title: CD34+ HSPCs - NFIC Overexprs

city: Cardiff

first: Namrata

last: Rastogi

address: Hadyn Ellis Building, Maindy Rd

department: European Cancer Stem Cell Research Institute, School of Biosciences

institute: Cardiff University

data_processing:
Data from 10X Genomics was imported into CellRanger software v.3.1.0. Raw sequencing BCL files from control and overexpression samples were demultiplexed into paired-end FASTQ files using “cellranger mkfastq”
“cellranger count” was then used to perform read alignment, UMI counting and secondary analysis separately for each sample.
Human reference genome GRCh38 was used as reference for generating counts from FASTQ files
FASTQ files were also analysed using Partek Flow single cell analysis module (Version: 6.0.17.1206) using the 10x Genomics Chromium™ Single Cell 3' v2 prep kit hg38_ensembl_release90_v2 was used for feature/gene annotation.
Differential gene expression analysis for monocyte cluster between NFIC overexpressed and control was performed using Partek Flow’s in-build algorithm
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including, ENSEMBLE Ids, Raw gene counts, FPKM values for each Sample; log2 Fold change values(Control vs NFIC Overexpression), p- value and adjusted p value

source_name: Cord Blood

growth_protocol: Human CD34+ HSPCs were isolated from cord blood and were cultured in differentiation media containing IMDM and cytokines; Flt3, IL3, IL6, G

extract_protocol:
10,000 sorted cells per sample were processed for single cell nuclei for RNA sequencing using 10X Genomics according to manufacturer’s instruction. Gel-Beads in emulsion (GEM) were generated using Chromium Next GEM Single Cell 3ʹGEM Kit v3.1 (10x Genomics).
cDNA libraries were constructed using Chromium Next GEM Single Cell 3ʹ Library Kit v3.1 (10x Genomics) and sequenced using Illumina NextSeq 500 system using the NextSeq 500/550 High Output v2 Kit.

treatment_protocol: HSPCs cells were infected with either control or NFIC overexpression using retronectin. Four days post infection cells were sorted for GFP and processed for sequencing.

value: CD34+ HSPCs

tag: lentiviral infection

value: NFIC overexpressing vector


title: H3K4me3, Armstrong

status: Public on Jan 04 2023

type: SRA

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

country: USA

institute: University of California, San Diego

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.38, discarding reads left with < 25 bp
Reads were aligned to the mouse genome (mm10) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were aligned to the yeast genome (sacCer3) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70
Spike-in normalization. The genomic coverage were then normalized by applying the scaling factor that is calculated from the number of mapped reads to mouse genome and yeast genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01, using Callpeak, and compared the sample to corresponding IgG samples using bdgcmp in FE (fold-enrichment) mode.
bigWig files were generated using bdg2bw from the bedgraph output from last step. Score represents the FE values at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
DNA extraction, digestion and purification was performed with the CUT&RUN Assay Kit by CST, #86652
ChIP-seq libraries were prepared using the SimpleChIp ChIp-Seq DNA Library Prep Kit (CST, #567945)  input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: tissue

value: spleen

tag: cell type

value: CD8 T Cell

tag: chip antibody


title: CD34+ HSPCs - Control

country: United Kingdom

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

value: Control vector


title: Batch 2 PBMC 10x Lane 2 (Batch2P02) GEX

city: Bethesda

first: William

last: Lau

state: MD

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

description: mRNA (cDNA) reads from multimodal scRNAseq

library_source: transcriptomic

data_processing:
fastq generation: CellRanger 6.0.1 (10x Genomics)
mapping, CellRanger 6.0.1 (10x Genomics)
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
secondary analysis: Seurat 4.0.3 (R package)
Multiple donor samples are combined within each lane. A demultiplexed dataset of all cells that passed QC is provided as an R Seurat object.
Assembly: hg19 (cellranger version 1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_1.2.0)
Supplementary files format and content: R Seurat object with count matrices
Library strategy: CITE-seq

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Frozen PBMC samples were thawed, recovered and washed using RPMI media with 10% FBS and 10mg/mL DNase I (STEMCELL 07470). Samples from different donors were pooled evenly before staining; single cells can be demultiplexed in silico using individual specific single nucleotide polymorphism (SNP) information during data analysis (see below; demultiplexing for each lane is provided in the *demux.best supplemental files). Multiple cell pools were prepared, such that cells from the same individual but different timepoints would be in different pools. PBMC pools were Fc blocked (Human TruStain FcX, BioLegend 422302) and stained with Totalseq-C human ‘hashtag’ antibodies (BioLegend), washed with staining buffer (2% BSA in PBS). This round of hashtag staining allows the different pools to be identified in the analysis, which when combined with the SNP-based demultiplexing, allows full identification of each sample. Hashtagged PBMC pools were combined and cells were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 137 surface proteins and SARS-CoV-2 S1 protein probe. Then, cells were washed three times, resuspended in PBS, and counted before proceeding immediately to the single cell partition step.
PBMC samples were partitioned into single cell Gel-Bead in Emulsion (GEM) mixed together with the reverse transcription (RT) mix using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v2 chemistry (10x Genomics, Pleasanton, CA), as previously described (PMID: 33713619). The RT step was conducted in the Veriti Thermo Cycler (ThermoFisher Scientific, Waltham, MA). Single cell gene expression and cell surface protein libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA) and quantified using Qubit Fluorometric (ThermoFisher). 10x Genomics 5’ Single cell gene expression, cell surface protein tag, TCR and BCR libraries were pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the following sequencing parameters: read1-100-cycle, i7-10-, i5-10, read2-100.
single cell RNAseq (10x Genomics 5' v2)

tag: unsorted or sorted

value: UnSorted

value: blood

value: PBMC


title: ChIPseq for NANOG in Zfp462KO_Rep2

city: Vienna

first: Ramesh

last: Yelagandula

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
ChIP-seq reads were trimmed using trim-galore v0.4.4 and thereafter aligned to the mm10 reference genome using bwa mem v0.7.17. A
A mapping quality filter with cutoff 1 was applied using samtools v1.10.
Duplicated reads were marked and excluded with picard MarkDuplicates v2.23.4 and the obtained bam files were used to generated bigwig files using deeptools bamCoverage v3.5.0 with the parameter -normalizeUsing RPKM.
Genome_build: mm10

source_name: ESCs

growth_protocol: Cells were grown at 37º C, 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin complexes were isolated either with antibody or Dynabeads M-280 Streptavidin
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

tag: mutants

value: Zfp462knock out

value: rabbit anti-NANOG/ab80892/abcam


title: H3K27me3, Clone13


title: Batch 2 PBMC 10x Lane 2 (Batch2P02) CSP

description: Cell Surface Protein Tag reads from multimodal scRNAseq

library_source: other

molecule: protein


title: H3K27me3, Armstrong


title: NAI-SCR_2-F4R4

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Raw read was evaluated quality by FastQC (v0.11.9) and removed PCR primmers by cutadaptor(v1.18). Trimmed data for ${treatment}_F1R1_F3R3.fq.gz and ${treatment}_F4R4.fq.gz were combined together. The combined data was mapped with ShapeMapper2 (v 2.1.3, parameters: --verbose --serial --nproc 16 --min-depth 1000). The RNA secondary structure was predicted by RNAfold (v 2.4.14, parameters: -p -d2 --shapeMethod=D).
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

source_name: HeLa cells

growth_protocol: HeLa cells expressing scramble tet-on shRNA or URB1-targetting  tet-on shRNA were maintained in DMEM, which was supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
The Tet inducible stable URB1-KD HeLa cell lines were seeded and induced with 1ug/mL doxycycline on 6 cm dishes for 6 days. After washed with DPBS, cells were incubated with 270 ?L of cell culture medium and 30 ?L of 10x SHAPE Chemical in DMSO with the final concentration of NAI (EMD Millipore) at 100 mM for 10 minutes at 37 °C. After removed reaction medium, RNAs were isolated by 1 mL Trizol reagent (Invitrogen) according to the manufacturer?s protocol. The same procedure was also performed in parallel for the untreated control samples, but with the addition of only DMSO. In the denaturing control (DC) reaction, RNAs were suspended in a denaturing buffer containing 50% formamide and were incubated at 95 °C before modification with SHAPE reagents. For DMS samples, after washed with DPBS, cells were treated with the addition of 15uL DMS and incubation at 37°C for 5min. Cell culture media with DMS was slowly decanted. Then cells were washed twice in 30% v/v BME (diluted in DPBS) and collected into a 15ml centrifuge tube using a scraper. Centrifuge cells at 1000 × g at 4°C for 3min and decant the BME solution. Wash the cells with 1ml DPBS twice and centrifuge the cells again. Isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment and were then used for SHAPE-MaP reverse transcription by adding 1 mL (200 U/mL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for 3' ETS. Second-strand synthesis was performed with TAQ DNA polymerase. The resulting PCR products were further isolated. Primers for SHAPE-MaP reverse transcription and second-strand synthesis (1st round PCR and nested PCR reactions) were listed in Supplementary Table S1. SHAPE-MaP libraries were prepared from 1 ng of DNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China. About 15-25 million mapped sequencing reads were obtained for each sample, with 88% of bases at or above Q30.
Isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment and were then used for SHAPE-MaP reverse transcription by adding 1 mL (200 U/mL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for 3' ETS. Second-strand synthesis was performed with TAQ DNA polymerase. The resulting PCR products were further isolated. Primers for SHAPE-MaP reverse transcription and second-strand synthesis (1st round PCR and nested PCR reactions) were listed in Supplementary Table S1.
SHAPE-MaP libraries were prepared from 1 ng of DNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China. About 15-25 million mapped sequencing reads were obtained for each sample, with 88% of bases at or above Q30.

treatment_protocol: Scramble and URB1-targetting shRNA expressing HeLa cells were were seeded and induced with 1 μg/ml doxycycline for 6 days.

tag: cell line

value: HeLa

tag: shRNA

value: shScr.

tag: treatment

value: NAI samples modified by NAI in DMSO


title: Batch 2 PBMC 10x Lane 1 (Batch2P01) GEX


title: Batch 2 PBMC 10x Lane 1 (Batch2P01) CSP


title: PRS_HiC_rep2

first: Qian

last: Bian

address: Jinzun Road No.115

department: Shanghai Institute of Precision Medicine, Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

description: E14.5 PRS-/- Meckel's cartilage Hi-C replicate2

data_processing:
Fasqt files of Hi-C samples were processed with Trim galore to remove low-quality reads and adapters.
Adaptor-trimmed Hi-C data were mapped to mm10 iteratively with bowtie2.
Mapped sequences were parsed into a Python data structure and assigned to DpnII fragments. HiC dataset object was created after fragment filtering, and generated hdf5 files were transformed to cool format with cooler cload hiclib and then balanced with cooler balance.
mm10
cool

source_name: chondrocytes

extract_protocol:
E14.5 Meckel’s cartilage bars were dissected from wild-type C57BL/6J  mouse embryos as previsouly described (Ishizeki, 1996 & Wiszniak, 2015) with modifications. E14.5 forelimb was dissected from wild-type mouse embryos with removal of surrounding connective tissues. Dissected forelimb cartilage was then digested following the same procedure as the digestion of Meckel’s cartilage.
Briefly, cells were crosslinked in 1% formaldehyde for 10 mins at room temperature and quenched with 0.2M glycine. Cells were pelleted, washed with 1ml HBSS and then resuspended with 1ml ice-cold Hi-C lysis buffer, incubated on ice for 30min and were further dounced with pestles to insure complete lysis. Chromatin was then opened up at the presence of 0.5% SDS at 65°C for 5 mins and quenched with Triton X-100 at the final concentration of 1%. Samples were then digested overnight with DpnII at 37°C on a thermomixer with interval shaking, followed by heat inactivation of DpnII and fill-in of the restriction fragment overhangs. Samples were then ligated with T4 DNA ligase at 16°C for 4hr, and crosslink reversal was performed by Proteinase K digestion. 3C libraries were then extracted and purified by phenol-chloroform isoamyalcohol extraction and ethonal precipitation. Efficiency of digestion and ligation was assessed by gel electrophoresis of quality controls. 3C libraries were then sheared to 200-700bp by Covaris sonication and Dynabeads MyOne Streptavidin T1 was used to perform biotin pull-down after washing. End repair, dA-tailing and ligation of libraries were performed with NEBNext Ultra II Ligation Module. Libraries was amplified on the streptavidin beads using Phusion DNA Polymerase, size-selected with AMPure XP beads, quantified by Qubit dsDNA High Sensitivity Assay and then sequenced on the NovaSeq platform.

