title: SSMT2

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

country: China

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),

description: the water temperature (25 °C) was maintained for 72 h

data_processing:
The abundance of each tag was normalized to one transcript per million to allow comparison between samples. The raw data was filtered to remove low quality sequences including ambiguous nucleotides and adaptor sequences. The remaining clean reads were assembled using trinity software (Haas et al., 2013) as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by LC Sciences before subsequent analysis. The assembled transcriptome contigs were subjected to similarity searches against the NCBI non-redundant (nr) protein database using BLASTx with e-value cutoff of  1e-10. Gene name and description was assigned to each contig based on the BLASTx hit with the highest score. GO analysis was conducted on the assembled transcriptome  using InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) and integrated protein databases with default parameters. The GO terms associated with transcriptome  contigs were then obtained for describing their biological processes, molecular functions and cellular components. For pathway enrichment analysis, all DEGs were mapped to terms in the KEGG database and searched for significantly enriched KEGG terms compared to the whole transcriptome background. Functional enrichment analysis, including GO and KEGG, were performed using the ultrageometric test to identify which DEGs were significantly enriched in GO terms (P-value ≤0.05) and metabolic pathways (q-value ≤0.05) compared with the whole transcriptome background (Kanehisa et al., 2006, 2008).
All the cleaned reads were mapped to the assembled reference transcriptome by Bowtie (Marioni et al., 2008). RSEM was then used to estimate and quantify gene and isoform abundances according to the Trinity-assembled transcriptome. Finally, we used edgeR to normalize the expression levels in each of these samples and obtain the differentially expressed transcripts by pairwise comparisons (Robinson et al., 2010). EdgeR uses a negative binomial distribution method for differential expression analysis
Supplementary_files_format_and_content: 1_Trinity_gene.fasta,3_gene_expression_all.xlsx
Supplementary_files_format_and_content: fasta,xlsx, assembly sequences and expression data.

organism: Megalobrama amblycephala

source_name: liver

growth_protocol: We obtained three hundred healthy M. amblycephala juvenile that were of a similar size (mean weight: 20.25±2.24g) from the Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, China. The fish transferred immediately to the aquatic laboratory and held in three 500-L fiberglass tank (N = 60 fish/tank). During acclimation, each tank was supplied with pre-aerated municipal water at 25±0.5°C (pH 7.45±0.08; chloride 15–18 mg L−1; dissolved oxygen 5.16–6.53 mg L−1; total ammonia <0.5 mg L−1; baseline nitrite <0.1 mg L−1) with natural light and photoperiod. Fish were fed with a commercial pelleted diet twice daily at a ration of 3% total body weight. The water exchange rate was 33% per day and fecal matter was removed daily from the aerated tanks. After fasting for 24 h, blunt snout bream were selected from the holding tank and transferred to six plastic tanks. One tank contained 50 fish that were subjected to heat stress, and the other contained 50 fish that acted as the control group with triplicates, respectively.

extract_protocol:
Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions
To remove residual genomic DNA, the RNA samples were incubated with 10 units of DNA-free DNAse I (Ambion, USA) for 30 min at 37°C. The quality and quantity of the purified RNA were determined by measuring the absorbances at 260 nm and 280 nm (A260/A280) using a Nanodrop ND-1000 spectrophotometer (LabTech, USA). RNA integrity was further verified by electrophoresis through a 1.5% (w/v) agarose gel. Poly(A) mRNA was isolated from each total RNA sample with oligo (dT) magnetic beads (Invitrogen). The purified mRNA was fragmented with the RNA fragmentation kit (Ambion) and used as template for first strand cDNA synthesis using random hexamer primers and reverse transcriptase (Invitrogen). The second strand cDNA was synthesized using RNase H (Invitrogen) and DNA polymerase I (New England Biolabs, USA). The Illumina Genomic DNA Sample Prep kit (Illumina, USA) was used to generate 100 bp + 100 bp paired-end cDNA libraries by following the manufacturer’s protocol. The libraries were loaded onto flow cell channels for sequencing using an Illumina Hiseq4000 at the LC-BIO (Hangzhou, China)

treatment_protocol: For the heat-treatment group, the water temperature (35 °C) was maintained for 72 h, at the same time, the control flounder were maintained at 25 °C. At the end of the feeding trial, all individuals from each replication were quickly removed and anesthetized in diluted MS-222 (tricaine methanesulfonate, Sigma, USA) at the concentration of 100 mg L−1. Five fish were randomly selected from each tank and blood sample was quickly drawn from the caudal vein using heparinized plastic syringes. Blood sample was transferred immediately to heparinized capillary tubes to separated by centrifuged, and the supernatant was pooled and stored at −70 °C for subsequent palma analysis. Three fish from each exposure group were sacrificed with anesthesia overdose to obtain liver samples that were stored at −80°C until RNA extraction for RNA-seq analysis.

tag: group

value: control


title: MM1

status: Public on May 30 2017

type: SRA

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Marine stickleback in marine water rep1

library_source: genomic

data_processing:
Basecalling with CASAVA 1.8.2 software
Reads were mapped  to gasAcu1 reference genome with Bismark software. For individual CpGs in each sample, we estimated total coverage and coverage with reads supporting DNA methylation
Genome_build: gasAcu1
Supplementary_files_format_and_content: DNA methylation values of individual CpGs are provided in 3 files: (1) a bed file (coord.bed.bz2) providing genomic coordinates of the profiled CpGs, (2) a table (space-delimited) with total read coverage (Cov.tab.bz2) of individual CpGs (rows) with bisulfite reads, columns represent  individual samples; (3) a table (space-delimited) showing read coverage (M.tab.bz2) with reads supporting cytosine methylation in a given positions, columns represent  individual samples. The lines and names of loci correspond between those three files.

molecule: genomic DNA

organism: Gasterosteus aculeatus

source_name: Marine stickleback in marine water

growth_protocol: Ten freshwater three-spined sticklebacks were collected in the Mashinnoye Lake, Republic of Karelia, Russia, in June-July 2014. The same number of marine three-spined sticklebacks were collected in the Kandalaksha Gulf Coast (15 km from the railway station Poyakonda, Republic of Karelia, Russia) during the same time frame. To equal physiological state of the fish, only males in breeding dress were collected.

extract_protocol:
DNA was isolated from gills (an organ, directly exposed to water environment) using standard method of DNA extraction from animal tissue (phenol-chloroform).
Two micrograms of genomic DNA from three-spined stickleback samples of G. aculeatus were digested using 60 U MspI (Fermentas, USA) in 50 μl at 37°С for 18–24 h, followed by QIAquick purification (Qiagen, Germany). The end of the digested DNA was repaired, and an adenine was added to the 3’ end of the DNA fragments according to the Illumina standard end repair and add_A protocol (Illumina, USA). Pre-annealed forked Illumina adaptors containing 5’- methylcytosine instead of cytosine was ligated to both ends of DNA fragments using standard Illumina adaptor ligation protocol (Illumina, USA). Ligated fragments were then separated by 2% agarose gel (Sigma-Aldrich, USA). Fragments between 170 bp and 350 bp, (includes adaptor length), were selected and cut from the gel. DNA from gel slices were purified using Qiagen Gel Extraction Kit (Qiagen, Germany). The sodium bisulfite treatment and subsequent clean-up of size selected DNA was performed with the EZ DNA MethylationTM Kit (ZymoResearch, USA) according to the manufacturer’s instructions. The bisulfite-treated DNA fragments were amplified using PCR and the following reaction: 5 μl of eluted DNA, 1 μl of NEB PE PCR two primers (1.0 and 2.0) and 45 μl Platinum PCR Supermix (Invitrogen, USA). The amplification conditions were as follows: 5 min at 95°C, 30 s at 98°C then 15 (10 s at 98°C, 30 s at 65°C, 30 s at 72°C), followed by 5 min at 72°C. The PCR reaction was purified by MinElute PCR Purification Kit (Qiagen), and final reduced representation bisulfite library was eluted in 15 μl EB buffer. The concentration of the final library was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: To explore immediate epigenetic response of a stickleback to changes in osmotic conditions of the environment, five marine fish were kept for 4 days in fresh water (M@F) and, vice versa, five freshwater fish were kept for 4 days in marine water (F@M). Control samples were kept in their native habitats (marine samples in marine water (M@M), freshwater samples in fresh water (F@F)) to equal captivity stress influence.

tag: original population

value: Marine

tag: treatment

tag: tissue

value: gills


title: Primary Retinal Pericytes (Cell System, USA)

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

country: USA

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

molecule: total RNA

organism: Homo sapiens

source_name: Primary Cells

growth_protocol: human embryonic stem cells (h1ESCs) directed towards mesendodermal differentiation in coculture with mouse bone marrow stromal cells OP9 for 2 days. APLNR+PDGFRa+ primitive posterior mesodermal cells were selected using magnetic sorting and grown in serum-free clonogenic cultures supplemented with FGF2.

extract_protocol:
Illustra RNA spin mini RNA isolation kit (GE healthcare).
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

treatment_protocol: 12 days mature colonies were differentiated into immature pericytes or immature smooth muscles cells under the influence of PDGF-BB or TGFb plus sphingosylphosphorylcholine (SPC), imPCs were further cultured on fibronectin and collagen coated plates in Pericytes Medium with added SB431542 (10μM) and PDGF-BB (50ng/ml) or SB431542 (10μM), PDGF-BB (10ng/ml), VEGF (10ng/ml), EGF2 (2ng/ml) for additional 6 days to generate Type 1 mature pericytes (PC1) and Type 2 mature pericytes (PC2) respectively.The SMCs were matured by culturing on human fibronectin and collagen-coated plates in complete EGM-2 medium (Lonza) with added PD0325901 MEK inhibitor (1μM) for an additional 6 days.

