title: SUDLH5_SENP6_OE_R3

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Genome_build: hg19

growth_protocol: cells were grown in RPMI + 10% FBS + P/S

extract_protocol:
Cells were lysed and RNA isolated with Qiagen RNeasy Isolation kit.
Libraries were prepared with NEBNext Ultra II Directional RNA Library (NEB, 188 #E7765L) and indexes were added by PCR with NEBNext Multiplex Oligos for Illumina (NEB, 189 #E7600) according to manufacturer’s protocols.

treatment_protocol: cells were seeded at equal densities and grown under standard conditions for 24h before harvest


title: MN_WT_ChIP_Ring1B

status: Public on Oct 11 2021

type: SRA

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

country: USA

institute: University of Miami Miller School of Medicine

description: ChIP DNA

library_source: genomic

data_processing:
For ChIP-Seq data processing, reads were aligned to the mouse reference genome mm10 and dm6 for spike-in samples, using Bowtie2 (v2.4.1) with default parameters. Reads of quality score less than 30 were removed using samtools (v1.9) and PCR duplicates were removed using picard (v2.18.11). Regions in mm10 genome blacklist was removed using bedtools (v2.27.1) and bigwig files were generated using deepTools (v3.2.1) and parameters: --binSize 50 --normalizeUsing RPKM --ignoreDuplicates  --ignoreForNormalization chrX --extendReads 250 for visualization in IGV. Peaks were called using MACS2 (v2.1.1) with parameters: -g mm --keep-dup 1 --nomodel --extsize 300. Motif discovery was performed using HOMER (v4.10) with default parameters. For visualization of ChIP-seq, uniquely aligned reads were normalized using dm6 spike-in. Heatmaps were performed using the functions computeMatrix followed by plotHeatmap and plotProfile from deepTools (v3.2.1).
For RNA-Seq data processing, reads were aligned to the mouse reference genome mm10 using STAR (v2.6.1d) with parameters: --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 1 --outSAMstrandField intronMotif  --outSAMmapqUnique 60 --twopassMode Basic --outSJfilterReads Unique --outFilterIntronMotifs RemoveNoncanonical. Gene counts were calculated using featureCounts (v1.6.3) with parameters: -p, -s 2, -t exon, and RefSeq mm10 annotation downloaded from GENCODE. The output gene count tables were used as input into DeSeq2 for normalization and differential expression analysis.
For scRNA-Seq data processing, raw non-demultiplexed fastq files were processed using zUMIs (v2.9.4) with STAR (v2.7.3a) to generate expression profiles for both the 5′ ends containing UMIs as well as combined full-length and UMI data. The parameters: find_pattern: ATTGCGCAATG, UMI (12-19), cDNA (23-50) was specified for Read 1. The UMI count table containing both intron and exon reads was used by Seurat for downstream analysis. Cells with more than 3000 genes detected and less than 5% of reads mapping to mitochondrial genome were retained. Data were normalized (scTransform) and used for principal component analysis dimensionality reduction, followed by louvain clustering and UMAP dimensionality reduction. Differential gene expression analysis between defined cell clusters was performed using R package presto.
Genome_build: mm10 and dm6
Supplementary_files_format_and_content: Bigwig files generated by deepTools (v3.2.1) are RPKM normalized track files; Narrowpeak files generated by MACS2 (v2.1.1) are peak files; featurecount.txt files generated by featureCounts (v1.6.3) are gene counts files. RDS files for scRNA-Seq are gene-cell matrix generated by zUMIs (v2.9.4) and Seurat object respectively.

molecule: genomic DNA

organism: Mus musculus

source_name: Differentiated motor neuron

growth_protocol: For motor neuron differentiation, mESCs were differentiated in AK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies. Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
Motor neurons differentiated for 6 days were dissociated with 0.05% trypsin, neutralized, fixed with 1% paraformaldehyde for 15 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina HiSeq 4000 platform.

tag: cell type

value: Differentiated motor neuron

tag: genotype

value: wild type

tag: antibody

value: Ring1B (Bethyl Laboratories, Cat# A302-869A)


title: SUDLH5_EV_R2

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: empty vector


title: PAAD_NX.40_P3

city: Tokyo

first: Kuniyo

last: Sueyoshi

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Preventive Medicine, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Illumina Genome Analyser IIx used for sequencing
Sequenced read were quantified by Salmon (version 0.8.1) software. Briefly, the human whole transcriptome (GENCODE, release 27, GRCh38.p10) and the mouse whole transcriptome (GENCODE, release M15, GRCm38.p5) of protein-coding genes were combined, and a quasi-mapping index of the dual-species was subsequently built with the --type quasi -k 31 preset. The estimation of the transcript abundance was executed by the Salmon quasi-mapping mode with the –l A preset.
The data of transcript-abundance was divided into human transcripts or mouse transcripts, representing cancer-reads or stroma-reads, respectively.
The transcripts of protein coding genes were extracted the whole transcripts. Subsequently the transcript-level read abundance was summarized to the gene-level abundance in Transcript per Million (TPM) value scaled by the library size and the transcript length with the tximport package (version 1.16.1) in R by using summarizeToGene function with the countsFromAbundance = "lengthScaledTPM" preset on the reference to the GRCh38.p10 (GENCODE, release 27) for cancer-reads or the GRCm38.p5 (GENCODE, release M15) for stromal-reads.
Genome_build: GRCh38.p10 for human, GRCm38.p5 for mouse
Supplementary_files_format_and_content: tab-delimited text files include raw transcript-abundance measurements computed by Salmon software for each Sample
Supplementary_files_format_and_content: Matrix table with scaled TPM values for every gene and every sample

organism:
Homo sapiens
Mus musculus

source_name: Patinent derived xenograft

growth_protocol: A total of 43 fresh tumor specimens of 9 distinctive tumor types were surgically resected, sectioned and frozen at −80°C. PDXs were established by the subcutaneous transplantation of the dissolved tissue fragments of 5 mm3 in size into the flank of five- to six-week-old NOD/SCID/γcnull mice (CLEA Japan, Tokyo, Japan). PDX samples were re-transplanted to reproduce the Nth passages (N: 2, 3, ...) of the corresponding PDX.

extract_protocol:
Tumors resected from the mice were frozen and the suspended in trizol reagent (Thermo Fisher Scientific Inc, Waltham, USA), and total RNA was extracted according to the manufacturer’s instruction.
One microgram of total RNA was used as the starting material for a 100-bp paired-end transcriptome-sequencing protocol using an Illumina GAIIx sequencer (Illumina, San Diego, CA, USA). Briefly, PolyA+ RNA was purified from total RNA and fragmented using divalent cations. RNA quality as assessed by RNA integrity number (RIN) using a bioanalyzer (Agilent). Double stranded cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen), and its overhang was converted into blunt end using T4 DNA polymerase. 3’ end of the blunt end was adenylated by Klenow fragment, and PE adapter was ligated. Without size selection, the cDNA library was amplified using PCR. For PCR amplification, 1ul of PCR primer PE 1.0 and 2.0, and 0.5 μL of Phusion DNA polymerase (Finnzymes Oy) were used in a final volume of 50 μL. The PCR condition was as follows: 98 °C for 5 min, then 15 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s, followed by 72 °C for 5 min before cooling to 4 °C. PCR primers were removed by QIA quick PCR Purification Kit. Each library was loaded into its own single Illumina flow cell lane, producing 100-mer paired-end reads for each sample.

treatment_protocol: No treatment procedure

tag: primary tumor type (human)

value: pancreatic ductal adenocarcinoma (PAAD)

tag: metastasis site

value: Lymph node

tag: originial tumor id

tag: passage of pdx

tag: host mice strain

value: NOD/SCID/γcnull mice


title: PAAD_NX.36_P3

value: Primary


title: ribo_pub1_3_b3_s2

city: Moscow

first: Sergey

middle: E.

last: Dmitriev

address: Leninskie Gory, 1

country: Russia

institute: Lomonosov Moscow State University

description: Ribosome-bound RNA

data_processing:
Reads were trimmed using cutadapt v. 2.10 with the following parameters for RNA-Seq (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length 20 -q 20) and Ribo-Seq samples (-a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --trimmed-only -q 20).
Additionally for Ribo-Seq, the reads were deduplicated with seqkit rmdup v. 0.10.1, and unique barcodes were then removed with cutadapt v. 2.10 (-q 20 --minimum-length 20 -u -4).
Afterwards, reads were aligned against eukaryotic rRNA sequence set obtained from silva-euk and rfam databases using bowtie2 v. 1.2.3. Only unmapped non-rRNA reads were saved for the further analysis.
Read mapping and counting against the Saccharomyces_cerevisiae.R64-1-1.95 (Ensembl) genome assembly was performed with STAR v. 2.7.9a.
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.95 (genome-build-accession GCA_000146045.2)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The cells were grown in YPD (2% glucose, 2% peptone, 1% yeast extract) at 30℃ and 220 rpm to exponential growth stage (OD=0.5-0.6).

extract_protocol:
Cell lysates were clarified by two sequential centrifugation steps - 3000g, 5 minutes, 4℃, and 20000g, 10 minutes, 4℃. Part of the cell lysate was used for mRNA isolation using Oligo(dT) beads.  Another part was treated with ribonuclease I for polysome disassembly and applied to a linear 10-50% sucrose gradient in fractionation buffer (20 mM Tris pH 8.0, 140 mM KCl, 15 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide, 1% Triton) and separated on a SW-41 rotor (Beckman) at 35000 rpm, 3 hours, 4℃. Subsequently, ribosome-bound RNA fragments were collected from the monosome fraction. Ribosome-bound RNA was isolated using acidic-phenol extraction.
cDNA libraries for Ribo-Seq and RNA-Seq were constructed in parallel using standard ribosomal profiling library construction protocol (described in Kasari et al., 2019 DOI: 10.1093/nar/gkz600). Importantly, cycloheximide was added to the lysis buffer but not to the growth media.

treatment_protocol: Cells were collected by vacuum filtration, separated from the filter with a plastic scraper and flash frozen in liquid nitrogen in a mortar and ground with a pestle with addition of polysome lysis buffer (20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide, 1% Triton) with constant addition of liquid nitrogen.