tag: strain

tag: genotype

value: PRS-/-

value: Meckel's cartilage


title: PRS_HiC_rep1

description: E14.5 PRS-/- Meckel's cartilage Hi-C replicate1


title: NAI-KD1_2-F4R4


title: FL_4C_Sox9_bait_rep2

description: E14.5 forelimb 4C-seq replicate2 (Sox9 promoter bait)

data_processing:
Reads matching the forward primer sequence were selected from the total fastq files to ensure an overall high quality of the raw data. The primer sequences were then removed from selected reads, which were then mapped to mm10 reference genome with Bowtie2.
For visualization of 4C-seq data, the coverage files in bedGraph format were built with a custom R script (https://github.com/bbcf/bbcfutils/blob/master/R/smoothData.R)(PMID: 33597753; PMID: 2447505), with a range of 5 fragments used to normalize the data per million reads (RPM).
The relative signal strength between MC and FL in the PRS-Sox9 loop bin (chr11: 111,650,000-111,660,000) was generated with wiggletools ratio at the window size of 100bp.
mm10
bedgraph
Library strategy: 4C-seq

extract_protocol: 4C-seq libraries were generated from microdissected E14.5 Meckel’s cartilage and forelimb cartilage as described previously(PMID: 31351925). Cells were crosslinked with 1% formaldehyde for 10 mins at room temperature, then treated with 0.2M glycine. The crosslinked cells were pelleted, washed with HBSS, and incubated with lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal CA-630 with cOmplete Protease Inhibitor Cocktail). Lysates were pelleted at 2500x g for 5min, washed with 1x NEB CutSmart Bffer, and chromatin was then opened up at the presence of 0.5% SDS at 65°C for 5mins and quenched with Triton X-100 at the final concentration of 1%. Samples were then digested overnight with Nlalll at 37°C. First round of ligation was carried in a total volume of 1.2ml with 50U T4 DNA ligase at 16°C for 4hr. The ligated products were then treated with 20 mg/ml Proteinase K overnight to reverse crosslinking. To generate 3C libraries, DNA purification was performed by phenol-chloroform isoamyl alcohol extraction and ethanol precipitation. 3C libraries were then treated with DpnII overnight at 37°C for the second round of restriction enzyme digestion, followed by overnight ligation at 16°C. The DNA was purified by phenol-chloroform isoamyl alcohol extraction and ethanol precipitation, and clean-up of 4C-seq libraries was then performed with PCR purification kit (Qiagen). Quality controls of the first and second rounds restriction enzyme digestion and ligation were assessed by gel electrophoresis.  Amplification of 4C-seq libraries was carried out with two rounds of PCR with the specificity of primers checked with test PCR. The first PCR step is to amplify the fragments ligated to Sox9 promoter viewpoint using the Expand Long Range PCR System (Roche). A total of four PCR reactions with 200 ng 4C-seq template per reaction was performed. 50μl aliquot of all pooled PCR reactions was purified with AMPure beads at 0.8x volume. The purified PCR products of the first round were amplified by universal primers containing the Illumina adapters required for flow cell binding of the amplicons, and then sequenced on the NovaSeq platform after purification with PCR purification kit (Qiagen).

value: wt

value: forelimb


title: ChIPseq for NANOG in WT_Rep1

value: Wild type


title: Batch 1 PBMC 10x Lane 16 (Batch1P16) GEX


title: ChIPseq for WIZ in Zfp462KO_Rep2

value: rabbit anti-WIZ/NBP1-80586/Novus


title: Batch 1 PBMC 10x Lane 16 (Batch1P16) CSP


title: ChIPseq for WIZ in WT_Rep2


title: NAI-KD4_2-F4R4


title: MC_4C_Sox9_bait_rep2

description: E14.5 Meckel's cartilage 4C-seq replicate2 (Sox9 promoter bait)


title: FL_4C_Sox9_bait_rep1

description: E14.5 forelimb 4C-seq replicate1 (Sox9 promoter bait)


title: ChIPseq for WIZ in Zfp462KO_Rep1


title: Batch 2 PBMC 10x Lane 3 (Batch2P03) CSP


title: NAI-SCR_1-F4R4


title: Batch 1 PBMC 10x Lane 15 (Batch1P15) GEX


title: ChIPseq for WIZ in WT_Rep1


title: NAI-KD1_1-F4R4


title: Batch 1 PBMC 10x Lane 15 (Batch1P15) CSP


title: ChIPseq for H3K27ac in Zfp462KO_Rep2

value: rabbit anti-H3K27ac/ab4729/abcam


title: ChIPseq for NANOG in Zfp462KO_Rep1


title: FL_H3K27Ac_rep3

description: E14.5 forelimb H3K27Ac CUT&Tag replicate3

data_processing:
Adaptor sequences in CUT&Tag fastq files were trimmed with trim galore.
Alignment of trimmed fastq files were performed with bowtie2 to mm10 with the following parameters: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Samtools was used for removing duplicated and mitochondrial reads in aligned bam files.
Peak calling was performed with SEACR.
mm10
bed
Library strategy: CUT&Tag

extract_protocol: CUT&Tag  was performed as previously described (55) with Hyperactive In-Situ ChIP Library Prep Kit for Illumina kit (Vazyme, TD901TD903) following the manufacturer’s instructions. Briefly, a total of 50,000 cells were harvested, washed, and incubated with 10μl activated ConA beads per sample at room temperature for 10 min. Cells bound in beads were then incubated with primary antibodies (H3K27Ac, Abcam; IgG rabbit, Abcam) overnight at 4°C, followed by binding with secondary antibody at room temperature for 1hr. After washing twice with 800μl Dig-wash buffer, pA/G-Tn5 adapter complex was added to the sample in 100μl Dig-300 buffer to a final concentration of 1:250 and incubated on a nutator at room temperature for 1hr. Tagmentation was then performed at room temperature for 1hr and stopped with 10μl 0.5M EDTA, 3μl 10% SDS, and 2.5μl 20 mg/ml Proteinase K. Phenol-chloroform isoamyl alcohol extraction and ethanol precipitation of DNA was performed,Template DNA was extracted with DNA extraction beads,  followed by PCR amplification and Illumina sequencing.


title: DMSO-KD4-F4R4

description:
NAI-KD4_1-F1R1_F3R3_F4R4_profile.txt
NAI-KD4_2-F1R1_F3R3_F4R4_profile.txt

value: DMSO samples only treated with DMSO


title: ChIPseq for H3K27ac in Zfp462KO_Rep1


title: NAI-KD4_1-F4R4


title: DMSO-KD1-F4R4

description:
NAI-KD1_1-F1R1_F3R3_F4R4_profile.txt
NAI-KD1_2-F1R1_F3R3_F4R4_profile.txt


title: Batch 1 PBMC 10x Lane 14 (Batch1P14) CSP


title: FL_H3K27Ac_rep1

description: E14.5 forelimb H3K27Ac CUT&Tag replicate1


title: DC-SCR-F4R4

description:
NAI-SCR_1-F1R1_F3R3_F4R4_profile.txt
NAI-SCR_2-F1R1_F3R3_F4R4_profile.txt

value: DC samples denatured by formamide at 95℃


title: Batch 1 PBMC 10x Lane 13 (Batch1P13) GEX

value: UnSorted


title: MC_H3K27Ac_rep3

description: E14.5 Meckel's cartilage H3K27Ac CUT&Tag replicate3


title: DC-KD4-F4R4


title: Batch 1 PBMC 10x Lane 13 (Batch1P13) CSP

value: blood


title: ChIPseq for H3K27ac in WT_Rep1


title: ChIPseq for H3K9me2 in Zfp462KO_Rep2

value: mouse anti-H3K9me2/ab1220/abcam


title: MC_4C_Sox9_bait_rep1

description: E14.5 Meckel's cartilage 4C-seq replicate1 (Sox9 promoter bait)


title: DMSO-SCR-F4R4


title: MC_H3K27Ac_rep2

description: E14.5 Meckel's cartilage H3K27Ac CUT&Tag replicate2


title: Batch 1 PBMC 10x Lane 12 (Batch1P12) GEX

value: PBMC


title: DC-KD1-F4R4


title: ChIPseq for H3K9me2 in Zfp462KO_Rep1

value: Zfp462knock out


title: SNU638-DEL-3

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

data_processing:
Illumina Casava software used for basecalling.
The FastQC (FastQC v0.11.3) and cut-adapt (v1.1) were used to filter sequencing reads of low quality.
Then reads were mapped to mouse genome build hg38 using STAR with default parameters. The HTseq (v0.9.1) was used for raw read counts. The DESeq2 (DESeq2 v3.1) was used for selecting differentially expressed genes (DEGs).
Genome_build: hg38
Supplementary_files_format_and_content: generation of raw abundance measurements, txt file

source_name: Gastric cancer cell line

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacture instruction
The RNA sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina)
RNA sequencing was performed using the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads

value: Homo Sapiens

value: SSTR2 deletion


title: ChIPseq for NANOG in WT_Rep2

value: rabbit anti-NANOG/ab80892/abcam


title: Batch 1 PBMC 10x Lane 12 (Batch1P12) CSP


title: Batch 1 PBMC 10x Lane 14 (Batch1P14) GEX


title: SNU638-DEL-2


title: ATACseq of Zfp462-KO_ZFP462-NT-Mid-Knock-In mESCs replicate2

data_processing:
ATAC-seq reads were processed using nfcore/atacseq v1.0.0 with standard settings.
Reads were trimmed using trim-galore v0.5.0, aligned to the mm10 genome using bwa mem v0.7.17 and duplicated reads were marked with picard MarkDuplicates v2.19.0.
Alignment was filtered using samtools v1.9 with parameters -q 1 -F 0x0400 -F 0x004 -F 0x0008 -f 0x001, thereby removing multimapping and duplicated reads.
Peaks were called from the filtered and sorted BAM using macs2 v2.1.2 with parameters --broad --BAMPE --keep-dup all --nomodel.
Assembly: mm10
Supplementary files format and content: peak files

source_name: mESCs

growth_protocol: Cell were grown at 37º C, 5% CO2

extract_protocol: ATACseq was performed as desrcibed in Buenrostro et al., 2013 using 50,000 cells.