tag: source cell type

value: Primary Cells

tag: cell subtype

value: Primary Retinal Pericytes


title: DMSO_Input_2

status: Public on May 29 2017

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description:
ChIP
Input for DMSO-treatd anti-acetylated histone ChIP

data_processing:
Reads were aligned using BWA with default parameters
Duplicate reads and reads mapping to multiple positions in the genome were removed
Reads were normalized to the total number of mapped reads
ChIP signals were normalized to input control
MACS2 was used to call ChIP-peaks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig read density for Histone data

growth_protocol: NCI-H1299 cells were grown in RPMI 1640 supplemented with 10% FCS

extract_protocol:
Genomic DNA was isolated using the DNeasy blood & tissue kit (Qiagen)
NEBNext Ultra Prep Kit for Illumina (NEB)

treatment_protocol: Cells were treated with 500 nM DAC, 500 nM SB939, or 500 nM DAC + 500 nM SB939 for 72, 18, 18, or 72+18 h, respectively

value: DMSO

tag: antibody

value: Input


title: SL-BPK275-1

city: Antwerpen

first: Bart

last: Cuypers

state: Antwerp

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: Adrem Data Lab

description:
Biological Replicate 1 of murine macrophages infected with Leishmania donovani BPK275 amastigotes, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt, SL_SEQ_PROAMA_DESEQ2.txt

data_processing:
Read Trimming with Trimmomatic v0.35 and settings LEADING:20 TRAILING:20 ILLUMINACLIP:adapter.fa:2:40:15 SLIDINGWINDOW:4:20 MINLEN:36. For SL-seq, an extra preceding Trimmomatic step was performed on the R2 FASTQ files to hard-trim the first 21 bases, which correspond to the SL sequence (HEADCROP:21)
Step for amastigote samples only:  Mapping with tophat2 to the human reference genome (hg38) to filter out reads originating from the human reference genome (standard settings)
Step for amastigote samples only:  Conversion of unmapped reads to FASTQ files with the samtools sort -n and samtools fastq functions (samtools-1.3.1) for further analysis
Mapping of the reads to the LdBPKv2 reference genome with bwa mem (version 0.7.15, default settings) and conversion to sorted bam file with samtools-1.3.1
Generation of count tables with htseq-count version 0.6.1 and settings '-r name -f bam -t gene -i ID -s no'
Differential expression was determined with the DESEQ2 package in R
Genome_build: HG38 and LdBPKv2
Supplementary_files_format_and_content: tab delimited tekst files of count tables and of differentially expression analysis by DESEQ2

organism:
Leishmania donovani
Homo sapiens

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium containing stationary phase L. donovani BPK275 promastigotes (macrophage:promastigote ratio of 1:10). After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Spliced-Leader Seq

tag: life stage

value: Intracellular Amastigote

tag: strain


title: SL-NI-1-DIL

description:
Biological Replicate 1 of unifected murine macrophages, library prepared with SL-seq
processed data file: SL_Macrophages_Dilutions_counttable.txt

extract_protocol:
THP-1 cells (ATCC TIB202) were treated with 0.1 μM phorbol myristate acetate (PMA, Sigma) at 37°C for 48 h, after which they were washed and incubated with complete RPMI medium. After 4 h incubation at 37°C, the cells were washed 3 times with PBS and incubated for 24 h at 37°C. RNA was subsequently extracted with the RNAqueous micro kit (Ambion).
Spliced-Leader Seq

value: Uninfected Control


title: SSMT1

description: the water temperature (35 °C) was maintained for 72 h

value: heat-treatment


title: DMSO_H3K14ac

description: ChIP


title: Mesenchymoangioblast (MAB) S.054024.0073097

source_name: human embryonic stem cells (h1ESCs) derived Mesenchymal stem cells

tag: cell type

value: Mesenchymoangioblast (MAB)


title: DMSO_H3K18ac

description: ChIP


title: DMSO_H4K8ac

description: ChIP


title: DMSO_H4K12ac

description: ChIP


title: DMSO_H2AK9ac

description: ChIP


title: ILL-LOG2

description:
Biological Replicate 2 of leishmania donovani logaritmic stage promastigotes, library prepared with the Illumina stranded mRNA kit
processed data file : ILL_SEQ_LOGSTAT_counttable.txt, ILL_SEQ_LOGSTAT_DESEQ2.txt

molecule: polyA RNA

organism: Leishmania donovani

source_name: Cell Culture

extract_protocol:
Promastigotes were cultured at 26°C in HOMEM supplemented with 20% heat-inactivated fetal bovine serum (Biochrom) and were harvested on day 4 (LOG stage, exponential growth). The parasites were washed 3 times by centrifugation at 18000 g at 0 °C and resuspended in ice-cold PBS buffer. RNA was subsequently extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN).
Illumina Stranded mRNA Seq

value: Logaritmic Phase Promastigotes


title: DMSO_H2BK5ac

description: ChIP


title: MM4

description: Marine stickleback in marine water rep3


title: DAC+SB_H2AK9ac

description: ChIP

value: DAC+SB


title: DAC+SB_H3K4ac

description: ChIP


title: DAC+SB_Input_2

description:
ChIP
Input for DAC+ SB anti-acetylated histone ChIP


title: DMSO_H3K23ac

description: ChIP


title: DAC+SB_H4K12ac

description: ChIP


title: DAC+SB_H3K18ac

description: ChIP


title: DAC+SB_H2BK5ac

description: ChIP


title: DAC+SB_H4K8ac

description: ChIP


title: DAC+SB_H3K14ac

description: ChIP


title: DAC+SB_H3K23ac

description: ChIP


title: DMSO_H3K4ac

description: ChIP


title: SB939_H2AK9ac

description: ChIP


title: SB939_H2BK5ac

description: ChIP


title: SB939_H4K12ac

description: ChIP


title: SB939_H3K4ac

description: ChIP


title: SB939_H3K18ac

description: ChIP


title: SB939_H3K14ac

description: ChIP


title: SB939_H4K8ac

description: ChIP


title: DAC_H2BK5ac

description: ChIP

value: DAC


title: SB939_H3K23ac

description: ChIP


title: DAC_H4K12ac

description: ChIP


title: DAC_H2AK9ac

description: ChIP


title: DAC_H3K18ac

description: ChIP


title: DAC_H4K8ac

description: ChIP


title: DAC_H3K23ac

description: ChIP


title: SB939_Input_2

description:
ChIP
Input for SB9393-treated anti-acetylated histone ChIP


title: DAC WGBS

description: WGBS

data_processing:
reads were aligned with HISAT 0.1.6-beta or BWA using default parameters for CAGE or ChIP/WGBS data, respectively
reads mapping to multiple positions in the genome were filtered
CAGEr, MACS2, and bsseq were used to call CAGE-clusters, ChIP-peaks, and methylation levels, respectively
Genome_build: hg19
Supplementary_files_format_and_content: processed files contain CpG methylation for WGBS data; bigWig read density for Histone data; consensus CAGE clusters are also provided for CAGE-seq data.

extract_protocol:
total RNA was isolated using the Rneasy kit (Qiagen); genomic DNA was isolated using the DNeasy blood & tissue kit (Qiagen)
For CAGE, ChIP-, and WGB-sequencing the CAGE™ Preparation Kit (DNAFORM.jp), NEBNext Ultra Prep Kit for Illumina (NEB), and EpiTect Bisulfite (Qiagen) + TruSeq DNA PCR-Free LT Sample Prep Kit (Illumina) were used, respectively

treatment_protocol: Cells were treated with 500 nM DAC, 500 nM SB939, 1500 nM SAHA, or 500 nM DAC + 500 nM SB939 for 72, 18, 18, or 72+18 h, respectively


title: DACSB WGBS

description: WGBS

value: DACSB


title: DMSO WGBS

description: WGBS


title: SB939_Input

description: ChIP


title: SB939_H3K9me3

description: ChIP


title: SB939_H3K36me3

description: ChIP


title: SB939_H3K9ac

description: ChIP


title: SB939_H3K4me3

description: ChIP


title: SB939_H3K4me1

description: ChIP


title: SB939_H3K27me3

description: ChIP


title: DAC_Input_2

description:
ChIP
Input for DAC-treated anti-acetylated histone ChIP


title: SAHA_H3K9me3

description: ChIP

value: SAHA


title: SAHA_H3K4me1

description: ChIP


title: SAHA_Input_20131128

description: ChIP


title: SB939 WGBS

description: WGBS


title: DAC_H3K14ac

description: ChIP


title: SAHA_H3K4me3

description: ChIP


title: SAHA_H3K9ac

description: ChIP


title: DAC_H3K4ac

description: ChIP


title: DMSO_H3K4me3

description: ChIP


title: SAHA_H3K36me3

description: ChIP


title: DMSO_Input

description: ChIP


title: DMSO_H3K9ac

description: ChIP


title: SAHA_H3K27ac

description: ChIP


title: TASOR_input

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using Bowtie2
Uniquely mapping reads imported into SeqMonk and EaSeq
Genome_build: GRCh37

