title: S_6

city: lanzhou

first: feng

last: cheng

state: GanSu

address: 335 Qilihe Rd,

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences

description: Treatment with terpinen-4-ol

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples

organism: Staphylococcus aureus

source_name: Treatment with terpinen-4-ol

extract_protocol:
Total RNA was extracted from planktonic cells using an RNA prep pure bacteria kit (Beijing Tiangen, Cat: #DP430) .Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: planktonic


title: S_5

status: Public on Sep 09 2020

type: SRA

country: China

description: Treatment with terpinen-4-ol

library_source: transcriptomic

molecule: total RNA

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD010_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PAL

tag: Sex

value: male

tag: age


title: SAM24370937 Bone Marrow WT_16hr

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: SAM24370937 Bone Marrow WT_16hr

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen)
and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

tag: samid

value: Bone Marrow

tag: genotype

value: WT

tag: time

value: 16 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD007_indexed


title: KYSE510_20 µM SFE-treated cells

type: RNA

city: beijing

first: sichong

last: han

address: No. 15 North Third Ring East Road, Chaoyang District

institute: beijing university of chemical technology

description: Gene expression data from hunam esophageal cancer KYSE510 cells with 20 µM SFE treatment

hyb_protocol: Following fragmentation, 5.2 µg of biotin-labeled ss-cDNA were hybridized for 16 h at 45℃ on Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Command Console Software was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: biotin

organism: Homo sapiens

source_name: KYSE510 with 20 µM SFE treatment

label_protocol: Total RNA was labeled and purified by Affymetrix FL-Ovation™ cDNA Biotin Module V2 according to the manufacturer’s instructions.

growth_protocol: KYSE510 cells were cultured in RPMI-1640 medium with 10% fetal bovine serum, 100 units/mL penicillin and 100 mg/mL streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: KYSE510 cells were seeded in 6-well plates with 20 µM SFE treatment or DMSO treatment as the negative control.After cultured for 48h, cells were treated with trizol reagent to extract total RNA.

tag: cell line

tag: cell type

value: human esophageal cancer cell line

tag: treatment

value: 20 µM Sulforaphene (SFE)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD001_indexed


title: KYSE510_DMSO-treated cells

description: Gene expression data from hunam esophageal cancer KYSE510 cells with DMSO treatment

source_name: KYSE510 with DMSO treatment

value: DMSO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD004_indexed


title: EC109_20 µM SFE-treated cells

description: Gene expression data from hunam esophageal cancer EC109 cells with 20 µM SFE treatment

source_name: EC109 with 20 µM SFE treatment


title: EC109_DMSO-treated cells

description: Gene expression data from hunam esophageal cancer EC109 cells with DMSO treatment

source_name: EC109 with DMSO treatment


title: SAM24370922 Bone Marrow KO_2hr

source_name: SAM24370922 Bone Marrow KO_2hr

value: N4bp1 KO

value: 2 hours


title: S_4

description: Treatment with terpinen-4-ol


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD001_indexed


title: S_3

description: Control

source_name: Control


title: SAM24370936 Bone Marrow KO_8hr

source_name: SAM24370936 Bone Marrow KO_8hr

value: 8 hours


title: S_2

description: Control


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D1_AD004_indexed


title: SAM24370915 Bone Marrow WT_1hr

source_name: SAM24370915 Bone Marrow WT_1hr

value: 1 hours


title: S_1

description: Control


title: SAM24370917 Bone Marrow KO_1hr

source_name: SAM24370917 Bone Marrow KO_1hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D1_AD002_indexed


title: Upf1_P_R3

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

description:
Strand specific library from polysomal RNA from upf1-3 pad4-1 leaf (biological replicate 3)
translatome_counts_genes

data_processing:
Kallisto version 0.43.0  for mapping to either AtRTD2 or AtRTD2-UPF1
3D RNA-seq for TMM normalisation
Limma-voom pipeline enabled in 3D RNA-seq for differential expression analysis
3D RNA-seq for DE DAS DTU analysis
transcriptome build: AtRTD2 or AtRTD2-UPF1
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separated file (csv) containing quantification of raw and normalized RNA-seq reads mapping to gene ID and transcript ID annotated in either AtRTD2 or AtRTD2-UPF1 transcriptome assembly

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Plants were germinated on 1/2MS media supplemented with 1% sucrose for 10 days and then transferred to soil and grown for 3 weeks (from germination to harvesting leaf) at 22°C ±1°C, 16/8 h (Light/Dark) period

extract_protocol:
RNA was extracted with RNA blue (Top bio), DNase digested with TURBO DNA-free (Ambion)
Ribosomal rRNA depleted single end libraries were generated using Scriptseq Complete kit (Plant) (Epicentre)

treatment_protocol: Not applicable

tag: ecotype

value: Columbia-0 (Col-0)

value: upf1-3 pad4-1

value: 3 week

tag: fraction

value: Polysomal RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD008_indexed


title: SAM24370938 Bone Marrow WT_16hr

source_name: SAM24370938 Bone Marrow WT_16hr


title: Upf1_P_R2

description:
Strand specific library from polysomal RNA from upf1-3 pad4-1 leaf (biological replicate 2)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD006_indexed


title: SAM24370921 Bone Marrow WT_2hr

source_name: SAM24370921 Bone Marrow WT_2hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD007_indexed


title: Upf1_P_R1

description:
Strand specific library from polysomal RNA from upf1-3 pad4-1 leaf (biological replicate 1)
translatome_counts_genes


title: SAM24370914 Bone Marrow WT_1hr

source_name: SAM24370914 Bone Marrow WT_1hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD002_indexed


title: Upf1_M_R3

description:
Strand specific library from monosomal RNA from upf1-3 pad4-1 leaf (biological replicate 3)
translatome_counts_genes

value: Monosmal RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D1_AD012_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D11_AD010_indexed

value: male


title: SAM24370919 Bone Marrow WT_2hr

source_name: SAM24370919 Bone Marrow WT_2hr

value: Bone Marrow


title: SAM24370923 Bone Marrow KO_2hr

source_name: SAM24370923 Bone Marrow KO_2hr


title: SAM24370913 Bone Marrow WT_1hr

source_name: SAM24370913 Bone Marrow WT_1hr

value: WT


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D11_AD001_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: Upf1_M_R2

description:
Strand specific library from monosomal RNA from upf1-3 pad4-1 leaf (biological replicate 2)
translatome_counts_genes


title: Upf1_M_R1

description:
Strand specific library from monosomal RNA from upf1-3 pad4-1 leaf (biological replicate 1)
translatome_counts_genes


title: SAM24370940 Bone Marrow KO_16hr

source_name: SAM24370940 Bone Marrow KO_16hr

value: 16 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD010_indexed


title: Pad4_P_R3

description:
Strand specific library from polysomal RNA from pad4-1 leaf (biological replicate 3)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD008_indexed


title: Pad4_P_R2

description:
Strand specific library from polysomal RNA from pad4-1 leaf (biological replicate 2)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD007_indexed


title: SAM24370910 Bone Marrow KO_untreated

source_name: SAM24370910 Bone Marrow KO_untreated

value: 0 hours


title: SAM24370930 Bone Marrow KO_4hr

source_name: SAM24370930 Bone Marrow KO_4hr

value: 4 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD004_indexed


title: SAM24370929 Bone Marrow KO_4hr

source_name: SAM24370929 Bone Marrow KO_4hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D12_AD001_indexed


title: Pad4_P_R1

description:
Strand specific library from polysomal RNA from pad4-1 leaf (biological replicate 1)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD002_indexed


title: Pad4_M_R3

description:
Strand specific library from monosomal RNA from pad4-1 leaf (biological replicate 3)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD012_indexed


title: Pad4_M_R2

description:
Strand specific library from monosomal RNA from pad4-1 leaf (biological replicate 2)
translatome_counts_genes