treatment_protocol: Rescue Experiment

value: mESCs

value: Zfp462-KO_ZFP462-NT-Mid-Knock-In mESCs


title: Batch 1 PBMC 10x Lane 11 (Batch1P11) GEX


title: FL_H3K27Ac_rep2

description: E14.5 forelimb H3K27Ac CUT&Tag replicate2

value: wt


title: ChIPseq for H3K27ac in WT_Rep2


title: ChIPseq for H3K9me2 in WT_Rep1


title: SNU638-DEL-1


title: Batch 1 PBMC 10x Lane 11 (Batch1P11) CSP


title: Input_for_antibody_ChIPs in Zfp462KO Rep2


title: SNU638-CON-3

value: Control


title: ATACseq of Zfp462-KO_ZFP462-FL-Knock-In mESCs replicate2

value: Zfp462-KO_ZFP462-FL-Knock-In mESCs


title: Batch 1 PBMC 10x Lane 10 (Batch1P10) GEX


title: Input_for_antibody_ChIPs in Zfp462KO Rep1


title: ATACseq of Zfp462-KO_ZFP462-FL-Knock-In mESCs replicate1


title: Input_for_antibody_ChIPs in WT_Rep2

value: Wild type


title: MC_H3K27Ac_rep1

description: E14.5 Meckel's cartilage H3K27Ac CUT&Tag replicate1

value: Meckel's cartilage


title: ATACseq of Zfp462-KO mESCs replicate2 (control for rescue experiment)

value: Zfp462-KO mESCs


title: SNU638-CON-1


title: Batch 1 PBMC 10x Lane 10 (Batch1P10) CSP


title: MKN74-OVER-3

value: SSTR2 overexpression


title: Input_for_antibody_ChIPs in WT_Rep1


title: ATACseq of wild type mESCs replicate2 (control for rescue experiment)

value: Wild type control mESCs


title: ATACseq of Zfp462-KO mESCs replicate1 (control for rescue experiment)


title: MKN74-OVER-2


title: Batch 1 PBMC 10x Lane 9 (Batch1P09) CSP

value: UnSorted

value: blood


title: ChIPseq for H3K9me2 in WT_Rep2

value: mouse anti-H3K9me2/ab1220/abcam


title: ChIPseq for HP1𝛾 in Zfp462KO_Rep2

value: Zfp462knock out

value: Dynabeads™ M-280Streptavidin/Invitrogen


title: MKN74-OVER-1

value: Homo Sapiens


title: Batch 1 PBMC 10x Lane 8 (Batch1P08) GEX

description: mRNA (cDNA) reads from multimodal scRNAseq

value: PBMC


title: ATACseq of Zfp462-KO_ZFP462-NT-Mid-Knock-In mESCs replicate1

value: mESCs


title: Batch 1 PBMC 10x Lane 8 (Batch1P08) CSP

description: Cell Surface Protein Tag reads from multimodal scRNAseq


title: ChIPseq for HP1𝛾 in WT_Rep2


title: MKN74-CON-3


title: CD4, replicate2, scRNAseq_HTO

city: Pittsburgh

first: Warren

last: Shlomchik

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

description:
10x Genomics
HTO ID for Replicate 2:
TATGCTGCCACGGTA: Spleen_2
GAGTCTGCCAGTATC: Skin_2
TATAGAACGCCAGGC: Colon_2
TGCCTATGAAACAAG: IEL_2
CCGATTGTAACAGAC: LP_2

data_processing:
Cell Ranger (version 3.1.0) was used to align the transcriptome sequencing reads and count the number of UMI-deduplicated reads mapped to each gene in single cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: multiplexed sample: Spleen, colon, skin, small intestine intraepithelila lymphocytes, small intestine lamina propria lymphocytes

extract_protocol:
Spleens were flushed with PBS, passed through a cell strainer, and lysed with red blood cell lysis buffer. Small intestines were excised, sectioned and incubated in RPMI containing 5mM EDTA, 1mM DTT and 3% v/v calf serum at 37°C for 20 minutes. The resulting digest was passed through a cell strainer and IELs isolated by centrifugation over a Histopaque gradient (Sigma). For LPL isolation, tissues were minced and digested with Liberase TL (Roche) (2.5mg/ml) and DNAse (Sigma) (0.02mg/ml) at 37°C for 30 minutes and passed through a cell strainer. Colons were processed the same as SI-LPLs without an IEL separation. For skin lymphocyte isolation, mouse ears were digested in HBSS CollagenaseIV (1mg/ml) at 37°C for 2 hours and the resulting digest  was passed through a cell strainer. Final cell suspensions were in FACS buffer containg 3% v/v calf serum and  2mM EDTA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: CD4 T cells

value: multiplexed sample:Spleen, colon, skin, small intestine intraepithelila lymphocytes, small intestine lamina propria lymphocytes

value: BALB/c RAG2-/- TS1 Tg

tag: age

value: 4 weeks post-transplantation


title: SNU638-CON-2

value: Control


title: ChIPseq for HP1𝛾 in WT_Rep1

value: Wild type


title: MKN74-CON-2


title: Batch 1 PBMC 10x Lane 9 (Batch1P09) GEX


title: Batch 1 PBMC 10x Lane 7 (Batch1P07) CSP


title: MKN74-CON-1


title: Batch 1 PBMC 10x Lane 6 (Batch1P06) GEX


title: MKN45-OVER-3


title: ChIPseq for HP1𝛾 in Zfp462KO_Rep1


title: Input_for_GLP ChIPseq_in_WT


title: CD4, replicate1, scRNAseq_HTO

description:
10x Genomics
HTO ID for Replicate 1:
ACCCACCAGTAAGAC: Spleen_1
GGTCGAGAGCATTCA: Skin_1
CTTGCCGCATGTCAT: Colon_1
AAAGCATTCTTCACG: IEL_1
CTTTGTCTTTGTGAG: LP_1


title: CD4, replicate1, scRNAseq_GEX

description: 10x Genomics


title: Input_for_GLP_ChIPseq in Zfp462KO


title: MKN45-OVER-2


title: ChIPseq for GLP in Zfp462KO_Rep2


title: Batch 1 PBMC 10x Lane 5 (Batch1P05) GEX


title: Batch 1 PBMC 10x Lane 6 (Batch1P06) CSP


title: ATACseq of wild type mESCs replicate1 (control for rescue experiment)


title: Batch 1 PBMC 10x Lane 5 (Batch1P05) CSP


title: ChIPseq for GLP in Zfp462KO_Rep1


title: ChIPseq for GLP in WT_Rep2


title: MKN45-OVER-1


title: MKN45-CON-3


title: Retina_Wfs1-KO_rep2

city: Milan

first: Edoardo

middle: Niccolò

last: Bellini

state: Lombardia

address: Via Olgettina 58

department: Neuroscience

country: Italy

institute: San Raffaele Hospital

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference human genome mm10, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode realise 31).
Assembly: mm10
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Retina

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: post natal day 240


title: Retina_Wfs1-KO_rep1


title: Batch 1 PBMC 10x Lane 7 (Batch1P07) GEX


title: CD4, replicate2, scRNAseq_GEX

description: 10x Genomics


title: ChIPseq for GLP in WT_Rep1


title: Retina_WT_rep3

value: wild type


title: MKN45-CON-2


title: Batch 1 PBMC 10x Lane 3 (Batch1P03) CSP

value: UnSorted


title: Input_for_ZFP462 ChIPseq_Rep2


title: Retina_WT_rep2


title: MKN45-CON-1


title: Retina_Wfs1-KO_rep3


title: Batch 1 PBMC 10x Lane 2 (Batch1P02) GEX

value: blood


title: Retina_WT_rep1


title: Batch 1 PBMC 10x Lane 2 (Batch1P02) CSP


title: ChIPseq for ZFP462 in NPCs_Rep2

source_name: NPCs


title: Input_for_ZFP462 ChIPseq_Rep1


title: AGS-OVER-2

value: SSTR2 overexpression


title: AGS-OVER-3


title: ChIPseq for ZFP462 in NPCs_Rep1


title: E12half_MC_ATAC_rep1

description: E14.5 Meckel's cartilage Hi-C replicate1

data_processing:
Trim galore was used to remove adaptor sequences of ATAC-seq data.
Cleaned data were then aligned to mouse genome (mm10) with bowtie2 (--very-sensitive -X 2000).
Samtools was used for removing duplicated and mitochondrial reads in aligned bam files.
Peak calling was performed with Genrich.
Genome_build: mm10
Supplementary_files_format_and_content: narrowpeak

extract_protocol:
E12.5 mandibular processes were dissected from wildtype embryo heads under stereomicroscope. Dissected tissues were then digested with trypsin and collagenase type II to acquire single-cell suspension for downstream library preparations.
ATAC-seq was performed as described previously with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Briefly, 50,000 cells were collected at 500×g for 5 min and resuspended in 50μl cold ATAC-seq lysis buffer and incubated on ice for 10min. Following centrifugation at 500×g at 4°C for 5 min, cells were pelleted and resuspended in 50μl transposition mix and then incubated at 37°C. The reaction was purified with VAHTS DNA Clean Beads and PCR amplified for 15 cycles. Purified ATAC-seq libraries were sequenced on the NovaSeq platform.

value: wt

value: Meckel's cartilage


title: AGS-OVER-1

value: Homo Sapiens


title: Batch 1 PBMC 10x Lane 3 (Batch1P03) GEX

value: PBMC


title: Batch 1 PBMC 10x Lane 1 (Batch1P01) GEX


title: Batch 1 PBMC 10x Lane 1 (Batch1P01) CSP


title: WTLPS_p65_HiChIP_rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

institute: Yonsei University College of Medicine

data_processing:
Library strategy: Hi-ChIP
Sequenced using Illumina NovaSeq6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MBoI restriction sites
Genome_build: mm10
Supplementary_files_format_and_content: hic contaning validpairs

source_name: BMDC

growth_protocol: Bone marrow cells prepared from CreER or CreER;CTCFfl/fl mice were culutred under the presence of murine GM-CSF for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq6000 platform.

treatment_protocol: Bone marrow-derived dendritic cells (BMDCs) were stimulated with LPS at the concentration of 100ng/ml for 3 hours.

value: dentritic cells

tag: passages

value: 8 weeks old

value: CreER

value: LPS


title: AGS-CON-3


title: ChIPseq for ZFP462_Rep2

value: Dynabeads™ M-280Streptavidin/Invitrogen


title: HCT116 treated with Activin+ HGF, rep3

city: Bishan

first: Hong

last: Peng

state: ChongQing

address: Shuangxing avenue 9

institute: AffiliatedBishan hospital of Chongqing Medical  University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: StringTie
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: colon and rectum

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara, Shiga, Japan), and 1 µg RNA was used to synthesize cDNA with the PrimeScript™RT reagent Kit with gDNA Eraser (Takara).
Libraries were constructed by depleting ribosomal RNA using the Human/Mouse/Rat Ribo-Zero rRNA Removal Kit for Illumina (Epicentre, Madison, WI, USA).

treatment_protocol: HCT116 cells were exposed to 100 ng/mL activin A (Peprotech, Rocky Hill, NJ, USA) for 5 days. The cells were then treated with 20 ng/mL HGF (Peprotech) for another 5 days.

value: colon and rectum

value: colorectal cancer cell

value: Activin+HGF


title: WTLPS_p65_HiChIP_rep1


title: ATACseq of wild type mNSCs replicate2

data_processing:
ATAC-seq reads were processed using nfcore/atacseq v1.0.0 with standard settings.
Reads were trimmed using trim-galore v0.5.0, aligned to the mm10 genome using bwa mem v0.7.17 and duplicated reads were marked with picard MarkDuplicates v2.19.0. Alignment was filtered using samtools v1.9 with parameters -q 1 -F 0x0400 -F 0x004 -F 0x0008 -f 0x001, thereby removing multimapping and duplicated reads.
Peaks were called from the filtered and sorted BAM using macs2 v2.1.2 with parameters --broad --BAMPE --keep-dup all --nomodel.
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak formatted peak sets for each replicate as called by macs2

source_name: mNSCs

growth_protocol:
mNSCs were grown at 37º C, 5% CO2
Cell were grown at 37º C, 5% CO2

value: mNSCs

value: Wild type


title: ChIPseq for ZFP462_Rep1


title: AGS-CON-2

value: Control


title: AGS-CON-1


title: WTLPS_K27Ac_HiChIP_rep2

value: H3K27ac (Abcam #ab4729)


title: HCT116 treated with Activin+ HGF, rep1


title: WTLPS_K27Ac_HiChIP_rep1


title: ATACseq of wild type mNSCs replicate1


title: HCT116 treated with Activin, rep3

value: Activin


title: ATACseq of Zfp462-/- cl.1 mESCs replicate3

description: ESC_Zfp462-/- cl.1_Rep3

growth_protocol:
mESCs were grown at 37º C, 5% CO2
Cell were grown at 37º C, 5% CO2

value: mESCs

value: Zfp462 knock out cl.1


title: HCT116 treated with Activin, rep2


title: E12half_MC_ATAC_rep2

description: E14.5 Meckel's cartilage Hi-C replicate2

value: wt

value: Meckel's cartilage


title: WT_K27Ac_HiChIP_rep1

value: dentritic cells


title: ATACseq of Zfp462-/- cl.1 mESCs replicate2

description: ESC_Zfp462-/- cl.1_Rep2


title: WT_K27Ac_HiChIP_rep2

value: 8 weeks old


title: ATACseq of Zfp462-/- cl.1 mESCs replicate1

description: ESC_Zfp462-/- cl.1_Rep1


title: HCT116 treated with NC, rep3

value: NC


title: KOLPS_K27Ac_HiChIP_rep2

value: CreER;CTCF fl/fl

value: LPS


title: PF13_Non_CD.Perifistule

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

description: Ileum biopsy perifistule

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7.3a (Dobin et al., 2013).
Differential gene expression and functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et al., 2016), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: raw_counts.tsv: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab: Tab-delimited text files include STAR gene counts.