tag: strain

tag: batch

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 pub1::KanMX


title: MN_Nrf1KO_clone2_ChIP_NRF1

description: ChIP DNA

value: NRF1 (Abcam, Cat# ab34682)


title: ribo_pub1_1_b3_s2

description: Ribosome-bound RNA


title: PAAD_NX.35_P3


title: ribo_pub1_2_b3_s2

description: Ribosome-bound RNA


title: SUDLH5_SENP6_OE_R2

value: reconstituted for SENP6


title: MN_Auts2KO_ChIP_NRF1

description: ChIP DNA


title: MN_WT_ChIP_H3K27ac

description: ChIP DNA

value: H3K27ac (Abcam, Cat# ab4729)


title: SUDLH5_EV_R3


title: SUDLH5_SENP6_OE_R1


title: SENP6_Input

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control.
Genome_build: hg19
Supplementary_files_format_and_content: bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 16 and 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

tag: cell line

tag: shRNA


title: PAAD_NX.38_P3


title: ribo_gir2_3_b2_s2

description: Ribosome-bound RNA

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 gir2::KanMX


title: ribo_pub1_4_b1_s2

description: Ribosome-bound RNA


title: ribo_gir2_1_b2_s2

description: Ribosome-bound RNA


title: EV_Input

value: EV


title: ribo_gir2_2_b2_s2

description: Ribosome-bound RNA


title: PAAD_NX.34_P3


title: NSCLC_NX.33_P3

value: non-small cell Lung cancer (NSCLC)

value: Brain


title: MN_WT_ChIP_NRF1

description: ChIP DNA


title: ribo_wt_4_b1_s2

description: Ribosome-bound RNA

value: wt

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: NSCLC_NX.32_P3


title: ribo_wt_3_b4_s2

description: Ribosome-bound RNA


title: SENP6_SUMO2_ChIPSeq


title: MN_Nrf1KO_clone1_ChIP_NRF1

description: ChIP DNA

value: Differentiated motor neuron


title: MN_Nrf1KO_ChIP_AUTS2

description: ChIP DNA

value: AUTS2 (Reinberg lab)


title: MN_Auts2KO_clone2_ChIP_AUTS2

description: ChIP DNA


title: ribo_wt_1_b1_s2

description: Ribosome-bound RNA


title: SUDLH5_EV_R1

value: empty vector


title: rna_pub1_5_b1_s2

description: Total RNA


title: NSCLC_NX.29_P5


title: MN_Auts2KO_clone1_ChIP_AUTS2

description: ChIP DNA


title: ribo_wt_2_b4_s2

description: Ribosome-bound RNA


title: NSCLC_NX.31_P3


title: SENP6_SUMO1_ChIPSeq


title: rna_pub1_4_b4_s2

description: Total RNA


title: NSCLC_NX.30_P3


title: MN_WT_ChIP_input

description: ChIP input DNA

extract_protocol:
Motor neurons differentiated for 6 days were dissociated with 0.05% trypsin, neutralized, fixed with 1% paraformaldehyde for 15 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
ChIP input DNA (∼10 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina HiSeq 4000 platform.

value: wild type


title: Seedlings, JKZ218_3818_YZ19_cdk8_ABA

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
Quality control was checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). RNA-Seq reads were trimmed using the fastx_trimmer command FASTX-Toolkit (hannonlab.cshl.edu/fastx_toolkit/index.html) with parameter “-f 11 -l 90” before alignment. The trimmed reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed file was generated using featureCounts with parameter "-p -t exon -g gene_id -a tair10_ensembl.gtf".

organism: Arabidopsis thaliana

extract_protocol: The total RNA was isolated with Trizol reagent (Invitrogen) according to the manufacturer’s instruction and RNA-sequencing were carried out by Shanghai stress center

value: treat with 50 μM ABA for 3 hours

tag: tissue

value: whole seedling

tag: age

value: 1 week


title: MN_WT_ChIP_AUTS2

description: ChIP DNA


title: EV_SUMO1_ChipSeq


title: KIRC_NX.28_P3

value: kidney renal clear cell carcinoma (KIRC)

value: Peritoneal dissemination

value: NOD/SCID/γcnull mice


title: Seedlings, JKZ218_3674_YZ11_cdk8_ABA


title: KIRC_NX.28_P2


title: Seedlings, JKZ218_3673_YZ10_cdk8_ABA


title: EV_SUMO2_ChipSeq


title: rna_pub1_2_b3_s2

description: Total RNA

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 pub1::KanMX


title: KIRC_NX.27_P3

value: Skin


title: E14_ESC_ChIP_NRF1

description: ChIP DNA

source_name: E14 mESC

growth_protocol: E14 mESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021).

extract_protocol:
E14 mESCs were fixed with 1% paraformaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS on the plates. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina HiSeq 4000 platform.

value: mESCs

value: NRF1 (Abcam, Cat# ab34682)


title: rna_pub1_3_b3_s2

description: Total RNA


title: rna_pub1_1_b3_s2

description: Total RNA

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 gir2::KanMX


title: Seedlings, JKZ218_3672_YZ09_WT_ABA

value: wild type (WT)


title: MN_WT_ChIP_H2AK119ub

description: ChIP DNA

value: H2AK119ub1 (Cell Signaling Technology, Cat# 8240)


title: KIRC_NX.27_P2


title: mBrain_ChIP_ NRF1_Mus

description: ChIP DNA

source_name: brain

growth_protocol: All mice were housed with a 12 hour light-dark cycle. Mixed cohorts of female and male mice were used for all experiments to minimize gender effects. Brain tissue was collected at postnatal Day 1.

extract_protocol:
The whole brains were homogenized with a glass douncing homogenizer. The cell homogenate was fixed with 1% paraformaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina HiSeq 4000 platform.

tag: developmental stage

value: Postnatal Day 1

value: NRF1 (Abcam, Cat# ab55744)


title: Seedlings, JKZ218_3671_YZ08_WT_ABA


title: E14_ESC_ChIP_AUTS2

description: ChIP DNA

value: AUTS2 (Reinberg lab)


title: GIST_NX.26_P3

value: gastrointestinal stromal tumor (GIST)

value: Primary


title: mBrain_ChIP_NRF1_Rb

description: ChIP DNA

value: wild type


title: Seedlings, JKZ218_3670_YZ07_WT_ABA

value: treat with 50 μM ABA for 3 hours

value: whole seedling

value: 1 week


title: rna_gir2_4_b1_s2

description: Total RNA


title: rna_gir2_3_b2_s2

description: Total RNA


title: mBrain_ChIP_PCGF3

description: ChIP DNA

value: PCGF3 (Reinberg lab)


title: GIST_NX.25_P4

value: NOD/SCID/γcnull mice


title: GIST_NX.25_P5


title: rna_gir2_2_b2_s2

description: Total RNA


title: Seedlings, JKZ218_3669_YZ06_cdk8

value: mock


title: rna_gir2_1_b2_s2

description: Total RNA


title: mBrain_ChIP_AUTS2_Rep2

description: ChIP DNA


title: GIST_NX.25_P3


title: rna_wt_5_b1_s2

description: Total RNA

value: wt

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: GBM_NX.24_P6

value: glioblastoma multiforme (GBM)


title: Seedlings, JKZ218_3667_YZ04_cdk8


title: rna_wt_4_b1_s2

description: Total RNA


title: ATAC-seq_NLS7_plus_DOX

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
complete processing pipeline avaialble at https://github.com/DoaneAS/atacflow
Read adapter trimming using ngtrim
Alignment to mm10 using bowtie2
PCR duplicate removeal by piccard tools
Peak calling using genrich
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: in vitro culture

extract_protocol:
Omni-ATAC-seq https://www.nature.com/articles/nmeth.4396
illumina nextera; paired-end 50bp reads

treatment_protocol: doxycycline added to growth medium

value: melanoma cell line

tag: sac microdomain

value: nuclear


title: rna_wt_3_b4_s2

description: Total RNA


title: GBM_NX.24_P5


title: Seedlings, JKZ218_3664_YZ01_WT

value: wild type (WT)


title: ATAC-seq_NLS6_plus_DOX


title: ATAC-seq_NLS6_no_DOX


title: mBrain_ChIP_RYBP

description: ChIP DNA

value: Postnatal Day 1

value: RYBP (Sigma, Cat# PRS2227)


title: GBM_NX.24_P4


title: Seedlings, JKZ218_3668_YZ05_cdk8


title: B6_H3K36me3_ChIPSeq (re-analysis)

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
H3K36me3 ChIP-seq, wild-type B6 mice
B6_H3K36me3_ChIP_Merge_RPM.bedgraph
H3K4me3_H3K36me3Peaks_B6.bed

data_processing:
Single-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.7.9a
ChIP-Seq reads were filtered to remove duplicates and to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bed

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. Cross-links were reversed and chromatin eluted by incubation at 68 degrees Celsius. After high-speed spin soluble chromatin was removed and used for ChIP with anti-H3K4me3.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: spermatocytes

value: 14 days post-partum

tag: chip antibody


title: EWS_NX.23_P9

value: Ewing’s sarcoma (EWS)