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD001_indexed


title: 28d MI SA P4 B4

city: Louisville

first: Steven

last: Jones

state: KY

address: 580 South Preston Street - Rm 321F

department: Diabetes and Obesity Center

institute: University of Louisville

description: CMCs isolated from failing heart

data_processing:
trim_fastqs: trimmomatic-0.36.jar PE -phred33 {input.fastq_1} {input.fastq_2} {output.trimmed_fastq_paired_1} {output.trimmed_fastq_unpaired_1} {output.trimmed_fastq_paired_2} {output.trimmed_fastq_unpaired_2}  ILLUMINACLIP:all_fastq_primers.fa:2:30:10  LEADING:7 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
hisat2 -p 8 --mm --dta-cufflinks --rna-strandness RF {params.index} -1 {input.fastq_1} -2 {input.fastq_2} -S {output.sam} > {output.stats} 2>&1
sam_to_bam:  samtools sort -@ {threads} -o {output} {input}
samtools index {input} {output}
StringTie_assembly: stringtie -p 8 -G {params.ref_gtf} {input} -A {output.genes} -o {output.gtf}
cuffdiff -p 12 Mus_musculus.GRCm38.91.gtf --output-dir CDIFF -p 12 CMC_Sham.1,CMC_Sham.2,CMC_Sham.3 CMC_HF.1,CMC_HF.2,CMC_HF.3 SJB2-19.gtf,SJB2-20.gtf,SJB2-21.gtf SJB2-22.gtf,SJB2-23.gtf,SJB2-24.gtf
Genome_build: GRCm38.91
Supplementary_files_format_and_content: tab-delimited text file including FPKM values and statistics.

source_name: cardiac mesenchymal cells (CMC)

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instruction.
RNA-seq was performed by Novogene (California, U.S.A.). From total RNA, rRNA was removed using Ribo-Zero rRNA Removal kit (Illumina, #MRZH11124). Then, rRNA-depleted total RNA was subjected to the library preparation using  NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs, #E7770). The insert size of 250~300bp were sequenced in a directional manner using The HiSeq 4000 System Illumina (pair-end, 2 × 150 bp).

treatment_protocol: Male, C57BL6/J male mice were subjected to 60 min of ischemia, then reperfused for 28 d; male mice from the same cohort were subjected to sham surgery (i.e., thoracotomy but no myocardial infarction). Slowly adherent CMCs were segregated based on their relatively late adherence to polystyrene culture plates, as we described previously

value: C57BL6/J male mouse

tag: tissue

value: Heart

value: cardiac mesenchymal cells (CMC)

tag: sample type

value: 28 days myocardial infarction


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C9_AD008_indexed


title: Upf1_T_R3

description:
Strand specific RNA library from upf1-3 pad4-1 leaf (biological replicate 3)
pad4_upf1_counts_genes.csv

value: Total RNA


title: 28d MI SA P4 B3

description: CMCs isolated from failing heart


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD008_indexed


title: Upf1_T_R2

description:
Strand specific RNA library from upf1-3 pad4-1 leaf (biological replicate 2)
pad4_upf1_counts_genes.csv

value: Columbia-0 (Col-0)


title: Ad-GFP

city: Tangshan

first: Dong

last: Ma

state: Hebei

address: No. 21 Bohai Avenue, Caofeidian New Town, Tangshan, Hebei Province

department: School of public health

institute: North China University of Science and Technology

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: mm8
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: primary VSMC

growth_protocol: Cells are cultured using IMDM basic medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: LY1 cells were infected with lentivirus vectors that encoded either shSirt6 or an empty vector (control) according to the manufacturers’ instruction

value: primary aorta

tag: cell

value: vascular smooth muscle cell (VSMC)


title: Ad-K5


title: Pad4_M_R1

description:
Strand specific library from monosomal RNA from pad4-1 leaf (biological replicate 1)
translatome_counts_genes

value: 3 week


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD004_indexed


title: 28d MI SA P4 B2

description: CMCs isolated from failing heart


title: Pad4_T_R3

description:
Strand specific RNA library from pad4-1 leaf (biological replicate 3)
pad4_upf1_counts_genes.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD006_indexed


title: Upf1_T_R1

description:
Strand specific RNA library from upf1-3 pad4-1 leaf (biological replicate 1)
pad4_upf1_counts_genes.csv

value: upf1-3 pad4-1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD001_indexed

value: PAL


title: Sham 3 SA P4

description: CMCs isolated from sham heart

value: sham


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD012_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C8_AD007_indexed


title: Sham 1 SA P4

description: CMCs isolated from sham heart


title: Pad4_T_R1

description:
Strand specific RNA library from pad4-1 leaf (biological replicate 1)
pad4_upf1_counts_genes.csv


title: Pad4_T_R2

description:
Strand specific RNA library from pad4-1 leaf (biological replicate 2)
pad4_upf1_counts_genes.csv


title: Sham 2 SA P4

description: CMCs isolated from sham heart


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD012_indexed


title: control_KO_RNA_seq_rep5

city: San Diego

first: Lingling

last: Wang

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

description: Co-upregulated genes in Mettl3 and Mettl14 depleted tumors.xlsx

data_processing:
Single-end reads were trimmed by cutadapt (v1.18)
Trimmed reads were aligned to mm10 mouse genome assembly by HISAT2 (v2.1.0) software using the default parameter in single-end model
Transcripts was quantified by HTSeq (0.11.2), differential expressed genes (DEGs) was then determined by DESeq2.
Peakcalling were performed by MACS2(v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05, conserved peaks in biological replicates was found by intersectBed in BEDtools
Genome_build: mm10

source_name: CT26 cells

growth_protocol: CT26 (CRL-2638; murine colon carcinoma) was cultured in DMEM, RPMI (Gibco) or McCoy's 5A medium (ATCC) supplemented with 10% fetal bovine serum (Gibco) at 37℃ in 5% CO2 incubators. After retroviral transdution and knockout by Mettl3, Mettl14 and control sgRNA, 2 × 106 CT26 cells were suspended in 200 μl of PBS/Matrigel (Corning) (1:1) and then subcutaneously inoculated into flank of each mouse. BALB/c mice bearing CT26 tumors were injected intraperitoneally (i.p.) with 200 μg (10 mg/kg) of anti–CTLA-4 (Bio X Cell, mCD152) and/or anti–PD1 (Bio X Cell, clone 29F.1A12) and IgG (Bio X Cell, clone 2A3, BE0089) antibodies on days 11, 14, 17, 20 and 23 as recommend.

extract_protocol:
Ribosomal depleted RNA was isolated from tumors using RiboMinus Transcriptom Isolation Kit (life technology, K1500-02). Poly(A)+ RNA was isolated from total RNA by Magnetic mRNA Isolation Kit (New England Biolabs, S1550S) followed by the procedures as recommended.
Purified mRNA samples were fragmented to 100~200 nucleotides with Fragmentation Reagents Kit (Invitrogen, AM8740) according to the manufacturer’s protocol. 10% of total fragmented RNA was reserved as an input sample and the rest of fragmented RNA was further used for m6A immunoprecipitation with the anti-N6-methyladenosine (m6A) antibody (abcam, ab151230) in 500ml IP binding buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) with RNase inhibitor at 4°C for 2h. And then adding the washed protein A/G magnetic beads (NEB) by IP binding buffer to the RNA-antibody immunoprecipitation mixture to rotate at 4°C for 2h. The collected magnetic beads were washed twice in IP binding buffer, twice in low salt reaction buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) and twice in high salt reaction buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). The bound RNA was eluted from beads by adding 30ml RLT buffer (QIAGEN) and incubated for 5 min at 25°C. Lastly, the eluted RNA was purified by ethanol precipitation and prepared for library generation using a TruSeq mRNA library preparation kit (Illumina),Sequencing was performed at IGM Genomics core, UCSD on an Illumina HiSeq4000 platform, single-end 75 model

tag: genotype/variation

value: control KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD008_indexed


title: control_KO_RNA_seq_rep4


title: HEK293T_quantseq_siSFPQ2_rep1

city: Aarhus C

first: Thomas

middle: B

last: Hansen

state: State...