source_name: Ileum biopsy

extract_protocol:
Total RNA was extracted from human biopsies using the RNeasy Lipid Tissue Mini kit (Qiagen), and checked for quality using Tapestation 4200 (Agilent, USA).
RNA-seq libraries were created using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, USA) starting from 400 ng of RNA.

value: Ileum biopsy

tag: diagnosis

value: Non-Crohn's disease with perifistule


title: PF18_Non_CD.Perifistule

description: Ileum biopsy perifistule


title: PF21_Non_CD.Perifistule

description: Ileum biopsy perifistule


title: PF17_Non_CD.Perifistule

description: Ileum biopsy perifistule


title: KOLPS_K27Ac_HiChIP_rep1


title: ATACseq of wild type mESCs replicate2

value: Wild type control


title: PF11_Non_CD.Perifistule

description: Ileum biopsy perifistule


title: HCT116 treated with NC, rep2

value: colon and rectum

value: colorectal cancer cell


title: ATACseq of wild type mESCs replicate3


title: KO_K27Ac_HiChIP_rep2


title: PF28_Non_CD.Perifistule

description: Ileum biopsy perifistule


title: HCT116 treated with NC, rep1


title: F21_Non_CD.Fistule

description: Ileum biopsy fistule

value: Non-Crohn's disease with fistule


title: ATACseq of wild type mESCs replicate1


title: KO_K27Ac_HiChIP_rep1

value: H3K27ac (Abcam #ab4729)


title: SUNE1, CBX1-Input, r1

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis.
BWA using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak scanning
SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
MACS (version: macs14)( -p 1e-3 -m 10,30) is a computational method that was designed to identify read-enriched regions from ChIP-seq data. The region would be defined as a peak when p-value<1e-5.
According to the genomic location information and gene annotation information of peak, peak related genes can be confirmed.
In different samples, the region of overlap >=50% of the shorter peak was considered as the common peak. We identified peaks with |M|>=1 and -log10 p-value>=3 in a comparison as significant differential peaks.
BWA (version 0.7.12)
Assembly: Homo sapiens (Version: v96)
Supplementary files format and content: The bed file include peak files. The bw file include peak related genes in processed data files.

extract_protocol:
The cells were fixed, quenched and lysed. The lysate was digested and the chromatin was sonicated to about 500 nt long and incubated with normal rabbit IgG, or the anti-FLAG-CBX1 antibody, and then incubated with ChIP-grade protein G magnetic beads. The DNA was eluted and purified using a DNA Clean-UP column and DNA column wash buffer. The purified DNA was used to perform sequencing (ChIP-seq).
ChIP DNA-end was repaired to overhang a 3’-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification. Finally we got qualified library for sequencing

value: nasopharyngeal carcinoma cell

value: FLAG (sigma, F1804)


title: WTLPS_HiC_rep2

data_processing:
Sequenced using Illumina NovaSeq6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MBoI restriction sites
Genome_build: mm10
Supplementary_files_format_and_content: hic contaning validpairs

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq6000 platform.

value: CreER


title: ESC_Zfp462-/- cl.2_4dayRA_Rep2

description: transcriptome profiling of Zfp462 knock out cl.2 neural progenitor cells with QuantSeq

data_processing:
RNA-seq reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20) and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Genome_build: mm10

source_name: Mouse cells from a differentiation assay

extract_protocol:
RNA was extracted using RNAeasy Qiagen kit
Libraries were prepared using a QuantSeq 3' mRNA kit from Lexogen

value: Zfp462 knock out cl.2

tag: growth protocol

value: Cells were grown at 37º C, 5% CO2

value: 4day retinoic acid


title: SUNE1, CBX1-Flag, r1


title: HCT116 treated with Activin, rep1

value: Activin


title: HCT116 treated with Activin+ HGF, rep2

value: Activin+HGF


title: F18_Non_CD.Fistule

description: Ileum biopsy fistule


title: WTLPS_HiC_rep1

value: dentritic cells

value: 8 weeks old


title: ESC_Zfp462-/- cl.2_2dayRA_Rep2

description: transcriptome profiling of Zfp462 knock out cl.2 neural lineage cells with QuantSeq

value: 2day retinoic acid


title: Sune1 cells, sgNC, r3

description:
gene_expression.bw
all.counts.Sune1sgCBX1_vs_Sune1V2.edgeR_differential.bw

data_processing:
Raw Reads are first processed to obtain high-quality Clean Reads by removing low quality sequences, removing joint contamination, and removing ribosome sequences (rRNA).
Clean Reads were compared to  GRCh38.91 reference genes using Hisat2 software.
Trimmed fragments from each subsequent gene segment were counted using Stringtie software to acquire FPKM values from each gene.
EdgeR software was used to quantify genes for difference analysis:Q value< 0.05 and FC>2.
Assembly:  GRCh38.91
Supplementary files format and content: bw, complete gene expression data and differential gene expression data.

growth_protocol: SUNE1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using a RNAeasy™ kit (R0027, Beyotime). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: nasopharyngeal carcinoma cells

value: sgNC


title: F17_Non_CD.Fistule

description: Ileum biopsy fistule

value: Ileum biopsy


title: WT_HiC_rep2


title: ESC_Zfp462-/- cl.2_2dayRA_Rep1


title: KOLPS_HiC_rep2

value: CreER;CTCF fl/fl

value: LPS


title: Sune1 cells, sgNC, r2


title: Sune1 cells, sgCBX1, r3


title: F11_Non_CD.Fistule

description: Ileum biopsy fistule

value: Non-Crohn's disease with fistule


title: F28_Non_CD.Fistule

description: Ileum biopsy fistule


title: Sune1 cells, sgNC, r1


title: KOLPS_HiC_rep1


title: WT_HiC_rep1


title: F13_Non_CD.Fistule

description: Ileum biopsy fistule


title: ESC_Zfp462-/- cl.2_Serum_LIF_Rep2

description: transcriptome profiling of Zfp462 knock out cl.2 cells cultured in Serum/LIF with QuantSeq Rep2

value: Serum/LIF


title: PF22_CD.Perifistule

description: Ileum biopsy perifistule

value: Crohn's disease with perifistule


title: PF26_CD.Perifistule

description: Ileum biopsy perifistule


title: ESC_Zfp462-/- cl.2_4dayEB_Rep1

description: transcriptome profiling of Zfp462 knock out cl.2 4day EBs with QuantSeq Rep1

value: after 4 days of LIF withdrawal


title: ESC_Zfp462-/- cl.2_4dayEB_Rep2

value: Zfp462 knock out cl.2


title: Sune1 cells, sgCBX1, r2


title: KO_HiC_rep2


title: ESC_Zfp462-/- cl.2_Serum_LIF_Rep1

description: transcriptome profiling of Zfp462 knock out cl.2 cells cultured in Serum/LIF with QuantSeq Rep1

value: Cells were grown at 37º C, 5% CO2


title: ESC_Zfp462-/- cl.2_4dayRA_Rep1

value: 4day retinoic acid


title: PF20_CD.Perifistule

description: Ileum biopsy perifistule


title: nasopharyngeal carcinoma,zyB732_input

description:
zyA_inputVSzyB_input_Gene_differential_expression.bw
zyAVSzyB_diffPeak_Gene_differential_expression.bw

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
HISAT2 was used to map reads to the genome of Homo sapiens (Version: v96) with default parameters. Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house.
Called peaks were annotated by intersection with gene architecture using ChIPseeker.
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR
Assembly: Homo sapiens (Version: v96)
Supplementary files format and content: Peak result and Gene expression result.

source_name: nasopharyngeal carcinoma

extract_protocol:
Total RNA of 4 paired NPC tissues with or without metastasis were extracted respectably using Trizol reagent.
Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method

value: nasopharyngeal carcinoma

value: non-metastasis


title: ESC_Zfp462-/- cl.2_Serum_LIF_2i_Rep2

description: transcriptome profiling of Zfp462 knock out cl.2 cells cultured in Serum/LIF/2i with QuantSeq Rep2


title: nasopharyngeal carcinoma,zyB1459_input


title: FL_ATAC_rep3

description: E14.5 forelimb ATAC-seq replicate3

data_processing:
Trim galore was used to remove adaptor sequences of ATAC-seq data.
Cleaned data were then aligned to mouse genome (mm10) with bowtie2 (--very-sensitive -X 2000).
Samtools was used for removing duplicated and mitochondrial reads in aligned bam files.
Peak calling was performed with Genrich.
mm10
narrowpeak

extract_protocol:
E14.5 Meckel’s cartilage bars were dissected from wild-type C57BL/6J  mouse embryos as previsouly described (Ishizeki, 1996 & Wiszniak, 2015) with modifications. E14.5 forelimb was dissected from wild-type mouse embryos with removal of surrounding connective tissues. Dissected forelimb cartilage was then digested following the same procedure as the digestion of Meckel’s cartilage.
ATAC-seq was performed as described previously with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Briefly, 50,000 cells were collected at 500×g for 5 min and resuspended in 50μl cold ATAC-seq lysis buffer and incubated on ice for 10min. Following centrifugation at 500×g at 4°C for 5 min, cells were pelleted and resuspended in 50μl transposition mix and then incubated at 37°C. The reaction was purified with VAHTS DNA Clean Beads and PCR amplified for 15 cycles. Purified ATAC-seq libraries were sequenced on the NovaSeq platform.

