer from fastx-toolkit version 0.0.13.2) to remove adapter remnants. Reads 64bp long were specifically selected (cutadapt version 1.15). The global quality of the reads was checked using the FastQC (version 0.11.2).
Bowtie2 (v2.2.4) was used to map the clean reads against the Xenopus laevis genome (release 9.2) downloaded from XenBase (https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/, accessed on 19 January 2023) only conserving uniquely mapped reads.
Reads were counted on gene annotations was accomplished by HTSeq-count (v0.9.1) in union mode.
Assembly: Xenbase: https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/, accessed on 19 January 2023)
Supplementary files format and content: tab-delimited text files included raw read counts

organism: Xenopus laevis

source_name: Brain tissue

extract_protocol:
RNA was harvested using RNAqueous-microkit from Thermofisher. Libraries are made from 50 ng of total RNA based on Qubit assays.
The transcriptome libraries were prepared from total RNA using Illumina TruSeq Stranded mRNA Sample Preparation kits (Illumina Inc., USA).

value: Brain tissue


title: 11_T4_10nM


title: H3K27ac_ChIP_786O_KO_Day0_Rep2


title: SP-_2_A


title: 10_T4_10nM


title: SP-_3_A


title: H3K27ac_ChIP_786O_EV_Day23_Rep2


title: 9_T4_10nM


title: H3K27ac_ChIP_786O_EV_Day5_Rep2


title: SP-_1_A


title: 8_Amnios_1X

value: Mixture 1x-treated


title: H3K27ac_ChIP_786O_EV_Day0_Rep2


title: MDA-MB-231 DSM OE

city: Gainesville

first: Daiqing

last: Liao

state: FL

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

data_processing:
ChIP-seq sequencing reads (Fastq files) were mapped to the human genome (GRCh37/hg19) using Bowtie2 (Langmead and Salzberg, 2012), where option –local was specified to trim or clip unaligned reads from one or both ends of the alignment. Genome browser BedGraph tracks and read density histograms were generated using SeqMINER. Peak finding and annotation to the nearest Refseq gene promoter was performed and de novo motif discovery was carried out using HOMER (Heinz et al., 2010).
Assembly: hg19
Supplementary files format and content: matrix table for peak distritbutions
Supplementary files format and content: matrix table for region distritbutions

source_name: Triple negative breast

growth_protocol: The panel of MDA_MB-231 derived cell lines (control, WT DAXX OE, and DSM OE) were cultured in complete DMEM.

extract_protocol:
The cells were resuspended in a swelling buffer in the presence of the protease inhibitor cocktail (Sigma) and then pelleted and resuspended in the SDS lysis buffer. The lysates were transferred to a Covaris microTUBE and sonicated with an E220 Covaris Ultrasonicator. Chromatin fragmentation (~500 bps) was verified through agarose gel electrophoresis. DNA was extracted using Qiagen mini prep based on manufacturer instructions.
DNA libraries were prepared for sequencing using standard ChIP Illumina protocols

value: Triple negative breast

value: DSM Overexpression


title: miRNA-seq Neu WT rep 2

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: miRNA-seq

data_processing:
Reads are trimmed with cutadapt.
Custom STAR genome index was generated for hybrid genome of human, fly, yeast, ERCC to facilitate spike-ins quantification. Reads are aligned to hybrid genome. Reads with MAPQ < 2 are filtered out.
Finally, usage of poly-A sites, obtained from PolyA_DB version 3, was defined as a sum of reads whose 3`-ends are falling within 20bp upstream and 10bp downstream of the poly-A sites.
Human counts are normalized to the total count of fly counts. Gene counts are obtained as a sum of normalized counts for all pA sites of a gene.
The abundance of mature miRNAs was quantified with mirdeep2 pipeline.
Genome_build: hg38

source_name: iPSC derived cortical neurons

growth_protocol: iPSC lines #37 (WT) and #20 (isogenic MECP2-null) from a female patient were previously described. Both cell lines were generated and cultured under the approval of the SickKids Research Ethics Board and the Canadian Institutes of Health Research Stem Cell Oversight Committee. iPSC lines were cultured in 5% CO2 on BD hESC-qualified matrigel (BD) in mTeSR medium (STEMCELL Technologies). Cultures were passaged using ReLeSR (STEMCELL Technologies) following the manufacture’s instruction every 6-7 days. For neuronal induction, iPSCs were aggregated as Embryoid Bodies (EBs) in low-attachment dishes in N2 media containing laminin (1 ml/ml) with 10 mM SB431542, 2 mM DSM, and 1x penicillin-streptomycin changed daily. After 7 days, EBs were plated on poly-L-ornithine + laminin-coated dishes and grown in N2 media + laminin (1 ml/ml). After 7 days, neural rosettes were manually picked and transferred to poly-L-ornithine + laminin-coated wells. After 7 days, neural rosettes were picked a second time, digested with Accutase and plated on poly-L-ornithine + laminin-coated wells. Resulting neural precursor cells (NPC) were grown as a monolayer and split every 5-7 days in NPC media containing DMEM/F12, N2, B27, 1x non-essential amino acid (NEAA), 2 mg/ml Heparin, 1 mg/ml laminin. To generate neurons, NPCs were plated on poly-L-ornithine + laminin-coated plates at a density of 106 cells per 10 cm dish and cultured for 3 weeks in neural differentiation medium (Neurobasal, N2, B27, 1 mg/ml laminin, 1x penicillin-streptomycin, 10ng/ml BDNF, 10ng/ml GDNF, 200 mM ascorbic acid, and 10 mM cAMP).

extract_protocol:
To calculate relative and absolute differences in the miRNA population in NEUWT and NEURTT, small RNAs were extracted from two replicates of both lines using the same number of cells followed by the addition of a set of spike-in RNAs. Small RNAs were extracted from 500,000 neurons of each line using the SPLIT RNA extraction Kit (Lexogen) according to the manufacturer’s instructions. A set of 52 RNA spike-ins (QIAseq miRNA Library QC Spike-Ins – Qiagen) that spanned a wide range of concentrations were added to the recovered RNAs according to the manufacturer’s instructions.
Sequencing libraries were made using the Small RNA library preparation kit NEBNext (NEB) according to the manufacturer’s instructions. Sequencing was performed on the Illumina HiSeq 2500 using the Rapid Run mode.

treatment_protocol:
NA
Neuronal cultures were enriched for all experiments to exclude contaminating glia and neuro progenitor cells present after differentiation. Enrichment of 3-week old neuronal cultures was made as described earlier. 3-week old heterogeneous neuronal cultures were enriched by a negative selection strategy using antibodies against surface markers CD44 and CD184 (recognizing NPCs, glial progenitors and astrocytes)4 using magnetic-activated cell sorting (MACS® - Miltenyi Biotec). After enrichment, neurons were re-seeded onto Matrigel-coated 6-well plates, cultured in neural differentiation medium, and allowed to recover for one extra week, for a total of 4 weeks neuronal differentiation.

tag: 4su labeling time before harvest, (hours)

value: wild type

value: line 37 (Cheung 2011, HMG)

tag: sequencing batch

value: C


title: miRNA-seq Neu RTT rep 1

description: miRNA-seq

value: MECP2 exons 3-4 deletion

value: line 20 (Cheung 2011, HMG)


title: 6_Amnios_1x


title: 7_Amnios_1x


title: SP-_0.5_A

value: mated to SP null male


title: miRNA-seq Neu WT rep 1

description: miRNA-seq


title: V_24_C

value: virgin


title: H3K27ac_ChIP_786O_KO_Day23_Rep1

value: 300nM DAC


title: V_12_C

value: head


title: RATE-seq Neu RTT SS rep2

description: 3` mRNA-seq

extract_protocol:
After 4sU incorporation, cells were quickly washed twice with ice-cold 1× PBS Total RNA and scraped into ice-cold 1.5 ml Eppendorf tubes.  Cells were collected by spinning at 1000g for 5 min at 4°C and cell pellets were resuspended in 1 mL of Trizol (Thermo Fisher Scientific). Total RNA was extracted according to manufacturer instructions. The SS sample was prepared from a 5μg aliquot of the 24 h time-point added with 0.5 μg of both 4sU labeled and unlabeled spike-in RNAs.
RNA-seq libraries were prepared for each time-points and seady-state sample using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) automated on the NGS WorkStation (Agilent) at The Centre for Applied Genomics (TCAG) according to the manufacturer’s instructions. PCR cycle numbers were determined using the PCR Add-on Kit for Illumina (Lexogen). All steady-state samples were processed with 250 ng of total RNA input. To minimize variability between time-points within a batch, RNA samples were processed with the same total RNA input with a minimum of 100 ng of total RNA used. Each sample was spiked-in with ERCC RNA Spike-In Control Mix 1 (Ambion) according to the manufacturer’s instructions prior to the start of library preparation. Library quality and quantity were measured at TCAG prior to sequencing with Bioanalyzer (Agilent) and KAPA qPCR (Roche). Sequencing was also performed at TCAG on the Illumina HiSeq 2500 with single-end 100bp read length yielding 40 to 50 million reads.