source_name: Input for IgG and TASOR ChIP

growth_protocol: RPMI 1640

extract_protocol:
Formaldehye-crosslinked chromatin was sheared by sonication to an average size of ~300bp and then immunoprecipitated with the relevant antibodies: rabbit anti-TASOR (Atlas Antibodies, HPA006735), rabbit IgG (Cell Signaling, #2729) or anti-V5 agarose affinity gel (Sigma-Aldrich, A7345).
NEBNext ChIP-seq Library Prep Kit (NEB)

tag: cell line

value: HeLa


title: V5-MORC2_input

source_name: Input for V5 ChIP in MORC2 knockout cells transduced with V5-ragged MORC2


title: DACSB_Input

description: ChIP


title: DACSB_H3K9ac

description: ChIP


title: DMSO_H3K4me1

description: ChIP


title: DMSO_H3K27ac

description: ChIP


title: DMSO_H3K36me3

description: ChIP


title: DMSO_H3K27me3

description: ChIP


title: DACSB_H3K4me1

description: ChIP


title: DACSB_H3K9me3

description: ChIP


title: DACSB_H3K4me3

description: ChIP


title: SAHA_H3K27me3

description: ChIP


title: SB939_H3K27ac

description: ChIP


title: DACSB_H3K27ac

description: ChIP


title: DACSB_H3K36me3

description: ChIP


title: V5_control_input

source_name: Input for V5 ChIP in MORC2 knockout cells


title: V5-MORC2_inHUSHKO_input

source_name: Input for V5 ChIP in HUSH triple knockout cells transduced with V5-tagged MORC2


title: V5 control

source_name: V5 ChIP in MORC2 knockout cells


title: Selected

data_processing:
Library strategy: Amplicon
Reads trimmed of constant sequences using fastx toolkit
Reads aligned to the reference GeCKO v2 library using Bowtie2
Raw counts generated for each sgRNA
Count tables analyzed using RSA algorithm
Supplementary_files_format_and_content: RSA output

source_name: KBM7 cells

growth_protocol: IMDM

extract_protocol:
Genomic DNA was extracted using the Puregene Core Kit A (Qiagen).
sgRNA sequences were amplified by PCR.

treatment_protocol: Genome-wide mutagenesis was carried out using the GeCKO v2 sgRNA library, and GFPbright cells were isolated through sequential rounds of FACS.


title: DAC_Input

description: ChIP


title: Unselected


title: DAC_H3K4me3

description: ChIP


title: MORC2 Knockout (DIVA)

data_processing:
Library strategy: LAM-PCR
Reads trimmed of adaptor sequences using fastx_trimmer
Aligned to the reference human genome using Bowtie2
Uniquely mapping reads imported into SeqMonk
Reads collapsed into a set of unique points of viral integrations
Genome divided into a set of 10 kb windows (overlapping by 5 kb) and the number of unique integrations sites in each window compared between wild-type and MORC2 knockout samples
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized number of unique lentiviral integration sites detected in each genomic window

source_name: HeLa cells

extract_protocol:
Genomic DNA was extracted using the Puregene Core Kit A (Qiagen).
Lentiviral integration sites were amplified using LAM-PCR

treatment_protocol: Cells were transduced twice with an HIV-1-derived lentiviral vector to achieve high multiplicity of infection.

tag: genotype

value: MORC2 KO


title: DAC_H3K9me3

description: ChIP


title: Wild-type (DIVA)

value: Wild-type


title: DAC_H3K9ac

description: ChIP


title: Wild-type ChIP-Seq

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using Bowtie2
Uniquely mapping reads imported into SeqMonk
H3K9me3 scores generated for a series of 1kb windows across the genome, discounting windows with low H3K9me3 levels (<40 reads in wild-type cells)
Genome_build: GRCh37
Supplementary_files_format_and_content: H3K9me3 scores for 1kb windows across the genome

extract_protocol:
Formaldehye-crosslinked chromatin was sheared by sonication to an average size of ~300bp and then immunoprecipitated with anti-H3K9me3 antibody ab8898 (Abcam)
NEBNext ChIP-seq Library Prep Kit (NEB)


title: R252W MORC2 sample

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using HISAT2
Uniquely mapping reads imported into SeqMonk and analysed using the RNA-seq quantiation pipeline
Genome_build: GRCh37

extract_protocol:
RNeasy kit (Qiagen) with on-column DNaseI digestion
Ribo-Zero Gold rRNA depletion (Epicentre) followed by TruSeq Stranded Total RNA Library Prep (Illumina)

treatment_protocol: Transduced with lentiviral vector encoding wild-type or R252W mutant MORC2; hygromycin selection used to eliminate untransduced cells.

tag: genotype/variation

value: MORC2 knockout, transduced with lentviral vector encoding R252W MORC2


title: Wild-type MORC2 sample

value: MORC2 knockout, transduced with lentiviral vector encoding wild-type MORC2


title: SETDB1 KO ChIP-Seq

value: SETDB1 Knockout


title: DAC_H3K4me1

description: ChIP


title: V5-MORC2_W505A_input

source_name: Input for V5 ChIP in MORC2 knockout cells transduced with a V5-tagged W505A MORC2 mutant


title: DAC_H3K36me3

description: ChIP


title: R252W MORC2

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using HISAT2
Uniquely mapping reads imported into SeqMonk and analysed using the RNA-seq quantitation pipeline
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized abundance measurements from edgeR

growth_protocol: DMEM

tag: transduced with

value: R252W MORC2


title: DAC Single-end CAGE-seq


title: SAHA Single-end CAGE-seq


title: Mock sample

value: MORC2 knockout, mock transduced


title: DACSB Single-end CAGE-seq


title: Mock rep1

value: Mock


title: DAC_H3K27ac

description: ChIP


title: MORC2 KO (RNA-Seq)

data_processing:
Reads trimmed of adaptor sequences using Trim Galore
Aligned to the reference human genome using HISAT2
Uniquely mapping reads imported into SeqMonk and analysed using the RNA-seq quantiation pipeline
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized abundance measurments from DEseq

extract_protocol:
miRNeasy kit (Qiagen) with on-column DNaseI digestion
Ribo-Zero Gold rRNA depletion (Epicentre) followed by TruSeq Stranded Total RNA Library Prep (Illumina)


title: SB939 Single-end CAGE-seq


title: Wild-type (RNA-Seq)


title: DMSO Single-end CAGE-seq

value: DMSO


title: Wild-type MORC2

value: Wild-type MORC2


title: TASOR

description: HeLa cells

source_name: TASOR ChIP in wild-type HeLa cells


title: MORC2 KO ChIP-Seq

value: MORC2 Knockout


title: DAC Paired-end CAGE-seq


title: DACSB Paired-end CAGE-seq


title: SB939 Paired-end CAGE-seq


title: IgG

description: HeLa cells

source_name: IgG control ChIP in wild-type HeLa cells


title: V5-MORC2 (W505A)

description: CW domain mutant W505A expressed in MORC2 knockout HeLa cells generated through CRISPR/Cas9-mediated gene disruption

source_name: V5 ChIP in MORC2 knockout cells transduced with a V5-tagged W505A MORC2 mutant


title: SAHA Paired-end CAGE-seq


title: DAC_H3K27me3

description: ChIP


title: SC_rep2_4Gts_8h_mRNA

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: fragmented rRNA-depleted mRNA

data_processing:
Reads were trimmed of adapter sequence: TGGAATTCTCGGGTGCCAAGG. Reads were mapped to the S288C genome using Tophat and requiring uniquely mapping reads. Read 5' ends maping to the first 8 codons of each ORF were discarded. ORF read counts were rescaled in DESeq to compute TEs.
Library strategy: Ribosome footprint profiling
Genome_build: SacCer3
Supplementary_files_format_and_content: YPA_footprint_offset8_rpkms.tsv: tab-seperated text of ribosome footprint RPKMs
Supplementary_files_format_and_content: YPA_mRNA_offset8_rpkms.tsv: tab-seperated text of mRNA RPKMs
Supplementary_files_format_and_content: SC_footprint_offset8_rpkms.tsv: tab-seperated text of ribosome footprint RPKMs
Supplementary_files_format_and_content: SC_mRNA_offset8_rpkms.tsv: tab-seperated text of mRNA RPKMs
Supplementary_files_format_and_content: YPA_TEs.tsv: tab-seperated text of TE values (footprint/mRNA)
Supplementary_files_format_and_content: SC_TEs.tsv: tab-seperated text of TE values (footprint/mRNA)
Supplementary_files_format_and_content: CIVIT_seq_RPM.tsv: tab-seperated text of CIVIT-seq RPM values (reads per million)
Supplementary_files_format_and_content: CIVIT_Seq_monosome_recruitment.tsv: tab-seperated text of CIVIT-seq monosome recruitment scores, and pool sequences
Supplementary_files_format_and_content: CIVIT_seq_monosome_recruitment_change.tsv: tab-seperated text of changes in CIVIT-seq monosome recruitment scores between WT and mutant transcript leader variants

organism: Saccharomyces cerevisiae

growth_protocol:
SC+2% raff/2% gal 30 minutes, 36°C for 8hours
cycloheximide added to  0.1mg/ml, and cultures immediately poured over ice and harvested by centrifugation, then frozen in liquid nitrogen, cell pellets thawed and lysed by glass bead beating

extract_protocol: Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).