value: Brain


title: Seedlings, JKZ218_3665_YZ02_WT

tag: genotype

value: whole seedling


title: EWS_NX.23_P8


title: ATAC-seq_NLS16_no_DOX

tag: treatment


title: KO-mg-ATAC-2_KO ATAC REP2

first: Sandhya

last: Chandrasekaran

address: 1470 Madison Avenue, 9-202, Hess Building

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Hi-C (.hic files):
Quality control was performed using the ‘pre-truncation method’ with HiC-Pro(v2.9).
Libraries were mapped to the Mus musculus reference genome (GRCm38.p5_M13) using bowtie2.2, and combined by matching sex and genotype.
HiC-Pro results were piped to Juicer(v1.14.8) to produce .hic format files using the parser tool ‘hicpro2juicebox’.
Resulting files were then processed into final KR matrix-balanced normalized contact maps with Juicebox.
Genome_build: GRCm38.p5_M13 or mm10
Supplementary_files_format_and_content: .hic files for Juicebox visualization and subcompartment calling
Hi-C (HOMER interactions):
Each read of the paired-end libraries was aligned independently using bwa-mem(v0.7.15), permitting split mapping to the GRCm38.p5_M13 reference annotation.
After mapping, forward and reverse reads were directly supplied to Homer(v4.8) for processing by first, merging the paired-end reads and later, filtering out self-ligation (spikes and continuous) artifacts.
Files were normalized based on sequencing depth and distance between loci, creating a background model necessary for calculating significant pairwise interactions.
Trans- interactions (1Mb resolution) were similarly calculated, but for significant interactions for loci >200Mbp apart (-minDist 200000000) to disregard intra-chromosomal interactions.
Supplementary_files_format_and_content: HOMER interactions (1Mb resolution, p<1e-50)
differential bins file (NeuN+ vs. NeuN-):
Raw .fastq reads were aligned to the Mus musculus reference genome (mm10) using bowtie2.
Only concordant reads were compressed into aligned .bam files, then sorted and indexed using the samtools/0.1.19 suite.
Following PCR duplicate removal, files were converted into .bed files using bedtools(v2.29.2)for further processing.
Differential analysis using diffReps was performed (1kb resolution) at a statistical significance threshold of p<0.001, for NeuN+ (tx) vs. NeuN- (ctrl).
Significantly called regions (spanning a length of 1kb or more) were labeled as NeuN+ enriched or NeuN- enriched according to their log2FoldChange values.
Supplementary_files_format_and_content: differential bins file (NeuN+ vs. NeuN-)
.txt files with BLAST scores for de novo alignments to the IAP-masked genome or IAPEzi:
Bioinformatics processing was performed with SMRT Link v5.1.0, run with default parameters, unless otherwise indicated.
Files were first demultiplexed with lima and circular consensus sequences (CCS) were generated with ccs for filtered sequences with matching paired-end adapters.
CCS reads were then mapped to an IAPEzi consensus sequence (dfam.org) using pbalign.
Passing reads were subsequently mapped to the mouse reference genes using bwa split mapping and filtered based on mapping score (=60).
Reads were then assigned as autosomal IAPEzi or autosomal non-IAPEzi IAP using the GenomicRanges subsetByOverlaps() function (R(v3.6.0)).
The other reads, those not mapping to IAPs denoted in the reference genome, were then blasted against the IAPEzi consensus sequence and IAP masked reference genome in parallel; reads with higher bit scores for the IAPEzi blast than the reference genome were defined as de novo. Full-length de novo insertions were defined as fragments representing >5833bp (0.9*6481).
Supplementary_files_format_and_content: .txt files with BLAST scores for de novo alignments to the IAP-masked genome or IAPEzi
.txt files with transcript alignments to genes and repeats:
Read pairs were aligned to the Mus musculus mouse reference genome (mm10) with Tophat2 short-read aligner.
Reads were counted using HTSeq against the Gencode vM4 Mouse annotation.
Genes were filtered based on the criteria that all replicates in either condition must have at least 5 reads per gene.
On the resulting filtered transcripts, a pairwise differential analysis between Setdb1 conditional mutant vs. control cortex was performed using the voomlimma R package, which converts counts into precision weighted log2 counts per million and determines differentially expressed genes using a linear model.
Significantly differentially expressed genes were identified using a cutoff of Benjamini-Hochberg adjusted p-value less than 0.05.
Discordant pairs were extracted from aligned .bam files using samtools with the following command: samtools view –b –F 2 and reads identifiable with specific flags were quantified and categorized.
Supplementary_files_format_and_content: .txt files with transcript alignments to genes and repeats
RNA-seq:
FastQC was first used for quality control analysis, and trim-galore was used to remove low-quality reads.
Paired-end cleaned data was aligned to reference genome (M. musculus, UCSC mm10) using Tophat2 v2.1.1.
Samtools v1.9 was used to sort and build the alignment files index.
FeatureCounts v1.6.3 from subread package was used to get gene expression level counts by determining the number of reads mapped to gene exons.
Differential analysis was generated by DESeq2.
Significant genes (log2FoldChange > 0.5, Padj < 0.05) were extracted for Gene Ontology Enrichment Analysis by using ShinyGO v0.61 (http://bioinformatics.sdstate.edu/go/).
Deeptools was used to generate normalized bigwig and visualized on IGV.
Supplementary_files_format_and_content: .txt and .xls counts files
peaks files:
FastQC was first used for quality control analysis, and trim-galore was used to remove low-quality reads.
Paired-end cleaned data was then aligned to reference genome (M. musculus, UCSC mm10) using Bowtie2 v2.3.4.3.
Samtools v1.9 was used to sort and build the alignment files index after removing duplications.
MACS2 was used for peak calling (--shift -100 --extsize 200 --nomodel).
Diffbind was used to generated differential change peaks. R packages “ChIPseeker”, “clusterProfiler” “org.Mm.eg.db” and “TxDb.Mmusculus.UCSC.mm10.knownGene” were used for peak annotation.
Significant differential peaks that are located on gene promoters were extracted to generate Gene Ontology Enrichment Analysis by ShinyGO v0.61 (http://bioinformatics.sdstate.edu/go/).
Deeptools was used to generate normalized bigwig and visualized on IGV.
Supplementary_files_format_and_content: .xls peaks files

source_name: KO ATAC

extract_protocol:
Hi-C (Jiang, et. al.): Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
ChIP-seq: Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
Hi-C (Arima): Cortical tissue was prepped for fluorescence activated nuclear sorting (FANS) as follows. Briefly, the dissected tissue was homogenized in a hypotonic lysis solution and fixed in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with 125 mM glycine. The nuclei were then purified by centrifugation at 4000xg and resuspended in a 1:1 solution of the hypotonic lysis solution and a 1.8M sucrose solution prior to re-centrifugation at 4000xg to isolate out cortical nuclei. The pellet was then resuspended in Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% BSA and 1:1000 anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Samples were incubated for 45 minutes while rotation and protected from light at 4C. DAPI (Invitrogen) was added immediately before sorting to label all nuclei.
PacBio: Genomic DNA was isolated from FACS-sorted NeuN+ or NeuN- nuclei of adult mouse cerebral cortex using phenol chloroform extraction and was subsequently sheared to ~10kb using g-Tube microcentrifuge tubes (Covaris, 010145).
RNA-Seq (RiboZero): Total RNA was first extracted from the prefrontal mouse cortices (n=12, 6WT/6KO), and prepared with RNeasy Lipid Tissue Mini kit (with on-column DNase1 treatment). The quantity and quality of RNA was checked using a bioanalyzer (Agilent RNA 6000 Nano Kit).
RNA-Seq (QIAseq): Single-cell suspension from adult brain tissues was prepared using Miltenyi’s Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677) and Debris Removal Solution Kit (Miltenyi Biotec, 130-109-398) according to manufacturer instruction with minor modifications. In brief, total brain tissues, except olfactory bulb and cerebellum, were collected quickly and washed with ice cold 1x HBSS. After chopped into small pieces using sharp blade, the brain tissues were transferred into the C-tube containing 1950ul of Enzyme mix 1 and 30ul of Enzyme mix 2 from the kit and incubated on Miltenyi’s gentle MACS Octo Dissociator with Heaters using program 37°C _ABDK_1 for 30 minutes. Afterwards, the digested tissue homogenate gently went through fire polished glass pippette 10 times, and then passed through a 70um cell strainer. Cells were collected via centrifuged at 300g for 10 minutes at 4 °C and resuspended in ice cold 1x HBSS. Debris Removal Solution was then added and overlayed with ice cold 1x HBSS. After centrifugation, three phases in the tube were clearly visualized, from top to bottom: 1x HBSS solution, debris and myelin layer, and single-cell suspension. Discard the top two phases completely, wash the cells in 1x HBSS, centrifuge to collect the cells, and then resuspended the cell pellet in 1 ml of 1x HBSS containing 1% fetal bovine serum. In order to minimize the unwanted microglia activation, single cell suspension was incubated in Fc receptor blocking Reagent (Miltenyi Biotec, 130-092- 575) for 10 min, and then the cell suspension was incubated with CD11b-microbeads (Miltenyi Biotec, 130-093-634) for 10 min at 4 °C in the dark, followed by positive selection with LS separation column (Miltenyi Biotec, 130-042-401). Flow cytometry analysis was performed to check the cell purity. The three different groups of cells (no enrichment, target and non-target cell population) were incubated in CD11b-FITC Monoclonal Antibody (M1/70) (eBioscience, 11-0112-81) at 1:2000 dilution for 30 min at 4 °C in the dark. Stained cells were examined using the Beckman flow cytometer.
ATAC-seq: Single-cell suspension from adult brain tissues was prepared using Miltenyi’s Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677) and Debris Removal Solution Kit (Miltenyi Biotec, 130-109-398) according to manufacturer instruction with minor modifications. In brief, total brain tissues, except olfactory bulb and cerebellum, were collected quickly and washed with ice cold 1x HBSS. After chopped into small pieces using sharp blade, the brain tissues were transferred into the C-tube containing 1950ul of Enzyme mix 1 and 30ul of Enzyme mix 2 from the kit and incubated on Miltenyi’s gentle MACS Octo Dissociator with Heaters using program 37°C _ABDK_1 for 30 minutes. Afterwards, the digested tissue homogenate gently went through fire polished glass pippette 10 times, and then passed through a 70um cell strainer. Cells were collected via centrifuged at 300g for 10 minutes at 4 °C and resuspended in ice cold 1x HBSS. Debris Removal Solution was then added and overlayed with ice cold 1x HBSS. After centrifugation, three phases in the tube were clearly visualized, from top to bottom: 1x HBSS solution, debris and myelin layer, and single-cell suspension. Discard the top two phases completely, wash the cells in 1x HBSS, centrifuge to collect the cells, and then resuspended the cell pellet in 1 ml of 1x HBSS containing 1% fetal bovine serum. In order to minimize the unwanted microglia activation, single cell suspension was incubated in Fc receptor blocking Reagent (Miltenyi Biotec, 130-092- 575) for 10 min, and then the cell suspension was incubated with CD11b-microbeads (Miltenyi Biotec, 130-093-634) for 10 min at 4 °C in the dark, followed by positive selection with LS separation column (Miltenyi Biotec, 130-042-401). Flow cytometry analysis was performed to check the cell purity. The three different groups of cells (no enrichment, target and non-target cell population) were incubated in CD11b-FITC Monoclonal Antibody (M1/70) (eBioscience, 11-0112-81) at 1:2000 dilution for 30 min at 4 °C in the dark. Stained cells were examined using the Beckman flow cytometer.
Hi-C (Jiang, et. al.): Nuclei were digested with 100U MboI, and the restriction fragment ends were labeled using biotinylated nucleotides and re-ligated. After reversal of the cross-linking, ligated DNA was purified and sheared to a length of ~400bp by sonication, and the biotin-tagged ligation junctions were subsequently pulled down with streptavidin beads (Invitrogen, Dynabeads MyOne Streptavidin T1, Catalog No. 65602) and prepared into libraries.
ChIP-seq: Nuclei were pelleted after FANS, resuspended in 300μl of micrococcal nuclease digestion buffer (10mM Tris pH 7.5, 4mM

tag: strain background

value: microglia

value: KO


title: KO-mg-ATAC-1_KO ATAC REP1


title: EWS_NX.23_P4

tag: primary tumor type (human)

tag: metastasis site

value: NOD/SCID/γcnull mice


title: ATAC-seq_NLS7_no_DOX


title: WT-mg-ATAC-3_WT ATAC REP3

source_name: WT ATAC

value: WT


title: rna_wt_1_b1_s2

description: Total RNA

value: wt


title: M2-WT-RNA_WT RNA REP5

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M2-WT-RNA

source_name: WT RNA

value: cortex


title: GBM_NX.24_P3

value: glioblastoma multiforme (GBM)