treatment_protocol:
When enriched neuronal cultures reached 4-week of differentiation, media was replaced with neuronal differentiation media supplemented with 100 μM 4sU (Sigma-Aldrich) reconstituted in DMSO. Neurons were harvested at 0.5, 1, 4, 8, and 24 h after the addition of 4sU (except for the MECP2-null line where the time-point 1h was omitted from both replicates due to low differentiation yields). Metabolic labeling was designed such that all time points were collected together. Neuronal viability in the presence of 100 μM 4sU was monitored up to 24 h of treatment on parallel cultures by using Trypan blue staining and live/dead cell counting.
Neuronal cultures were enriched for all experiments to exclude contaminating glia and neuro progenitor cells present after differentiation. Enrichment of 3-week old neuronal cultures was made as described earlier. 3-week old heterogeneous neuronal cultures were enriched by a negative selection strategy using antibodies against surface markers CD44 and CD184 (recognizing NPCs, glial progenitors and astrocytes)4 using magnetic-activated cell sorting (MACS® - Miltenyi Biotec). After enrichment, neurons were re-seeded onto Matrigel-coated 6-well plates, cultured in neural differentiation medium, and allowed to recover for one extra week, for a total of 4 weeks neuronal differentiation.

value: A


title: 4_Ctrl

value: Control


title: H3K27ac_ChIP_786O_KO_Day0_Rep1


title: miRNA-seq Neu RTT rep 2

description: miRNA-seq


title: RATE-seq Neu RTT 24h rep2

description: 3` mRNA-seq

extract_protocol:
After 4sU incorporation, cells were quickly washed twice with ice-cold 1× PBS Total RNA and scraped into ice-cold 1.5 ml Eppendorf tubes.  Cells were collected by spinning at 1000g for 5 min at 4°C and cell pellets were resuspended in 1 mL of Trizol (Thermo Fisher Scientific). Total RNA was extracted according to manufacturer instructions. 50 µg of total neuronal RNA was mixed with 5 µg unlabeled yeast RNA and 5 µg 4sU-labeled S2 fly RNA in a total volume of 120 µL. 1 mg/mL HPDP-biotin (ThermoFisher Scientific) was reconstituted in dimethylformamide by shaking at 37°C for 30 min at 300 RPM. 120 µL of 2.5× citrate buffer (25 mM citrate, pH 4.5, 2.5 mL EDTA) and 60 µL of 1 mg/mL HPDP-biotin were added to the premixed RNA sample for each time point. The solution was incubated at 37°C for 2 h at 300 RPM on an Eppendorf ThermoMixer F1.5 in the dark. Samples were extracted twice with acid phenol, pH 4.5, and once with chloroform. RNA was precipitated with 18 µL 5M NaCl, 750 µL 100% ethanol, and 2 µL GlycoBlue (Invitrogen) overnight at −20°C. Precipitated RNA was pelleted for 30 min at 21,000g at 4°C. The RNA pellet was resuspended in 200 µL of 1× wash buffer (10 mM Tris-HCl, pH 7.4, 50 mM NaCl, 1 mM EDTA). Biotinylated RNA was purified using the µMACS Streptavidin microbeads system (Miltenyi Biotec). 50 µL Miltenyi beads per sample were pre-blocked with 48 µL 1× wash buffer and 2 µL yeast tRNA (Invitrogen), rotating for 20 min at room temperature. µMACS microcolumns were washed 1× with 100 µL nucleic acid equilibration buffer (Miltenyi Biotec), followed by 5× washes with 100 µL 1× wash buffer. Beads were applied to microcolumns in 100 µL aliquots and again washed 5× with 100 µL 1× wash buffer. Beads were demagnetized and eluted off the column with 2× 100 µL 1× wash buffer, and columns were placed back on the magnetic stand. A total of 200 µL beads was mixed with each sample of biotinylated RNA and rotated at room temperature for 20 min. Samples were applied to the microcolumns in 100 µL aliquots, washed 3× with 400 µL wash A buffer (10 mM Tris-HCl, pH 7.4, 6 M urea, 10 mM EDTA) prewarmed to 65°C, and washed 3× with 400 µL wash B buffer (10 mM Tris-HCl, pH 7.4, 1 M NaCl, 10 mM EDTA). RNA was eluted with 5× 100 µL of 1× wash buffer supplemented with 0.1 M DTT, and flow-through was collected in a tube. Purified RNA was precipitated with 30 µL 5 M NaCl, 2 µL GlycoBlue, and 1 mL 100% ethanol, incubated at −20°C overnight. Samples were spun at 21,000g at 4°C for 30 min and resuspended in 20 µL water. RNA quality was assessed by running 3 µL of samples on a 1.5% agarose gel.
RNA-seq libraries were prepared for each time-points and seady-state sample using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) automated on the NGS WorkStation (Agilent) at The Centre for Applied Genomics (TCAG) according to the manufacturer’s instructions. PCR cycle numbers were determined using the PCR Add-on Kit for Illumina (Lexogen). All steady-state samples were processed with 250 ng of total RNA input. To minimize variability between time-points within a batch, RNA samples were processed with the same total RNA input with a minimum of 100 ng of total RNA used. Each sample was spiked-in with ERCC RNA Spike-In Control Mix 1 (Ambion) according to the manufacturer’s instructions prior to the start of library preparation. Library quality and quantity were measured at TCAG prior to sequencing with Bioanalyzer (Agilent) and KAPA qPCR (Roche). Sequencing was also performed at TCAG on the Illumina HiSeq 2500 with single-end 100bp read length yielding 40 to 50 million reads.


title: 3_Ctrl


title: V_8_C

value: Canton-S


title: RATE-seq Neu RTT 8h rep2

description: 3` mRNA-seq


title: H3K27ac_ChIP_786O_EV_Day5_Rep1

value: WT

value: H3K27ac (Active Motif Cat# 39685, RRID:AB_2793305)


title: 2_Ctrl

value: Brain tissue


title: H3K27ac_ChIP_786O_EV_Day23_Rep1


title: RATE-seq Neu RTT 4h rep2

description: 3` mRNA-seq


title: V_6_C


title: 1_Ctrl


title: RATE-seq Neu RTT 30min rep2

description: 3` mRNA-seq


title: H3K27ac_ChIP_786O_EV_Day0_Rep1


title: V_4_C


title: 5_Amnios_1x

value: Mixture 1x-treated


title: H3K27ac_ChIP_786O_KO_Day5_Rep1


title: RATE-seq Neu RTT SS rep1

description: 3` mRNA-seq


title: V_3_C


title: V_5_C


title: H3K27me3_ChIP_786O_KO_Day23_Rep2

value: H3K27me3 (Cell Signaling Technology Cat# 9733, RRID:AB_2616029)


title: V_2_C


title: wild-type osteoclast 1

city: Ann Arbor

first: Lingxin

last: Zhu

address: 210 Washtenaw Ave, Life Sciences Institute, Room 5008

institute: Univeristy of Michigan in Ann Arbor

description:
Gene expression data
136683

data_processing:
Data were aligned using the STAR aligner and featureCounts v1.6.4 software, and reads per kilobase of transcript per million mapped read values on gene level were estimated for ensemble transcriptome.
DESeq2 was used to estimate significance between any two experimental groups.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow-derived

growth_protocol: Bone marrow cells were isolated from wild-type mice and myeloid specific Zeb1-deleted mice cultured on plastic substrata for differentiation into osteoclasts with M-CSF and RANKL.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The construction of libraries was generated using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.
QuantSeq 3’ mRNA-Seq Library

treatment_protocol: Bone marrow-derived macrophages were cultured with 20 ng/ml M-CSF and 30 ng/ml RANKL for 0 or 4 days