value: wt

value: forelimb


title: PF16_CD.Perifistule

description: Ileum biopsy perifistule


title: FL_ATAC_rep2

description: E14.5 forelimb ATAC-seq replicate2


title: PF10_CD.Perifistule

description: Ileum biopsy perifistule


title: ESC_Zfp462-/- cl.2_Serum_LIF_2i_Rep1

description: transcriptome profiling of Zfp462 knock out cl.2 cells cultured in Serum/LIF/2i with QuantSeq Rep1


title: nasopharyngeal carcinoma,zyB994_input


title: FL_ATAC_rep1

description: E14.5 forelimb ATAC-seq replicate1


title: PF8_CD.Perifistule

description: Ileum biopsy perifistule


title: PF7_CD.Perifistule

description: Ileum biopsy perifistule


title: ESC_Zfp462-/- cl.1_4dayRA_Rep1

description: transcriptome profiling of Zfp462 knock out cl.1 neural progenitor cells with QuantSeq

value: Zfp462 knock out cl.1


title: nasopharyngeal carcinoma,zyB539_input


title: nasopharyngeal carcinoma,zyA1392_input

value: metastasis


title: FL_HiC_rep2

description: E14.5 forelimb Hi-C replicate2

data_processing:
Fasqt files of Hi-C samples were processed with Trim galore to remove low-quality reads and adapters.
Adaptor-trimmed Hi-C data were mapped to mm10 iteratively with bowtie2.
Mapped sequences were parsed into a Python data structure and assigned to DpnII fragments. HiC dataset object was created after fragment filtering, and generated hdf5 files were transformed to cool format with cooler cload hiclib and then balanced with cooler balance.
mm10
cool

extract_protocol:
E14.5 Meckel’s cartilage bars were dissected from wild-type C57BL/6J  mouse embryos as previsouly described (Ishizeki, 1996 & Wiszniak, 2015) with modifications. E14.5 forelimb was dissected from wild-type mouse embryos with removal of surrounding connective tissues. Dissected forelimb cartilage was then digested following the same procedure as the digestion of Meckel’s cartilage.
Briefly, cells were crosslinked in 1% formaldehyde for 10 mins at room temperature and quenched with 0.2M glycine. Cells were pelleted, washed with 1ml HBSS and then resuspended with 1ml ice-cold Hi-C lysis buffer, incubated on ice for 30min and were further dounced with pestles to insure complete lysis. Chromatin was then opened up at the presence of 0.5% SDS at 65°C for 5 mins and quenched with Triton X-100 at the final concentration of 1%. Samples were then digested overnight with DpnII at 37°C on a thermomixer with interval shaking, followed by heat inactivation of DpnII and fill-in of the restriction fragment overhangs. Samples were then ligated with T4 DNA ligase at 16°C for 4hr, and crosslink reversal was performed by Proteinase K digestion. 3C libraries were then extracted and purified by phenol-chloroform isoamyalcohol extraction and ethonal precipitation. Efficiency of digestion and ligation was assessed by gel electrophoresis of quality controls. 3C libraries were then sheared to 200-700bp by Covaris sonication and Dynabeads MyOne Streptavidin T1 was used to perform biotin pull-down after washing. End repair, dA-tailing and ligation of libraries were performed with NEBNext Ultra II Ligation Module. Libraries was amplified on the streptavidin beads using Phusion DNA Polymerase, size-selected with AMPure XP beads, quantified by Qubit dsDNA High Sensitivity Assay and then sequenced on the NovaSeq platform.


title: Sune1 cells, sgCBX1, r1

value: nasopharyngeal carcinoma cells


title: FL_HiC_rep1

description: E14.5 forelimb Hi-C replicate1


title: KO_HiC_rep1

value: dentritic cells

value: 8 weeks old


title: MC_ATAC_rep3

description: E14.5 Meckel's cartilage ATAC-seq replicate3

value: Meckel's cartilage


title: nasopharyngeal carcinoma,zyA1259_input


title: nasopharyngeal carcinoma,zyA973_input


title: ESC_Zfp462-/- cl.1_2dayRA_Rep1

description: transcriptome profiling of Zfp462 knock out cl.1 neural lineage cells with QuantSeq

value: 2day retinoic acid


title: PF2_CD.Perifistule

description: Ileum biopsy perifistule

value: Ileum biopsy


title: MC_ATAC_rep2

description: E14.5 Meckel's cartilage ATAC-seq replicate2


title: ESC_Zfp462-/- cl.1_4dayEB_Rep2

description: transcriptome profiling of Zfp462 knock out cl.1 4day EBs with QuantSeq Rep1


title: F26_CD.Fistule

description: Ileum biopsy fistule

value: Crohn's disease with fistule


title: nasopharyngeal carcinoma,zyA694_input


title: ESC_Zfp462-/- cl.1_4dayEB_Rep1

value: after 4 days of LIF withdrawal


title: nasopharyngeal carcinoma,zyB732_IP

description:
zyAVSzyB_diffPeak_result.bw
zyAVSzyB_diffPeak_Gene_differential_expression.bw

data_processing:
library strategy: m6A-seq
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
HISAT2 was used to map reads to the genome of Homo sapiens (Version: v96) with default parameters. Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house.
Called peaks were annotated by intersection with gene architecture using ChIPseeker.
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR
Assembly: Homo sapiens (Version: v96)
Supplementary files format and content: Peak result and Gene expression result.


title: F22_CD.Fistule

description: Ileum biopsy fistule


title: MC_ATAC_rep1

description: E14.5 Meckel's cartilage ATAC-seq replicate1


title: ESC_Zfp462-/- cl.1_Serum_LIF_Rep2

description: transcriptome profiling of Zfp462 knock out cl.1 cells cultured in Serum/LIF with QuantSeq Rep2

value: Serum/LIF


title: MC_HiC_rep2

description: E14.5 Meckel's cartilage Hi-C replicate2


title: ESC_Zfp462-/- cl.1_4dayRA_Rep2

value: Cells were grown at 37º C, 5% CO2


title: nasopharyngeal carcinoma,zyB1459_IP


title: F20_CD.Fistule

description: Ileum biopsy fistule


title: ESC_Zfp462-/- cl.1_2dayRA_Rep2


title: PF6_CD.Perifistule

description: Ileum biopsy perifistule

value: Crohn's disease with perifistule


title: ESC_Zfp462-/- cl.1_Serum_LIF_Rep1

description: transcriptome profiling of Zfp462 knock out cl.1 cells cultured in Serum/LIF with QuantSeq Rep1


title: F16_CD.Fistule

description: Ileum biopsy fistule


title: MC_HiC_rep1

description: E14.5 Meckel's cartilage Hi-C replicate1


title: nasopharyngeal carcinoma,zyB994_IP

value: nasopharyngeal carcinoma


title: ESC_Zfp462-/- cl.1_Serum_LIF_2i_Rep2

description: transcriptome profiling of Zfp462 knock out cl.1 cells cultured in Serum/LIF/2i with QuantSeq Rep2


title: ESC_Zfp462+/R1257*_Rep3

data_processing:
RNA-seq reads were trimmed using trimgalore v0.5.0 and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) with parameter -s 2.
Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1.
Genome_build: mm10

growth_protocol: mESCs were grown at 37º C, 5% CO2

extract_protocol:
RNA was extracted using RNAeasy Qiagen kit
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)
polyA selection

value: mESCs

value: Zfp462 heterozygous mutant


title: nasopharyngeal carcinoma,zyB539_IP

value: non-metastasis


title: F10_CD.Fistule

description: Ileum biopsy fistule


title: ESC_Zfp462+/R1257*_Rep2


title: ESC_Zfp462+/R1257*_Rep1


title: ESC_WT_4dayRA_Rep2

description: transcriptome profiling control neural progenitor cells with QuantSeq

value: WT control

value: 4day retinoic acid


title: ESC_Zfp462-/- cl.1_Serum_LIF_2i_Rep1

description: transcriptome profiling of Zfp462 knock out cl.1 cells cultured in Serum/LIF/2i with QuantSeq Rep1

value: Zfp462 knock out cl.1


title: F14_CD.Fistule

description: Ileum biopsy fistule


title: nasopharyngeal carcinoma,zyA1392_IP

value: metastasis


title: ESC_Zfp462-/- cl.2_Rep3

value: Zfp462 knock out cl.2


title: F6_CD.Fistule

description: Ileum biopsy fistule


title: ESC_WT_4dayRA_Rep1


title: nasopharyngeal carcinoma,zyA973_IP


title: ESC_Zfp462-/- cl.2_Rep2


title: ESC_WT_2dayRA_Rep2

description: transcriptome profiling of control neural lineage cells with QuantSeq_Rep2


title: nasopharyngeal carcinoma,zyA1259_IP


title: ESC_Zfp462-/- cl.2_Rep1


title: ESC_WT_2dayRA_Rep1

description: transcriptome profiling of control neural lineage cells with QuantSeq_Rep1


title: F2_CD.Fistule

description: Ileum biopsy fistule


title: ESC_Zfp462-/- cl.1_Rep3


title: THP-1 NFIC N3

description: Replicate 3 (NFIC shRNA)

data_processing:
Paired-end reads from Illumina sequencing were trimmed with Trim Galore and assessed for quality using FastQC
Reads were mapped to the human GRCh38 reference genome using STAR and counts were assigned to transcripts using featureCounts with the GRCh38.96 HEnsembl gene build GTF.  Both the reference genome and GTF were downloaded from the Ensembl FTP site
Differential gene expression analysis was performed using DESeq2 package
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including, ENSEMBLE Ids, Raw gene counts, FPKM values for each Sample; log2 Fold change values(Knockdown vs control), p- value and adjusted p value

source_name: AML cell line

growth_protocol: THP-1 cells were grown in IMDM supplemented with 10% FBS and penicillin and streptomycin solution. Cells were subcultred every two days at a density of 300K cells/ml

extract_protocol:
Total RNA was isolated from sorted cells using All Prep DNA/RNA kit (Qiagen) according to the protocol.
Library was generated using NEB Next® Ultra RNA Library Prep Kit (Illumina) according to manufacturer’s protocol. Libraries were analysed by pair-end sequencing using Novaseq 6000 S4

treatment_protocol: THP-1 cells were infected with either scrambled shRNA or shRNA against NFIC using retronectin. Four days post infection cells were sorted for GFP and processed for sequencing

value: Acute myleoid leukemia (AML)

value: NFIC shRNA


title: THP-1 NFIC N2

description: Replicate 2 (NFIC shRNA)


title: ESC_WT_4dayEB_Rep2

description: transcriptome profiling of control cells cultured in no LIF with QuantSeq_Rep2


title: ESC_Zfp462-/- cl.1_Rep2


title: ESC_WT_4dayEB_Rep1

description: transcriptome profiling of control cells cultured in no LIF with QuantSeq_Rep1


title: ESC_WT_Serum_LIF_Rep2

description: transcriptome profiling of control cells cultured in Serum/LIF with QuantSeq_Rep2


title: ESC_Zfp462-/- cl.1_Rep1


title: F8_CD.Fistule

description: Ileum biopsy fistule

value: Ileum biopsy


title: ESC_WT_Serum_LIF_Rep1

description: transcriptome profiling of control cells cultured in Serum/LIF with QuantSeq_Rep1


title: ESC_WT_Rep3

value: control cells


title: THP-1 Control C4

description: Replicate 3 (Control)

value: Scrambled shRNA


title: THP-1 Control C3

description: Replicate 2 (Control)


title: Bdnf_4Cseq_rep2

city: London

first: Emily

last: Brookes

state: London

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

data_processing:
trimming reads
4cseqpipe (perl, van de Werken, Nat Methods, 2012)
Genome_build: mm10
stat files (output of fastq2raw)
Supplementary_files_format_and_content: 4cseqpipe output

source_name: Cortical neurons (NPC, PMN, CN)

growth_protocol: For neuronal progenitor cultures, cortices were dissected from E12.5 C57BL/6J mouse embryos in dissection buffer (2.5 mM Hepes pH 7.4, 30 mM glucose, 1 mM CaCl2, 1 mM MgSO4, 4 mM NaHCO3, 1X HBSS) supplemented with 1 U/ml Dispase I (Sigma) and 0.6 mg/ml DNase I (Sigma). Dissected cortices were digested in dissociation media (1 mM Hepes pH 7.4, 20mM glucose, 98 mM Na2SO4, 30 mM K2SO4, 5.8 mM MgCl2, 0.25 mM CaCl2, 0.001% Phenol red) supplemented with 20 U/ml of papain (Worthington) for 25 min at 37°C. After digestion, cortices were washed, dissociated and plated on Nunc dishes (Thermo Fisher Scientific) coated with 40 μg/ml poly-D-lysine (Sigma) and 2 μg/ml Laminin (BD Bioscience) in DMEM/F12 medium supplemented with 1X B27, 1X N2, 1 mM glutamine, 1 mM NaHCO3 and 10 ng/ml of bFGF (Thermo Fisher Scientific). Cells were plated more densely for NPC cultures harvested after 2 days in vitro (DIV) than for PMN cultures harvested at 7 DIV (90 mm dish for 4C-seq: NPC 2.5 x 10^6 cells, PMN 1 x 10^6 cells). For PMN cultures, after 2 DIV half of the medium was replaced with Neurobasal medium supplemented with 1X B27, 1 mM glutamine and 200 ng/ml NT3 (Alomone labs). After 5 DIV, half of the medium was replaced with Neurobasal medium supplemented with 1X B27, 1 mM glutamine, 200 ng/ml NT3 (Alomone labs) and 20 μM 5-Fluoro-2ʹ-deoxyuridine (FdU; Merck). Cells were maintained in 37°C, 5% CO2 incubators. For cortical neuron cultures, cortices were dissected from E15.5 C57BL/6J mouse embryos and dissociated as above. Neurons were cultured on Nunc dishes (Thermo Fisher Scientific) coated as above and plated in MEM supplemented with 10% fetal bovine serum, 5% horse serum, 1 mM glutamine and 1X penicillin-streptomycin. After 2-6 hours, culture medium was replaced with Neurobasal medium supplemented with 1X B27, 1 mM glutamine, 1X penicillin-streptomycin and 10 μM fluorodeoxyuridine (Merck). Cells were cultured at 37°C, 5% CO2 for 6 days, and one day before the experiment, 2/3 of the plating medium was replaced with medium lacking B27.