value: Primary

tag: originial tumor id

tag: passage of pdx


title: ATAC-seq_LacZ12_plus_DOX

value: melanoma cell line


title: F2-WT-RNA_WT RNA REP2

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F2-WT-RNA


title: M1-WT-RNA_WT RNA REP4

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M1-WT-RNA


title: ATAC-seq_NLS16_plus_DOX

value: nuclear


title: ATAC-seq_LacZ6_no_DOX


title: Seedlings, JKZ218_3666_YZ03_WT

value: wild type (WT)

value: mock

value: 1 week


title: EWS_NX.23_P6

tag: host mice strain


title: M3-WT-RNA_WT RNA REP6

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M3-WT-RNA


title: EWS_NX.23_P7


title: KO-mg-RNA-3_KO RNA REP3

description:
QIAseq
KO-mg-RNA-3

source_name: KO RNA


title: WT-mg-ATAC-1_WT ATAC REP1


title: M3-KO-RNA_KO RNA REP6

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M3-KO-RNA


title: ATAC-seq_LacZ6_plus_DOX


title: EWS_NX.23_P10


title: F3-WT-RNA_WT RNA REP3

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F3-WT-RNA


title: WT-mg-ATAC-2_WT ATAC REP2


title: ATAC-seq_LacZ12_no_DOX


title: EWS_NX.23_P5


title: KO-mg-ATAC-3_KO ATAC REP3


title: ATAC-seq_LacZ10_plus_DOX


title: COAD_NX.21_P5

value: colorectal carcinoma (COAD)

value: Liver


title: M2-KO-RNA_KO RNA REP5

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M2-KO-RNA


title: F1-WT-RNA_WT RNA REP1

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F1-WT-RNA


title: KO-mg-RNA-2_KO RNA REP2

description:
QIAseq
KO-mg-RNA-2


title: COAD_NX.22_P3


title: ATAC-seq_LacZ10_no_DOX


title: F3-KO-RNA_KO RNA REP3

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F3-KO-RNA


title: rna_wt_2_b4_s2

description: Total RNA

tag: strain

tag: batch

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: NLS.7.t6

data_processing:
Transcript quantification using salmon 1.2.0
Genome_build: GRCm38 Ensembl Release 97
Supplementary_files_format_and_content: Transcript quantification quant.sf file

molecule: polyA RNA

source_name: melanoma

extract_protocol:
Trizol total RNA extraction
Truseq stranded mRNA (Illumina); paired-end

tag: treament

tag: cell line number


title: COAD_NX.20_P3


title: NLS.7.t48

tag: tissue


title: F2-KO-RNA_KO RNA REP2

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F2-KO-RNA


title: WT-mg-RNA-2_WT RNA REP2

description:
QIAseq
WT-mg-RNA-2


title: WT-mg-RNA-3_WT RNA REP3

description:
QIAseq
WT-mg-RNA-3


title: COAD_NX.20_P2


title: COAD_NX.19_P2


title: KO-mg-RNA-1_KO RNA REP1

description:
QIAseq
KO-mg-RNA-1


title: EWS_NX.23_P3

value: Ewing’s sarcoma (EWS)

value: Brain


title: WT-mg-RNA-1_WT RNA REP1

description:
QIAseq
WT-mg-RNA-1

value: microglia


title: NLS.6.t6


title: NLS.16.t6


title: KO NeuN+ HiC REP4

description:
Jiang, et. al.
processed data file:
insituWTKO-A01519_stedb1_pooled_males_neurons_allValidPairs.hic
M2-KO-HiC-NeuN+

source_name: KO NeuN+ HiC

value: KO


title: KO-TAC-3

city: Iowa City

first: Ajit

last: Vikram

state: IA

address: 285 Newton Road

department: Internal Medicine

institute: University of Iowa

data_processing:
The expression ratio of WT-TAC and KO-TAC, the significance of difference (p values), and gene IDs were uploaded to the Ingenuity Pathway Analysis tool of the Qiagen Inc.
In this dataset, we performed expression analysis based on the experimental log-ratio. The Ingenuity knowledge base was used as the reference set, and both direct and indirect relationships were considered.
A cutoff of -0.3 and 0.3 was set up for the analysis, which provided us with 2441 analysis-ready molecules (1352; downregulated, 1089; upregulated). The Excel sheet from the IPA software was downloaded and used as a processed data.
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat (v2.1.0) using the mouse (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RawReadCounts_Vikram.txt

source_name: Heart, miR-204 KO

extract_protocol:
The RNA was quantified using a fluorometric RiboGreen assay and RNA integrity was assessed using capillary electrophoresis and generating an RNA Integrity Number (RIN) (Agilent BioAnalyzer 2100). The samples with higher than 500 ng and RIN of 8 or greater were used to generate Illumina sequencing libraries using Illumina's TruSeq RNA Sample Preparation Kit (Cat. # RS-122-2001 or RS-122-2002) or Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2101).
The libraries were amplified using 15 cycles of PCR and final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen) and via Q-PCR. Indexed libraries are then normalized, pooled, and size-selected to 320 bp (tight) using the PippinHT instrument. Pooled libraries are denatured and diluted to the appropriate clustering concentration. The libraries are then loaded onto the NovaSeq paired-end flow cell and clustering occurs onboard the instrument. Once clustering is complete, the sequencing reaction immediately begins using Illumina's 2-color SBS chemistry. Upon completion of reading 1, a 7 base pair index read is performed in the case of single indexed libraries. If dual indexing was used during library preparation, 2 separate 8 or 10 base pair index reads are performed. Finally, the clustered library fragments are re-synthesized in the reverse direction thus producing the template for paired-end read 2. Base call files for each cycle of sequencing are generated by Illumina Real-Time Analysis (RTA) software. The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute. Primary analysis and de-multiplexing are performed using Illumina's bcl2fastq v2.20. The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.

value: Heart

value: Transaortic constriction surgery

tag: time point

value: 5 weeks after surgery


title: KO-TAC-2


title: COAD_NX.17_P7

value: NOD/SCID/γcnull mice


title: NLS.7.t0

tag: sac microdomain


title: KO NeuN+ HiC REP2

description:
Jiang, et. al.
processed data file:
insituHi-C-FEM-Pool1-A015A19_pooled_allValidPairs.hic
F2-KO-HiC-NeuN+

value: cortex


title: KO NeuN+ HiC REP1

description:
Jiang, et. al.
processed data file:
insituHi-C-FEM-Pool1-A015A19_pooled_allValidPairs.hic
F1-KO-HiC-NeuN+


title: KO NeuN+ HiC REP3

description:
Jiang, et. al.
processed data file:
insituWTKO-A01519_stedb1_pooled_males_neurons_allValidPairs.hic
M1-KO-HiC-NeuN+


title: F1-KO-RNA_KO RNA REP1

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
F1-KO-RNA


title: NLS.16.t48

value: melanoma cell line


title: NLS.6.t0


title: NLS.16.t0


title: COAD_NX.18_P3


title: COAD_NX.19_P4


title: M1-KO-RNA_KO RNA REP4

description:
RiboZero
processed data file:
rna-total-counts.xls
counttab.repeat.rna.kowt.ALL.txt
M1-KO-RNA


title: KO-TAC-1


title: COAD_NX.17_P5


title: WT-TAC-2

source_name: Heart, WT

value: WT


title: COAD_NX.17_P6


title: WT NeuN- H3K27ac REP3

description:
processed data file:
h3k27ac-diffReps.txt
M3-WT-H3K27ac-NeuN-

source_name: WT NeuN- H3K27ac


title: NLS.6.t48

value: nuclear


title: WT-TAC-3


title: LacZ.10.t48


title: COAD_NX.14_P3


title: 4TO7-Exo

city: Shanghai

first: Lixing

last: Zhan

state: Shanghai

address: 320 Yue-yang Road

department: Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include TPM values for each Sample ...

source_name: 4TO7 breast tumor

growth_protocol: The orthotopic transplanted 4TO7 breast cancer tissues were ablated and cut into small pieces at 2 weeks after tumor inoculation and cultured in RPMI-1640 medium without FBS for 12 hours, after which the medium was collected and centrifuged at 800 × g for 10 min, followed by a centrifugation step of 20,000 × g for 20 min to remove cellular debris. The supernatant was recovered and filtered using a 0.2-um filter. The collected media was then subjected to ultracentrifugation at 100,000 × g for 90 min at 4°C and the supernatant was discarded. The pellet was washed once in a large volume of PBS, ultracentrifuged again and resuspended in Trizol for exosomal RNA extraction.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kreamer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254,QIAGEN, GmBH, Germany)RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: Orthotopic implanted 4TO7 breast tumor

tag: age

value: 2 week after tumor inoculation


title: COAD_NX.13_P3

value: colorectal carcinoma (COAD)