value: Bone marrow-derived

value: Primary osteoclast

value: wild-type

value: M-CSF plus RANKL-induced


title: RATE-seq Neu RTT 8h rep1

description: 3` mRNA-seq

value: MECP2 exons 3-4 deletion

value: line 20 (Cheung 2011, HMG)


title: H3K27me3_ChIP_786O_EV_Day23_Rep2


title: wild-type osteoclast 3

description:
Gene expression data
136685


title: RATE-seq Neu RTT 24h rep1

description: 3` mRNA-seq


title: wild-type osteoclast 2

description:
Gene expression data
136684


title: RATE-seq Neu RTT 4h rep1

description: 3` mRNA-seq


title: H3K27me3_ChIP_786O_EV_Day5_Rep2


title: V_0.5_C

value: virgin


title: RATE-seq Neu RTT 30min rep1

description: 3` mRNA-seq


title: H3K27me3_ChIP_786O_KO_Day0_Rep2


title: H3K27me3_ChIP_786O_KO_Day5_Rep2

value: 300nM DAC


title: H3K27me3_ChIP_786O_EV_Day0_Rep2


title: wild-type BMDM 3

description:
Gene expression data
136673

value: Primary bone marrow-derived macrophage

value: M-CSF-induced


title: V_1_C

value: head


title: RATE-seq Neu WT 24h rep2

description: 3` mRNA-seq

value: wild type

value: line 37 (Cheung 2011, HMG)

value: B


title: V_8_B

value: Canton-S


title: RATE-seq Neu WT 8h rep2

description: 3` mRNA-seq


title: RATE-seq Neu WT SS rep2

description: 3` mRNA-seq


title: V_5_B


title: Zeb1ΔM/ΔM osteoclast 1

description:
Gene expression data
136680


title: Zeb1ΔM/ΔM osteoclast 2

description:
Gene expression data
136681


title: H3K27me3_ChIP_786O_KO_Day0_Rep1


title: wild-type BMDM 2

description:
Gene expression data
136672


title: V_12_B


title: H3K27me3_ChIP_786O_KO_Day5_Rep1


title: Zeb1ΔM/ΔM osteoclast 3

description:
Gene expression data
136682


title: H3K27me3_ChIP_786O_EV_Day0_Rep1

value: WT


title: V_24_B


title: V_2_B


title: V_6_B


title: wild-type BMDM 1

description:
Gene expression data
136671


title: RATE-seq Neu WT 4h rep2

description: 3` mRNA-seq


title: RATE-seq Neu WT 1h rep2

description: 3` mRNA-seq


title: H3K27me3_ChIP_786O_KO_Day23_Rep1

value: H3K27me3 (Cell Signaling Technology Cat# 9733, RRID:AB_2616029)


title: Zeb1ΔM/ΔM BMDM 3

description:
Gene expression data
136670

value: Bone marrow-derived


title: V_3_B


title: Zeb1ΔM/ΔM BMDM 2

description:
Gene expression data
136669


title: RATE-seq Neu WT 30min rep2

description: 3` mRNA-seq


title: V_4_B


title: H3K27me3_ChIP_786O_EV_Day5_Rep1


title: H3K27me3_ChIP_786O_EV_Day23_Rep1


title: H3K4me3_ChIP_786O_KO_Day5_Rep2

value: H3K4me3 (Millipore Sigma, 05-1339, RRID:AB_1977251)


title: PAH/aKO_Rep2

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: PAH_Adra1a KO_heart

extract_protocol:
We used CRISPR/Cas9 system to generate female Adra1a-deficient hAGT transgenic mice with a frameshift mutation that leads to a knockout of the Adra1a gene. Then, we generated PAH/KO mice by mating female Adra1a-deficient hAGT transgenic mice with male hRN transgenic mice. Whole hearts were frozen in liquid nitrogen and were crushed into powder with a Multi-beads Shocker (Yasui Kikai Co.). Total RNA was extracted using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Reads were mapped on GRCm38 (mm10) mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age

value: Gestational days 19

tag: Sex

value: female

tag: genotype/variation

value: PAH_Adra1a KO

value: Heart


title: RATE-seq Neu WT SS rep1

description: 3` mRNA-seq

tag: treatment

value: A


title: RATE-seq Neu WT 24h rep1

description: 3` mRNA-seq

tag: genotype


title: H3K4me3_ChIP_786O_KO_Day0_Rep2


title: PAH/aKO_Rep4

tag: tissue


title: Zeb1ΔM/ΔM BMDM 1

description:
Gene expression data
136668

tag: cell type


title: H3K4me3_ChIP_786O_KO_Day23_Rep2

tag: cell line

value: 300nM DAC


title: RATE-seq Neu WT 8h rep1

description: 3` mRNA-seq


title: PAH/aKO_Rep1


title: V_12_A

tag: timepoint

value: virgin


title: V_1_B


title: H3K4me3_ChIP_786O_EV_Day0_Rep2


title: PAH/aKO_Rep3


title: RATE-seq Neu WT 30min rep1

description: 3` mRNA-seq


title: RATE-seq Neu WT 1h rep1

description: 3` mRNA-seq


title: V_24_A


title: RATE-seq Neu WT 4h rep1

description: 3` mRNA-seq


title: H3K4me3_ChIP_786O_EV_Day23_Rep2


title: H3K4me3_ChIP_786O_EV_Day5_Rep2


title: V_8_A


title: PAH_Rep3

value: PAH


title: PAH_Rep1


title: V_6_A

value: head


title: H3K4me3_ChIP_786O_KO_Day23_Rep1


title: V_5_A


title: V_0.5_B


title: D16 ADGRG1+ CD8TEM bulk TCR

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v6.0.0) and the GRCh38 genome annotation
clonotypes in bulk TCR sequencing were characterized IMSEQ software
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression, CITEseq) and contig table (VDJ)
Supplementary files format and content: IMSEQ output table (bulk TCR)
Library strategy: bulk VDJ profiling

source_name: blood

extract_protocol:
Cell sorting of CD8 T-cells for the functional studies and TCRβ bulk sequencing analysis was performed at the FACS Melody (Becton Dickinson, Franklin Lakes, NJ, USA).
DNA was isolated using AllPrep DNA Micro Kit (QIagen) and the recombined TCRβ locus was amplified.
single-cell immune profiling (totalSeq: scRNAseq, CITEseq, single-cell VDJ sequencing), bulk TCR

value: blood

tag: donor


title: PAH_Rep4


title: PAH_Rep2


title: Control_Rep4

source_name: Wild type_heart

value: Wild type


title: H3K4me3_ChIP_786O_KO_Day0_Rep1


title: V_2_A


title: Control_Rep3


title: V_3_A


title: RK012, scRNAseq

city: Shinjukuku

first: Shogo

last: Hashimoto

state: Tokyo

address: 35 shinanomachi

department: Department of Orthopaedic Surgery

institute: Keio university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing: The reads were mapped to rat UCSC6.0 using Cell Ranger 6.0.1. More than 200 million reads were acquired from each sample.

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
All tissues were homogenized using a Minute Single Nucleus Isolation Kit for Neuronal Tissues/Cells (Invent Biotech. BN-020)
single-nucleus suspensions were mixed with Single Cell Master Mix containing template switch oligonucleotide and loaded together with 3′ gel beads and partitioning oil into a Chip G according to the manufacturer’s instructions (10x Genomics). RNAs within single nuclei were uniquely barcoded and reverse transcribed within droplets. The RT reaction was performed on a Veriti PRO Thermal Cycler (Applied Biosystems) at 53°C for 45 minutes. Then, cDNAs were amplified using cDNA primer mix from the kit via PCR for 13 cycles, and then the manufacturer’s instructions were followed. Each library was barcoded with different indexes from a Dual Index Kit TT Set A plate (10x Genomics). The size profiles of the libraries were examined by a Bioanalyzer (Agilent), and the amount of RNA was quantified by KAPA Library Quantification Kits (Kapa Biosystems). All libraries were sequenced on the HiSeq X platform (Illumina) as 150 bp paired-end reads.