extract_protocol:
4C-seq experiments were performed as described previously (Sofueva et al., 2013). To crosslink proteins with DNA, the medium was removed from neuronal cultures, and crosslinking buffer (0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 25 mM HEPES-KOH, pH 8.0) containing 1% formaldehyde was added for 10 min at room temperature. The cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM. Cells were rinsed three times with ice-cold PBS containing protease inhibitor cocktail and 1 mM PMSF, collected by scraping and centrifuged at 3000 rpm at 4°C for 10 minutes.  Cell pellets were lysed in 10 ml lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40 supplemented with protease inhibitor cocktail and 1 mM PMSF) on ice for 20 min. Nuclei were collected by centrifugation (1800 rpm, 5 min, 4oC), resuspended in 1.2X DpnII buffer and transferred to Protein LoBind tubes. SDS was added to 0.3% final concentration and nuclei were incubated 1h at 37oC in thermomixer shaking at 900 rpm (30s on, 30s off). Triton-20 was added to 2% final concentration and nuclei were incubated 1h 37oC in a thermomixer shaking at 900 rpm (30s on, 30s off). 750 Units of DpnII (NEB) was added and incubated overnight at 37oC in a thermomixer shaking at 900 rpm (30s on, 30s off). The next day, the DpnII buffer was replaced with fresh 1.2X DpnII buffer supplemented with 0.3% SDS and 2% Triton and another 750 Units of DpnII and incubated overnight at 37oC in thermomixer shaking at 900 rpm (30s on, 30s off). Samples of undigested and DpnII-digested DNA was reverse crosslinked and run on a gel to confirm that most DNA fragments were <3 kb after digestion.Nuclei were centrifuged (1800 rpm, 3 min) and washed twice with 1X T4 DNA ligase buffer before resuspending in 100 µl 1X T4 DNA ligase buffer with 1600 Units T4 DNA ligase (NEB). In nucleo ligation was carried out overnight at 16oC without shaking before confirming that high molecular weight products were obtained. Samples were then reverse crosslinked in the presence of proteinase K overnight at 65oC before phenol:chloroform extraction and ethanol precipitation. DNA was quantified using Qubit high sensitivity assays (Thermo Fisher Scientific)6-10 µg of DNA was digested with 120 Units Csp6I enzyme (Thermo Fisher Scientific) [3-5 Csp6I digests per sample] overnight at 37oC in thermomixer shaking at 900 rpm (30s on, 30s off). After confirmation that Csp6I-digested products are <3kb, Csp6I was heat inactivated at 65oC for 20 min before phenol:chloroform extraction and ethanol precipitation. DNA was resuspended in 6 ml total volume to allow proximity ligation by 1600 Units T4 DNA ligase overnight at 16oC. Samples were purified by phenol:chloroform extraction and ethanol precipitation, followed by PCR purification columns (Qiagen), before quantitation using with Qubit high sensitivity assays (Thermo Fisher Scientific).
4C-seq libraries were generated using Expand Long Template polymerase (Roche) and primers designed using the 4C-seq primer database (van de Werken et al., 2012). Forward primers were generated with the Illumina p1 sequence (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), a two-nucleotide barcode to allow multiplexing of samples, and then the primer sequence. Reverse primers were generated with the Illumina p2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT). 6-10 PCRs were set up per sample to generate library diversity. PCRs were run using the following program: 3 min 94oC; then 29 cycles of 10s 94oC, 1 min 55oC, 3 min 68oC; then 10 min 68oC. PCR products were purified using the High Pure PCR product purification kit (Roche). Libraries were quantified with Qubit high sensitivity assays, assessed using the Agilent Tapestation, and run on an Illumina MiSeq (MiSeq Reagent Kit v3, 150-cycle).
4C-seq

treatment_protocol: Cortical neurons were treated with 50mM KCl for 45 min before harvesting


title: ESC_WT_Serum_LIF_2i_Rep2

description: transcriptome profiling of control cells cultured in Serum/LIF/2i with QuantSeq_Rep2


title: nasopharyngeal carcinoma,zyA694_IP


title: ESC_WT_Rep2


title: Bdnf_4Cseq_rep1


title: ESC_WT_Serum_LIF_2i_Rep1

description: transcriptome profiling of control cells cultured in Serum/LIF/2i with QuantSeq_Rep1


title: THP-1 Control C1

description: Replicate 1 (Control)


title: ESC_WT_Rep1


title: DS6 Myc, liver

type: RNA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix 430_2 mouse expression arrays

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed with RMA using R/affy package and quantile normalized.

label: Biotin

source_name: 1867 (Rps6-deficient + Alb-c-Myc liver)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug of RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 week-old mice of the appropriate genotypes were humanely euthanized between 10am and noon.  Livers were isolated and prioritized for immediate RNA extraction.

extract_protocol: RNAStat extraction of total liver RNA was performed according to manufacturers instructions.  RNA quality/integrity was determined by standard agarose electrophoresis of 1-2 micrograms of each RNA to visualize intact 28S and 18S rRNAs (~2:1 ratio).

treatment_protocol: No special treatment. A small piece of freshly isolated liver (~ 50 milligrams) was immediately homogenized in 4 mls of RNAStat and processed according to manufacturers instructions.  Total liver RNA was isolated from 3 mice from each group (non-fasted 5 week-old males) and equal amounts of each of the 3 individual RNAs were combined to produce a single RNA sample/group for the array analysis.

value: liver

value: S6-deficient + Alb-c-Myc


title: DS6, liver

source_name: 1865 (Rps6-deficient liver)


title: Muscle, simulated reads, GTEX-ZYW4

status: Public on Jan 03 2023

city: Philadelphia

first: Yoseph

last: Barash

state: Pennsylvania

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

data_processing:
Publicly available gene- and transcript-level quantifications were downloaded from the GTEx v8 portal for each of the 300 samples
Simulated paired-end fastq files were generated by the BEERS simulator (Grant et al., 2011) using the reference hg38 genome sequence, transcript models from GENCODE v26, and the publicly available TPM values for the transcripts from each donor. Simulated read depth was determined by the gene-level quantification table to count the total number of gene mapping reads for each sample. To simulate strand-specific reads with uniform coverage with no errors, substitutions, or intron retention events, we ran the BEERS simulator using the following command-line options: -strandspecific -outputfq -error 0 -subfreq 0 -indelfreq 0 -intronfreq 0 -palt 0 -fraglength 100,250,500.
Simulated fastq files were aligned to the hg38 genome assembly using STAR (v2.5.3a) and transcript abundances were estimated using Salmon (v0.14.0)
Assembly: hg38
Supplementary files format and content: tab-deliminated text files including Salmon TPM quantifications for each sample

molecule: polyA RNA

source_name: Muscle (simulated)

extract_protocol: simulated RNA-seq

value: Muscle (simulated)

value: WT


title: Muscle, simulated reads, GTEX-ZYT6


title: WT, liver

source_name: 1864 (Wild type liver)

value: Wild-type


title: Muscle, simulated reads, GTEX-ZVZP


title: Muscle, simulated reads, GTEX-ZWKS


title: Muscle, simulated reads, GTEX-ZVTK


title: THP-1 NFIC N1

description: Replicate 1 (NFIC shRNA)


title: Muscle, simulated reads, GTEX-ZEX8


title: Muscle, simulated reads, GTEX-ZF2S


title: Muscle, simulated reads, GTEX-ZLV1


title: Myc, liver

source_name: 1866 (Alb-c-Myc liver)