value: Liver


title: WT NeuN+ H3K27ac REP3

description:
processed data file:
h3k27ac-diffReps.txt
M3-WT-H3K27ac-NeuN+

source_name: WT NeuN+ H3K27ac


title: COAD_NX.15_P3


title: LacZ.10.t0


title: WT NeuN- H3K27ac REP2

description:
processed data file:
h3k27ac-diffReps.txt
M2-WT-H3K27ac-NeuN-


title: WT NeuN+ H3K27ac REP2

description:
processed data file:
h3k27ac-diffReps.txt
M2-WT-H3K27ac-NeuN+


title: WT NeuN- H3K27ac REP1

description:
processed data file:
h3k27ac-diffReps.txt
M1-WT-H3K27ac-NeuN-


title: MN_scRNA

source_name: Differentiated motor neuron

extract_protocol:
Motor neurons cultured for 6 days were dissociated with 0.05% trypsin and stained with 0.2 uM Calcein AM and 8 uM Ethidium homodimer-1 at RT for 15 min. Single viable cells were sorted using Fluorescence Activated Cell Sorting to single wells of 96-well fully-skirted Eppendorf PCR plates in 3 uL lysis buffer (5% PEG8000, 0.1% Triton X-100, 0.5 unit/ul RNAse Inhibitor, 0.5 uM OligodT30VN, 0.5 mM dNTP in nuclease free water). The plates were immediately covered, spun at 2600 rpm for 1 min at 4°C, and stored at −80°C until library construction.
Plates with cells in lysis buffer were incubated at 72 °C for 10 min for lysing the cells and denaturing the RNA. Next, 1 µl of reverse transcription mix (25 mM Tris-HCl, pH 8, 30 mM NaCl, 1 mM GTP, 2.5 mM MgCl2, 8 mM DTT, 0.5 unit/ul RNAse Inhibitor, 2 µM Smart-seq3, 2  unit/ul Maxima H-minus reverse transcriptase enzyme, was added to each well for reverse transcription and template switching at 42 °C for 90 min followed by 10 cycles of 50 °C for 2 min and 42 °C for 2 min and the reaction was inactivated at 85 °C for 5 min. cDNA pre-amplification was performed by adding 6 µl of PCR mix (1×Kapa HiFi HotStart buffer, 0.02  unit/ul KAPA HiFi DNA polymerase, 0.5 mM MgCl2, 0.3 mM dNTPs, 0.5 µM Smartseq3 forward PCR primer and 0.1 µM Smartseq3 reverse PCR primer) with program: 3 min at 98°C for initial denaturation, 19 cycles of 20 s at 98°C, 30 s at 65°C and 6 min at 72°C, followed by a final elongation for 5 min at 72°C. Pre-amplified cDNA was purified by 0.6x volume of AMpure XP beads, eluted in 14 ul nuclease free water, quantified using the Quant-iT PicoGreen dsDNA Assay Kit and size distributions were checked on a high-sensitivity DNA chip. cDNA was then diluted to 200 pg/µl, and 1 ul was used for tagmentation by mixing with 1 µl of tagmentation buffer (10 mM TAPS, pH 8.5, 5 mM MgCl2, 8% PEG8000, 0.08 ul Tn5 mix (illumina)). The reaction was performed at 55°C for 7 min, followed by heat inactivation at 80°C for 5 min. Library amplification of the tagmented samples was performed using custom-designed index primers and by adding 5 µl of PCR mix (1× Phusion High-Fidelity buffer, 0.01  unit/ul Phusion High-Fidelity DNA Polymerase, 0.2 mM dNTPs, 0.1 µM forward indexed primer and 0.1 µM reverse indexed primer). Amplification was performed as program: 3 min 72°C; 30 s at 95°C; 12 cycles of (10 s at 95°C; 30 s at 55°C; 30 s at 72°C); and 5 min at 72°C. Samples from all the wells were pooled, and then purified with Ampure XP beads at a 1:0.6 ratio. Libraries were quantified by Qubit™ dsDNA HS Assay Kit and quality checked on a high-sensitivity DNA chip. The size averaged at ~1 Kb should be expected. scRNA-seq libraries were sequenced as 100 bp paired-end reads on the Illumina NovaSeq 6000 platform and importantly, ~20% phiX spike-in was added to resolve the low complexity issue in the first 20 bps.

tag: cell type

value: Differentiated motor neuron

value: wild type, Auts2KO, Auts2_HX*,Nrf1KO


title: PBS3_IP

first: Fangzhou

last: Teng

address: No. 12, Urumchi Middle Road, Jingan District

department: Department of Integrative Medicine

institute: Huashan Hospital, Fudan University

data_processing:
FASTP software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and input samples were also verified using FASTP.
Clean reads of all libraries were aligned to the Mus musculus genome from Ensembl version 101 by HISAT2.
The methylated m6A peaks and differentially methylated peaks were identified by R package exomePeak.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker.
Genome_build: Mus musculus Ensembl version 101
Supplementary_files_format_and_content: tab-delimited text files include m6A peak information for each group

source_name: lung tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN >7.0, and confirmed by electrophoresis with agarose gel. Approximately more than 25 μg of total RNA was used to deplete ribosomal RNA using the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribosomal-depleted RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min.
The fragmented RNA was incubated with m6A antibody as immunoprecipitation (IP) RNA was used for MeRIP-seq. In detail, the RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The fragmented RNA without IP as input RNA was used for RNA-seq. Then both the input and IP RNA were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. The 2×150bp paired-end sequencing (PE150) was performed on an illumina Novaseq 6000.

value: lung

tag: Sex

value: Female

tag: disease state

value: normal


title: WT-TAC-1

value: Heart

tag: genotype

tag: treatment

value: Transaortic constriction surgery


title: PBS2_IP


title: COAD_NX.11_P3

source_name: Patinent derived xenograft

tag: primary tumor type (human)

tag: metastasis site

value: NOD/SCID/γcnull mice


title: LacZ.12.t48


title: WT NeuN- H3K79me2 REP3

description:
processed data file:
h3k79me2-diffReps.txt
F3-WT-H3K79me2-NeuN-

source_name: WT NeuN- H3K79me2

tag: strain background

value: cortex


title: LacZ.12.t0

value: melanoma cell line


title: COAD_NX.16_P3

tag: originial tumor id

tag: passage of pdx

tag: host mice strain


title: PBS2_input

tag: strain


title: PBS3_input


title: WT NeuN+ H3K27ac REP1

description:
processed data file:
h3k27ac-diffReps.txt
M1-WT-H3K27ac-NeuN+

value: WT


title: mito10_noDOX_1L_S56_L006

data_processing:
Transcript quantification using salmon 1.2.0
Genome_build: GRCm38 Ensembl Release 97
Supplementary_files_format_and_content: TPM

growth_protocol: xenograft

extract_protocol:
Trizol total RNA
Tru-seq mRNA stranded (Illumina); paired-end stranded

treatment_protocol: doxycycline oral

tag: treament

value: mito

value: melanoma xenograft


title: PBS1_IP

value: BALB/c

tag: tissue


title: mito10_plusDOX_1L1R_S58_L006


title: mito10_plusDOX_none_S59_L006


title: COAD_NX.09_P3


title: COAD_NX.12_P3

value: Brain


title: NLS6_plusDOX_none_S51_L006

value: nuclear


title: COAD_NX.10_P3

value: colorectal carcinoma (COAD)


title: NES22_plusDOX_none_S55_L006

value: cytoplasma


title: WT NeuN+ H3K79me2 REP3

description:
processed data file:
h3k79me2-diffReps.txt
F3-WT-H3K79me2-NeuN+

source_name: WT NeuN+ H3K79me2


title: WT NeuN- H3K79me2 REP2

description:
processed data file:
h3k79me2-diffReps.txt
F2-WT-H3K79me2-NeuN-


title: NLS6_noDOX_1L_S48_L006


title: COAD_NX.08_P3

value: Liver


title: mito10_noDOX_1L1R_S57_L006


title: COAD_NX.06_P3


title: NLS6_noDOX_1L2R_S49_L006


title: COAD_NX.04_P9


title: COAD_NX.07_P3


title: OVA3_input

value: lung

value: asthma


title: OVA3_IP

value: Female


title: PBS1_input

value: normal


title: OVA2_input


title: OVA2_IP


title: NLS6_plusDOX_1L_S50_L006


title: OVA1_IP


title: COAD_NX.05_P3


title: NES22_noDOX_1R_S52_L006


title: WT NeuN- H3K9me3 REP4

description:
processed data file:
h3k9me3-diffReps.txt
M2-WT-H3K9me3-NeuN-

source_name: WT NeuN- H3K9me3


title: WT NeuN+ H3K79me2 REP2

description:
processed data file:
h3k79me2-diffReps.txt
F2-WT-H3K79me2-NeuN+


title: OVA1_input


title: NES22_plusDOX_1L_S54_L006


title: WT NeuN+ H3K79me2 REP1

description:
processed data file:
h3k79me2-diffReps.txt
F1-WT-H3K79me2-NeuN+


title: COAD_NX.04_P8


title: C57 NeuN- HiC REP2

description:
Arima
M1-C57-HiC-NeuN+

source_name: C57 NeuN- HiC


title: COAD_NX.04_P7


title: WT NeuN- H3K9me3 REP2

description:
processed data file:
h3k9me3-diffReps.txt
F2-WT-H3K9me3-NeuN-


title: WT NeuN- H3K79me2 REP1

description:
processed data file:
h3k79me2-diffReps.txt
F1-WT-H3K79me2-NeuN-


title: mixture of pre-let-7a-1 variants (1:0.5:0.25)

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description: Mixture of pre-let-7a-1 WT, pre-let-7a-1-1U, pre-let-7a-1-4U at 1:0.5:0.25 ratio

data_processing:
The resulting DNA sequences obtained from NGS were treated with cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC) (Martin, 2011) to remove the adapter sequences.
The trimmed paired-end sequencing reads were then joined using fastq-join (with default parameters).
Low quality reads were discarded using fastq_quality_filter (-q 30 -p 90) (FASTX- Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
The remaining sequencing reads were then aligned to the pre-generated reference sequences using Bowtie (local alignment mode) (Langmead and Salzberg, 2012). Only perfectly mapped reads were selected for further analysis.
Genome_build: Pre-generated reference sequences contained the pre-miRNA sequences and their variants.
Supplementary_files_format_and_content: Bed files containing read count number for each mapped reference sequence.

organism: synthetic construct

source_name: synthetic

extract_protocol: 2500 ng of total RNA from human cells or 250 fmol of synthesized pre-miRNAs were ligated by T4 RNA ligase 1. The ligated pre-miRNAs were then reverse-transcribed by Superscripts IV (Invitrogen, 18090010) and RT primers that formed 25–30 base pairs with pre-miRNAs. The reverse complementary sequence of the 3'-adapter (5'- TGGAATTCTCGGGTGCCAAGG-3') was included in the RT primers. The resulting cDNAs were first amplified using the reverse primer (5'-CCTTGGCACCCGAGAATTCCA-3') and the forward primer containing the 5'-adapter sequence (5'- GTTCAGAGTTCTACAGTCCGACGATC-3'). The resulting PCR products were then amplified using RPIx and RP1 primers to generate the DNA libraries for next-generation sequencing (NGS). The DNA libraries were sequenced by Illumina Nextseq 500 sequencer using Nextseq Mid Output 1250 (2x75) cycles kit.

tag: sample type

value: synthesized pre-miRNA


title: C57 NeuN- HiC REP1

description:
Arima
F1-C57-HiC-NeuN-


title: synthesized pre-let-7a-1-6U

description: Cloning of synthesized pre-let-7a-1-6U


title: COAD_NX.04_P13

extract_protocol:
Tumors resected from the mice were frozen and the suspended in trizol reagent (Thermo Fisher Scientific Inc, Waltham, USA), and total RNA was extracted according to the manufacturer’s instruction.
One microgram of total RNA was used as the starting material for a 100-bp paired-end transcriptome-sequencing protocol using an Illumina GAIIx sequencer (Illumina, San Diego, CA, USA). Briefly, PolyA+ RNA was purified from total RNA and fragmented using divalent cations. RNA quality as assessed by RNA integrity number (RIN) using a bioanalyzer (Agilent). Double stranded cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen), and its overhang was converted into blunt end using T4 DNA polymerase. 3’ end of the blunt end was adenylated by Klenow fragment, and PE adapter was ligated. Without size selection, the cDNA library was amplified using PCR. For PCR amplification, 1ul of PCR primer PE 1.0 and 2.0, and 0.5 μL of Phusion DNA polymerase (Finnzymes Oy) were used in a final volume of 50 μL. The PCR condition was as follows: 98 °C for 5 min, then 15 cycles of 98 °C for 10 s, 65 °C for 30 s, and 72 °C for 30 s, followed by 72 °C for 5 min before cooling to 4 °C. PCR primers were removed by QIA quick PCR Purification Kit. Each library was loaded into its own single Illumina flow cell lane, producing 100-mer paired-end reads for each sample.