value: spinal cord

tag: strain

value: SDrat

value: 17 weeks

value: HGF releasing scaffold implantation


title: RK011, scRNAseq

description: 10x Genomics

value: WT

value: scaffold implantation


title: H3K4me3_ChIP_786O_EV_Day5_Rep1

value: H3K4me3 (Millipore Sigma, 05-1339, RRID:AB_1977251)


title: H3K4me3_ChIP_786O_KO_Day5_Rep1


title: Control_Rep2

value: Gestational days 19

value: female


title: V_1_A

data_processing:
Read trimming: Sequencing adaptors were removed using Trimmomatic (version 0.39), which was also used to trim low quality bases at the 5’ end of reads (using parameters TRAILING:20 and SLIDINGWINDOW:5:20). Reads with a minimum length of 30 bases were retained.
Alignment: STAR (version 2.7.5a)
Read counting on gene-level: HTSeq (version 0.11.2); Read counting on exon level: scripts provided as part of R package DEXSeq (Anders et al. 2012).
Each sample was sequenced five times. We used PCA to verify the absence of a sequencing lane effect, after which we merged all five fastq files of each sample and repeated alignment and read counting based on the merged fastq files.
Gene-level filtering: Raw counts were filtered to keep only genes with at least three counts per million in at least three samples and genes encoded in mitochondrial DNA were removed. We removed three samples that were outliers in PCA (C_V_6, C_SP+_2 and C_SP+_3). Exon-level filtering: As a first filtering step, we only kept exons from genes that were analyzed in the gene-level analysis and removed exons that could not be unambiguously assigned to only one gene. For the second filtering step, after normalization (see below), we removed 20% of exons with the lowest normalized counts. Finally, we removed exons that are shared across all transcript isoforms of their gene, or that are present in a gene that has only one annotated transcript isoform. As for the gene-level analysis, we removed three outlier samples (C_V_6, C_SP+_2 and C_SP+_3).
Gene-level normalization: counts per million were calculated in edgeR, using TMM normalization. Exon-level normalization: exons were normalized as recommended in Soneson et al. 2016.
Batch effect correction: to correct for high immune gene expression in a random subset of samples, Combat-seq was applied to both gene and exon counts.
Assembly: dm6 version r6.24 for gene-level alignment; BDGP6.32 for exon-level alignment
Supplementary files format and content: Matrix table with raw gene-level and exon-level read counts. Both gene and exon read counts were corrected for batch effects using ComBat-seq.

extract_protocol:
Flash frozen flies were vortexed to dislodge heads. Heads were collected in Trizol. RNA was extracted and DNA was removed using the Directzol RNA microprep kit (Zymo).
Poly(A)-selected, stranded libraries were made using the NEBnext Ultra II Directional RNA library prep kit and the Poly(A) mRNA magnetic isolation module (New England Biolabs, MA).

value: Canton-S


title: H3K4me3_ChIP_786O_EV_Day23_Rep1

data_processing:
ChIP-seq reads were trimmed with Trim Galore to remove adapter sequences and aligned to the hg38 genome using bwa (bwa mem) . Duplicate reads were removed from aligned reads using Picard MarkDuplicates. Reproducible histone peaks (broad peaks for H3K36me3, H3K27me3 & narrow peaks for H3K4me3, H3K9me3, H3K27ac) were identified by using MACS2 followed by IDR identification and filtering using idr-threshold < 0.05.
The reads from total RNA-seq libraries were trimmed for adapter sequences and aligned to the hg38 genome using HISAT2 with proper capture of RNA strand orientation. The bam files were normalized into CPM bedgraph files using deeptools "bamCoverage" command.
Assembly: hg38
Supplementary files format and content: Total RNAseq are processed and presented as CPM normalized bedgraph files. For ChIP-seq, MACS2-identified peaks are presented as bed files.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) followed by on-column DNase I digestion according to the manufacturer’s protocol. Genomic DNAs were purified using phenol–chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat# 08098140702). ChIP assays were performed following the native ChIP protocol. ChIP assays were performed following the native ChIP protocol (Ohtani et al., 2018) with minor modifications.
Total RNA-seq 786-O EV/KO Rep1 were sequenced 75 bp single end.  Total RNA-seq 786-O EV/KO Rep2 and other kidney cancer cell line total RNA-seq libraries were sequenced 50 bp paired-end. All ChIP-seq libraries were sequenced 50 bp paired-end.


title: RK010, scRNAseq

description: 10x Genomics

value: no treatment


title: Efm_BacDrop

description: Efm

organism: Enterococcus faecalis

source_name: An E. faecium human commensal isolate

value: untreated

tag: method

value: BacDrop

tag: accession no.


title: Normal

type: RNA

city: Bunkyoku

first: Takahiro

last: Seimiya

address: 7-3-1 Hongo

institute: The university of Tokyo

hyb_protocol: Purification  Mix Hy3, Hy5 labeled RNA and add 75 μL of Nuclease Free water.  Add 10 μL of 3 M NaOAc and mix well.  Add 110 μL of Isopro  Centrifuge at 14,000 g at 4 ℃ for 20 min.  Discard sup., add 500 μL of 80 ％ EtOH, and centrifuge at 14,000 g at 4 ℃ for 5 min.  Discard sup., and dry out for 3 min with speed-vac.  Elute with 4 μL DMSO, 15 μL Nuclease Free water, 6 μL Labeling Buffer  Add 25 μL of “2 x Hybridization Buffer” (pre-heated at 56 ℃).  Hybridization  Denature the solution at 95 ℃ for 5 min.  Centrifuge at 12,000 g at 4 ℃ for 2 min.  Add 30 μL of 20 x salt Buffer to ditch of “Hybridization Chamber”.  Slide is capped by “MASTUNAMI Gap Cover Glass (CG00044 or 24*60 25PCS)”.  Fill the gap with 45 μL of the solution.  Incubate in 56 ℃ water bath for 16-20 hr.

scan_protocol: Wash  Separate gap cover glass from the slide in “Wash buffer A” (pre-heated at 56 ℃).  Wash with “Wash buffer A” (pre-heated at 56 ℃) for 2 min.  Wash briefly (one plunge) with “Wash buffer B”.  Wash with “Wash buffer B” for 2 min.  Wash with “Wash buffer C” for 2 min.  Centrifuge at 1000 rpm for 5 min.  Scan  Scanner; G2505C (Agilent)  Software; Agilent Scan Control (Agilent)  Green and Red PMT: 100 %, Scan resolution: 10 um,

data_processing: Data Analysis  Software; Feature Extraction 10.7.3.1 (Agilent)  ・Probe Name  ・Gene Name  ・rProcessed Signal (Hy5)  ・gProcessed Signal (Hy3)  Calculate the average of replicated spots (Hy3 or Hy5 data).  Calculate the average of Hy3/Hy5 of each replicated spots (Normalized data).

source_name: Normal pancreas

label_protocol: CIP reaction （miRCURY LNA microRNA Array Hi-Power Labeling kit）  Total RNA: 250ng - 1,000 ng, Nuclease Free Water → Total 3 μL ** over 84 ng/μL **  (Mixture: 1 rxn.)  -----------------------------  CIP Buffer: 0.5 μL  Spike-in control: 1 μL  CIP enzyme: 0.5 μL  -----------------------------  Total: 2 μL  Incubate at 37 ℃ for 30 min, at 95 ℃ for 5 min.  on ice for 2–15 min.  Labeling （miRCURY LNA microRNA Array Hi-Power Labeling kit）  (Mixture: 1 rxn.)  -------------------------------  Labeling Buffer: 3 μL  DMSO: 2 μL  Labeling enzyme: 1 μL  -------------------------------  Total: 6 μL  Add  CIP reaction: 5 μL  Fluorescent label: 1.5 μL  (Sample: Hy3, Reference: Hy5)  Incubate at 16 ℃ for 2 hr, at 65 ℃ 15 min.

extract_protocol: Pancreatic cancerous tissues from gene-modified mice and normal pancreas tissues from control mice were frozen in liquid nitrogen immediately after resection and stored at −80℃. Frozen tissues were crushed without thawing using the SK mill (Tokken, Chiba, Japan) and immediately immersed in ice-cold Isogen reagent for RNA extraction (Nippon Gene, Tokyo, Japan).