address: C.F. Moellers Alle 3, build 1130

country: Denmark

institute: MBG, Aarhus University

description:
HEK293T_peakcall_minus_featureCounts.txt
HEK293T_peakcall_plus_featureCounts.txt

data_processing:
Reads were mapped onto hg19 with STAR (v2.7) and quantified with featureCounts (v2.0.0) using gencode annotations (v28lift37 for hg19).
CircRNAs were predicted and quantified using ciri2 v2.0.6 and find_circ v1.2 adhering to default settings
Quantseq reads were mapped onto hg19 using STAR (v2.7). The resulting bam-files were merged and divided into plus and minus-strand alignments. Then, using MACS2 peakcall  (v2.2.6, https://github.com/macs3-project/MACS) with parameters [--nomodel --shift 0 –g 2.9e9], quantseq peaks were extracted. Each peak was then subsequently quantified using featureCounts (v2.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Merged raw counts provided by ciri2, find_circ or featureCounts

source_name: Knockdown in HEK293T using siSFPQ2, rep1

growth_protocol: HEK293T cells (Invitrogen), HepG2 (ATCC) were cultured in Dulbecco’s modified Eagle’s media (DMEM) with GlutaMAX (Thermo Fisher Scientific) supplemented with 10% foetal bovine serum (FBS) and 1% penicillin/streptomycin sulphate (P/S). All cells were kept at 37°C in a humidified chamber with 5% CO2.

extract_protocol:
RNA was extracted using TriZOL
For total RNA sequencing of HEK293T, RNA from SFPQ, NONO, and CTRL KD were rRNA depleted using RiboCop rRNA Depletion Kit V1.2 (Lexogen) according to manufacturer’s protocol. Subsequent cDNA libraries were prepared using SENSE Total RNA-Seq Library Prep Kit (Lexogen) following manufacturer’s protocol. For 3’end sequencing, cDNA libraries from HEK293T were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen). Total RNAseq was done as 100nt paired-end sequencing and performed using the Illumnia platform (HiSEQ4000, BGI, Copenhagen), while for 3’end sequencing, 75nt single-end sequencing was performed at MOMA (Aarhus University Hospital) on a NextSeq500. For total RNA sequencing of HepG2 cells, library preparation and sequencing was performed at BGI (Copenhagen) using BGIseq.

treatment_protocol: Knockdown of SFPQ and NONO were carried out using transient transfections of siRNAs accordingly: For HEK293T, approximately 250.000 cells were plated in a 6-well dish and transfected with a final concentration of 22.5 nM siRNA using siLentFect Lipid Reagent (Bio-Rad) accordingly to manufacturer’s protocol. 48 hours post transfection, the cells were replenished with new media and re-transfected using Lipofectamine 2000 (Thermo Fisher Scientific). After additional 48 hrs, cells were harvested. For HepG2, approximately 400.000 cells were plated in a 6-well dish and reverse transfected with a final siRNA concentration of 50 nM using Lipofectamine RNAiMax (Thermo Fisher Scientific). 48 hrs post transfection, the cells were trypsinized before reverse transfected for the second hit using Lipofectamine 2000 (Thermo Fisher Scientific). After 48 hrs, the cells were harvested

value: Knockdown using siSFPQ2

tag: library kit


title: HEK293T_quantseq_siSFPQ2_rep2

source_name: Knockdown in HEK293T using siSFPQ2, rep2

value: QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD006_indexed

tag: strain


title: control_KO_RNA_seq_rep2


title: control_KO_RNA_seq_rep3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD001_indexed

tag: brain region


title: HEK293T_quantseq_siSFPQ1_rep2

source_name: Knockdown in HEK293T using siSFPQ1, rep2

value: Knockdown using siSFPQ1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD004_indexed

tag: Sex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD012_indexed

tag: age


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD010_indexed


title: HEK293T_quantseq_siSFPQ1_rep1

source_name: Knockdown in HEK293T using siSFPQ1, rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C7_AD006_indexed


title: Mettl14_KO_RNA_seq_rep5

value: Mettl4 KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD002_indexed


title: control_KO_RNA_seq_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD008_indexed


title: HEK293T_quantseq_siNONO1_rep2

source_name: Knockdown in HEK293T using siNONO1, rep2

value: Knockdown using siNONO1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD004_indexed


title: HEK293T_quantseq_siNONO2_rep1

source_name: Knockdown in HEK293T using siNONO2, rep1

value: Knockdown using siNONO2


title: HEK293T_quantseq_siNONO2_rep2

source_name: Knockdown in HEK293T using siNONO2, rep2


title: Mettl14_KO_RNA_seq_rep4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD006_indexed


title: Mettl14_KO_RNA_seq_rep3


title: HEK293T_quantseq_siNONO1_rep1

source_name: Knockdown in HEK293T using siNONO1, rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C6_AD007_indexed


title: HEK293T_quantseq_siCTRL2_rep2

source_name: Knockdown in HEK293T using siCTRL2, rep2

value: Knockdown using siCTRL2


title: HEK293T_quantseq_siCTRL2_rep1

source_name: Knockdown in HEK293T using siCTRL2, rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C4_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C4_AD002_indexed


title: Mettl14_KO_RNA_seq_rep1


title: Mettl3_KO_RNA_seq_rep5

value: Mettl3 KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD010_indexed


title: HEK293T_quantseq_siCTRL1_rep1

source_name: Knockdown in HEK293T using siCTRL1, rep1

value: Knockdown using siCTRL1


title: Mettl3_KO_RNA_seq_rep3


title: Mettl3_KO_RNA_seq_rep4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD010_indexed


title: HT1080_Nice-seq_rep1

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

data_processing:
Library strategy: NicE-Seq
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools.
Peak calling was done with MACS2 v. 2.1.2
Differential peak analysis was done by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

growth_protocol: HCT116, HeLa, HT1080 and HUT78 cell line were routinely grown in McCoy's and DMEM media with 10% fetal bovine serum respectively, media being replaced every 3 days.

extract_protocol:
HCT116 and Hela cells were sorted using FACS for cell cycle specific phases. HUT78 were treated with 1 micromolar of Romidepsin for 6 hours.
After open chromatin labeling using fluorescein-dATP and biotin-dCTP in the nucleotide mix, DNA was extracted using phenol-chloroform method. The libraries were made using NEBNext Ultra DNA Library Prep Kit (E7370S, New England Biolabs).
For RNA-seq, RNA extraction was performed using Quick RNA Miniprep from Zymo Res (R1054) and RNA sequencing was performed using NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760S) according to manufacturer's recommendations.

treatment_protocol: HCT116 cells were treated with 2 mM thymidine for 24h. Then the cells are released for 3h and 100 ng/mL of nocodazole was added for 12 h. HUT78 were treated with 1 micromolar of Romidepsin for 6 hours.

value: Fibrosarcoma

tag: replicate

value: Technical replicate1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C3_AD004_indexed


title: Mettl3_KO_RNA_seq_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD008_indexed


title: HCT116_Nocodazole_G2M_NicE-seq_rep2

value: Colorectal cancer cells

tag: cell cycle phase

value: Technical replicate2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C4_AD008_indexed

value: PAL


title: Mettl3_KO_RNA_seq_rep1


title: control_KO_input_rep2

description: Supressed m6A modification with Co-upregulated genes in Mettl3 and Mettl14 depleted tumors.xlsx

tag: chip antibody

tag: molecule

value: Ribosomal depleted RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD004_indexed

value: male


title: HCT116_Nocodazole_G2M_NicE-seq_rep1

tag: cell line

tag: cell type


title: Mettl14_KO_RNA_seq_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C2_AD001_indexed


title: HEK293T_quantseq_siCTRL1_rep2

source_name: Knockdown in HEK293T using siCTRL1, rep2

tag: treatment


title: HCT116_G2M_NicE-seq_rep2


title: control_KO_merip_rep2

value: anti-N6-methyladenosine (m6A) antibody (abcam, ab151230)

value: control KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD010_indexed


title: HT1080_Nice-seq_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD007_indexed


title: HUT 78_Treated_RNA-seq_rep3

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools.
Peak calling was done with MACS2 v. 2.1.2
Differential peak analysis was done by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: HUT 78_Treated_RNA seq

value: T cell lymphoma

value: 1 micromolar of Romidepsin for 6 hrs

value: Technical replicate3


title: control_KO_input_rep1


title: control_KO_merip_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD001_indexed


title: Mettl4_KO_input_rep1

value: Mettl4 KO


title: HUT 78_Treated_RNA-seq_rep1


title: Mettl14_KO_merip_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD012_indexed


title: HUT 78_Treated_RNA-seq_rep2


title: Mettl14_KO_merip_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD004_indexed


title: HUT 78_control_RNA-seq_rep3

source_name: HUT 78_Control_RNA seq

value: control


title: Mettl4_KO_input_rep2


title: HUT 78_control_RNA-seq_rep2


title: HUT 78_control_RNA-seq_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD012_indexed