value: NOD/SCID/γcnull mice


title: COAD_NX.04_P10


title: WT NeuN- H3K9me3 REP3

description:
processed data file:
h3k9me3-diffReps.txt
M1-WT-H3K9me3-NeuN-

value: cortex


title: NES22_noDOX_1L2R_S53_L006

tag: sac microdomain


title: WT NeuN+ H3K9me3 REP1

description:
processed data file:
h3k9me3-diffReps.txt
F1-WT-H3K9me3-NeuN+

source_name: WT NeuN+ H3K9me3


title: WT NeuN+ H3K9me3 REP3

description:
processed data file:
h3k9me3-diffReps.txt
M1-WT-H3K9me3-NeuN+


title: mixture of pre-let-7a-1 variants (1:0.1:0.01)

description: Mixture of pre-let-7a-1 WT, pre-let-7a-1-1U, pre-let-7a-1-4U at 1:0.1:0.01 ratio


title: C57 NeuN+ HiC REP2

description:
Arima
M1-C57-HiC-NeuN+

source_name: C57 NeuN+ HiC


title: WT NeuN+ H3K9me3 REP4

description:
processed data file:
h3k9me3-diffReps.txt
M2-WT-H3K9me3-NeuN+


title: C57 NeuN+ HiC REP1

description:
Arima
F1-C57-HiC-NeuN+


title: COAD_NX.04_P11


title: WT NeuN+ H3K9me3 REP2

description:
processed data file:
h3k9me3-diffReps.txt
F2-WT-H3K9me3-NeuN+


title: COAD_NX.03_P3


title: noIgG_P28-5_synch

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Library strategy: CUT&RUN
Alignment to the mm10 genome was performed using bowtie2.
BAM files were generated by using bowtie2 and samtools.
BAM files were converted to bigWig format, using Deeptools , bamCoverage, bigWigCompare
Replicate bigWIg were averaged using WiggleTools
Genome_build: mm10
Supplementary_files_format_and_content: BED files listing ARID2 target regions

source_name: Spermatogenic cells from P28.5 synchronized testes

extract_protocol:
Spermatogenic cells were isolated from P28 and P28.5 synchronized testes by digesting tubules with collagnease and trypsin followed by filteration through a 40 micron sieve.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing.

treatment_protocol: Synchronous spermatogenesis was established in mice using the potent Retinoic acid (RA) synthesis inhibitor, WIN18,446  [(N,N'-1,8-Octanediylbis(2,2-dichloroacetamide)]. Briefly, neonatal mice are gavage-treated with WIN18,446 (100mM; 100ug/g of body weight) from P1-P10; as a result, the testis contains only undifferentiated type A spermatogonia. At P11 WIN 18,446 is discontinued and the mice are given a single dose of 10 ul exogenous RA (10ug/ul) via subcutaneous injection (30-gauge needle) to initiate spermatogenesis.  Prophase-I (pachynema/diplonema) and metaphase spermatocyte enriched populations were isolated from P28 and P28.5 seminiferous tubules

tag: antibody

value: no IgG


title: BRCA_NX.01_P3

value: breast invasive carcinoma (BRCA)


title: WT NeuN- HiC REP3

description:
Jiang, et. al.
processed data file:
09_18_18_glia_pooled_neurons_males_allValidPairs.hic
M1-WT-HiC-NeuN-

source_name: WT NeuN- HiC

value: WT


title: WT NeuN- H3K9me3 REP1

description:
processed data file:
h3k9me3-diffReps.txt
F1-WT-H3K9me3-NeuN-


title: BRCA_NX.02_P4


title: BRCA_NX.02_P5


title: synthesized pre-let-7a-1-2U

description: Cloning of synthesized pre-let-7a-1-2U


title: synthesized pre-let-7a-1-4U

description: Cloning of synthesized pre-let-7a-1-4U


title: synthesized pre-let-7a-1-1U

description: Cloning of synthesized pre-let-7a-1-1U


title: BRG1ab_CnR_P28-5_synch

value: anti-BRG1-abcam (ab110641)


title: WT NeuN- HiC REP2

description:
Jiang, et. al.
processed data file:
female_glia_allValidPairs.hic
F2-WT-HiC-NeuN-


title: WT NeuN- HiC REP1

description:
Jiang, et. al.
processed data file:
female_glia_allValidPairs.hic
F1-WT-HiC-NeuN-


title: synthesized pre-let-7a-1-5U

description: Cloning of synthesized pre-let-7a-1-5U


title: COLO205 cells, NP-2

city: Zunyi

first: Xue-feng

last: Yang

address: The Second Affiliated Hospital of Zunyi Medical University, Xinpu New District, Zunyi City, Guizhou Province

institute: The Second Affiliated Hospital of Zunyi Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.100 whole genome using HISAT2
Fragments Per Kilo bases per Million fragments (FPKM) were calculated using  HTSeq.
Genome_build: GRCh38.100
Supplementary_files_format_and_content: Excel file includes read counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: COLO205 cells were treated with nonylphenol (NP, 10-6 M) or DMSO  for 24 h.

tag: cell line

tag: cell type

value: colorectal cancer cells

value: NP


title: synthesized pre-let-7a-1-3U

description: Cloning of synthesized pre-let-7a-1-3U


title: ARID2_CnR_P28-5_synch_m2

value: anti-ARID2 Thermofisher (PA5-35857)


title: Light SHH during neural induction_rep2

first: Riccardo

last: De Santis

address: 1230 York Ave

institute: The Rockefeller univeristy

data_processing:
FASTQ file were aligned using Cell Ranger (v.2.0.2) against hg19 reference genome.
Count matrix were further processed using Python in the Scanpy environment (https://pypi.org/project/scanpy/)
The raw matrices were filtered to have a minimum of 500 detected genes per cell and genes were filtered to be expressed in at least 5 cells.
Cells with over 15% mitochondrial UMIs were discarded.
Clustering analysis was performed using Leiden algorithm on normalized counts and visualized in a low-dimensional space using UMAP plots (n.neighbors = 50, PCA components= 20).
Genome_build: Hg19
Supplementary_files_format_and_content: We uploaded the Cell ranger count matrix and cluster annotation in the metadata csv.

source_name: Neural progenitors

growth_protocol: hESCs (RUES2) were differentiated using dual SMADs inhibition (SB431542 and LDN193189) to induce an anterior forebrain fate, and in the presence of DOX for 24 hours to confer light sensitivity

extract_protocol: 10X genomics v3 library

treatment_protocol: Blue light was shone on day 2 during neural induction through a 1 mm rectangular mask overnight to activate SHH in a specially restricted domain

value: ES-derived neural progenitor cells

tag: hesc line

value: hESC RUES2 NIHhESC-09-0013

tag: scrna-seq platform

value: 10X genomics v3


title: BRG1G7_CnR_P28-5_synch


title: WT NeuN- HiC REP4

description:
Jiang, et. al.
processed data file:
09_18_18_glia_pooled_neurons_males_allValidPairs.hic
M2-WT-HiC-NeuN-

tag: genotype


title: ARID2_CnR_P28-5_synch_m1


title: SPRET NeuN+ HiC REP2

description:
Arima
M1-SPRET-HiC-NeuN+

organism: Mus spretus

source_name: SPRET NeuN+ HiC

value: SPRET/EiJ


title: COLO205 cells, control-2

tag: treatment

value: DMSO


title: SPRET NeuN- HiC REP2

description:
Arima
M1-SPRET-HiC-NeuN+

source_name: SPRET NeuN- HiC


title: ARID2_CnR_P28_synch_d1

source_name: Spermatogenic cells from P28 synchronized testes


title: COLO205 cells, NP-1


title: BRG1G7_CnR_P28_synch


title: WT NeuN+ HiC REP4

description:
Jiang, et. al.
processed data file:
09_21_18_A002A005_male_neurons_pooled_allValidPairs.hic
M2-WT-HiC-NeuN+

source_name: WT NeuN+ HiC


title: SPRET NeuN+ HiC REP1

description:
Arima
F1-SPRET-HiC-NeuN+


title: Tbx1-Cre_Tbx1cKO_lineage 3

status: Public on Oct 10 2021

city: Bronx

first: Hiroko

last: Nomaru

address: 1300 Morris Park ave

institute: Albert Einstein College of Medicine

data_processing:
We removed Nextera Transposase Sequence primers in the range 33 to 47 bp using cutadapt78 with the following option -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA.
Sequences were then aligned to the mouse genome (mm9) using Bowtie2 2.3.4.3 with default parameters.
A customized R script was used to remove reads with mates mapping to different chromosomes, or with discordant pairs orientation, or with a mate-pair distance >2 kb, or PCR duplicates (defined as when both mates are aligned to the same genomic coordinates).
After the mitochondrial genome were also removed, ATAC peaks in each sample were identified using MACS2 2.1.2.179 with the option -- nomodel --shif100 --extsize 200.
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: pharyngeal mesoderm

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted. After nuclear extraction, nuclear pellets were incubated with Tb5 transpose. Then transposed DNAs were extracted with columns
ATAC-seq libraries were prepare with Nextera DNA Sample Preparation Kit (Illumina)

value: Swiss Webster

value: Pharyngeal apparatus and heart with back

tag: developmental stage


title: SPRET NeuN- HiC REP1

description:
Arima
F1-SPRET-HiC-NeuN-

tag: strain background


title: ARID2_CnR_P28_synch_d2


title: Light SHH during neural induction_rep1


title: Tbx1-Cre_lineage 3


title: WT NeuN+ HiC REP1

description:
Jiang, et. al.
processed data file:
neurons_fem_wt_allValidPairs.hic
F1-WT-HiC-NeuN+


title: Tbx1-Cre_lineage 2


title: noIgG_P28_synch


title: NPC_rep2

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

data_processing:
Reads were aligned to the mouse genome (build GRCm38/mm10) using STAR aligner version 2.5.4b
StringTie-ls was used to assemble transcripts
kallisto-ls was used for transcript quantification
Isoform switching analysis was performed using the R package IsoformSwitchAnalyzeR version 1.4.0
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

growth_protocol: Mouse NPCs were isolated from Mettl14 WT and cKO mouse embryonic cortices and cultured in Neurobasal medium (GIBCO BRL) containing 20 ng/ml FGF2, 20 ng/ml EGF, 5 mg/ml heparin, 2% B27 (v/v, GIBCO BRL), Glutamax (Invitrogen), Penicillin/Streptomycin (Invitrogen) on culture dishes precoated with Matrigel matrix (2%, Corning).