tag: gender

value: male

value: 7 weeks

value: pancreas

source_name: reference(blends equal amounts of each  samples)


title: H3K4me3_ChIP_786O_EV_Day0_Rep1

tag: chip antibody


title: KrasG12D+Tgfbr2-/-

source_name: KrasG12D+Tgfbr2-/- mouse pancreatic cancer


title: V_4_A

source_name: head

value: head

value: virgin


title: Plate 9

status: Public on Jan 26 2023

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

data_processing:
Fastq files were obtained from the sequencing facility (running Illumina NextSeq2000 with HighOutput75 cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
The counts matrix was loaded to R (v.4.0.3), and Seurat (v3.2.0) was used for downstream analyses. Quality control was performed to remove poor quality cells. Cells with less than 600 genes detected were removed. We further excluded cells having mitochondrial gene expression above 3 median absolute deviations (MADs) from the median value.
Genome_build: GRCm39 with additional artificial chromosomes including for TdTomato, EGFP and for 92 ERCC spike-in genes.
Supplementary_files_format_and_content: csv file containing gene UMI counts, csv file containing additional cell-specific metadata, csv containing phenotypic information including protein expression

source_name: spleen

extract_protocol:
RNA was extracted and reverse transcribed as previously published (PMID: 32194545; 32690951). In brief, single cells were FACS-sorted into ice-cold 96-well PCR plates (Thermofisher) containing 2µl lysis mix per well. Immediately after cell sorting, each plate was covered with an adhesive film (Thermofisher), briefly spun down in a benchtop plate centrifuge, and frozen on dry ice. The plates containing single cells in lysis mix were thawed on ice, briefly spun down in a benchtop plate centrifuge, and incubated in a thermal cycler for 3 minutes at 72°C (lid temperature 72°C). Immediately after, the plate was placed back on ice and prepared for the reverse transcription reaction, with SuperScript II (Thermofisher) in presence of RnaseOUT (Thermofisher), DTT (Thermofisher), betaine (Sigma-Aldrich), MgCl2 (Sigma-Aldrich), and well-specific template switching oligonucleotide. Plates with single-cell cDNA were stored at -20°C until further processing. For cDNA amplification, KAPA HiFi HotStart ReadyMix (Roche Diagnostics) was used with adapted primers.
Libraries were prepared as previously published (PMID: 32194545; 32690951). In brief, amplified cDNA from each well of a 96-well plate were pooled, purified with two rounds of 0.6X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene) and finally eluted in nuclease free water. After tagmentation and neutralization, tagmented cDNA was amplified with Nextera PCR Mastermix containing Nextera i5 primer (Illumina), and custom i7 primer mix.
Libraries generated from multiple 96-well plates of single cells and carrying distinct i7 barcodes were pooled for sequencing on an Illumina NextSeq2000 platform, with 100-cycles P2 flow cells, targeting 5 × 105 reads per cell in paired-end single-index mode with the following cycles: Read1 (Read1_SP, 67 cycles), Read i7 (i7_SP, 8 cycles), and Read2 (Read2_SP, 16 cycles).

treatment_protocol: Mice were untreated, or infected for 36 hours or 48 hours upon intraperitoneal injection of MCMV.

tag: mouse strain

value: ZeST

value: spleen

value: infected (MCMV)

tag: time point


title: Plate 7


title: Plate 8


title: Plate 6


title: Plate 4


title: Plate 5


title: Plate 2


title: Plate 20


title: Plate 3


title: Plate 14

value: uninfected


title: Control_Rep1

tag: strain background

tag: age

value: Wild type

value: Heart


title: Plate 13


title: Plate 12


title: xenopus laevis sperm-HiC_spikein_rep2

city: Shenzhen

first: Chuihui

last: Hou

state: Guangdong

address: Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Hi-C raw sequencing reads were aligned to reference genome using distiller-nf mapping pipeline with default parameters (https://github.com/mirnylab/distiller-nf).
Assembly: xl9
Supplementary files format and content: hic contact map

source_name: xenopus laevis sperm

extract_protocol:
Male Xenopus laevis were injected with 150 U HCG. After 2 hours, two X. laevis testes collected in 1 ml 1xMBS and homogenized using razor blades. The solution was filtered with 40um strainer and its volume was brought down to 14ml. Then, through twice 180G horizontal centrifugation, we can obtain pure sperm in the supernatant. Ovulation and cross-fertilization were carried out according to the protocol described previously with some modification (Gibeaux., 2018).
1-2 millions X.laevis sperm were cross-linked with 1% formaldehyde for 10 min using vacuum infiltration. (Human K562 cells were added as spike-in control.) Isolated nuclei were digested with 80U of DpnII (NEB, R0543L) at 37°C for 4 hrs. Restriction fragment overhangs were marked with biotin-labeled nucleotides. After labeling, chromatin fragments in proximity were ligated with 4000U T4 DNA ligase for 6 hrs at 16°C. Chromatin was reverse cross-linked, purified, and precipitated using ethanol. Biotinylated ligation DNA was sheared to 250-500bp fragments followed by pull-down with MyOne Streptavidin T1 beads (Life technologies, 65602). Immobilized DNA fragments were end-repaired, A-tailed, and ligated with adaptors. Fragments were then amplified with the Q5 master mix (NEB, M0492L). Hi-C libraries were sequenced on the Illumina HiSeq X10 platform (PE 2×150 bp reads).

value: sperm


title: V_0.5_A


title: xenopus laevis sperm-HiC_spikein_rep1


title: Jurkat LAI redo HIVDEP gDNA Rep1

city: SEATTLE

first: Vanessa

last: Montoya

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Screen conducted with LAI again (termed LAI-redo) to test reproducibility of HIV-CRISPR screening with HIVDEP library/
Jurkat_LAIredo_210507.anno.txt

data_processing:
For the HiSeq2500 datasets, image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4. For the NextSeq2000 datasets Real Time Analysis v3.7.17 was used, followed by bcl2fastq v2.20.
Samples were demultiplexed using FASTX toolkit. Specifically, FASTX barcode splitter was used to separate reads by barcode matching.
HiSeq dataset reads were trimmed and aligned to the respective guide libraries using Bowtie v1.0.0, followed by tabulation of read counts using R. Guide-level quantification for the NextSeq data was performed using Liu lab's MAGeCK software.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: Described in samples section on a per sample basis. [description field]
Supplementary files format and content: Tab delimited files with read counts for each guide sequence
Library strategy: CRISPR

growth_protocol: Jurkat-CCR5 ZAP KO cells are grown in RPMI-1640 supplemented with 10% FBS, 10nM HEPES, and Pen/Strep. Cells are passaged between 2 x 10^5 cells/mL and 2 x 10^6 cells/mL.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen, Cat No 51183)
Described in samples section on a per sample basis.
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: 3 x 10^6 (>500X coverage) Jurkat-CCR5 ZAP KO cells were each transduced with the TKOv3, HuEpi, PIKA, or HIVDEP libraries (MOI<1) and selected in  0.4 ug/mL puromycin for 10-14 days. Knockout cell pools were infected with viral strains LAI, VSV-G psuedotyped LAI, LAIΔVpr, Q23.BG505, or CH470 TF . Each condition is performed with two replicates. After the treatment, cells and viral supernatants were harvested.

value: Human T lymphocyte

value: Pooled KO cells containing HIVDEP library infected with LAI and gDNA extracted 3dpi (Replicate 1)

tag: group

value: Jurkat LAI redo HIVDEP


title: Jurkat CH470 TF HIVDEP vRNA Rep1

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
viral RNA
Jurkat_CH470_HIVDEP_210507.anno.txt

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Cat No 52904)
Described in samples section on a per sample basis.
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

tag: treatment

value: Pooled KO cells containing HIVDEP library infected with CH470 TF, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)

value: Jurkat CH470 TF HIVDEP


title: Jurkat CH470 TF HIVDEP gDNA Rep2

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Jurkat_CH470_HIVDEP_210507.anno.txt

value: Pooled KO cells containing HIVDEP library infected with CH470 TF and gDNA extracted 3dpi (Replicate 2)


title: Jurkat LAI redo HIVDEP gDNA Rep2

value: Pooled KO cells containing HIVDEP library infected with LAI and gDNA extracted 3dpi (Replicate 2)


title: Jurkat LAI redo HIVDEP vRNA Rep1

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
viral RNA
Screen conducted with LAI again (termed LAI-redo) to test reproducibility of HIV-CRISPR screening with HIVDEP library/
Jurkat_LAIredo_210507.anno.txt

value: Pooled KO cells containing HIVDEP library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)


title: Jurkat CH470 TF HIVDEP gDNA Rep1

value: Pooled KO cells containing HIVDEP library infected with CH470 TF and gDNA extracted 3dpi (Replicate 1)


title: Jurkat Q23BG505 HIVDEP  gDNA Rep1

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Jurkat_Q23BG505_210303.anno.txt

value: Pooled KO cells containing HIVDEP library infected with Q23.BG505 and gDNA extracted 3dpi (Replicate 1)

value: Jurkat Q23.BG505 HIVDEP


title: Jurkat Q23BG505 HIVDEP  gDNA Rep2

value: Pooled KO cells containing HIVDEP library infected with Q23.BG505 and gDNA extracted 3dpi (Replicate 2)