title: Mettl3_KO_input_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B2_AD007_indexed


title: HUT 78_Romidepsin_NicE-seq_BR2_2

data_processing:
Library strategy: NicE-seq
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools.
Peak calling was done with MACS2 v. 2.1.2
Differential peak analysis was done by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: HUT 78_Treated_NicE-seq

value: Biological replicate2, Technical replicate2


title: Mettl3_KO_merip_rep2

source_name: CT26 cells

value: Mettl3 KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B2_AD010_indexed


title: HUT 78_Romidepsin_NicE-seq_BR2_1

value: Biological replicate2, Technical replicate1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B2_AD008_indexed


title: Mettl3_KO_input_rep1


title: HUT 78_Romidepsin_NicE-seq_BR1_2

value: Biological replicate1, Technical replicate2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B2_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD006_indexed


title: HUT 78_Romidepsin_NicE-seq_BR1_1

value: Biological replicate1, Technical replicate1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD004_indexed


title: KO iPS- Microglia + anti-TREM2 antibody 2

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Rd

institute: University of California, Irvine

data_processing:
RNA-sequencing read integrity was verified using FastQC
BBDuk was used to trim adapters and filter out poor quality reads
Reads were mapped to the hg19 reference genome using HISAT aligner
Complete clustering linkage was measured by pearson coefficient
Lowly expressed genes (expression count summed over all samples < 10) were removed before differential expression analysis
Differential Expression of TPM was calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Expressions_Table

source_name: Differentiated in vitro  from iPSCs

growth_protocol: Growth protocols explicitly defined in Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer’s pathology in vivo (Nature Communications)

extract_protocol:
Samples were lysed in RLT and isolated using Rneasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 24 hrs

tag: genotype

value: KO

value: 20 ug/mL anti-TREM2 antibody


title: KO iPS- Microglia + anti-TREM2 antibody 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD001_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD010_indexed


title: HUT 78_DMSO_NicE-seq_BR2_2

source_name: HUT 78_Control_NicE-seq


title: HUT 78_DMSO_NicE-seq_BR2_1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD006_indexed


title: KO iPS- Microglia + anti-TREM2 antibody 1


title: WT iPS- Microglia + anti-TREM2 antibody 4

value: WT


title: Mettl3_KO_merip_rep1

value: Ribosomal depleted RNA


title: KO iPS- Microglia + anti-TREM2 antibody 4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD008_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD002_indexed


title: WT iPS- Microglia + anti-TREM2 antibody 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD004_indexed


title: HCT116_G2M_NicE-seq

value: Colorectal cancer cells


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD001_indexed


title: WT iPS- Microglia + anti-TREM2 antibody 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B12_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B11_AD006_indexed


title: WT iPS- Microglia + anti-TREM2 antibody 1


title: HCT116_S_NicE-seq_rep2

value: S

value: Technical replicate2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B11_AD004_indexed


title: HUT 78_DMSO_NicE-seq_BR1_2

value: T cell lymphoma


title: HUT 78_DMSO_NicE-seq_BR1_1


title: KO iPS- Microglia + IgG isotype control 4

value: 20 ug/mL IgG


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B11_AD001_indexed


title: KO iPS- Microglia + IgG isotype control 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD010_indexed


title: HCT116_S_NicE-seq_rep1

value: Technical replicate1


title: HeLa_G2M_NicE-seq

value: HeLa

value: Cervical cancer cells


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD008_indexed


title: HeLa_G1_NicE-seq


title: HCT116_G1_NicE-seq_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD006_indexed


title: KO iPS- Microglia + IgG isotype control 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD004_indexed


title: HCT116_G1_NicE-seq_rep1


title: epe1D

city: Edinburgh

first: Sito

last: Torres-Garcia

address: 6.4 Michael Swann Building. Max Born Crescent

country: United Kingdom

institute: Wellcome Centre for Cell Biology. University of Edinburgh

data_processing:
ChIP-Seq: Raw reads were de-multiplexed and trimmed using Trimmomatic (v0.35) to remove adapter contamination and regions of poor sequencing quality. Trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using Bowtie2 (v2.3.3). Resulting bam files were processed using Samtools (v1.3.1) and picard-tools (v2.1.0) for sorting, removing duplicates and indexing. Ratios IP/input were calculated using BamCompare (deepTools v2.0) in SES mode for normalisation.
RNA-Seq: Raw read were de-multiplexed. Adapter-trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using STAR (v2.2.1) and processed using Samtools (v1.3.1). Differential expression was analysed using the Bioconductor Rsamtools (v2.0.3), GenomicFeatures (v1.36.4) and DESeq2 (v.1.24) R libraries. Log2 fold changes were shrunk using the apeglm method58 and a MA-plot was generated using R. BigWig coverage files for forward and reverse strands were generated using BamCoverage (deepTools v2.0).
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: ChIP-Seq: bigWig files of ratio IP/input. RNA-Seq: bigWig files of coverage for forward and reverse strands

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL

extract_protocol:
Cells were lysed by bead beating and chromatin was sheared by sonication. Lysates were incubated with antibody and Protein-G Dynabeads overnight. Immunoprecipitated genomic DNA was recovered using PCR purification columns.
Libraries were prepared for Illumina sequencing with 1-5 ng of ChIP or 10 ng of input DNA using NEXTflex adaptors and Ampure XP beads. Barcoded libraries were pooled and sequenced following Illumina HiSeq2000, NextSeq or MiniSeq workflows.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature

value: h- epe1D

tag: phenotype

value: epe1D phenotype

value: no treatment

value: 5.1.1 mouse monoclonal anti-H3K9me2 antibody kindly provided by Takeshi Urano (Nakagawachi et al. 2003. Oncogene)


title: clr5-Q264STOP_meu27-S100Y

value: h- clr5-Q264STOP meu27-S100Y

value: clr5-Q264STOP meu27-S100Y phenotype


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD001_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD012_indexed


title: WT iPS- Microglia + IgG isotype control 4

value: WT


title: striatum, WT3

first: Bianca

middle: H

last: Habermann

address: 163, Avenue de Luminy

country: France

institute: Aix-Marseille University, CNRS, IBDM UMR 7288

data_processing:
We used STAR (Dobin et al., 2013) with standard parameters to align RNA-Seq reads to the latest release of the mouse genome (mm10) downloaded from UCSC (as of March 2020). Read counting was performed using featureCounts (Liao et al., 2014). One replicate of control and one of Camk2a-cKO were discarded before further analysis due to inconsistent clustering during principal component analysis. Differential expression analysis was done using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Tshz3_CamK2A-CRE_DESeq2.xlsx

source_name: striatum

extract_protocol:
1 µg of total RNA from wild-type (WT) and Tshz3 mutant (KO) striatum at postnatal day 34 (P34) was prepared using Rneasy Plus Universal Mini Kit gDNA eliminator (Qiagen ™). Three independent replicates, each containing striata from 3-4 mice (P34), were prepared for analysis.
RNA-seq libraries were prepared  with the "Truseq stranded mRNA sample preparation kit" (low throughput protocol) from Illumina.

tag: tissue

value: striatum

value: Postnatal day 34 (P34)

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD006_indexed


title: WT iPS- Microglia + IgG isotype control 2


title: striatum, KO3

description:
St9
Discarded before further analysis due to inconsistent clustering during principal component analysis.

value: TSHZ3 KO


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD004_indexed


title: striatum, WT1

description:
St10
Discarded before further analysis due to inconsistent clustering during principal component analysis.


title: striatum, WT2


title: WT iPS- Microglia + IgG isotype control 1


title: KO iPS-Microglia 4

value: KO


title: KO iPS-Microglia 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD001_indexed


title: KO iPS-Microglia 2


title: KO iPS- Microglia + IgG isotype control 1

value: 20 ug/mL IgG


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A8_AD012_indexed


title: KO iPS-Microglia 1


title: WT iPS-Microglia 4


title: WT iPS- Microglia + IgG isotype control 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A8_AD006_indexed


title: WT iPS-Microglia 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A8_AD004_indexed


title: cKO_naïve_1yo [7306]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with HiSat2 version 2.1.0 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on October 2019
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma separated files include DeSeq2 rlog counts for each Sample.