title: SC_rep2_4Gts_2h_mRNA

description: fragmented rRNA-depleted mRNA

growth_protocol:
SC+2% raff/2% gal 30 minutes, 36°C for 2hours
cycloheximide added to  0.1mg/ml, and cultures immediately poured over ice and harvested by centrifugation, then frozen in liquid nitrogen, cell pellets thawed and lysed by glass bead beating


title: V5-MORC2

description: V5 epitope-tagged wild-type MORC2

source_name: V5 ChIP in MORC2 knockout cells transduced with V5-ragged MORC2


title: SC_rep2_WT_8h_mRNA

description: fragmented rRNA-depleted mRNA


title: E12_brain_H2AZcKO_RNA-seq

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Brain

extract_protocol:
Cerebral cortex was dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: development stage

value: brain

tag: tissue subtype

value: telencephalic tissue


title: E12_brain_H2AZfl/fl_RNA-seq


title: SC_rep2_WT_2h_mRNA

description: fragmented rRNA-depleted mRNA


title: P30-rd10_rep2

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

data_processing:
Paired-end sequencing of 125 bases length was performed on HiSeq 2500 system (Illumina)
Pass-filtered reads were mapped using TopHat v2.1.0 and aligned to UCSC mouse reference genome mm10.
Count table of the gene features was obtained using HT-Seq
Normalization, differential expression analysis and FPKM (fragments per kilobase of exon per million fragments mapped) values were computed using EdgeR
Genome_build: UCSC mouse reference genome mm10.
Supplementary_files_format_and_content: tab-delimited text files include counts from HT-Seq and List of Differentially expressed genes with FPKM values for each Sample, fold change, adjusted p-value

source_name: rd10 mouse retina at age postnatal day 30

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Nucleospin RNA Plus kit, which includes DNase treatment. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described (Brooks et al. 2012). The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing

value: Retina

tag: age

value: post natal day 30


title: 60D_Round_2_techReplicate2

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

description:
36227_2
DESeq2.ENCORvsSpheroid.60days.txt

data_processing:
Basecalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Homo sapiens genome (hg38) and a maxiumum of 6 missmatches. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2015_01, hg38). rRNA loci are masked on the genome for downstream analysis.
Aligned reads are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with UCSC RefSeq annotation (hg38) of genes with at least one protein-coding transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator.
Furthermore, the aligned reads were counted with HTSeq (0.6.1p1) and the genes were subjected to differential expression analysis with DESeq2 (v1.6.3).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited "cufflinks" .txt files include FPKM values for each sample (standard output Cufflinks); tab-delimited "DESeq2" .txt files contain the differential expression analysis plus mean FPKM values (DESeq2)

source_name: 60D, Round

growth_protocol: Human ESCs were differentiated to 3D brain tissue according to the original cerebral organoid protocol (Lancaster et al. Nature 2013)

extract_protocol:
RNA was isolated from individual organoids using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific, cat. #KIT0204) (20 days timepoint) or Trizol Reagent (Thermo Fisher Scientific, cat. # 15596018) (60 days timepoint) according to the manufacturers instructions.
RNA concentration and integrity was analyzed using RNA 6000 Nano Chip (Agilent techReplicatenologies, cat. #5067-1511). RNA was enriched for mRNA using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, cat. # 61006). Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, cat. # E7420L). Barcoded samples were multiplexed and sequenced 50bp SE on a HighSeq2500 (Illumina). Sample preparation and sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at).

treatment_protocol: Human ESCs were differentiated using the enCOR approach, with microscaffolds and pulse of CHIR

value: embryonic stem cells

tag: time

value: 60 days in vitro

tag: method used

value: Spheroid

value: wildtype


title: 60D_Fiber_3_techReplicate2

description:
36225_2
DESeq2.ENCORvsSpheroid.60days.txt

source_name: 60D, Fiber

value: ENCOR


title: P30-rd10_rep1

tag: tissue


title: SC_rep2_WT_8h_footprints

description: ribosome-protected mRNA fragments


title: SC_rep2_4Gts_2h_footprints

description: ribosome-protected mRNA fragments


title: V5-MORC2 (in HUSH KO)

description: V5 epitope-tagged MORC2 in HUSH triple knockout cells

source_name: V5 ChIP in HUSH triple knockout cells transduced with V5-tagged MORC2

value: HeLa


title: 60D_Round_1_techReplicate2

description:
36226_2
DESeq2.ENCORvsSpheroid.60days.txt


title: 60D_Fiber_2_techReplicate2

description:
36224_2
DESeq2.ENCORvsSpheroid.60days.txt


title: SC_rep2_4Gts_8h_footprints

description: ribosome-protected mRNA fragments


title: DMSO Paired-end CAGE-seq

tag: treatment


title: SC_rep1_4Gts_8h_mRNA

description: fragmented rRNA-depleted mRNA


title: 20D_Round_3_techReplicate2

description:
36222_2
DESeq2.ENCORvsSpheroid.20days.txt

source_name: 20D, Round

value: 20 days in vitro


title: P30-C57_rep3

source_name: wild type mouse retina at age postnatal day 30

value: wild type


title: SC_rep1_4Gts_2h_mRNA

description: fragmented rRNA-depleted mRNA


title: P30-C57_rep1


title: 20D_Round_2_techReplicate2

description:
36221_2
DESeq2.ENCORvsSpheroid.20days.txt


title: P30-rd10_rep3


title: 18M-PIAS3-KO_rep3

data_processing:
Paired-end sequencing of 100 bases length was performed on HiSeq 2500 system (Illumina)
Pass-filtered reads were mapped using TopHat v2.1.1 and aligned to UCSC mouse reference genome mm10.
Count table of the gene features was obtained using FeatureCounts
Normalization, differential expression analysis and FPKM (fragments per kilobase of exon per million fragments mapped) values were computed using EdgeR
Genome_build: UCSC mouse reference genome mm10.
Supplementary_files_format_and_content: tab-delimited text files include counts from FeatureCounts and List of Differentially expressed genes with FPKM values for each Sample, fold change, adjusted p-value

source_name: PIAS3 KO mouse retina at 18M

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described (Brooks et al. 2012). The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing

value: 18 months

value: PIAS3 KO


title: 18M-PIAS3-KO_rep2


title: SC_rep1_WT_2h_mRNA

description: fragmented rRNA-depleted mRNA


title: 20D_Fiber_3_techReplicate2

description:
36219_2
DESeq2.ENCORvsSpheroid.20days.txt

source_name: 20D, Fiber


title: 18M-PIAS3-KO_rep1


title: 18M-C57_rep2

source_name: wild type mouse retina at 18M


title: 60D_Fiber_1_techReplicate2

description:
36223_2
DESeq2.ENCORvsSpheroid.60days.txt


title: SC_rep2_WT_2h_footprints

description: ribosome-protected mRNA fragments


title: 20D_Fiber_2_techReplicate2

description:
36218_2
DESeq2.ENCORvsSpheroid.20days.txt


title: 20D_Fiber_1_techReplicate2

description:
36217_2
DESeq2.ENCORvsSpheroid.20days.txt


title: DACSB_H3K27me3

description: ChIP

value: DACSB


title: SC_rep1_WT_8h_footprints

description: ribosome-protected mRNA fragments


title: SC_rep1_4Gts_8h_footprints

description: ribosome-protected mRNA fragments


title: SC_rep1_4Gts_2h_footprints

description: ribosome-protected mRNA fragments


title: 18M-C57_rep1


title: 60D_Round_3_techReplicate1

description:
36228_1
DESeq2.ENCORvsSpheroid.60days.txt


title: P30-C57_rep2


title: 60D_Round_2_techReplicate1

description:
36227_1
DESeq2.ENCORvsSpheroid.60days.txt


title: 60D_Round_1_techReplicate1

description:
36226_1
DESeq2.ENCORvsSpheroid.60days.txt


title: P21-PIAS3-KO_rep3

source_name: PIAS3 KO mouse retina at age postnatal day 21

value: post natal day 21


title: YPA_4Gts_2h_mRNA

description: fragmented rRNA-depleted mRNA

growth_protocol:
YPA+2% raff/2% gal 30 minutes, 36°C for 2hours
cycloheximide added to  0.1mg/ml, and cultures immediately poured over ice and harvested by centrifugation, then frozen in liquid nitrogen, cell pellets thawed and lysed by glass bead beating


title: 18M-C57_rep3


title: 60D_Fiber_3_techReplicate1

description:
36225_1
DESeq2.ENCORvsSpheroid.60days.txt


title: SC_rep1_WT_8h_mRNA

description: fragmented rRNA-depleted mRNA


title: 20D_Round_1_techReplicate2

description:
36220_2
DESeq2.ENCORvsSpheroid.20days.txt


title: P21-PIAS3-KO_rep2


title: P21-PIAS3-KO_rep1


title: YPA_4Gts_pre_shift_mRNA

description: fragmented rRNA-depleted mRNA

growth_protocol:
YPA+2% raff, 25°C
cycloheximide added to  0.1mg/ml, and cultures immediately poured over ice and harvested by centrifugation, then frozen in liquid nitrogen, cell pellets thawed and lysed by glass bead beating


title: 60D_Fiber_2_techReplicate1

description:
36224_1
DESeq2.ENCORvsSpheroid.60days.txt


title: P21-C57_rep3

source_name: wild type mouse retina at age postnatal day 21


title: SC_rep1_WT_2h_footprints

description: ribosome-protected mRNA fragments


title: YPA_WT_2h_mRNA

description: fragmented rRNA-depleted mRNA


title: 60D_Fiber_1_techReplicate1

description:
36223_1
DESeq2.ENCORvsSpheroid.60days.txt


title: P21-C57_rep2


title: YPA_WT_0h_mRNA

description: fragmented rRNA-depleted mRNA

growth_protocol:
YPA+2% raff/2% gal 30 minutes, 25°C
cycloheximide added to  0.1mg/ml, and cultures immediately poured over ice and harvested by centrifugation, then frozen in liquid nitrogen, cell pellets thawed and lysed by glass bead beating


title: 20D_Round_2_techReplicate1

description:
36221_1
DESeq2.ENCORvsSpheroid.20days.txt


title: YPA_4Gts_0h_mRNA

description: fragmented rRNA-depleted mRNA


title: 20D_Round_3_techReplicate1

description:
36222_1
DESeq2.ENCORvsSpheroid.20days.txt


title: YPA_4Gts_2h_footprints

description: ribosome-protected mRNA fragments


title: P21-C57_rep1


title: SAM24313603 Skin CD34+ cells control NaCl

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

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.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts + RPKM

source_name: RNA

extract_protocol: After FACS, RNA was extracted from samples using the RNeasy Micro kit (cat # 74004; Qiagen) according to the manufacturer's instructions including the on-column DNase digestion. RNA quality was evaluated using Bioanalyzer.