title: Jurkat Q23BG505 HIVDEP vRNA Rep2

description:
HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
viral RNA
Jurkat_Q23BG505_210303.anno.txt

value: Pooled KO cells containing HIVDEP library infected with Q23.BG505, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)


title: Jurkat Q23BG505 HIVDEP vRNA Rep1

value: Pooled KO cells containing HIVDEP library infected with Q23.BG505, viral supernatants collected, and vRNA extracted 3dpi (Replicate 1)


title: Plate 1

value: ZeST

value: spleen

value: infected (MCMV)


title: NSPCs, ctrl, ko, 2-3 rep

city: Lausanne

first: Valentina

last: Scandella

address: Rue du Bugnon 7

country: Switzerland

institute: University of Lausanne

data_processing:
BRB-seq libraries are multiplexed paired-end libraries containing multiple barcoded samples that needs to be demultiplexed
Barcodes were demultiplexed using the barcode mapping file AMP0017_L2_barcodes.txt
We used STAR v2.7.9a (in STARsolo mode) to align, demultiplex (using a barcode mapping file), and produce read counts as well as UMI count matrix for all samples
STARsolo was used with the following extra parameters: --soloUMIdedup NoDedup 1MM_Directional --soloCBmatchWLtype 1MM --clipAdapterType CellRanger4 --outSAMmapqUnique 60 --runThreadN  --soloStrand Forward --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --soloUMIlen 9 --soloCellFilter None --soloCBwhitelist barcodes_v4_setC_star.txt --soloFeatures Gene --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM --outFilterMultimapNmax 1
Read count normalization (DESEq2) was performed using R
Assembly: mm10 (Ensembl GRCm38 r102)
Supplementary files format and content: Tab-delimited text files including raw counts and UMI values for each sample
Supplementary files format and content: Tab-delimited text files including normalized counts using DESeq2 for library depth normalization

source_name: Neural stem/progenitor cells

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 500 ng of RNA was used
The libraries were generated using MERCURIUS BRB-seq kit (PN 10813, Alithea) following the user guide. In brief, the RNA samples were reverse transcribed using barcoded oligo-dT primers. Illumina libraries were prepared with cDNA following tagmentation protocol and sequencing on the Illumina Nextseq instrument (Alpern et al, 2019).
RNA-seq (paired-end, multiplexed, including UMI)

value: Neural stem/progenitor cells

tag: genotype

value: MPC1 WT + MPC1 KO


title: Plate 10

tag: tissue

value: uninfected


title: 168-PEARL457rep_1

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Beltraan Baguena, 8-11

department: Molecular Biology Lab

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

data_processing:
Sequencing was performed by using Oncology Biomarker Panel from HTG Edgeseq which interrogates the expression of 2560 genes.
Base-calling: Illumina Basespace
Generation of read counts: HTG Edgeseq Parser v. 5,2,823,5648
Normalization: R Bioconductor DESeq2 v. 1,28,1
Assembly: hg19
Supplementary files format and content: Table with median transformation normalized counts
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast Cancer

extract_protocol:
Total RNA was prepared from 5µm FFPE tissue sections of microdissected ITF using the Agencourt FormaPure kit (A33341; Beckman Coulter, Indianapolis, IN, USA) and following the manufacturer’s instructions. RNA concentration was determined with Qubit 4 Fluorometer and Qubit® RNA HS Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
HTG EdgeSeq Chemistry was employed to synthetize the RNA-Seq library. Briefly, target capture was performed by hybridizing the mRNA with Nuclease Protection Probes (NPPs). The S1 nuclease was added to the mix, producing a stoichiometric amount of target mRNA/NPP duplexes. This reaction was blocked by enzyme heat denaturation of S1. The samples were randomized before inclusion in the HTG EdgeSeq system to reduce potential biases in the run. Each hybridized sample was used as template to set up PCR reactions with specially designed tags, sharing common sequences that are complementary to both 5’-end and 3’-sequences of the probes, and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode used for sample identification and multiplexing. After PCR amplification, a clean-up procedure was performed using Agencourt AMPure XP (Beckman Coulter). The library was quantified by quantitative PCR, using KAPA Library Quantification (Roche), according to the manufacturer’s instructions. All samples and controls were quantified in triplicate and no template control was included in any run.

value: Breast Cancer

tag: cell type

value: Tumor

value: Palbociclib


title: 168-PEARL474rep_1

value: Capecitabine


title: 168-PEARL310rep_1


title: 168-PEARL466rep_1


title: 168-PEARL507_1


title: 168-PEARL300rep_1


title: Jurkat CH470 TF HIVDEP vRNA Rep2

tag: cell line

value: Human T lymphocyte

value: Pooled KO cells containing HIVDEP library infected with CH470 TF, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

value: Jurkat CH470 TF HIVDEP


title: Jurkat LAI redo HIVDEP vRNA Rep2

value: Pooled KO cells containing HIVDEP library infected with LAI, viral supernatants collected, and vRNA extracted 3dpi (Replicate 2)