growth_protocol: Naive T cells were isolated direcly

extract_protocol:
Spleen was manually homogenized and naive CD4+ T cells were FACS sorted as CD3+CD4+CD25-CD62L+CD44-
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries
75 bp single-end run was performed on a HiSeq2000

treatment_protocol: No treatment, cells were directly processed for RNAseq

tag: genetic background

tag: mouseid

value: Naive CD4+ T cells


title: ctrl_naïve_1yo [7302]

tag: genotype/variation

value: control


title: WT iPS-Microglia 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD012_indexed

tag: strain


title: cKO_naïve_1yo [7305]


title: cKO_naïve_1yo [7307]


title: WT iPS-Microglia 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD007_indexed

tag: brain region


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD008_indexed

tag: Sex


title: ctrl_naïve_1yo [7301]


title: striatum, KO2

tag: age


title: 3860: cKO_8h_stim

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with HiSat2 version 2.1.0 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on October 2018
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 rlog counts for each Sample.

source_name: Naive CD4+ T cells

growth_protocol: Naive CD4+ T cells were isolated directly, stimulation and control were cultured in IMDM medium supplemented with 10% FCS, 1% Pen/Strep, 1% L-glutamine, 5mM HEPES, 0.5 mM sodium pyruvate and 55µM β-mercaptoethanol

treatment_protocol: Naive T cells were stimulated with 1 ug/ml of anti-CD3 and anti-CD28 antibodies


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A9_AD002_indexed


title: HEK293T_siNONO2_rep1

description:
HEK293T_featureCounts.txt
HEK293T_ciri2.txt
HEK293T_find_circ.txt

value: Knockdown using siNONO2

tag: library kit

value: SENSE Total RNA-Seq Library Prep Kit (Lexogen)

tag: ribodepleted

value: RiboCop rRNA Depletion Kit V1.2 (Lexogen)


title: HEK293T_siSFPQ2_rep2

source_name: Knockdown in HEK293T using siSFPQ2, rep2

value: Knockdown using siSFPQ2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD006_indexed


title: 3859: ctrl_8h_stim

value: Control


title: HEK293T_siCTRL1_rep2

value: Knockdown using siCTRL1


title: striatum, KO1

tag: replicate


title: HEK293T_siNONO1_rep1

value: Knockdown using siNONO1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD002_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD004_indexed


title: HEK293T_siSFPQ1_rep2

source_name: Knockdown in HEK293T using siSFPQ1, rep2

value: Knockdown using siSFPQ1


title: HEK293T_siCTRL2_rep2

value: Knockdown using siCTRL2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD012_indexed


title: ctrl_naïve_1yo [7300]


title: 3856: cKO_naïve


title: 3855: ctrl_naïve


title: 3857: ctrl_8h_unstim


title: 3858: cKO_8h_unstim


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD010_indexed


title: HEK293T_siSFPQ2_rep1

source_name: Knockdown in HEK293T using siSFPQ2, rep1


title: 3850: cKO_8h_stim


title: HEK293T_siNONO1_rep2

source_name: Knockdown in HEK293T using siNONO1, rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD007_indexed


title: HEK293T_siCTRL2_rep1


title: 3849: ctrl_8h_stim


title: HEK293T_siNONO2_rep2

source_name: Knockdown in HEK293T using siNONO2, rep2


title: 3848: cKO_8h_unstim


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD004_indexed


title: 3846: cKO_naïve


title: 3847: ctrl_8h_unstim


title: HEK293T_siCTRL1_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD001_indexed


title: 3845: ctrl_naïve


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD012_indexed


title: 3840: cKO_8h_stim


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD008_indexed


title: 3839: ctrl_8h_stim


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD007_indexed


title: PC3 control HDAC2 rep2

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

description: Sample 46

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19/GRCh37) using BWA (v0.5.9) with defautl parameters. Reads from spike-in samples were mapped to the meta reference genome containing hg19 and dm6 chromosomes.
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from MNase digested, sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: PC-3 control and GDC-resistant cells was treated with vehicle, iCBP112 or SAHA for 24 hours.

value: prostate cancer

tag: passages

tag: chip antibody

value: Rabbit polyclonal anti-HDAC2 #ab7029


title: PC3 GDC-resist HDAC1 rep2

description: Sample 44

tag: cell type

value: Rabbit polyclonal anti-HDAC1 #ab7028


title: 3837: ctrl_8h_unstim


title: 3838: cKO_8h_unstim


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD006_indexed

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: PC3 control HDAC2 rep1

description: Sample 45


title: PC3 GDC-resist HDAC2 rep1

description: Sample 47


title: 3836: cKO_naïve


title: 3835: ctrl_naïve


title: PC3 GDC-resist HDAC2 rep2

description: Sample 48


title: HEK293T_siSFPQ1_rep1

source_name: Knockdown in HEK293T using siSFPQ1, rep1

tag: cell line

tag: treatment


title: PC3 control HDAC1 rep1

description: Sample 41


title: Primary spermatocytes 2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Swift BS-Seq sequences were trimmed with Trim Galore (v0.4.4; Cutadapt v1.9.1) with the options --clip_r1 12 --clip_r2 12, and Truseq libraries with the options --clip_r1 8 --clip_r2 8. Trimmed sequences were mapped to a personalised FVB/NJ mouse genome using Bismark (Krueger and Andrews, 2011) (v0.18.2). The personalised FVB/NJ genome was constructed by incorporating all high confidence SNPs from the latest VCF file released by the Mouse Genomes Project (mouse mgp.v5.merged.snps_all.dbSNP142.vcf; http://www.sanger.ac.uk/science/data/mouse-genomes-project) into the GRCm38 mouse reference using the genome preparation of SNPsplit (https://github.com/FelixKrueger/SNPsplit ; option --full_sequence). The CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Primary spermatocytes

extract_protocol:
Spermatocytes and spermatids were isolated from testes using 25ug/mL liberase TM (Roche) followed by elutriation and percoll gradient centrifugation. Caput, corpus, cauda, and vas deferens were dissected and genomic DNA was isolated from all samples by lysing in extraction buffer (4.24 M guanidine thiocyanate (Sigma), 100 mM NaCl (Ambion), 1% N-Laurylsarcosine (Sigma), 150 mM DTT (Promega) and 200 ug/mL Proteinase K (Sigma)) at 56C for 2 hours followed by isopropanol precipitation. Samples were then sonicated on a Covaris S-220 to achieve a median size of 200-250 base pairs. DNA fragments were cleaned up using phenol:choloroform:isoamyl alcohol and phase-lock tubes. 500 ng of DNA was used as input for 2 rounds of sodium bisulfite conversion using the EZ DNA Methylation – Lightning Kit (Zymo).
Library construction was performed using TruSeq DNA Methylation Kit (Illumina) and Accel-NGS Methyl-Seq DNA Library Kit (Swift) according to the manufacturer’s instructions. For TruSeq (Illumina) libraries, 50ng bisulfite converted DNA was used and individual libraries were barcoded using the TruSeq DNA Methylation Index PCR Primers (IIlumina) to allow for multiplexed sequencing of libraries. Size selection and DNA purification was performed using Ampure XP beads (Agencourt) according to the TruSeq DNA Methylation kit protocol. For Accel-NGS Methyl-Seq (Swift) libraries, 30ng bisulfite converted DNA was used and barcoded following the (Swift) manufacturer’s instructions including 6 rounds of PCR. All final libraries were analyzed by Fragment Analyzer and quantitated using the Qubit as well as the KAPA Library Quantitation qPCR kit.
Bisulfite-Seq (Accel-NGS Methyl-Seq (Swift))
Bisulfite-Seq (Truseq)

value: FVB


title: Vas deferens sperm 2

source_name: Vas deferens sperm


title: PC3 GDC-resist p300 rep2

description: Sample 40

value: Rabbit monoclonal anti-p300 CST#54062


title: PC3 GDC-resist p300 rep1

description: Sample 39


title: Early round spermatids 2

source_name: Early round spermatids


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD012_indexed


title: cell line B, fish

city: New York

first: Maayan

last: Baron

state: NY

address: 435 E. 30th Street, 8th Floor

institute: NYU

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method was processed using a custom-built pipeline, (available at https://github.com/flo-compbio/singlecell). Briefly, the location of the known “W1” adapter sequence of the inDrop RT primer, was located in the barcode read (read 2). Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, UMI sequence was extracted, and reads with low confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The, reads containing the mRNA sequence (read 1) were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously (Grün et al. 2014) The genome and gff file used included the zebrafish genome and the BRAF human vector. Single-cell transcriptomes with UMIs>750, mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis.
Raw sequencing data obtained from the Spatial Transcriptomics (ST) method were processed using a publicly available pipeline (https://github.com/jfnavarro/st_pipeline). Briefly, quality trimming is performed to remove low quality bases and reads with long nucleotide stretches (> 15). Read 2 (transcript sequence) is mapped with STAR 2.5.1 and Read 1 (spatial barcode) is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq-count; to get a final read count annotated reads are grouped by spatial barcode.
Raw sequencing data obtained from the CEL-Seq2 method were processed using a publicly available pipeline (https://github.com/yanailab/celseq2).
Genome_build: Danio_rerio.GRCz10
Supplementary_files_format_and_content: For inDrop data: tab-delimited files with genes as rows and cells as columns.
For ST data: tab-delimited files with spots (x and y coordinates for the ST array) as columns and genes as rows.
For CEL-Seq data: csv files with genes as rows and cells as columns.