extract_protocol:
Total RNA fraction was isolated from cultured NPC samples with Trizol reagent (Thermo Fisher) followed by total RNA extraction using the RNA Clean and Concentrator-25 (Zymo Research). mRNA was isolated from total RNA with Dynabeads mRNA purification kit (Thermo Fisher).
For samples WT1 through WT4 and KO1 through KO4, RNA sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina, and each band of each sample used a unique index PCR primer (NEBNext Multiplex Oligos for Illumina). Libraries were multiplexed 1:1 for sequencing in the NextSeq 500 (Illumina) yielding approximately 100 million 2×75-bp paired-end reads per sample. For sample WT_control, libraries was prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced in Illumina HiSeq 2500 yielding approximately 30 million 50 bp single-end reads.

tag: genotype/variation

value: Wild type

value: neural progenitor cells (NPCs)


title: 5 synthesized pre-miRNAs

description: Cloning of synthesized 5 human pre-miRNAs, including pre-mir-216a, pre-let-7a-1, pre-let-7a-2, pre-let-7c, pre-let-7g

value: synthesized pre-miRNA


title: 249_rep3

city: Montpellier

first: Laurent

last: Laplaze

address: 911 avenue Agropolis

department: DIADE

country: France

institute: IRD

description: Pennisetum glaucum

data_processing:
Illumina RTA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Splice junction mapping using TopHat2.
Counting using HTSeq-count.
Mapping was performed against predicted CDS available as PM.genechr.trans.cds.txt.
Genome_build: Pearl millet genome of reference IDs: ASM217483v2 (1532771 [UID] 5927848 [GenBank])
Supplementary_files_format_and_content: Lignee337_vs_Lignee249_Raw_Counts_RNA-Seq.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Cenchrus americanus

source_name: Root tip

growth_protocol: Plants were grown in hydropony in 1/2 Hoagland solution at 27 °C (12 h light/12 h dark).

extract_protocol:
RNA were extracted using the RNeasy kit (Qiagen).
Libraries were constructed with the TruSeq Stranded mRNA Sample Preparation (Illumina).

tag: line

tag: phenotype

value: High primary root growth

value: Primary root tip (2 cm apex)

value: 15 days after germination

tag: growth condition

value: Hydropony


title: Mesp1-Cre_lineage 3

tag: strain

value: Pharyngeal apparatus and heart


title: 337_rep1

description: Pennisetum glaucum

value: Low primary root growth

tag: tissue


title: 337_rep2

description: Pennisetum glaucum


title: WT NeuN+ HiC REP2

description:
Jiang, et. al.
processed data file:
neurons_fem_wt_allValidPairs.hic
F2-WT-HiC-NeuN+

value: cortex

value: WT


title: Tbx1-Cre_Tbx1cKO_lineage 1


title: Tbx1-Avi;BirA 2

data_processing:
We removed adapters using cutadapt with -a option and a set of adapters detected with FASTQC.
Sequences were then trimmed using TrimGalore with option –length 0, then sequences were aligned to the mouse genome (mm9) using Bowtie2 2.3.4. with default parameters.
Only uniquely mappable reads were retained ahd  the reads with mates mapping to different chromosomes, or with discordant pairs orientation, or with a mate-pair distance >2 kb, or PCR duplicates (defined as when both mates are aligned to the same genomic coordinate) were removed.
ChIP-seq peaks in each sample were identified using MACS2 2.1.2.1 with default parameters. Then, a consensus list of enriched regions was obtained using the intersectBed function from the BedTools 2.29 with the default minimum overlap and retaining only the peak regions common to at least two out of the three replicates.
Peaks were filtered by removing those overlapping with blacklist regions (Encode mm9 black regions Version 2) using findOverlapsOfPeaks of ChIPpeakAnno.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak, bed

source_name: whole embryo

extract_protocol:
After dissected out, total twenty whole embryos were minced and cross-linked with 1% formaldehyde. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries and their input were prepare with Accel-NGS 2S Plus DNA Library Kit (Swift Bioscience)

value: Mix

value: Tbx1 3'-Avi; FVB;129P2-Gt(ROSA)26Sortm1.1(BirA)Mejr/J double homozygous


title: 249_rep1

description: Pennisetum glaucum


title: WT NeuN+ HiC REP3

description:
Jiang, et. al.
processed data file:
09_21_18_A002A005_male_neurons_pooled_allValidPairs.hic
M1-WT-HiC-NeuN+


title: COLO205 cells, control-1

value: colorectal cancer cells


title: Tbx1 Ctrl E9.5

description: scRNA-seq

data_processing:
Cell Ranger (v 3.1.0) was used to align reads of scRNA-seq data to the mouse reference genome (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted and then the cells were loaded in a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using Chromium Single Cell 3’ Library & Gel Bead Kit v2.
RNA libraries were prepared for sequencing using standard 10x Genomics protocols.


title: 337_rep3

description: Pennisetum glaucum


title: BRG1ab_CnR_P28_synch

value: anti-BRG1-abcam (ab110641)


title: Mesp1E9.5

data_processing: Cell Ranger (v 3.1.0) were used to align reads of scRNA-seq data to the mouse reference genome (mm10).

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted and then the cells were loaded in a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using Chromium Single Cell 3’ Library & Gel Bead Kit v2
RNA libraries were prepared for sequencing using standard 10xGenomics protocols

value: Swiss Webster


title: 249_rep2

description: Pennisetum glaucum


title: Tbx1-Cre_Tbx1cKO_lineage 2

value: Pharyngeal apparatus and heart with back


title: Mesp1-Cre_lineage 1


title: Tbx1-Cre_lineage 1


title: Mesp1-Cre_lineage 2


title: Tbx1-Avi;BirA 1


title: MEL_Input_DNA-seq_rep2

city: Mishima

first: Satoru

last: Ide

address: 1111 Yata

institute: National Institute of Genetics

data_processing:
Library strategy: PI-PRICh
Illumina Miseq reporter software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CUTADAPT and PRINSEQ using a composite set of Illumina adapters, a minimum quality score of 20 and a minimum length of 25.
Reads containing (TTAGGG)5 or (CCCTAA)5 repeats were extracted  using the grep command in the UNIX system.
Genome_build: mm10

source_name: Mouse erythrocytes leukemia cells

growth_protocol: MEL cells were grown in DMEM medium containing 10% FBS at 37°C (5% CO2) in the  bottle roller.

extract_protocol:
To extract DNA, the pull-down chromatin fractions were incubated in de-crosslinking buffer (50 mM Tris-HCl pH 8.0, 200 μg/mL Protease K, 2% SDS) overnight at 65°C. An equal volume of phenol: chloroform: isoamyl alcohol (25:24:1,v/v) (311-90151, Wako) was added and vortexed, and centrifuge at 16,000 g for 5 min at room temperature. The upper aqueous phase was transferred to a new tube. This step was repeated. One-tenth volume of 3 M sodium acetate, glycogen, and the double volume of ethanol were added and incubated for 2 hr at -80°C. After centrifugation at 20,000 g for 30 min at 4ºC, the pellet was retained, washed with 70% ethanol, and dried up. The dried pellet was dissolved in 10 μg/mL RNase A in DNA dilution buffer attached to DNA SMART ChIP-Seq Kit (634865, Takara). After incubation for 1 hr at 37°C, DNA was purified by the phenol-chloroform extraction and ethanol precipitation to remove RNase A.
DNA libraries were synthesized by the DNA SMART ChIP Seq Kit (634865, Takara).

treatment_protocol: The cells were washed with PBS and crosslinked with 3.7% formaldehyde in PBS for 30 min at room temperature.  Following the chromatin sample preparation, the region-specific chromatin isolation were  performed by TH59-DB and masked TH59-DB (negative control) probes.

value: mouse erythrocytes leukemia

tag: pull-down fraction

value: Input


title: MEL_masked_TH59-DB

data_processing:
Illumina Miseq reporter software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CUTADAPT and PRINSEQ using a composite set of Illumina adapters, a minimum quality score of 20 and a minimum length of 25, and then mapped to mm10 whole genome using Hisat2 with parameters -p 12 -no--mixed --no-discordant --un-conc
Fragments Per Kilobase of trannscript per Megabase of library size (FPKM) were calculated using Cufflinks and featureCounts. In short, the mapped fragments in TH59-DB pulled-down fractions were assembled into transcripts and annotated using Cufflinks software. The number of fragments falling in this transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample

extract_protocol:
To extract RNA, the input and isolated chromatin with masked TH59-DB and TH59-DB were incubated in de-crosslinking buffer (32 mM Tris-HCl pH 8.0, 320 μg/mL Protease K, 0.8% SDS) for 6 hr at 65°C. An equal volume of acidic phenol was added, then vortexed, and incubated for 5 min at room temperature. After adding an equal volume of chloroform: isoamyl alcohol (24:1, v/v) and centrifuging at 16,000 g for 5 min at 4°C, the upper aqueous phase was transferred to a new tube. This step was repeated. One-tenth volume of 3 M sodium acetate, glycogen, and double volume of ethanol were added and incubated overnight at -80°C. After centrifugation at 20,000 g for 30 min at 4ºC, the pellet was retained, washed with 70% ethanol, and dried up. The dried pellet was dissolved in diethylpyrocarbonate (DEPC)-treated water (36415-54, Nakarai) and kept at -80°C until use.
RNA libraries were synthesized by the SMARTer Stranded Total RNA-Seq Kit v2 (634411, Takara).

value: performed by masked_TH59-DB


title: MEL_Input


title: MEL_TH59-DB

value: performed by TH59-DB


title: MEL_Input_DNA-seq_rep1


title: SW622-cy3-treated-inflamed-2

type: RNA

city: Philadelphia

first: Mariana

last: Franco Fragoso

state: PA

address: 333 Cottman Avenue

department: Cancer Prevention and Control

institute: Fox Chase Cancer Center

hyb_protocol: Hybridization was performed on Agilent 4x44K mouse genomic arrays. Cy3-labeled aRNA was mixed with Cy5-labeles reference aRNA and hybrized onto Agilent G2545A Hybridization oven using In situ Hybridization Kit Plus (Agilent Technologies).

scan_protocol: Images were scanned on an Agilent G2505B scanner and quantified using Agilent Feature Extraction (v9.1.1.1)

data_processing: Agilent Feature Extraction (FE) software (v9.1.1.1) was used to generate Cy3 & Cy5 ProcessedSignal intensities and to flag poor quality spots.