value: Jurkat LAI redo HIVDEP


title: 168-PEARL269rep_1


title: 168-PEARL069rep_1


title: 168-PEARL288rep_1


title: 168-PEARL048rep_1


title: 168-PEARL307rep_1


title: 168-PEARL293rep_1


title: 168-PEARL262rep_1


title: 168-PEARL508_1


title: 156-PEARL_506_1


title: 168-PEARL019rep_1


title: 168-PEARL008rep_1


title: 168-PEARL510_1


title: 156-PEARL_492_1


title: 156-PEARL_505_1


title: 156-PEARL_499_1


title: 156-PEARL_488_1


title: 156-PEARL_487_1


title: 156-PEARL_484_1


title: 156-PEARL_467_1


title: 156-PEARL_452_1


title: 156-PEARL_446_1


title: 156-PEARL_332bis_1


title: 156-PEARL_424_1


title: 156-PEARL_441_1


title: 156-PEARL_439_1


title: 168-PEARL035rep_1


title: 155-PEARL_412_1


title: 155-PEARL_409_1


title: 155-PEARL_195_1


title: 155-PEARL_199_1


title: 155-PEARL_197_1


title: 155-PEARL_198_1


title: 168-PEARL001rep_1


title: 155-PEARL_196_1


title: 155-PEARL_194_1


title: 156-PEARL_327bis_1


title: 155-PEARL_201_1


title: 155-PEARL_349_1


title: 155-PEARL_191_1


title: 155-PEARL_193_1


title: 155-PEARL_187_1


title: 155-PEARL_186_1


title: 155-PEARL_189_1


title: 155-PEARL_188_1


title: 155-PEARL_184_1


title: 155-PEARL_185_1


title: 155-PEARL_183_1


title: 155-PEARL_405_1


title: 154-PEARL-500rep-1


title: 154-PEARL-497rep-1


title: 154-PEARL_496_1


title: 155-PEARL_192_1


title: 154-PEARL_504_1


title: 154-PEARL_502_1


title: 154-PEARL_501_1


title: 154-PEARL_503_1


title: 154-PEARL_498_1


title: 154-PEARL_486_1


title: 154-PEARL_485_1


title: 154-PEARL_481_1


title: 154-PEARL_491_1


title: 154-PEARL_479_1


title: 154-PEARL_493_1


title: 154-PEARL_489_1


title: 154-PEARL_490_1


title: 154-PEARL_482_1


title: 154-PEARL_480_1


title: 154-PEARL_475_1


title: 154-PEARL_477_1


title: 154-PEARL_478_1


title: 154-PEARL_476_1


title: 154-PEARL_472_1


title: 154-PEARL_473_1


title: 154-PEARL_471₁


title: 154-PEARL-179rep-1


title: 154-PEARL_470_1


title: 154-PEARL_469_1


title: 154-PEARL_468_1


title: 154-PEARL_494_1


title: 154-PEARL_495_1


title: 154-PEARL_464_1


title: 154-PEARL_462_1


title: 154-PEARL_461_1


title: 154-PEARL_465_1


title: 154-PEARL_460_1


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title: 154-PEARL_459_1


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title: 154-PEARL_455_1


title: 154-PEARL_456_1


title: 154-PEARL_447_1


title: 154-PEARL_453_1


title: 154-PEARL_448_1


title: 154-PEARL_450_1


title: 154-PEARL_451_1


title: 154-PEARL_445_1


title: 154-PEARL_443_1


title: 154-PEARL_438_1


title: 154-PEARL_440_1


title: 154-PEARL_182_1


title: 154-PEARL_180_1


title: 154-PEARL_436_1


title: 154-PEARL_178_1


title: 154-PEARL_181_1


title: 154-PEARL_437_1


title: 154-PEARL_177rep_1


title: 154-PEARL_171_1


title: 154-PEARL_174rep_1


title: 154-PEARL_175_1


title: 154-PEARL_449_1


title: 154-PEARL_170_1


title: 154-PEARL_176rep_1


title: 154-PEARL_169_1


title: 154-PEARL_165rep_1


title: 154-PEARL_166rep_1


title: 154-PEARL_163_1


title: 154-PEARL_173_1


title: 154-PEARL_442_1


title: 154-PEARL_164_1


title: 154-PEARL_157_1


title: 154-PEARL_156_1


title: 154-PEARL_160_1


title: 154-PEARL_444rep_1


title: 154-PEARL_161_1


title: 154-PEARL_159_1


title: 154-PEARL_162_1


title: 154-PEARL_168_1


title: 154-PEARL_155_1


title: 154-PEARL_151_1


title: 154-PEARL_152_1


title: 153-PEARL_435_1


title: 153-PEARL_433_1


title: 154-PEARL_149_1


title: 154-PEARL_167_1


title: 153-PEARL_434_1


title: 154-PEARL_148_1


title: 153-PEARL_432_1


title: 153-PEARL_427_1


title: 153-PEARL_428_1


title: 153-PEARL_430_1


title: 153-PEARL_425_1


title: 153-PEARL_422_1


title: 153-PEARL_429_1


title: 154-PEARL_158_1


title: 153-PEARL_426_1


title: 153-PEARL_421_1


title: 153-PEARL_423_1


title: 153-PEARL_420_1


title: 153-PEARL_408_1


title: 153-PEARL_411_1


title: 153-PEARL_419_1


title: 153-PEARL_414_1


title: 153-PEARL_416_1


title: 153-PEARL_413_1


title: 154-PEARL_153_1


title: 153-PEARL_410_1


title: 153-PEARL_407_1


title: 153-PEARL_406_1


title: 154-PEARL_154_1


title: 153-PEARL_403_1


title: 153-PEARL_400_1


title: 153-PEARL_402_1


title: 153-PEARL_398_1


title: 153-PEARL_399_1


title: 153-PEARL_395_1


title: 153-PEARL_404_1


title: 153-PEARL_397_1


title: 153-PEARL_393_1


title: 153-PEARL_391_1


title: 153-PEARL_389_1


title: 153-PEARL_390_1


title: 153-PEARL_392_1


title: 153-PEARL_418_1


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title: 153-PEARL_388_1


title: 153-PEARL_386_1


title: 153-PEARL_382_1


title: 153-PEARL_383_1


title: 153-PEARL_381_1


title: 153-PEARL_385_1


title: 153-PEARL_384_1


title: 153-PEARL_380_1


title: 153-PEARL_379_1


title: 153-PEARL_377_1


title: 153-PEARL_374_1


title: 153-PEARL_378_1


title: 153-PEARL_372_1


title: 153-PEARL_396_1


title: 153-PEARL_373_1


title: 153-PEARL_369_1


title: 153-PEARL_376_1


title: 153-PEARL_366_1


title: 153-PEARL_375_1


title: 153-PEARL_365_1


title: 153-PEARL_364_1


title: 153-PEARL_370_1


title: 153-PEARL_371_1


title: 153-PEARL_359_1


title: 153-PEARL_363_1


title: 153-PEARL_361_1


title: 153-PEARL_358_1


title: 153-PEARL_360_1


title: 153-PEARL_362_1


title: 153-PEARL_352_1


title: 153-PEARL_357_1


title: 153-PEARL_355_1


title: 153-PEARL_354_1


title: 153-PEARL_353_1


title: 153-PEARL_350_1


title: 153-PEARL_348_1


title: 153-PEARL_351_1


title: 153-PEARL_347_1


title: 153-PEARL_367_1


title: 152-PEARL_341_1


title: 153-PEARL_221_1


title: 153-PEARL_250_1


title: 152-PEARL_340_1


title: 153-PEARL_346_1


title: 153-PEARL_243_1


title: 153-PEARL_284_1


title: 153-PEARL_230_1


title: 153-PEARL_081_1


title: 153-PEARL_130_1


title: 152-PEARL_343_1


title: 152-PEARL_339_1


title: 152-PEARL_337_1


title: 152-PEARL_338_1


title: 152-PEARL_335_1


title: 152-PEARL_334_1


title: 152-PEARL_333_1


title: 152-PEARL_331_1


title: 152-PEARL_328_1


title: 152-PEARL_329_1


title: 152-PEARL_330_1


title: 152-PEARL_342_1


title: 152-PEARL_325_1


title: 152-PEARL_344_1


title: 152-PEARL_326_1


title: 152-PEARL_324_1


title: 152-PEARL_322rep_1


title: 152-PEARL_323rep_1


title: 152-PEARL_321_1


title: 152-PEARL_317_1


title: 152-PEARL_319_1


title: 152-PEARL_316_1


title: 152-PEARL_314_1


title: 152-PEARL_336_1


title: 152-PEARL_318_1


title: 152-PEARL_312_1


title: 152-PEARL_313_1


title: 152-PEARL_315_1


title: 152-PEARL_309_1


title: 152-PEARL_311_1


title: 152-PEARL_305_1


title: 152-PEARL_308_1


title: 152-PEARL_302_1


title: 152-PEARL_298_1


title: 152-PEARL_297_1


title: 152-PEARL_299_1


title: 152-PEARL_295_1


title: 152-PEARL_294_1


title: 152-PEARL_320_1


title: 152-PEARL_292_1


title: 152-PEARL_289_1


title: 152-PEARL_290_1


title: 152-PEARL_291_1


title: 152-PEARL_285_1


title: 152-PEARL_281_1


title: 152-PEARL_282_1


title: 152-PEARL_287_1


title: 152-PEARL_286_1


title: 152-PEARL_278rep_1


title: 152-PEARL_275_1


title: 152-PEARL_304_1


title: 152-PEARL_279_1


title: 152-PEARL_280_1


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title: 152-PEARL_274_1


title: 152-PEARL_301_1


title: 152-PEARL_273_1


title: 152-PEARL_276_1


title: 152-PEARL_272_1


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title: 152-PEARL_296_1


title: 152-PEARL_268_1


title: 152-PEARL_266_1


title: 152-PEARL_264_1


title: 152-PEARL_263_1


title: 152-PEARL_261_1


title: 152-PEARL_260_1


title: 152-PEARL_259_1


title: 152-PEARL_223_1


title: 152-PEARL_016_1


title: 152-PEARL_045_1


title: 149-PEARL256_1


title: 149-PEARL253_1


title: 149-PEARL257_1


title: 149-PEARL249_1


title: 149-PEARL254_1


title: 149-PEARL258_1


title: 149-PEARL240_1


title: 149-PEARL238_1


title: 149-PEARL237_1


title: 153-PEARL_356_1


title: 149-PEARL241_1


title: 152-PEARL_265_1


title: 152-PEARL_007_1


title: 149-PEARL233_1


title: 149-PEARL246_1


title: 149-PEARL229_1


title: 152-PEARL_267_1


title: 149-PEARL225_1


title: 149-PEARL216_1


title: 149-PEARL218_1


title: 149-PEARL211_1


title: 149-PEARL209_1


title: 149-PEARL234_1


title: 149-PEARL208_1


title: 149-PEARL205_1


title: 149-PEARL203_1


title: 149-PEARL248_1


title: 149-PEARL236_1


title: 149-PEARL147_1


title: 149-PEARL146_1


title: 149-PEARL144_1


title: 149-PEARL141_1


title: 149-PEARL137_1


title: 149-PEARL138_1


title: 149-PEARL143_1


title: 149-PEARL213_1


title: 149-PEARL134_1


title: 149-PEARL136_1


title: 149-PEARL140_1


title: 149-PEARL139_1


title: 149-PEARL135_1


title: 149-PEARL133_1


title: 149-PEARL132_1


title: 149-PEARL126_1


title: 149-PEARL204_1


title: 149-PEARL131_1


title: 149-PEARL128_1


title: 149-PEARL124_1


title: 149-PEARL127_1


title: 149-PEARL120_1


title: 149-PEARL122_1


title: 149-PEARL123_1


title: 149-PEARL119_1


title: 149-PEARL117_1


title: 149-PEARL145_1


title: 149-PEARL118_1


title: 149-PEARL116_1


title: 149-PEARL115_1


title: Stag2_KO_SMC1_R2

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

data_processing:
Alignment of reads to the reference mouse genome (mm9) was performed using ‘Bowtie2′ (version 2.4.2) under default settings.
Duplicates were removed using GATK4 (version 4.1.9.0).
Peak calling was carried out using MACS2 (version 2.2.7.1) after setting the q value (FDR) to 0.05 and using the ‘–extsize’ argument with the values obtained in the ‘macs2 predictd’ step.
Assembly: mm9
Supplementary files format and content: bigWig files

source_name: MEF

growth_protocol: MEFs were isolated from E12.5 embryos and cultured in DMEM supplemented with 20% FBS at 37 ºC under 90% humidity and 5% CO2.