value: CD34+ cells control

value: skin

value: NaCl


title: SAM24313604 Skin CD34+ cells DT-treated DT

value: CD34+ cells DT-treated

value: DT


title: YPA_4Gts_pre_shift_footprints

description: ribosome-protected mRNA fragments


title: YPA_4Gts_0h_footprints

description: ribosome-protected mRNA fragments


title: 20D_Fiber_2_techReplicate1

description:
36218_1
DESeq2.ENCORvsSpheroid.20days.txt

value: embryonic stem cells


title: YPA_WT_2h_footprints

description: ribosome-protected mRNA fragments


title: 20D_Fiber_1_techReplicate1

description:
36217_1
DESeq2.ENCORvsSpheroid.20days.txt


title: YPA_WT_0h_footprints

description: ribosome-protected mRNA fragments


title: 20D_Fiber_3_techReplicate1

description:
36219_1
DESeq2.ENCORvsSpheroid.20days.txt


title: SAM24314502 Skin CD34+ cells DT-treated DT


title: SAM24314503 Skin CD34+ cells control NaCl


title: E13_brain_H2AZ_ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the following configurations.
Quality control checks on raw sequence data by FastQC.
Peaks were called using MACS with the following setting: FDR=10%, Enrichment Fold (H2AZ/input), p-value <= 10-5.
Gene Ontology based on top300 peaks (the 300 most enrichments, p-value<=10-5, FDR<=0.1).
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: brain

extract_protocol:
Briefly, E13 neural progenitor cells were crosslinked with 1% formaldehyde solution (50 mM, HEPES-KOH, pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1% formaldehyde) for 10 minutes at room temperature, and the reaction was quenched with glycine. After washing two times with ice-cold PBS, cells were resuspending the cells in lysis buffer 1(50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibitors) for 10 minutes at 4℃. Nuclei were isolated at at 4000rpm for 5 minutes at 4°C and resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x protease inhibitors), and then rocked gently at room temperature for 10 minutes. Nuclei was sonicated in lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 1x Protease Inhibitor) using a Scientz-IID sonicator. Chromatin was immunoprecipitated overnight at 4℃with 50 μl Protein A bead (Dynabeads, Invitrogen) pre-coupled with 2 μg appropriate antibodies. Beads were washed three times with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, Tris-HCl, pH 8.1) and three times with high-salt buffer buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, Tris-HCl, pH 8.1). After reverse crosslinking was performed, DNA was eluted and purified using a DNA purification kit (Tiangen).
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.

value: brain

value: neural progenitor cells

tag: chip antibody

tag: molecule subtype

value: Chromatin IP against H2AZ


title: E13_brain_input

value: nono (input)

value: input DNA


title: SAM24314504 Skin CD34+ cells DT-treated DT


title: NF90+NF110 KO RIP-seq IP rep3

status: Public on May 28 2017

city: Boston

first: Hu

last: Jin

state: MA

address: 10 Shattuck St

department: Biomedical Informatics

institute: Harvard Medical School

data_processing:
Both RNA-seq and RIP-seq reads were mapped to the mm10 reference genome using Tophat2 v2.0.10 with options -g 1 --prefilter-multihits.
Cuffnorm from Cufflinks v2.2.1 was used with the gtf file from UCSC mm10 (Illumina iGenomes July 17, 2015 version) as transcript annotation to evaluate relative expression level of genes (fragments per kilobase of transcript per million mapped reads (FPKM)).
Genes belonging to the following categories were removed from subsequent analysis: tRNA, Mt-tRNA, rRNA, scRNA, snRNA, snoRNA, miRNA, and misc-RNA.
HTSeq-count v0.6.1 was used to summarize read counts for each gene.
The resulting read count matrices were used in DESeq2 analysis of differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm.xlsx contains fpkm value for genes (calculated by Cuffnorm); "deseq2.xlsx" contains library-size normalized read count (calculated by DESeq2) for genes and data calculated by DESeq2 for calling differentially expressed genes between different conditions.

source_name: embryonic stem cells

extract_protocol:
Total RNA was collected using TRIzol (ThermoFisher Scientific) according to the manufacturer’s protocol.
For NF45 WT and NF45 KO ESCs, 1ug of RNA per sample was processed using the Illumina TruSeq Stranded mRNA Sample Prep kit according to the manufacturer’s protocol. For NF90/NF110 WT, NF90+NF110 KO, and NF110 KO ESCs, 1ug of RNA per sample was processed using the KAPA Stranded RNA-Seq with RiboErase kit according to the manufacturer’s protocol. RIP was performed essentially as previously described. ESCs were harvested, pelleted, and lysed in 10 pellet volumes of polysome lysis buffer (100mM KCl, 5mM MgCl2, 10mM HEPES pH 7.5, 0.5% NP40 substitute, 1mM DTT) with cOmplete protease inhibitors (Roche), 100U/ml Superase-In (ThermoFisher Scientific), and 400uM vanadyl ribonucleoside complex (NEB). Lysates were freeze-thawed once, incubated with 100U/ml Turbo DNase (ThermoFisher Scientific) for 15min at 37C, and then cleared by centrifugation at maximum speed for 15min at 4C. Aliquots of the cleared lysate were taken at this step to serve as input for Western blot and qRT-PCR analysis. Antibodies for immunoprecipitation (5ug NF90/NF110 Ab/1ml lysate [BD Biosciences clone 21/DRBP76], 6ul normal rabbit IgG/1ml lysate [ThermoFisher Scientific]) were conjugated to 40ul/1ml lysate Protein G Dynabeads (ThermoFisher Scientific) in polysome lysis buffer for 2 hours at room temperature. Lysates were then incubated with Protein G Dynabead-conjugated antibodies for 4hr at 4C. Immunoprecipitates were washed 3x with polysome lysis buffer and then 3x with polysome lysis buffer containing 1M urea. An aliquot of the immunoprecipitate was taken for Western blot, while the rest of the immunoprecipitate, along with the qRT-PCR input lysate, was incubated with 1.2mg/ml proteinase K (Roche) and 2x proteinase K buffer (100mM Tris-HCl pH7.5, 12.5mM EDTA, 150mM NaCl, 2% SDS) for 30min at 55C. Samples were then lysed in TRIzol LS (ThermoFisher Scientific), and RNA was extracted and used for qRT-PCR or sequencing.

value: NF90+NF110 KO

tag: antibody


title: YPA_WT_pre_shift_mRNA

description: fragmented rRNA-depleted mRNA

tag: strain


title: 20D_Round_1_techReplicate1

description:
36220_1
DESeq2.ENCORvsSpheroid.20days.txt

tag: cell type

value: 20 days in vitro

value: Spheroid

value: wildtype


title: NF90+NF110 KO RIP-seq input rep3


title: NF90+NF110 KO RIP-seq IP rep1


title: SAM24314501 Skin CD34+ cells control NaCl


title: YPA_WT_pre_shift_footprints

description: ribosome-protected mRNA fragments


title: NF110 KO RIP-seq input rep3

value: NF110 KO


title: NF110 KO RIP-seq IP rep1


title: NF110 KO RIP-seq IP rep2


title: NF90+NF110 KO RIP-seq input rep2


title: NF110 KO RIP-seq IP rep3


title: NF90/NF110 WT RIP-seq IP rep3

value: NF90/NF110 WT


title: NF90/NF110 WT RIP-seq IP rep1


title: NF90/NF110 WT RIP-seq IP rep2


title: NF110 KO RIP-seq input rep2


title: DEX_MP_1

city: Heidelberg

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

data_processing:
Basecalls performed using Off-Line Basecaller  v1.9.4
Sequenced reads were aligned to TAIR10 whole genome using CLC Genomics Workbench version 6 with the following parameters: Additional upstream bases = 0; Additional downstream bases = 0; Maximum number of mismatches allowed (applies to short reads) = 0; Minimum length fraction (applies to long reads) = 0,9; Minimum similarity fraction (applies to long reads) = 0,8; Unspecific match limit = 1; Use colorspace encoding = No; Use strand specific assembly = No; Strand = Forward; Minimum paired distance = 180; Maximum paired distance = 250; Count paired reads as two = No; Minimum exon coverage fraction = 0,2; Minimum number of reads = 10; Minimum length of putative exons = 50
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis from WT (Col-0) were grown on soil for three weeks in short days (8h light 16h dark, constant 21°C) and then transfered to long days (16h light 8h dark) to stimulate flowering.