label_protocol: Labeled antisense (aRNA) probes for microarray hybridization were generated in the second round of applification in the presence of UTP after Cy3 fluorescent dye (Amersham Biosciences Corp., Piscataway, NJ) incorporation. 100ng of a mouse universal reference RNA (BD Biosciences Clontech, Palo Alto, CA) was amplified in parallel and labeled with Cy5 fluorescent dye (Amersham Biosciences Corp.)

growth_protocol: Female Swiss Webster mice (7 weeks of age) were maintained in the animal facility and received food and water ad libitum. Animals were treated with AOM (7.4 mg/kg, i.p.) and 4% DSS for 3 cycles (one cycle = 7 days of DSS plus 21 days of water). At the time of the sacrifice, colons were cut into sections and snap frozen on OCT compound. Frozen sections were cut at 5um at -20oC and kept at -80oC until sample collection by Laser Capture Microdissection.

extract_protocol: Total RNA was isolated using PicoPure RNA Isolation Kit (Arcturus Bioscience). All RNAs were subjected to DNAse treatment. Quality was assessed on RNA 6000 Pico LabChip and evaluated on Agilent Bioanalyzer 2100 using Eukaryote Total RNA Pico Assay. Total RNA was submitted to two rounds of amplification using RiboAmp Kit (Arcturus Biosciences) and Paradise Reagent System.

treatment_protocol: Treated groups received 5-ASA through the experiment.

value: inflamed

value: treated

source_name: Ref

value: Ref


title: Tbx1-Avi;BirA 3


title: SW548-cy5-untreated-polypoid-2

value: polyp


title: SW546-cy3-untreated-polypoid-1


title: SW645-cy3-treated-polypoid-2


title: SW637-cy3-treated-polypoid-1


title: SW545-cy5-untreated-inflamed-2


title: SW548-cy3-untreated-polypoid-2


title: SW545-cy3-untreated-inflamed-2


title: MEL_TH59-DB_rep2

data_processing:
Illumina Miseq reporter software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CUTADAPT and PRINSEQ using a composite set of Illumina adapters, a minimum quality score of 20 and a minimum length of 25, and then mapped to mm10 whole genome using Hisat2 with parameters -p 12 -no--mixed --no-discordant --un-conc
Fragments Per Kilobase of trannscript per Megabase of library size (FPKM) were calculated using Cufflinks and featureCounts. In short, the mapped fragments in TH59-DB pulled-down fractions were assembled into transcripts and annotated using Cufflinks software. The number of fragments falling in this transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample ...


title: MEL_masked_TH59-DB_rep2


title: MEL_Input_rep2


title: SW549-cy5-untreated-inflamed-1


title: SW645-cy5-treated-polypoid-2


title: MEL_TH59-DB_DNA-seq_rep2


title: zikv_GFP_rep2

city: Beijing

first: Wenze

last: Huang

address: Tsinghua street

institute: Tsinghua University

description:
ZIKV_IGG_bam.bedgraph
ZIKV_IGG_bam.bw

data_processing:
For the sequencing data, the 1st reads were used for further analysis. The 5’- and 3’-adapter sequences were removed using Trimmomaitc version 0.30.
Sequencing data was de-duplicated and the cleaned reads were then mapped to the human rRNA index with bowtie2 version 2.2.5.
The unmapped reads were then mapped to the ZIKV and the SARS-CoV-2 genome with bowtie2 version 2.2.5.
Peak calling was conducted using Piranha version 1.2.1.
Per-base coverages were calculated using bedtools.
Genome_build: NC_045512.2,AY632535.2
Supplementary_files_format_and_content: RBP binding peak and read count abundances per position in the virus reference genome
Supplementary_files_format_and_content: bedGraph
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: peak

source_name: ZIKV infected HUH-7 cell line

growth_protocol: Caco2-N cells were cultured on 10cm dishes and infected with SARS-CoV-2-GFP∆N virus with a MOI 0.05 for 48 hours. Huh7 cells were cultured on 10cm dishes and infected with ZIKV (MR766) with a MOI 0.5 for 48h. Then cells were washed 3 times using cold PBS and crosslinked using UV254.

extract_protocol:
The crosslinked cells were resuspended using 1 mL lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS and 0.5% sodium deoxycholate) supplemented with protease inhibitor. Cells were lysed on ice for 30min. To fragment the RNA, 10 μL of RNase I dilution (1:1000 in lysis buffer) and 2 μL Turbo DNase were added, then the cell lysates were incubated for 3 min at 37 °C with shaking at 1100 rpm. The digested lysate was then immediately transferred to ice for 3 min, followed by centrifugation of lysates at 18,000 RCF for 10 min at 4 °C. IGF2BP1 antibody (10 μg, MBL, RN007P) or HSP90AB1 antibody (10 μg, Proteintech, 11405-1-AP) was conjugated to 100 μL protein A/G beads (Pierce, 88802). Rabbit IgG (10 μg) was also conjugated to protein A/G beads used for protein pull-down control. The conjugated beads were added to lysates and rotated for 1h at 4 °C. Beads were washed twice with lysis buffer and four times with wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20); all washes lasted 5min with rotation at 4 °C.
Co-purified RNA was dephosphorylated using T4 polynucleotide kinase (NEB, M0201L) following the manufacturer’s instructions. The beads were washed twice with PNK wash buffer, following once with high-salt wash buffer (50 mM Tris-HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS and 0.5% sodium deoxycholate). Discard the high-salt wash buffer, beads were resuspended using PK buffer (100 mM Tris-HCl, pH 7.4, 50 mM NaCl, 10 mM EDTA) supplemented with 10 μL of proteinase K (20 μg/μL stock) then incubated at 37 °C for 20 min with shaking at 1100 rpm. TRIzol LS reagent (800 μL, Invitrogen, 10296028) was added to the tubes for RNA extraction as the manufacturer’s instructions.
The sequencing library of IGF2BP1 or HSP90AB1 uvCLAP was prepared as the protocol described in the SMARTer smRNA-Seq Kit for Illumina User Manual.

treatment_protocol: No

value: IgG

tag: target

value: ZIKV genome

tag: agent

value: ZIKV infected


title: zikv_IGF2BP1_rep3

description:
ZIKV_IGF2BP1_bam.bedgraph
ZIKV_IGF2BP1_bam.bw

tag: antibody


title: zikv_GFP_rep1

description:
ZIKV_IGG_bam.bedgraph
ZIKV_IGG_bam.bw


title: MEL_TH59-DB_DNA-seq_rep1

tag: cell type


title: zikv_IGF2BP1_rep4


title: SW637-cy5-treated-polypoid-1


title: sars2_IGG_L1_rep2

description:
SARS_CoV_2_IGG_L1_bam.bedgraph
SARS_CoV_2_IGG_L1_bam.bw

source_name: SARS-CoV-2 infected Caco2 cell line

value: SARS-CoV-2 genome

value: SARS-CoV-2 infected


title: zikv_IGF2BP1_rep1

description:
ZIKV_IGF2BP1_bam.bedgraph
ZIKV_IGF2BP1_bam.bw
ZIKV_IGF2BP1_peaks.narrowPeak


title: sars2_IGG_L1_rep1


title: SW549-cy3-untreated-inflamed-1


title: sars2_HSP90AB1_rep2

description:
SARS_CoV_2_HSP90AB1_bam.bedgraph
SARS_CoV_2_HSP90AB1_bam.bw


title: SW546-cy5-untreated-polypoid-1


title: sars2_IGG_rep2

description:
SARS_CoV_2_IGG_bam.bedgraph
SARS_CoV_2_IGG_bam.bw


title: HMVII-ST-2

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

institute: Peking University Cancer Hospital

data_processing:
Library examination：RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlusTM Real-Time PCR System (Library valid concentration>10 nM).
Library clustering and sequencing: The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: HMVII cell line

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

value: HMVII

value: melanoma cell line

value: di-ABZI


title: HMVII-ST-1


title: HMVII-E-2


title: SW626-cy5-treated-inflamed-1


title: A875-E-2

source_name: A875 cell line


title: sars2_IGF2BP1_rep2

description:
SARS_CoV_2_IGF2BP1_bam.bedgraph
SARS_CoV_2_IGF2BP1_bam.bw


title: HMVII-E-1


title: A875-E-1


title: sars2_IGG_rep1


title: hESC_HERVH KO_RNA-seq_rep2

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

description: rRNA depleted

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count for each gene

source_name: hESCs

growth_protocol: Human ES cell line H9 was cultured and maintained in mTesR1 medium (Stem Cell Technologies).

extract_protocol:
RNA was extracted from cells using TRI Reagent (Molecular Research Center, Inc) and further purified using Zymo RNA clean and concentrator-5 kit (Zymo Research) with DNase I treatment. DNA was extracted using phenol/chloroform followed by ethanol precipitation.
Sequencing libraries were prepared as described previously in Bowman SK et al. (2013).

treatment_protocol: Cells were treated with 4-Thiouridine for 16 hours and with LNA-GapmeRs for 24 hours, respectively, before harvesting for further experiments.

value: Untreated

value: Deletion of HERVH element on Chr2


title: A875-NC-2

value: DMSO


title: HMVII-COM-2


title: sars2_IGF2BP1_rep1

description:
SARS_CoV_2_IGF2BP1_bam.bedgraph
SARS_CoV_2_IGF2BP1_bam.bw
SARS_CoV_2_IGF2BP1_peaks.narrowPeak


title: hESC_HERVH KO_RNA-seq_rep1

description: rRNA depleted


title: sars2_HSP90AB1_rep1

description:
SARS_CoV_2_HSP90AB1_bam.bedgraph
SARS_CoV_2_HSP90AB1_bam.bw
SARS_CoV_2_HSP90AB1_peaks.narrowPeak


title: zikv_IGF2BP1_rep2


title: HMVII-NC-2


title: A875-COM-2


title: hESC_HERVH KD_RNA-seq_rep1

description: rRNA depleted

value: LNA-GapmeRs treated

value: wild type (CHD7-HA)


title: A875-NC-1


title: A875-ST-2


title: HMVII-COM-1


title: hESC_CHD7 KO_RNA-seq_rep2

description: rRNA depleted


title: hESC_WT_PAR-CLIP_rep2

data_processing:
Library strategy: PARCLIP-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by deeptools bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

value: 4-Thiouridine treated

value: wild type

value: CHD7 (Abcam, ab31824)


title: hESC_WT_RNA-seq_rep2

description: rRNA depleted


title: SW626-cy3-treated-inflamed-1

value: inflamed

value: treated

value: Ref


title: hESC_WT_PAR-CLIP_input2

value: IgG (Abcam, ab37415)


title: A875-COM-1


title: A875-ST-1