extract_protocol:
Cells were fixed for 15 min in 1% formaldehyde and after quenching and lysis, sonication with performed in Covaris instrument. Around 50 micrograms of antibody was added to immunoprecipitated chromatin from 10 million cells. 5% mouse ES cell chromatin was added for calibration.
At least 5 ng of DNA were processed through subsequent enzymatic treatments with "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7805). Briefly, a short fragmentation of 10 min was followed by end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8-12 cycles). Resulting average fragment size is 300 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on Illumina NextSeq 500 (with v2.5 reagent kits) following manufacturer's recommendations.

treatment_protocol: Conditional knock out MEFs (Stag2 f/Y; Cre-ERT2 and Pds5A f/f; Pds5B f/f; Cre-ERT2) were cultured in medium with 1 μM 4-hydroxy tamoxifen for 4 and 5 days, respectively. For CTCF elimination, a clone of immortalized Ctcf f/f MEFs was infected with Adeno-Cre viruses (University of Iowa) at 250 pfu/cell in DMEM supplemented with 2% FBS. Medium was replaced after 24 h and cells were collected 9 days later for immunoblot and chromatin immunoprecipitation analyses.

value: MEF

value: Embryonic fibroblasts

value: Stag2 KO

value: 4 days 1 uM 4OHT

tag: antibody

value: SMC1A, custom made


title: Stag2_KO_SMC1_R1


title: 149-PEARL114_1


title: 149-PEARL113_1


title: Stag2_WT_SMC1_R1

value: Stag2 WT


title: Stag2_WT_SMC1_R2


title: 149-PEARL109_1


title: 149-PEARL125_1


title: Stag2_pool-WT-KO_INPUT_R1R2

value: None + 4 days 1 uM 4OHT


title: 149-PEARL108_1


title: Pds5_DKO_SMC1_R2

value: Pds5 DKO

value: 5 days 1 uM 4OHT


title: Pds5_DKO_SMC1_R1


title: 149-PEARL106_1

value: Breast Cancer

value: Tumor


title: Pds5_WT_SMC1_R2

value: Pds5 WT


title: 149-PEARL105_1

value: Capecitabine


title: Pds5_WT_SMC1_R1


title: 149-PEARL104_1


title: Pds5_pool-WT-DKO_INPUT


title: 149-PEARL102_1

value: Palbociclib


title: Pds5_KOB_SMC1_R2

value: Pds5 KOB


title: 149-PEARL103_1


title: Pds5_KOB_SMC1_R1


title: Pds5_KOA_SMC1_R2

value: Pds5 KOA


title: 149-PEARL100_1


title: 148-PEARL_098_1


title: Pds5_KOA_SMC1_R1


title: 149-PEARL111_1


title: 149-PEARL110_1


title: 148-PEARL_097_1


title: WT_STAG2_R1

value: WT

value: STAG2, custom made


title: WT_CTCF

value: MEF

value: Embryonic fibroblasts

value: CTCF 07-729 (Millipore)


title: WT_STAG2_R2


title: 148-PEARL_095_1


title: 148-PEARL_096_1


title: WT_Pds5B_R2

value: PDS5B, custom made


title: 148-PEARL_094_1


title: 148-PEARL_093_1


title: WT_Pds5B_R1


title: 148-PEARL_092_1


title: 148-PEARL_091_1


title: WT_Pds5A_R1

value: PDS5A, custom made


title: 149-PEARL101_1


title: Pds5_KOA-KOB_INPUT

value: Pds5 KOA KOB


title: WT_INPUT_Pds5


title: TELS S41 embryos hybrid RNA-seq__rep2

data_processing:
Raw fastq RNA-seq reads and adapter sequences were removed by Trimmomatic v0.38. Clean reads were mapped to the combined X.tropicalis v10.0 and X.laevis v9.2 reference genome using STAR v2.7.9a
Genome_build: xv10_xl9
Supplementary_files_format_and_content: gene abundance

organism: Xenopus tropicalis x Xenopus laevis

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S41

extract_protocol:
Ovulation and cross-fertilization were carried out according to the protocol described previously with some modification (Gibeaux., 2018). Briefly, Female Xenopus laevis were injected with 500 U HCG. After 12 hours, male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, X. laevis females were squeezed gently to deposit eggs onto clean 9 cm Petri dishes and two X. tropicalis testes collected in 0.5 ml 1xMBS and homogenized using razor blades. Any liquid in the Petri dishes was removed and the per dish eggs were fertilized with mix solution containing 0.1 ml of sperm and 0.9 ml H2O. Eggs were swirled in the solution to individualize eggs as much as possible and incubated for 10 min. Jelly coats were removed with a 2% cysteine solution (add NaOH adjust the pH to 7.8-8.0). After extensive washing (at least four times) with 0.1xMBS, embryos were incubated at 23 °C.
Total RNA was isolated from hybrid embryos using the TransZol Up Plus RNA Kit (Transgen, ER501-01). Libraries were prepared with a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) according to the manufacturer's instructions. The libraries were sequenced on an Illumina HiSeq 2500 platform, and 150-base paired-end reads were produced. Two biological replicates were generated for control and dark-treated seedlings.

value: embryo


title: 148-PEARL_088_1


title: 148-PEARL_089rep_1


title: 148-PEARL_090rep_1


title: TELS S41 embryos hybrid RNA-seq__rep1


title: 148-PEARL_087_1


title: TELS S34 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S34


title: 148-PEARL_086_1


title: 148-PEARL_085_1


title: TELS S24 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S24


title: TELS S34 embryos hybrid RNA-seq__rep1


title: 148-PEARL_084_1


title: 148-PEARL_082_1


title: TELS S24 embryos hybrid RNA-seq__rep1


title: TELS S13 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S13


title: WT_Pds5A_R2


title: 148-PEARL_078_1


title: TELS S16 embryos hybrid RNA-seq__rep1

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S16


title: 148-PEARL_077rep_1


title: TELS S16 embryos hybrid RNA-seq__rep2


title: TELS S12 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S12


title: 148-PEARL_076_1


title: TELS S13 embryos hybrid RNA-seq__rep1


title: 148-PEARL_075_1


title: 148-PEARL_074_1


title: TELS S12 embryos hybrid RNA-seq__rep1


title: 148-PEARL_073rep_1


title: TELS S11 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S11


title: 148-PEARL_071rep_1


title: 148-PEARL_070rep_1


title: TELS S11 embryos hybrid RNA-seq__rep1


title: 148-PEARL_072rep_1


title: TELS S10 embryos hybrid RNA-seq__rep1

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S10


title: 148-PEARL_068_1


title: TELS S9 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S9


title: TELS S9 embryos hybrid RNA-seq__rep1


title: 148-PEARL_066_1


title: 148-PEARL_067_1


title: TELS S7 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S7


title: 148-PEARL_080rep_1


title: 148-PEARL_064_1


title: TELS S7 embryos hybrid RNA-seq__rep1


title: TELS S8 embryos hybrid RNA-seq__rep1

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S8


title: 148-PEARL_063_1


title: 148-PEARL_062_1


title: TELS S5 embryos hybrid RNA-seq__rep2

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S5


title: 148-PEARL_061_1


title: 148-PEARL_065_1


title: 148-PEARL_059_1


title: TELS S10 embryos hybrid RNA-seq__rep2


title: 148-PEARL_060_1


title: TELS S8 embryos hybrid RNA-seq__rep2


title: TELS S3 embryos hybrid RNA-seq__rep1

source_name: xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S3


title: 148-PEARL_058_1


title: 148-PEARL_056_1