value: Alb-c-Myc


title: Muscle, simulated reads, GTEX-ZE9C


title: Muscle, simulated reads, GTEX-ZTPG


title: Muscle, simulated reads, GTEX-XV7Q


title: Muscle, simulated reads, GTEX-ZDYS


title: Muscle, simulated reads, GTEX-Y5LM


title: Muscle, simulated reads, GTEX-XPT6


title: Muscle, simulated reads, GTEX-Y5V6


title: Muscle, simulated reads, GTEX-XBEW


title: Muscle, simulated reads, GTEX-XOT4


title: Muscle, simulated reads, GTEX-WYVS


title: Muscle, simulated reads, GTEX-WYJK


title: Muscle, simulated reads, GTEX-Y3I4


title: Muscle, simulated reads, GTEX-YEC4


title: Muscle, simulated reads, GTEX-WK11


title: Muscle, simulated reads, GTEX-WRHU


title: Muscle, simulated reads, GTEX-VJYA


title: Muscle, simulated reads, GTEX-ZV7C


title: Muscle, simulated reads, GTEX-V955


title: Muscle, simulated reads, GTEX-UJHI


title: Muscle, simulated reads, GTEX-VJWN


title: Muscle, simulated reads, GTEX-V1D1


title: Muscle, simulated reads, GTEX-U4B1


title: Muscle, simulated reads, GTEX-WEY5


title: Muscle, simulated reads, GTEX-SNOS


title: Muscle, simulated reads, GTEX-SJXC


title: Muscle, simulated reads, GTEX-QEG4


title: Muscle, simulated reads, GTEX-QEL4


title: Muscle, simulated reads, GTEX-QV31


title: Muscle, simulated reads, GTEX-POYW


title: Muscle, simulated reads, GTEX-OIZI


title: Muscle, simulated reads, GTEX-PLZ6


title: Muscle, simulated reads, GTEX-QDVJ


title: Muscle, simulated reads, GTEX-P4PQ


title: Muscle, simulated reads, GTEX-PX3G


title: Muscle, simulated reads, GTEX-PWN1


title: Muscle, simulated reads, GTEX-14753


title: Muscle, simulated reads, GTEX-12696


title: Muscle, simulated reads, GTEX-P4QS


title: Muscle, simulated reads, GTEX-1399R


title: Muscle, simulated reads, GTEX-1314G


title: Muscle, simulated reads, GTEX-1212Z


title: Muscle, simulated reads, GTEX-145MN


title: Muscle, simulated reads, GTEX-146FH


title: Muscle, simulated reads, GTEX-146FQ


title: Muscle, simulated reads, GTEX-TML8


title: Muscle, simulated reads, GTEX-145LT


title: Muscle, simulated reads, GTEX-145MI


title: Muscle, simulated reads, GTEX-139TU


title: Muscle, simulated reads, GTEX-139T4


title: Muscle, simulated reads, GTEX-132AR


title: Muscle, simulated reads, GTEX-PWCY


title: Muscle, simulated reads, GTEX-OIZG


title: Muscle, simulated reads, GTEX-18QFQ


title: Muscle, simulated reads, GTEX-111CU


title: Muscle, simulated reads, GTEX-18A6Q


title: Muscle, simulated reads, GTEX-1399U


title: Muscle, simulated reads, GTEX-18D9U


title: Muscle, simulated reads, GTEX-17F98


title: Muscle, simulated reads, GTEX-17EUY


title: Muscle, simulated reads, GTEX-14LLW


title: Muscle, simulated reads, GTEX-16MT8


title: Muscle, simulated reads, GTEX-15F5U


title: Muscle, simulated reads, GTEX-15DZA


title: Muscle, simulated reads, GTEX-15UF6


title: Muscle, simulated reads, GTEX-16NPX


title: Muscle, simulated reads, GTEX-16NPV


title: Muscle, simulated reads, GTEX-14JG6


title: Muscle, simulated reads, GTEX-14ICL


title: Muscle, simulated reads, GTEX-14E6E


title: Muscle, simulated reads, GTEX-14AS3


title: Muscle, simulated reads, GTEX-14A5H


title: Muscle, simulated reads, GTEX-14E1K


title: Muscle, simulated reads, GTEX-13QJ3


title: Muscle, simulated reads, GTEX-13PLJ


title: Muscle, simulated reads, GTEX-13SLW


title: Muscle, simulated reads, GTEX-13OVI


title: Muscle, simulated reads, GTEX-18A67


title: Muscle, simulated reads, GTEX-13NZA


title: Muscle, simulated reads, GTEX-13O3P


title: Muscle, simulated reads, GTEX-13NYS


title: Muscle, simulated reads, GTEX-14PII


title: Muscle, simulated reads, GTEX-12WSF


title: Muscle, simulated reads, GTEX-11WQC


title: Muscle, simulated reads, GTEX-11NSD


title: Muscle, simulated reads, GTEX-11UD1


title: Muscle, simulated reads, GTEX-15G1A


title: Muscle, simulated reads, GTEX-11H98


title: Muscle, simulated reads, GTEX-1RAZR


title: Muscle, simulated reads, GTEX-11DXX


title: Muscle, simulated reads, GTEX-11EQ8


title: Muscle, simulated reads, GTEX-1R9PM


title: Muscle, simulated reads, GTEX-1PIGE


title: Muscle, simulated reads, GTEX-1PIEJ


title: Muscle, simulated reads, GTEX-1N2EF


title: Muscle, simulated reads, GTEX-1O9I2


title: Muscle, simulated reads, GTEX-1N2DW


title: Muscle, simulated reads, GTEX-1M4P7


title: Muscle, simulated reads, GTEX-1LSNL


title: Muscle, simulated reads, GTEX-11UD2


title: Muscle, simulated reads, GTEX-1MUQO


title: Muscle, simulated reads, GTEX-1LVAM


title: Muscle, simulated reads, GTEX-1KD5A


title: Muscle, simulated reads, GTEX-1JN76


title: Muscle, simulated reads, GTEX-1JMQL


title: Muscle, simulated reads, GTEX-1K9T9


title: Muscle, simulated reads, GTEX-1KANC


title: Muscle, simulated reads, GTEX-1LB8K


title: Muscle, simulated reads, GTEX-1J8QM


title: Muscle, simulated reads, GTEX-1JMQI


title: Muscle, simulated reads, GTEX-11LCK


title: Muscle, simulated reads, GTEX-1QW4Y


title: Muscle, simulated reads, GTEX-1RAZA


title: Muscle, simulated reads, GTEX-1J8Q3


title: Muscle, simulated reads, GTEX-1IOXB


title: Muscle, simulated reads, GTEX-1J1R8


title: Muscle, simulated reads, GTEX-1IDJF


title: Muscle, simulated reads, GTEX-1L5NE


title: Muscle, simulated reads, GTEX-1I1GU


title: Muscle, simulated reads, GTEX-1IDJC


title: Muscle, simulated reads, GTEX-1LNCM


title: Muscle, simulated reads, GTEX-1HSMQ


title: Muscle, simulated reads, GTEX-1I1GS


title: Muscle, simulated reads, GTEX-1HSGN


title: Muscle, simulated reads, GTEX-1HC8U


title: Muscle, simulated reads, GTEX-1GZ4H


title: Muscle, simulated reads, GTEX-1GN1W


title: Muscle, simulated reads, GTEX-1HFI7


title: Muscle, simulated reads, GTEX-1H3VY


title: Muscle, simulated reads, GTEX-1LG7Z


title: Muscle, simulated reads, GTEX-1F7RK


title: Muscle, simulated reads, GTEX-1CAMS


title: Muscle, simulated reads, GTEX-1CB4J


title: Muscle, simulated reads, GTEX-1CB4F


title: Muscle, simulated reads, GTEX-1CAMQ


title: Muscle, simulated reads, GTEX-1B97I


title: Muscle, simulated reads, GTEX-1B932


title: Muscle, simulated reads, GTEX-1IGQW


title: Muscle, simulated reads, GTEX-1C6VQ


title: Muscle, simulated reads, GTEX-1AX8Z


title: Muscle, simulated reads, GTEX-1FIGZ


title: Cerebellum, simulated reads, GTEX-ZF28

source_name: Cerebellum (simulated)

value: Cerebellum (simulated)


title: Muscle, simulated reads, GTEX-1AX9J


title: Cerebellum, simulated reads, GTEX-ZZPT


title: Cerebellum, simulated reads, GTEX-ZAK1


title: Cerebellum, simulated reads, GTEX-XLM4


title: Cerebellum, simulated reads, GTEX-XMD1


title: Cerebellum, simulated reads, GTEX-ZAJG


title: Muscle, simulated reads, GTEX-1HSMP


title: Cerebellum, simulated reads, GTEX-Z93S


title: Cerebellum, simulated reads, GTEX-ZVT3


title: Cerebellum, simulated reads, GTEX-WWYW


title: Cerebellum, simulated reads, GTEX-WVLH


title: Cerebellum, simulated reads, GTEX-WL46


title: Cerebellum, simulated reads, GTEX-WHSE


title: Cerebellum, simulated reads, GTEX-UTHO


title: Cerebellum, simulated reads, GTEX-T6MN


title: Cerebellum, simulated reads, GTEX-T5JC


title: Cerebellum, simulated reads, GTEX-RU72


title: Cerebellum, simulated reads, GTEX-S7SE


title: Cerebellum, simulated reads, GTEX-QVJO


title: Cerebellum, simulated reads, GTEX-R55E


title: Cerebellum, simulated reads, GTEX-QMR6


title: Cerebellum, simulated reads, GTEX-RNOR


title: Cerebellum, simulated reads, GTEX-ZAB4


title: Cerebellum, simulated reads, GTEX-X4XX


title: Cerebellum, simulated reads, GTEX-QDT8


title: N_STR_WT_4609

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
The fastq files were generated after BCL conversion and demultiplexing using the bcl2fastq (v2.20.0.422) from Illumina
Fastq files were aligned to mus musculus reference genome (mm10 obtained from UCSC) using STAR_2.5.2b.
Reads in exons were counted using featureCounts v1.5.1 with mm10 entrez annotations obtained from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts

source_name: STR Nes-Cre WT

growth_protocol: Mice were maintained in a 129Ola/ICR/C57bl6 mixed genetic background. The mice were group-housed in a specific pathogen free stage with ad libitum access to food and water under a 12-h light-dark cycle (lights on at 6 a.m.) at relative humidity of 50-60 % and room temperature 21±1 °C. Bedding (aspen chips, Tapvei) and nest material (Tapvei) were changed weekly and wooden blocks (Tapvei) were provided for enrichment.

extract_protocol:
Adult male mice were deeply anesthetized with CO2, followed by cervical dislocation and decapitation. The brain was quickly dissected and immersed in ice-cold PBS. Brain regions of interest were isolated from 2-mm slices cut using a brain matrix. Samples were snap frozen and stored at -80 °C. Total RNA was isolated using Trizol Reagent (Thermo Fisher Scientific) according to manufacturer's recommendations. Total RNA was quality checked on an Agilent 2200 TapeStation system. RNA quantity was measured using a NanoDrop ND-1000 Spectrophotometer.Tissue collection and processing were performed by researchers blinded to the genotypes of the animals. In all experiments, wild-type littermates were used as controls.
200 ng RNA/sample was used for library preparation using TruSeq Stranded mRNA protocol (Illumina). The yield and quality of the amplified libraries was analysed using Qubit (Thermo Fisher) and the Agilent 2200 TapeStation system. The indexed cDNA libraries were normalised and combined, and the pools were sequenced on the Illumina Nextseq for a 75-cycle v2.5 sequencing run, generating 75 bp single-end reads.