extract_protocol:
15-20 cm tall plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously  (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes
The RNA-seq library was prepared by the following the dUTP library and Illumina RNA ligation method.

value: 2nd internode

value: DEX


title: NF90+NF110 KO RIP-seq input rep1


title: DEX_MP_2


title: Mock_MP_3

value: Mock


title: NF90/NF110 WT RIP-seq input rep3


title: DEX_MP_3


title: DMSO_H3K9me3

description: ChIP

data_processing:
reads were aligned with HISAT 0.1.6-beta or BWA using default parameters for CAGE or ChIP/WGBS data, respectively
reads mapping to multiple positions in the genome were filtered
CAGEr, MACS2, and bsseq were used to call CAGE-clusters, ChIP-peaks, and methylation levels, respectively
Genome_build: hg19
Supplementary_files_format_and_content: processed files contain CpG methylation for WGBS data; bigWig read density for Histone data; consensus CAGE clusters are also provided for CAGE-seq data.

value: DMSO


title: NF45 KO RNA-seq rep1

value: NF45 KO


title: NF45 WT RNA-seq rep2

value: embryonic stem cells

value: NF45 WT


title: NF90/NF110 WT RIP-seq input rep2


title: NF90/NF110 WT RIP-seq input rep1


title: NF45 KO RNA-seq rep2


title: Mock_MP_2


title: NF45 WT RNA-seq rep1


title: NF90+NF110 KO RIP-seq IP rep2


title: 60D_Round_3_techReplicate2

description:
36228_2
DESeq2.ENCORvsSpheroid.60days.txt

value: 60 days in vitro


title: Mock_MP_1


title: NF110 KO RIP-seq input rep1


title: DEX_bdl_3


title: Mock_bdl_3


title: WT-2

city: Munich

first: Longchang

last: Jiang

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University München

data_processing:
alignment: TopHat v2.1.0 using default settings
expression levels: HTSeq v0.6.1 using default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each transcript

source_name: Adenoma from small intestine

extract_protocol:
Adenomas were isolated from small intestine, flash frozen into liquid nitrogen, and RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 18 weeks


title: WT-3


title: KO-2


title: KO-3


title: Mock_bdl_2


title: WT-1


title: DEX_bdl_1


title: H37Rv_rep2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Sequencing data were processed using the Illumina Pipeline Software version 1.82.
Reads were mapped against the H37Rv reference strain genome sequence (NC_000962.2) using Bowtie2. Read counts over features was done using htseq-count  and the annotation from Tuberculist (http://tuberculist.epfl.ch/).  To take advantage of strand specificity of the libraries and to maximize detection of putative unknown transcriptionally active regions we included also the reverse orientation of each feature, as well as intergenic regions.
Differential gene expression (DGE) analysis was done using DESeq.
Genome_build: NC_000962.2

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis H37Rv parental wild-type strain

growth_protocol: Strains were grown at 37°C either in Middlebrook 7H9 broth (Difco) supplemented with 10 % albumin-dextrose-catalase, 0.2 % glycerol and 0.05 % Tween 80 or in Sauton’s liquid medium supplemented with 0.005 % Tween 80. Where necessary, the medium was buffered with 10 % MES (pH = 5, 6) or MOPS (pH = 7). Cultures were plated on Middlebrook 7H10 (Difco) agar supplemented with 10 % oleic acid-albumin-dextrose-catalase and 0.2 % glycerol.

extract_protocol:
Exponential phase M. tuberculosis cultures were harvested by centrifugation, pellets were resuspended in TRIzol Reagent (ThermoFisher) and stored at -80° until further processing. Total RNA was extracted by bead-beating as previously described (32). Integrity of RNA was checked by agarose gel electrophoresis, the purity and amount of RNA were assessed using a Nanodrop instrument and Qubit Fluorometric Quantitation (ThermoFisher) respectively. SuperScript III First-Strand Synthesis System (Invitrogen) was used to generate randomly primed cDNA from 500 ng of RNA, according to the manufacturer’s recommendations.
300 ng of total RNA were mixed with 5 x Fragmentation buffer (Applied Biosystems), incubated for 4 minutes at 70°C and then transferred immediately to ice. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer’s recommendations, and subsequently treated with Antarctic phosphatase (New England Biolabs). RNA was then re-phosphorylated at the 5’-end with polynucleotide kinase (New England Biolabs) and purified with RNeasy MinElute columns (Qiagen). To ensure strand-specificity, v1.5 sRNA adapters (Illumina) were ligated at the 5’- and 3’-ends using RNA ligase. Reverse transcription was carried out using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). Twelve cycles of PCR amplification using Phusion DNA polymerase were then performed and the resulting library was purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions.

treatment_protocol: Hygromycin (50 μg ml−1), kanamycin (25 µg ml−1), streptomycin (25 μg ml−1), chloramphenicol (30 μg ml−1) or 2.5 % sucrose were added when needed. For cloning procedures, One shot® TOP10 chemically competent Escherichia coli (Invitrogen) were grown in Luria–Bertani (LB) broth or on LB agar with hygromycin (200 μg ml−1), kanamycin (50 μg ml−1) or spectinomycin (25 μg ml−1). All chemicals were purchased from Sigma-Aldrich, unless otherwise stated.

tag: parental strain

value: cell culture

value: wild type


title: KO-1

tag: genotype


title: Δhns_rep2

source_name: Mycobacterium tuberculosis Rv3852 (hns) knockout mutant

value: hns knockout mutant


title: DEX_bdl_2


title: Δhns_rep1


title: U87 whole genome bisulfite p11

status: Public on May 27 2017

first: Shuli

last: Xia

address: 707 N Broadway

institute: Kennedy Krieger Institute

data_processing:
Tophat2 was used to map all RNA-seq reads to human genome (hg19) then Cufflink was employed to summarize the gene/transcript expression based on mapped reads.
KLF4 ChIP-Seq data were mapped by Bowtie2, followed by MACS 1.4 being used to call peaks with cutoff of p < 1E-5
The peaks of H3K27ac was recognized by MACS2 as broad peaks based on their ChIP-Seq data mapped by Bowtie2. The cutoff of broad peak call was q < 0.1.
An R package, DEGseq, was taken on RNA-seq data to identify differentially expressed genes (DEGs) for p < 0.001 between 0 hr and 48 hr in KLF4 WT and R458A cells, respectively.
WGBS were aligned using Bismark, context-dependent methylation were extracted using bismark_methylation_extractor from merged bam files and format with coverage2cytosine.
Genome_build: hg19

source_name: Human glioblastoma cells

growth_protocol: U87 cells grown in MEM +10% FCS medium

extract_protocol:
RNA was extracted for RNA-seq, genomic DNA was extracted for ChIP-seq and WGBS
Library was constructed by microarray facility at Johns Hopkins University using commercially available kits (illumina)

treatment_protocol: for +Dox samples, cells were treated with doxycycline at 1 ug/ml for 48h

value: Brain

value: Human glioblastoma cells

tag: passage

value: in vitro for a long time


title: Mock_bdl_1


title: U87 whole genome bisulfite p8


title: U87 whole genome bisulfite p9


title: U87 whole genome bisulfite p6


title: U87 whole genome bisulfite p7


title: U87 whole genome bisulfite p5


title: U87 whole genome bisulfite p4


title: U87 whole genome bisulfite p1


title: U87 whole genome bisulfite p3


title: U87 whole genome bisulfite p2


title: U87DOX whole genome bisulfite p9


title: U87DOX whole genome bisulfite p10


title: U87DOX whole genome bisulfite p8


title: H37Rv_rep1


title: U87DOX whole genome bisulfite p7


title: U87 whole genome bisulfite p10


title: U87DOX whole genome bisulfite p5


title: U87DOX whole genome bisulfite p6


title: U87DOX whole genome bisulfite p4


title: U87DOX whole genome bisulfite p3


title: RNA-seq WT rep1


title: RNA-seq WT 5Aza+DOX rep2


title: U87DOX whole genome bisulfite p1


title: RNA-seq WT+DOX 48h rep1


title: RNA-seq WT rep2


title: RNA-seq WT+DOX 48h rep2


title: U87DOX whole genome bisulfite p2


title: RNA-seq WT 5Aza control rep2


title: RNA-seq WT 5Aza+DOX rep1


title: RNA-seq WT 5Aza control rep1


title: RNA-seq R458A+DOX 48h rep2


title: RNA-seq R458A control rep2


title: RNA-seq R458A control rep1


title: RNA-seq R458A+DOX 48h rep1


title: KLF4_ChIP-seq R458A


title: KLF4_ChIP-seq WT


title: KLF4_ChIP-seq Input


title: H3K9me3_ChIP-seq for WT at 0hr


title: H3K9me3_ChIP-seq for R458A at 0hr


title: H3K27me3_ChIP-seq for WT at 0hr


title: H3K9me3_ChIP-seq for R458A at 48hr


title: H3K9me3_ChIP-seq for WT at 48hr


title: H3K27me3_ChIP-seq for R458A at 0hr


title: H3K27me3_ChIP-seq for R458A at 48hr


title: H3K27ac_ChIP-seq for WT at 48hr


title: H3K27ac_ChIP-seq for R458A at 48hr


title: H3K27ac_ChIP-seq for WT at 0hr


title: H3K27ac_ChIP-seq for R458A at 0hr


title: ago4-4/6-2/9-1/AGO4-D742A Rep1

city: State College

first: Michael

middle: J.