organism: Danio rerio

source_name: melanoma cell line cells in a fish

extract_protocol:
For inDrop and CEL-Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin-EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15-30 min to soften tissue, every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC, 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then, sample was filtered twice using 5 mL polystyrene round-bottom tube with 35um cell-strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken.
For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X-PBS, and 4-5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry, sterile 10-cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue-mold with OCT and snap-frozen in liquid nitrogen-chilled isopentane. Tissue blocks were stored at -80°C until further use. Prior to cryosectioning, the cryostat was cleaned with 100% ethanol, and equilibrated to an internal temperature of -18°C for 30 minutes. Once equilibrated, OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15-20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays, and stored at -80°C until use, maximum of two weeks.
Prior to fixation and staining, the ST array was removed from the -80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature, followed by warming on a 37°C heat block for 1 minute. Tissue was fixed for 10 minutes with 3.6% formaldehyde in 1X PBS, and subsequently rinsed in 1x PBS. Next, the tissue was dehydrated with isopropanol for 1 minute followed by staining with hematoxylin and eosin. Slides were mounted in 65 µl 80% glycerol and brightfield images were taken on a Leica 397 SCN400 F whole-slide scanner at 40X resolution.
For inDrop library construction the cells and reverse transcription (RT) reaction was carried out as previously described in Klein et al., 2015. RNA amplification and library preparation were carried out according to this protocol incorporating the changes introduced in Zilionis et al. 2017.
Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England Biolabs). RNA was fragmented for 3 minutes with 1X fragmentation reagent prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).
For spatial transcriptomics (ST) library construction, we followed the previously published ST protocol from Stahl et al. Science 2016, with minor changes. Briefly, after brightfield imaging of stained tissue, tissue was permeabilized with collagenase and 0.1% pepsin prior to an overnight RT step with SuperScript III on the ST slide. Tissue was digested away with proteinase K and 1% 2-mercaptoethanol prior to cleavage of probes from the slide surface with USER enzyme. Second strand synthesis was performed with DNA Pol I and RNase H (New england biolabs) followed by an in vitro transcription amplification step with the MEGAScript T7 kit (Thermofisher). Amplified RNA then underwent a second RT with random hexamers and SuperScript II (Invitrogen), eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).
For CEL-Seq2 sample, cells were sorted using fluorescence activated cell sorting (FACS) into 384 well plate contacting 1.2ul primer mix and library was constructed according to the CEL-Seq2 protocol (Hashimshony et al. 2016).

tag: time

tag: type

value: CEL-Seq


title: cell line B, cultured

source_name: melanoma cell line cells


title: PC3 control p300 rep2

description: Sample 38


title: PC3 control HDAC1 rep2

description: Sample 42


title: PC3 GDC-resist HDAC1 rep1

description: Sample 43


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD006_indexed


title: PC3 control p300 rep1

description: Sample 37


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD004_indexed


title: Corpus sperm 2

source_name: Corpus sperm


title: cell line A, cultured


title: Cauda sperm 2

source_name: Cauda sperm


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD010_indexed


title: PC3 GDC-resist CBP rep2

description: Sample 36

value: Rabbit monoclonal anti-CBP CST# 7425


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD002_indexed


title: ZF3, ST

source_name: tumor tissue section

value: ST


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A4_AD001_indexed


title: PC3 GDC-resist CBP rep1

description: Sample 35


title: ZF2, time point 2

source_name: tumor cells

value: inDrop


title: PC3 control CBP rep2

description: Sample 34


title: ZF2, time point 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD008_indexed


title: ZF1,tumor 2,time point 3


title: Caput sperm 2

source_name: Caput sperm


title: Vas deferens sperm 1


title: Primary spermatocytes 1


title: PC3 GDC-resist H4-ac rep2

description: Sample 32

value: anti-Histone H4-ac (K5/K8/K12-ac ) Thermol Fisher#PA5-40083


title: PC3 control CBP rep1

description: Sample 33


title: Early round spermatids 1


title: Later round spermatids 2

source_name: Later round spermatids


title: ZF1,tumor 2,time point 2


title: Later round spermatids 1


title: cell line A, fish


title: PC3 GDC-resist H4-ac rep1

description: Sample 31


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD007_indexed


title: PC3 control H4-ac rep2

description: Sample 30


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD004_indexed


title: ZF1,tumor 1,time point 4


title: ZF1,tumor 2,time point 1


title: Corpus sperm 1


title: PC3 control H4-ac rep1

description: Sample 29


title: Cauda sperm 1


title: ZF1,tumor 1,time point 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD001_indexed


title: Caput sperm 1


title: ZF1,tumor 1,time point 2


title: PC3 GDC-resist H3K9/K14-ac rep2

description: Sample 28

value: Rabbit polyclonal anti-Histone H3K9/K14-ac # ab232952


title: ZF1,tumor 1,time point 1


title: PC3 control H3K9/K14-ac rep2

description: Sample 26


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A2_AD008_indexed


title: PC3 GDC-resist H3K9/K14-ac rep1

description: Sample 27


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A2_AD007_indexed


title: PC3 GDC-resist + SAHA H3K27-ac (S2 cell Spike-in) rep2

description: Sample 24

value: Rabbit polyclonal anti-Histone H3K27-ac #ab4729


title: vIRF1_mut-3

city: Nanjing

first: Liuxue

last: Sheng

state: Jiangsu

address: Tian Yuan East Road

institute: Nanjing Medical University

data_processing:
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters,then mapped to hg19 whole genome using BWA-MEM or Tophat.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts and RPM values for each sample

source_name: EA.HY926 cell line

extract_protocol:
TRIzol Protocol
RNA is extracted from cells and fragmented. RNA is converted to cDNA by reverse transcription. DNA Fragments are converted into the library by ligation to sequencing adapters containing specific sequences designed to interact with the NGS platform, the surface of the flow-cell (Illumina). The next step involves clonal amplification of the library, by cluster generation for Illumina. The final step generates the actual sequence via the chemistries for each technology.

value: EA.HY926 cell line

tag: agent

value: vIRF1 mutant virus


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A2_AD012_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A2_AD002_indexed


title: vIRF1_mut-1


title: KSHV-2

value: KSHV


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A2_AD001_indexed


title: KSHV-3


title: PC3 GDC-resist + iCBP112 H3K27-ac (S2 cell Spike-in) rep2

description: Sample 22

value: prostate cancer


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A3_AD002_indexed


title: PC3 control H3K9/K14-ac rep1

description: Sample 25


title: PC3 GDC-resist + SAHA H3K27-ac (S2 cell Spike-in) rep1

description: Sample 23


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD012_indexed


title: PC3 GDC-resist + iCBP112 H3K27-ac (S2 cell Spike-in) rep1

description: Sample 21


title: KSHV-1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD010_indexed


title: PC3 GDC-resist+vehicle H3K27-ac (S2 cell Spike-in) rep2

description: Sample 20


title: vIRF1_mut-2


title: PBS-3

value: PBS


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD008_indexed


title: PC3 GDC-resist+vehicle H3K27-ac (S2 cell Spike-in) rep1

description: Sample 19


title: total mRNA siEIF3E U251 cells from 1st experiment

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: Biological replicate 1 of 4. Cytoplasmic RNA; sieIF3e treated U251 cells

hyb_protocol: Oligoarray  hybridization was performed in Agilent chambers according to the manufacturer’s instructions

scan_protocol: Scanned on an Ion Proton (Lifetechnologies) according to the manufacturer’s instructions