tag: strain background

value: 129Ola/ICR/C57bl6 mixed

value: GDNF cKU x Nestin-Cre

value: 2 months

value: wt/wt

value: Brain

tag: tissue subtype

value: striatum


title: N_STR_WT_4545


title: Cerebellum, simulated reads, GTEX-PWO3


title: Cerebellum, simulated reads, GTEX-WZTO


title: Cerebellum, simulated reads, GTEX-OHPN


title: N_STR_WT_4529


title: Cerebellum, simulated reads, GTEX-Q2AG


title: Cerebellum, simulated reads, GTEX-12126


title: Cerebellum, simulated reads, GTEX-18465


title: Cerebellum, simulated reads, GTEX-NPJ7


title: Cerebellum, simulated reads, GTEX-1269C


title: Cerebellum, simulated reads, GTEX-P44H


title: N_STR_HOM_4575

source_name: STR Nes-Cre HOM

value: cKU/cKU


title: N_STR_HOM_4627


title: N_STR_HOM_4569


title: N_STR_WT_4394


title: Cerebellum, simulated reads, GTEX-147GR


title: N_STR_WT_4612


title: N_STR_HOM_4580


title: Cerebellum, simulated reads, GTEX-183WM


title: Cerebellum, simulated reads, GTEX-147F4


title: Cerebellum, simulated reads, GTEX-145MH


title: Cerebellum, simulated reads, GTEX-145MG


title: Cerebellum, simulated reads, GTEX-145LU


title: N_STR_HOM_4568


title: N_STR_WT_4326


title: N_STR_HET_4628

source_name: STR Nes-Cre HET

value: wt/cKU


title: Cerebellum, simulated reads, GTEX-145LS


title: N_STR_HOM_4393


title: N_STR_HET_4606


title: Cerebellum, simulated reads, GTEX-144GL


title: N_STR_HET_4579


title: Cerebellum, simulated reads, GTEX-139TT


title: Cerebellum, simulated reads, GTEX-139TS


title: Cerebellum, simulated reads, GTEX-132Q8


title: N_STR_HET_4577


title: N_STR_HET_4578


title: Cerebellum, simulated reads, GTEX-131YS


title: N_STR_HET_4566


title: Cerebellum, simulated reads, GTEX-131XH


title: N_SN_WT_4609

source_name: SN Nes-Cre WT

value: substantia nigra


title: Cerebellum, simulated reads, GTEX-111FC


title: N_SN_WT_4612


title: Cerebellum, simulated reads, GTEX-17JCI


title: N_SN_WT_4545


title: Cerebellum, simulated reads, GTEX-17HII


title: N_SN_WT_4394


title: N_SN_WT_4329


title: N_SN_WT_4529


title: N_SN_HOM_4627

source_name: SN Nes-Cre HOM


title: Cerebellum, simulated reads, GTEX-17HG3


title: Cerebellum, simulated reads, GTEX-16YQH


title: N_SN_HOM_4575


title: Cerebellum, simulated reads, GTEX-16Z82


title: Cerebellum, simulated reads, GTEX-17HHY


title: Cerebellum, simulated reads, GTEX-16XZZ


title: Cerebellum, simulated reads, GTEX-15SHU


title: N_STR_HET_4564


title: N_SN_HOM_4580


title: N_SN_HOM_4569


title: Cerebellum, simulated reads, GTEX-15EO6


title: N_SN_HOM_4393


title: Cerebellum, simulated reads, GTEX-15G19


title: N_SN_HET_4628

source_name: SN Nes-Cre HET


title: N_SN_HET_4606


title: N_SN_HOM_4568


title: Cerebellum, simulated reads, GTEX-15DYW


title: Cerebellum, simulated reads, GTEX-14PJM


title: Cerebellum, simulated reads, GTEX-14E7W


title: Cerebellum, simulated reads, GTEX-14DAQ


title: Cerebellum, simulated reads, GTEX-14E6D


title: N_SN_HET_4578


title: N_SN_HET_4566


title: N_SN_HET_4577


title: N_PFC_WT_4612

source_name: PFC Nes-Cre WT

value: prefrontal cortex


title: N_SN_HET_4564


title: Cerebellum, simulated reads, GTEX-14ABY


title: Cerebellum, simulated reads, GTEX-13X6K


title: Cerebellum, simulated reads, GTEX-14A5I


title: N_PFC_WT_4529


title: N_PFC_WT_4609


title: N_PFC_WT_4575


title: N_PFC_WT_4396


title: Cerebellum, simulated reads, GTEX-13VXU


title: Cerebellum, simulated reads, GTEX-13SLX


title: N_SN_HET_4579


title: Cerebellum, simulated reads, GTEX-14JFF


title: Cerebellum, simulated reads, GTEX-13S7M


title: N_PFC_WT_4329


title: N_PFC_WT_4394


title: N_PFC_WT_4326


title: Cerebellum, simulated reads, GTEX-13OVL


title: N_PFC_HOM_4569

source_name: PFC Nes-Cre HOM


title: N_PFC_HOM_4580


title: Cerebellum, simulated reads, GTEX-13QIC


title: Cerebellum, simulated reads, GTEX-13O3O


title: Cerebellum, simulated reads, GTEX-14BMV


title: N_PFC_HOM_4568


title: Cerebellum, simulated reads, GTEX-13NYB


title: Cerebellum, simulated reads, GTEX-13O3Q


title: N_PFC_HOM_4393


title: Cerebellum, simulated reads, GTEX-13X6J


title: Cerebellum, simulated reads, GTEX-13JVG


title: Cerebellum, simulated reads, GTEX-13X6I


title: N_PFC_HET_4606

source_name: PFC Nes-Cre HET


title: Cerebellum, simulated reads, GTEX-13JUV


title: N_PFC_HET_4579


title: N_PFC_HET_4578


title: Cerebellum, simulated reads, GTEX-13G51


title: Cerebellum, simulated reads, GTEX-13FHP


title: N_PFC_HET_4566


title: N_PFC_HET_4577


title: A_STR_WT_3677

source_name: STR AAV-Cre WT

value: GDNF cKU +AAV-Cre

value: 5-7 months

value: bilateral striatal AAV-Cre injection at 3-5 months


title: Cerebellum, simulated reads, GTEX-12WSE

value: WT


title: N_PFC_HET_4564


title: A_STR_WT_3588


title: Cerebellum, simulated reads, GTEX-13FHO


title: Cerebellum, simulated reads, GTEX-12ZZX


title: Cerebellum, simulated reads, GTEX-12WSM


title: A_STR_WT_3587


title: A_STR_WT_3649


title: Cerebellum, simulated reads, GTEX-12WSC


title: Cerebellum, simulated reads, GTEX-12WSD


title: A_STR_WT_3576


title: Cerebellum, simulated reads, GTEX-11ZUS


title: A_STR_HOM_3749

source_name: STR AAV-Cre HOM


title: Cerebellum, simulated reads, GTEX-12WSH


title: Cerebellum, simulated reads, GTEX-11ZTS


title: Cerebellum, simulated reads, GTEX-11ONC


title: A_STR_HOM_3690


title: A_STR_HOM_3687


title: Cerebellum, simulated reads, GTEX-11OC5


title: A_STR_HOM_3607


title: Cerebellum, simulated reads, GTEX-11O72


title: Cerebellum, simulated reads, GTEX-11NV4


title: A_STR_HOM_3570


title: A_STR_HOM_3606


title: A_STR_HOM_3567


title: Cerebellum, simulated reads, GTEX-11GSP


title: A_STR_HET_3750

source_name: STR AAV-Cre HET


title: A_STR_WT_3585


title: Cerebellum, simulated reads, GTEX-11GSO


title: Cerebellum, simulated reads, GTEX-11EI6


title: A_STR_HET_3676


title: A_STR_WT_3578


title: Cerebellum, simulated reads, GTEX-11DXY


title: Cerebellum, simulated reads, GTEX-1RDX4


title: Cerebellum, simulated reads, GTEX-1R46S


title: Cerebellum, simulated reads, GTEX-11DZ1


title: A_STR_HET_3586


title: A_STR_HET_3652


title: A_STR_HET_3610


title: Cerebellum, simulated reads, GTEX-1PWST


title: Cerebellum, simulated reads, GTEX-1R9PO


title: Cerebellum, simulated reads, GTEX-11NUK


title: A_STR_HET_3577


title: A_SN_WT_3677

source_name: SN AAV-Cre WT


title: A_SN_WT_3649


title: Cerebellum, simulated reads, GTEX-1MJK2


title: Cerebellum, simulated reads, GTEX-1P4AB


title: A_SN_WT_3588


title: A_SN_WT_3587


title: Cerebellum, simulated reads, GTEX-1KWVE


title: A_STR_HET_3688


title: Cerebellum, simulated reads, GTEX-1KD4Q


title: A_SN_WT_3585


title: A_SN_WT_3578


title: Cerebellum, simulated reads, GTEX-1KANB


title: Cerebellum, simulated reads, GTEX-1JN1M


title: A_SN_HOM_3749

source_name: SN AAV-Cre HOM


title: A_SN_HOM_3690


title: Cerebellum, simulated reads, GTEX-1JMLX


title: A_SN_HOM_3611


title: A_SN_WT_3576


title: Cerebellum, simulated reads, GTEX-1JJEA


title: Cerebellum, simulated reads, GTEX-1JJ6O


title: Cerebellum, simulated reads, GTEX-1PIIG


title: A_SN_HOM_3607


title: A_SN_HOM_3687


title: Cerebellum, simulated reads, GTEX-1IL2V


title: Cerebellum, simulated reads, GTEX-1IKOH


title: A_SN_HOM_3570


title: Cerebellum, simulated reads, GTEX-1I1HK


title: A_SN_HOM_3606


title: Cerebellum, simulated reads, GTEX-1HSKV


title: A_SN_HET_3676

source_name: SN AAV-Cre HET


title: Cerebellum, simulated reads, GTEX-1HSMO


title: A_SN_HET_3610


title: Cerebellum, simulated reads, GTEX-1I1CD


title: A_SN_HET_3688


title: Cerebellum, simulated reads, GTEX-1H3VE


title: A_SN_HET_3586


title: Cerebellum, simulated reads, GTEX-1H3O1


title: A_SN_HET_3577


title: Cerebellum, simulated reads, GTEX-1H3NZ


title: Cerebellum, simulated reads, GTEX-1H1CY


title: A_SN_HOM_3567


title: Cerebellum, simulated reads, GTEX-1GZ2Q


title: A_PFC_WT_3588

source_name: PFC AAV-Cre WT


title: A_PFC_WT_3649


title: A_PFC_WT_3587


title: Cerebellum, simulated reads, GTEX-1HCVE

source_name: Cerebellum (simulated)


title: Cerebellum, simulated reads, GTEX-1GZ4I


title: Cerebellum, simulated reads, GTEX-1IDJH


title: A_PFC_WT_3578


title: Cerebellum, simulated reads, GTEX-1GTWX


title: A_PFC_WT_3585


title: Cerebellum, simulated reads, GTEX-1F75W


title: A_PFC_HOM_3749

source_name: PFC AAV-Cre HOM


title: Cerebellum, simulated reads, GTEX-1GF9W


title: A_SN_HET_3652


title: A_SN_HET_3750


title: Cerebellum, simulated reads, GTEX-1F75A


title: A_PFC_HOM_3690


title: A_PFC_HOM_3687


title: Cerebellum, simulated reads, GTEX-1F48J


title: Cerebellum, simulated reads, GTEX-1F6I4


title: A_PFC_HOM_3606


title: A_PFC_HOM_3607


title: Cerebellum, simulated reads, GTEX-1EMGI


title: Cerebellum, simulated reads, GTEX-1EU9M


title: A_PFC_HOM_3570


title: Cerebellum, simulated reads, GTEX-1EKGG


title: Cerebellum, simulated reads, GTEX-1GN73


title: A_PFC_HOM_3567


title: A_PFC_WT_3576


title: A_PFC_HET_3750

source_name: PFC AAV-Cre HET


title: Cerebellum, simulated reads, GTEX-1GF9V


title: Cerebellum, simulated reads, GTEX-1CB4H


title: Cerebellum, simulated reads, GTEX-1CB4G


title: A_PFC_HET_3688


title: A_PFC_HET_3610


title: A_PFC_HET_3652


title: Cerebellum, simulated reads, GTEX-1C6VR


title: Cerebellum, simulated reads, GTEX-1C64N


title: A_PFC_HET_3586


title: A_PFC_HOM_3611


title: Cerebellum, simulated reads, GTEX-1B8L1


title: A_PFC_HET_3676


title: Cerebellum, simulated reads, GTEX-1A8G7


title: Cerebellum, simulated reads, GTEX-1C6WA


title: Cerebellum, simulated reads, GTEX-1B933


title: Cerebellum, simulated reads, GTEX-1A8G6


title: spt650-2alpha-input

city: Boston

first: Catherine

middle: LW

last: Miller

state: MA

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50

data_processing:
Briefly, data was aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2 (Langmead and Salzberg, 2012). Sequences were trimmed with cutadapt and processed using samtools (Li et al., 2009), bedtools, and deeptools (Ramírez et al., 2016) to generate genome coverage tracks. Samples are spike-in normalized.
Assembly: S. cerevisiae R64-2-1, S. pombe ASM294v2

organism: Saccharomyces cerevisiae

growth_protocol: All S. cerevisiae strains used in this study are in the S288C background. All S. cerevisiae liquid cultures were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30°C . For spike-in normalization, S. pombe liquid cultures were grown in YES (0.5% yeast extract, 3% glucose, 225 mg/l each of adenine, histidine, leucine, uracil, and lysine) at 32°C.

extract_protocol: Libraries were prepared with Qiagen GeneRead Kit according to manufacturers instructions.

treatment_protocol: Yeast strains were grown to an OD~0.2 and then synchronized by treatment with alpha factor for 2 hours. Visual inspection confirmed >90% of cells had shmoo-like morphology.

value: S. cerevisiae (S. pombe spike-in)

value: alpha arrested


title: spt6YW-3alpha-input

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-YW


title: spt6YW-1alpha-input

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-YW


title: spt6YW-4alpha-input


title: spt650-3alpha-input

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50


title: WT-4alpha-input

description: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3


title: spt650-4alpha-input


title: spt650-1alpha-input


title: iCLIP_SRSF6_Hyp4h_Rep3.fq.gz

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description: iCLIP

data_processing:
iCLIP data were processed according to: Busch et al. (2020): iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods PMID:31751605
Assembly: hg38
Supplementary files format and content: BW files containing the genomic coordinates and counts of uniquely mapped X-links for each replicate separated by strand. Bed files containing the genomic coordinates and counts of reproducible binding sites from merged replicates over all conditions.

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2 and 21% oxygen (Normoxia) or 0.2% oxygen (Hypoxia).

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was size selected by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonucleotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: Huppertz et al., (2014): iCLIP: protein-RNA interactions at nucleotide resolution. Methods. PMID:24184352

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

value: HeLa

tag: antibody

value: anti-EGFP

tag: protocol

value: SRSF6-GFP Hypoxia 4h

tag: barcode sequence


title: Cerebellum, simulated reads, GTEX-1B8SG

tag: tissue

value: Cerebellum (simulated)


title: iCLIP_SRSF6_Hyp4h_Rep2.fq.gz

description: iCLIP


title: A_PFC_HET_3577

value: 129Ola/ICR/C57bl6 mixed


title: WT-3alpha-input

source_name: his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3

tag: cell type


title: iCLIP_SRSF6_Norm_Rep3.fq.gz

description: iCLIP

value: SRSF6-GFP Normoxia


title: iCLIP_SRSF6_Norm_Rep2.fq.gz

description: iCLIP


title: WT-1alpha-input