last: Axtell

address: 208 Mueller Lab

department: Department of Biology

institute: The Pennsylvania State University

data_processing:
Small RNA-seq libraries listed here as well as libraries prepared from Col-0 wild-type (GSE79119) were merged and run with ShortStack 3.3 with options --adapter TGGAATTC --mincov 50. All sRNA-seq libraries were aligned to the Arabidopsis TAIR10 reference genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include non-redundant trimmed reads with raw sequencing count.

growth_protocol: All Arabidopsis thaliana plants were grown at 21oC with 16 h light/8 h dark in a growth room.

extract_protocol:
Total RNA from immature Arabidopsis inflorescence and fully expanded maize leaves was extracted using the miRNeasy Mini kit (Qiagen) per the manufacturer's instructions.
Small RNA libraries were prepared using the TruSeq Small RNA kit (Illumina) per the manufacturer's instructions.

tag: ecotype

tag: genotype/variation

value: Inflorescence


title: ago4-4/6-2/9-1/AGO4-D742A Rep2


title: ago4-4/6-2/9-1/wtAGO4 Rep3


title: ago4-4/6-2/9-1/wtAGO4 Rep2


title: ago4-4/wtAGO4 Rep3

value: Ws


title: ago4-4/AGO4-D742A Rep1


title: ago4-4/wtAGO4 Rep1


title: ago4-4/AGO4-D742A Rep3


title: ago4-4/AGO4-D742A Rep2


title: ago4-4/6-2/9-1/wtAGO4 Rep1


title: ago4-4/wtAGO4 Rep2


title: ago4-4/6-2/9-1 Rep2


title: ago4-4/6-2/9-1 Rep3


title: ago4-4 Rep2


title: ago4-4 Rep3


title: H3K27me3_ChIP-seq for WT at 48hr


title: ago4-4 Rep1


title: Ws Rep1

source_name: wild type_inflorescence


title: 9591_WT-plus_AGTTCC_L012

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: RNA subjected to RNAseq

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to mm9 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: Genome Reference Consortium GRCm37
Supplementary_files_format_and_content: normalized counts in txt format for all samples

source_name: Wild-type, C57BL/6J

extract_protocol:
The RNA was purified with RNeasy miniprep kit (Qiagen) following the manual. RNA quality was determined with an Agilent Bioanalyzer (RNA integrity number [RIN] > 7.5 for all samples).
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2  (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: Two groups of mice—wild-type (C57BL/6J) and CAMKIIγ-/- at 4-5 weeks of age—were given a single intraperitoneal injection of N-methyl-N-nitrosourea (MNU, 75 mg/kg) on Day 1 followed by an observation period; and the mice were observed weekly for tumor formation. MNU was dissolved in cold PBS immediately before treatment and injected within 1 hour.

value: wildtype

value: thymus

tag: +/- mnu treatment

value: MNU+

tag: treatment time

value: MNU:6 months


title: Ws Rep2


title: Ws Rep3


title: 9590_WT-minus_AGTCAA_L012

description: RNA subjected to RNAseq

value: MNU-

value: Vehicle:6 months


title: 9592_KO-minus_ATGTCA_L012

description: RNA subjected to RNAseq

source_name: CAMKIIg-/-, C57BL/6J

value: CAMKIIgamma-/-


title: 9593_KO-plus_CCGTCC_L012

description: RNA subjected to RNAseq


title: ago4-4/6-2/9-1/AGO4-D742A Rep3


title: ago4-4/6-2/9-1 Rep1


title: WT animals 1, 2, 3 pooled (hippocampus)

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

description: MACE (massive analysis of cDNA ends)

data_processing:
Sequencing on Illumina HiSeq 2000, basecalling pipeline: HiSeq Control Software 1.5.15.1, RTA 1.13.48.0, CASAVA-1.8.2, Flow cell version: HiSeq Flow Cell v3, Kit version: TruSeq SBS Kit v3
Sequences were cleaned from duplicates ("TrueQuant"), Bases with low sequencing quality were trimmed.
The trimmed reads were mapped to NCBI RefSeq mouse sequences and UCSC genome version mm9.2 using "SOAP2.2" with the following parameters “-p 16 -r 2 -v 5 -w 10 -g 1“
Expression analysis was performed by in-house scripts and DEGSeq (R-package)
Genome_build: NCBI RefSeq mouse sequences, mm9.2
Supplementary_files_format_and_content: Tab-delimited text files contain read counts, normalized read counts, p-values, fold changes

source_name: hippocampus

extract_protocol:
After cervical dislocation, cerebellum, midbrain and liver were dissected from homozygous wild-type (Atxn2+/+) and knock-out (Atxn2-/-) mice at 6, 12 and 24 weeks of age. Total RNA was extracted from these tissues by homogenization in 1 ml of Trizol® Reagent per 50 – 100 mg of tissue using a Pellet Pestle® Motor tissue homogenizer (Kontes, The Glass Company). One µg total RNA was digested with a DNase I Amplification Grade Kit (Invitrogen, Karlsruhe) in a reaction volume of 10 µl per tube in order to eliminate DNA during RNA purification prior to reverse transcription (RT-PCR) amplification.
For preparation of MACE libraries, poly-adenylated mRNA was isolated from 1 μg of the large fraction of total RNA using Dynabeads® mRNA Purification Kit (Life Technologies GmbH) and cDNA was produced by first and second strand synthesis using the SuperScript® III First-Strand Synthesis System (Life Technologies GmbH). , but with modified, barcoded poly-T adapters that are suitable to bind on the Illumina Hiseq2000 flow cell and that are biotinylated at the very 5′ end. After cDNA production, the biotinylated cDNA was random-fragmented to reach an average size of 250 bps, the 3′ends were captured by streptavidin beads and GenXPro’s TrueQuant adapters were ligated. Ten barcoded samples were sequenced simultaneously in one lane of an Illumina Hiseq2000 with 1 × 100 bps.

value: hippocampus

tag: age

value: 6 months

value: WT


title: WT animals 1, 2, 3 pooled (liver)

description: MACE (massive analysis of cDNA ends)

source_name: liver

value: liver


title: KO animals 1, 2, 3 pooled (liver)

description: MACE (massive analysis of cDNA ends)


title: WT animals 1, 2, 3 pooled (cerebellum)

description: MACE (massive analysis of cDNA ends)

source_name: cerebellum

value: cerebellum


title: Mouse_Input_ExVivo_Rep2

status: Public on May 26 2017

city: La Jolla

first: Dylan

middle: Derik

last: Skola

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

institute: UCSD

data_processing:
Tag directories for the ChIP-seq experiments were combined into an ex vivo and in vitro pool for each target in both mouse and human. The tag directories for the input DNA were likewise combined. Peaks were then called on the pooled tags with the pooled input DNA as background using HOMER’s findPeaks command with the following parameters for the PU.1 ChIP-seq: “-style factor -size 200 -minDist 200” and the following parameters for the H3K27ac and H3K4me2 ChIP-seq: “-style histone -size 500 -minDist 1000 -region.” The “-tbp” parameter was set to the number of replicates in the pool.   For identifying regions that are deacetylated in vitro, peaks for H3K27ac replicates were called individually, then merged using bedtools. A matrix containing the number of reads in each merged peak in each replicate was generated using HOMER’s annotatePeaks command with the following parameters: “-size given -noadj -tbp 1”. The read count matrix was then loaded into R and the limma package with voom normalization was used to identify peaks where the reads were reduced more than two-fold in vitro at an FDR of 0.05.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol:
For ChIP-Seq experiments, a cross-linking step with paraformaldehyde was performed immediately after staining but before microglia sorting. Briefly, a subset of human cells, and mouse cells to be used for ChIP-Seq, were washed once after staining, fixed at RT with 1% paraformaldehyde in PBS (Affymetrix 19943 1 LT) for 10 minutes, incubated for 5 min at RT with glycine to a final concentration of 0.125 M for PFA quenching, and washed twice with cold staining buffer. Microglia were then sorted as described above. After sorting, microglia were pelleted and snap-frozen in liquid nitrogen and stored at -80 C until chromatin immunoprecipitation.   Chromatin immunoprecipitation for histone modification H3K4me2, H3K27ac and transcription factor PU.1 was performed as followed, using 500,000 to 2 million microglia per assay. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in water) for 10 min on ice. Lysate were centrifuge at 800 x rcf for 5 min at 4°C, and pellets were resuspended in 200 l of sonication/immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 15 min each, alternating stages of 30 sec “sonication-on” with 60 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 x rcf at 4°C. Two microliters of supernatant were then set aside for input library sequencing controls. Supernatants were then immunoprecipitated on a rotator for 2 h at 4°C with antibody pre-bound to 20 l Protein A Dynabeads (Life Technologies 10001D). The following antibodies were used: H3k4me2 (Millipore, 07030), 2.0 l from stock per sample; H3K27ac (Active Motif, 39135), 1.5 l from stock per sample; and PU.1 (Santa Cruz, sc-352), 3.0 g per sample.   Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in water) and eluted with 1% SDS/TE at room temperature in a final volume of 100 l.   Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 l of 5 M NaCl (final concentration 300 mM) was added to each samples immersed in 100 l SDS/TE. Crosslinking was then reversed by overnight incubation at 65°C in a hot air oven. Potentially contaminated RNA was then digested for 1 h at 37°C with 0.33 mg/ml RNase A, proteins digested for 1 h at 55°C with 0.5 mg/ml proteinase K, and DNA extracted using Sera-Mag SpeedBeads (Thermo Scientific, 6515205050250).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.
Mice were euthanized with CO2 and quickly perfused intracardially with ice-cold DPBS (Mediatech 21-031CV). Whole brains were removed and gently mechanically homogenized on ice as described above. Cells were fractionated by Percoll gradient centrifugation, washed, FC blocked with CD16/32 antibody (1:50, eBioscience 14-0161, clone 93) on ice for 15 min, stained 1:100 with CD11b-APC (BioLegend 101212, clone M1/70) and CD45-Alexa Fluor 488 (BioLegend 103122, clone 30-F11). Microglia were then purified by cell sorting as specified above, with microglia defined as live-CD11b+CD45Low single cells. Typical yield was roughly 250,000 microglia per mouse brain.