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

label_protocol: labelling with Cy3 was performed with 100 ng of  RNA

growth_protocol: Human glioblastoma cell lines  U251 (obtained from C. Simon’s laboratory, UPENN, Philadelphia, PA, USA) were used and routinely maintained in Dulbecco’s Modified Eagle Medium (Lonza, Portsmouth, NH, USA) supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37C° in 5% CO2-humidified incubators as previously described.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Human U251  glioblastoma cells were transfected with 20 nmol/L of siScramble (siScr, Qiagen, Venlo, Limburg, The Netherlands) or 20 nmol/L of siRNA against human INT6/eIF3e (si3e: SI02662499, FlexiTube EIF3E siRNA, 20 nmol, 5'-CCCAAAGGUCGCGAUAAUAUU-3', Qiagen; or si3e#2: Dharmacon ON-TARGET plus SMART pool EIF3E siRNA 3646, 10 nmol) for 72h

tag: tissue/cell type

value: Human glioblastoma cell line

value: siRNA eif3e (siEIF3E)

tag: molecule subtype

value: Cytoplasmic RNA


title: PBS-2


title: polysome mRNA siSCR U251 cells from 4th experiment

description: Biological replicate 4 of 4. heavy polysome-associated RNA; siScr treated U251 cells

tag: genotype/variation

value: siRNA Scramble/control (siSCR)

value: heavy polysome-associated RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD006_indexed

city: La Jolla

tag: brain region

value: male

tag: strain


title: polysome mRNA siSCR U251 cells from 3rd experiment

description: Biological replicate 3 of 4. heavy polysome-associated RNA; siScr treated U251 cells


title: total mRNA siEIF3E U251 cells from 2nd experiment

description: Biological replicate 2 of 4. Cytoplasmic RNA; sieIF3e treated U251 cells


title: polysome mRNA siEIF3E U251 cells from 2nd experiment

description: Biological replicate 2 of 4. heavy polysome-associated RNA; sieIF3e treated U251 cells

value: siRNA eif3e (siEIF3E)


title: polysome mRNA siEIF3E U251 cells from 1st experiment

description: Biological replicate 1 of 4. heavy polysome-associated RNA; sieIF3e treated U251 cells


title: polysome mRNA siEIF3E U251 cells from 3rd experiment

description: Biological replicate 3 of 4. heavy polysome-associated RNA; sieIF3e treated U251 cells


title: PC3 control+vehicle H3K27-ac (S2 cell Spike-in) rep2

description: Sample 18


title: total mRNA siEIF3E U251 cells from 3rd experiment

description: Biological replicate 3 of 4. Cytoplasmic RNA; sieIF3e treated U251 cells


title: polysome mRNA siSCR U251 cells from 2nd experiment

description: Biological replicate 2 of 4. heavy polysome-associated RNA; siScr treated U251 cells


title: PBS-1


title: PC3 control+vehicle H3K27-ac (S2 cell Spike-in) rep1

description: Sample 17


title: CF-U-3

city: Chongqing

first: wang

last: xianxing

address: No. 2 Tiansheng Rd., Beibei District

institute: State Key Laboratory of Silkworm Genome Biology, the Institute of Sericulture and Systems Biology, Southwest University

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the hg38 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: GRCh38 (hg38)

growth_protocol: Pancreatic cancer cell line  were used for our research.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After transfecting CFPAC-1  cells with siUBE2C for 36 hours,  three matched control samples

tag: tissue

value: Pancreatic cancer cell line

value: UBE2C knock-down


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD002_indexed

tag: Sex

tag: age


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD004_indexed


title: CF-U-1


title: NC3 mRNAseq

city: Suzhou

first: Shuyu

last: Zhang

address: Ren Ai Road 199

institute: Suzhou University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4)
guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM

source_name: skin cells

growth_protocol: Human skin fibroblasts WS1 cells were routinely cultured with DMEM high glucose complete medium(include 10% FBS and 5% Penicillin and streptomycin antibody), in 37℃ 5% CO2  environment.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
RNA-seq.10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: WS1 cells were divided into two groups and each group had four repeats, one group was infected by IFI6-overexpressed lentivirus and another was infected by NC lentivirus. The two groups of cells were then irradiated with a single 5 Gy dose of radiation at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation the two groups of cells were collected.

value: skin cells of NC

value: skin cells with 5 Gy radiation

value: human skin fibroblasts WS1 cells


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A12_AD012_indexed


title: NC2 mRNAseq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD002_indexed


title: polysome mRNA siSCR U251 cells from 1st experiment

description: Biological replicate 1 of 4. heavy polysome-associated RNA; siScr treated U251 cells


title: CF-U-2


title: NC4 mRNAseq


title: CF-N-3

value: control


title: total mRNA siSCR U251 cells from 4th experiment

description: Biological replicate 4 of 4. Cytoplasmic RNA; siScr treated U251 cells

value: siRNA Scramble/control (siSCR)


title: Total RNAseq wt 7mM CAF rep 2

source_name: Total RNAseq wt 7mM CAF

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s instructions. Contaminating DNA was removed by treating with Turbo DNase (Invitrogen). rRNA was removed using the Ribo-Zero Gold rRNA removal kit (Yeast) (Illumina).
Libraries were prepared for Illumina sequencing with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced using NextSeq workflow.

tag: genotype

value: h- ED972 wild-type (wt)

tag: phenotype

value: wild-type phenotype

value: treated with 7 mM CAF for 18 hr


title: CF-N-1


title: CF-N-2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A12_AD010_indexed

value: PAL


title: Total RNAseq wt 7mM CAF rep 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD001_indexed


title: IFI64 mRNAseq

value: skin cells with IFI6 overexpression


title: Total RNAseq wt no treatment rep 2

source_name: Total RNAseq wt no treatment

value: no treatment


title: total mRNA siSCR U251 cells from 1st experiment

description: Biological replicate 1 of 4. Cytoplasmic RNA; siScr treated U251 cells

value: Human glioblastoma cell line

value: Cytoplasmic RNA


title: ChIPseq Meis in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc10.V5)] replicate 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard (v 2.8.2)
Alignment: ChIP-seq reads were aligned to the mm10 genome using Bowtie (v1.0.1) (Langmead, Trapnell, Pop, & Salzberg, 2009), using options “-q --best --strata -m 1 --chunkmbs 1024”.
Binding Event Detection: Genome-wide TF binding events.txt were called in each condition using MultiGPS (v0.74) (Mahony et al., 2014). EdgeR (v3.22.5) was used within the MultiGPS framework to test whether genomic sites were differentially bound by TFs (Robinson, McCarthy, & Smyth, 2010). A genomic site was defined as shared by TFs if significant binding events.txt were called in both TF ChIP-seq experiments (q-value < 0.001), and the TFs did not display differential read enrichment at that site as estimated by EdgeR (q-value > 0.01). A binding event was defined as “TF1>TF2” if a MultiGPS peak was called in TF1 ChIP-seq (q-value < 0.001), TF1 exhibited a greater log fold-change with respect to the input ChIP-seq than TF2, and TF1 and TF2 were significantly differentially bound as defined by EdgeR (q-value < 0.01). A similar strategy was applied to perform multi-way ChIP-seq comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

source_name: ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected 24h and 48h after Doxycycline (Dox) treatment. Crosslinking was performed at room temperature in 1mM DSG (ProteoChem) for 15min, followed by the addition of 1% FA (vol/vol) for an additional 15min. After quenching with Glycine, cells were divided into ~25-30x106 aliquots, pelleted by centrifugation and frozen at -80°C. After thawing cells on ice, lysis was performed in 5mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1× protease inhibitors (Roche, 11697498001) for 10 min at 4 °C. Cells were centrifuged for 5min, resuspended in 5mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1× protease inhibitors, and incubated for 10 min at 4 °C on a rotating platform. Cells were centrifuged for 5min and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1× protease inhibitors). Sonication was performed by splitting each sample to 2 Bioruptor tubes with sonication beads and using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off into an average size of approximately 200 bp. Immunoprecipitation was performed for 16h at 4 °C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with 5 µg of one of the following antibodies: mouse monoclonal antibody to Flag (Sigma, F1804) or rabbit polyclonal antibody to HA (Abcam, ab9110).
lllumina DNA sequencing libraries were prepared with one third of the ChIP sample or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Unligated adapters were removed using Agencourt AmpureXP beads (Beckman Coulter). Amplification was performed by PCR with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Final quantification of the library was performed using the KAPA library amplification kit on the Roche Lightcycler 480 before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ChIP-seq experiments, 3-3.5x10^6 mESCs were plated in 245mm x 245mm square dishes (Corning).

tag: strain genotype/variation

value: EB + 3 Days RA + SAG, D2+24hours Dox

value: Embryoid Bodies

tag: chip target

value: Meis

tag: chip antibody

value: sc-10599 (Santa Cruz)


title: total mRNA siSCR U251 cells from 3rd experiment

description: Biological replicate 3 of 4. Cytoplasmic RNA; siScr treated U251 cells

tag: cell line


title: ChIPseq Meis in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc9.V5)] replicate 1

tag: treatment

tag: cell type


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD012_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: Total RNAseq wt no treatment rep 1


title: IFI61 mRNAseq

value: skin cells with 5 Gy radiation


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A12_AD008_indexed


title: ChIPseq Meis in EB-Day3[D0+RA+SAG][D2+24hDox(iHoxc6.V5)] replicate 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD007_indexed


title: NC1 mRNAseq

value: skin cells of NC

value: human skin fibroblasts WS1 cells


title: control rep4

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description: WXZ

data_processing:
Transcriptome high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software and circRNAs were detected and identified with DCC software. Raw junction reads for all samples were normalized by total mapped reads number and log2 transformed. Differentially expressed circRNAs were identified by volcano plot between two groups, and fold change between two samples. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software. Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs. Alternative splicing was performed by SplAdder software.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel files include raw and normalized values for each Sample

source_name: exosome derived follicular fluid

extract_protocol:
Exosomes from follicular fluid were isolated by ExoQuick-TC Exosome Precipitation Solution Kit (System Biosciences).Total RNA was extracted from the exosome with using TRIzol reagent (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: non-PCOS

tag: sample type

value: exosomes in follicle fluid


title: Female EAE CysCKO rep 3

city: Calgary

first: Shalina

last: Ousman

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
bcl2fastq v2.20.0.422 (default params)
kallisto 0.42.4 (quant -b 100 --single -l 180 -s 20 -i /export/common/dbs/kallisto/mm10.refMrna)
raw counts rounded to integer
Genome_build: Mouse RefSeq mRNA July 2017 (mm10)
Supplementary_files_format_and_content: Raw Mapped Read Counts vs RefSeq transcripts

source_name: CD11b+ cells

extract_protocol:
CD11b+ cells were isolated by positive selection from spleens and RNA retrieved with an RNeasy Mini Kit. All samples were subjected to reverse transcription and Multiple Displacement Amplification with REPLI-g SensiPhi DNA Polymerase and oligo-dT primers as per the QIAGEN REPLI-g Single Cell RNA Library preparation kit and the manufacturer’s protocol. Libraries were prepared with 1 ug of total RNA using the QIAGEN GeneRead Adaptor I Set A 12-plex index adapters as per the REPLI-g single cell RNA library prep kit’s protocol and subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2 75 cycle sequencing kit as per the standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen-derived

tag: disease

value: EAE

value: Female

value: CysC knockout


title: IFI63 mRNAseq

value: skin cells with IFI6 overexpression


title: control rep3

description: WWY


title: Female EAE CysCKO rep 4


title: control rep1

description: GQ


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A12_AD007_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD007_indexed


title: control rep2

description: LJL


title: Female EAE CysCKO rep 2


title: Female EAE CysCKO rep 1


title: IFI62 mRNAseq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD010_indexed


title: Female EAE WT rep 4

value: wildtype


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD006_indexed


title: Female EAE WT rep 3


title: PCOS rep5

description: DBB

value: PCOS


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD006_indexed


title: PCOS rep4

description: CYT


title: control rep5

description: YJW


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD004_indexed


title: Female EAE WT rep 2


title: Female EAE WT rep 1

value: naive


title: PCOS rep3

description: ZLZ


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD008_indexed


title: PCOS rep2

description: YL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD002_indexed


title: G. lacustris, 1.5 degrees C, sample 4

city: Leipzig

first: Polina

last: Lipaeva

address: Permoserstraße 15

department: Biotox

institute: Helmholtz Centre for Environmental Research - UFZ

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of approx. 11 individuals of G. lacustris were acclimated at 6 degrees C for 14 days, gradually cooled down to 1.5 °C at a rate of 1-1.5 °C/d over about 6 days. Afterwards animals were kept at 1.5 degrees C for 1 month.

data_processing:
Raw reads were mapped onto transcriptome assemblies with the align_and_estimate_abundance.pl script from the Trinity v2.9.1 toolkit. We used salmon v1.1.0 as an abundance estimation method.
Differential expression was performed with DESeq2 v1.26.0. In-house scripts for data analysis are available at GitHub, see https://github.com/PolinaLip/Amphipods_ColdAdaptation_RNA.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files on series record)
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, tab-delimited text files) and DESeq2 output files (tab-delimited text files)

organism: Gammarus lacustris

source_name: whole body

extract_protocol:
Frozen coarse powder of amphipods was homogenized in 1 ml of Qiazol Reagent (Qiagen) using an MM400 mixer mill (Retsch). Total RNA of amphipods was manually isolated using an RNeasy Mini kit (Qiagen). All samples were treated with DNase (TURBO DNA-free Kit).
mRNA purification from total RNA was performed using an Oligotex mRNA Mini Kit. RNA concentration and quality were evaluated using Qubit 2.0 fluorometer and Agilent Bioanalyzer 2100. Twenty-four RNA-seq libraries were prepared from 20 ng of mRNA using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 14 days before the experiment. Please refer to description of individual samples for species- and sample-specific details. After the temperature expositions, animals were frozen in liquid nitrogen. The frozen animals were ground to coarse powder in a mortar, which was stored at -80 degrees C until further sample processing.

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

tag: depth

value: adult

value: 1.5 degree C


title: G. lacustris, 1.5 degrees C, sample 3


title: G. lacustris, 1.5 degrees C, sample 2


title: Female naïve CysCKO rep 3


title: PCOS rep1

description: MNN


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD001_indexed

tag: brain region

value: male


title: Female naïve CysCKO rep 2

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD012_indexed


title: Female naïve CysCKO rep 1

tag: tissue


title: Female naïve WT rep 3

tag: Sex


title: G. lacustris, 1.5 degrees C, sample 1


title: G. lacustris, 12 degrees C, sample 4

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of approx. 11 individuals of G. lacustris were acclimated at 6 degrees C for 14 days, then the temperature was gradually increased to 12 °C by 1-1.5 °C/day over about 6 days, and animals were kept at 12 degrees C for 1 month.

value: 12 degree C


title: G. lacustris, 12 degrees C, sample 3


title: SC_VitC_3_hMeDIP

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
5hmc-precipitated DNA
Counts of reads in each peak

data_processing:
Library strategy: hMeDIP-Seq
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the RN6 transcriptome using STAR or to RN6 genome using BWA
For hMeDIP samples, peaks were called using the Irreproducible Discovery Rate
Genome_build: RN6
Supplementary_files_format_and_content: Count files were generated using HTSeq-count.

organism: Rattus norvegicus

extract_protocol:
Qiagen RNEasy or Qiagen DNA Mini
Epicentre RiboZero or Active Motif hMeDIP

treatment_protocol: Cells were taken upon passage 3

value: Primary Schwann Cells

tag: passage

value: Passage 3

value: VitC


title: SC_VitC_3_Genomic_Input

description:
Genomic Input
Counts of reads in each peak

source_name: SC_VitC_Genomic Input


title: SC_VitC_2_hMeDIP


title: G. lacustris, 12 degrees C, sample 1


title: Female naïve WT rep 2

value: Spleen-derived

value: Female

tag: genotype


title: SC_VitC_2_Genomic_Input


title: Male EAE CysCKO rep 4

value: EAE

value: Male