tag: culture protocol

tag: time in culture

value: ex vivo

tag: ligands in culture


title: Mouse_Input_ExVivo_Rep6


title: Mouse_Pu1_ExVivo_Rep2

description: mouse_pu1_exvivo_vsInput_yes_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed


title: Mouse_H3K27ac_7day_Rep1

description: mouse_h3k27ac_invitro_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed

value: Isolated microglia were plated in 48-, 24, or 6-well plates at the following numbers, respectively:80,000 to 125,000, 150,000 to 200,000, and 1.5 million. Culture media consisted of DMEM/F12 (Life Technologies, 113300-032) supplemented with 5% FBS (heat inactivated, Omega Scientific, FB-12) and 1x Anti-Anti (Life Technologies, 152240-062). No media changes were performed for the duration of the culture experiments. Interleukin-34 (R&D, human 5265-IL-010; mouse 5195-ML-010) was supplemented daily at a concentration of 20 ng/ml. Recombinant human or mouse TGF-b1 cytokine (R&D, human 240-B-002; mouse 7666-MB-005) was supplements daily as a concentration of 10 ng/ml. At the end of the culture experiments, microglia were washed once with cold PBS and either lysed with 150 ml Oligo d(t) beads lysis/binding buffer (100 mM Tris-HCl ph 7.5, 500 mM LiCl, 10 mM EDTA ph 8.0, 1% LiDS, 5 mM DTT, in water) or 150 ml ATAC-Seq lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water; see below), or cross-linked, scraped off the wells and pelleted in preparation of ChIP-Seq experiments (see below).

value: 7 d


title: dTgDox_3

city: Jerusalem

first: uriya

last: Bekenstein

address: Safra

department: Dept. of Biological Chemistry

country: Israel

institute: HUJI

description: Frontal cortex RNA of mouse

data_processing:
86-bp long reads. percent of quality (Q30) reads was 94-95%.
Reads were aligned (90% mapping) to the mouse transcriptome (TopHat2), Using the DeSeq software via R platform
Supplementary_files_format_and_content: ENSEMBLE ID PER ANIMAL, AS TEXT FILE

source_name: Fronral cortex

extract_protocol:
RNA was extracted by miRNeasy kit (QIAGEN), RNA quality determined with 6000-Nano Bioanalyzer (Agilent, Santa Clara, CA.), and samples with RIN values ranged between 8 and 8.9 were used
Sequencing-compatible poly A-terminated single-end libraries were generated using an RNA Library prep kit (NEBNext® Multiplex, E7330S, New England Biolabs) following manufacturer’s instructions, with 12 amplification rounds
poly A-terminated single-end libraries: Libraries were sequenced on a NextSeq Series Sequencing System (The HUJ Center for Genomic Technologies) using two Illumina chips (Illumina 500® NextSeq High Output v2 Kit, FC-404-2005, Illumina).

treatment_protocol: Mice were anesthetized with isoflurane prior to cervical dislocation and their brain regions including frontal cortices were dissected and collected

value: FVB/N

tag: dox, days

tag: Sex

value: Male


title: Mouse_ATAC_7day_Rep1

description: mouse_atac_invitro_vsInput_no_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed

data_processing:
Tag directories for the ATAC-seq experiments were combined into an ex vivo and in vitro pool for both mouse and human. Peaks were then called on the pooled tags using HOMER’s findPeaks command with the following parameters: “-style factor -size 200 -minDist 200” with the “-tbp” parameter was set to the number of replicates in the pool.
Library strategy: ATAC-Seq
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol:
80,000 isolated microglia were lysed in 50 l lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water) on ice and nuclei were pelleted by centrifugation at 500 x rcf for 10 min. Nuclei were then resuspended in 50 l transposase reaction mix (1x Tagment DNA buffer (Illumina 15027866), 2.5 l Tagment DNA enzyme I (Illumina 15027865), in water) and incubated at 37 C for 30 min on a PCR cycler. DNA was then purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205) and eluted with 10 l of elution buffer. DNA was then amplified with PCR mix (1.25 M Nextera primer 1, 1.25 M Nextera primer 2-bar code, 0.6x SYBR Green I (Life Technologies, S7563), 1x NEBNext High-Fidelity 2x PCR MasterMix, (NEBM0541)) for 8-12 cycles, run on a gel for size selection of fragments (160-290 bp), extracted from gel and single-end sequenced for 51 cycles on a HiSeq 4000 or NextSeq 2500.
Mice were euthanized with CO2 and quickly perfused intracardially with ice-cold DPBS (Mediatech 21-031CV). Whole brains were removed and gently mechanically homogenized on ice as described above. Cells were fractionated by Percoll gradient centrifugation, washed, FC blocked with CD16/32 antibody (1:50, eBioscience 14-0161, clone 93) on ice for 15 min, stained 1:100 with CD11b-APC (BioLegend 101212, clone M1/70) and CD45-Alexa Fluor 488 (BioLegend 103122, clone 30-F11). Microglia were then purified by cell sorting as specified above, with microglia defined as live-CD11b+CD45Low single cells. Typical yield was roughly 250,000 microglia per mouse brain.


title: Mouse_H3K27ac_ExVivo_Rep2

description: mouse_h3k27ac_exvivo_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed


title: Mouse_Input_7day_Rep1


title: Mouse_H3K27ac_7day_Rep2


title: KO animals 1, 2, 3 pooled (hippocampus)

description: MACE (massive analysis of cDNA ends)

tag: tissue


title: Mouse_RNA_ExVivo_Rep4

description:
mouse_rna_read_counts_sample_ids.csv
mouse_rna_tpm_trimmed_sample_ids.csv

data_processing:
The “analyzeRepeats” function of HOMER was used to generate a table of read counts for each experiment using the parameters “-raw -count exons -strand both -condenseGenes” as well as a table of reads per kilobase per million reads (RPKM) values using “-rpkm -normMatrix 1e7 -count exons -strand both -condenseGenes.” The RPKM values were converted to transcripts per million (TPM) by normalizing the expression values in each experiment to a total count of one million. The base-2 logarithm of the TPM values was taken after adding a pseudocount of 1 TPM to each gene.The raw count data from HOMER analyzerepeat.pl program were imported in R (version 3.3.1) and preprocessed with Bioconductor packages. Expression data was filtered with average logTPM value > 2.0.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol: Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was then performed. RNA/DNA samples in 10 l of water were incubated for 2.5 hours at 16 C with 5 l the following mix (3x Blue Buffer (Enzymatics), 1.0 l PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 l Sera-Mag SpeedBeads (Thermo Scientific, 651520505025) resuspended in 30 l 20%PEG 8000/2.5 M NaCl and incubation at RT for 15 min and placed on magnet for two rounds of bead washing with 80% EtOH. Beads were then air-dried for 10-12 min and DNA was eluted off the beads by adding 40 l of water. Supernatant was then collected on magnet and placed on ice or stored at -20 C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.      Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was


title: dTgDox_2

description: Frontal cortex RNA of mouse


title: Ntg_1

description: Frontal cortex RNA of mouse

value: PTRE-miR-211 (non CamK)


title: dTgDox_1

description: Frontal cortex RNA of mouse


title: dTg_1

description: Frontal cortex RNA of mouse


title: Ct_6

description: Frontal cortex RNA of mouse

value: CamK


title: dTg_4

description: Frontal cortex RNA of mouse


title: dTg_2

description: Frontal cortex RNA of mouse


title: dTg_3

description: Frontal cortex RNA of mouse


title: dTg_5

description: Frontal cortex RNA of mouse


title: Ct_5

description: Frontal cortex RNA of mouse


title: Mouse_Input_7day_Rep2


title: Ct_3

description: Frontal cortex RNA of mouse


title: Ct_4

description: Frontal cortex RNA of mouse


title: Ct_2

description: Frontal cortex RNA of mouse


title: WM989-A6G3_Fluidigm COL20_ROW38_sample20

city: Philadelphia

first: Eduardo

middle: A

last: Torre

state: PA

department: Bioengineering

institute: University of Pennsylvania

description: fluidigmRPM

data_processing:
Drop-seq data processing was performed using Drop-seq_tools-1.0.1 ( http://mccarrolllab.com/dropseq/ ), and following protocol described in seqAlignmentCookbook_v1.1Aug2015.pdf
Data were aligned to reference genome builds hg38 (Human) and mm10 (Mouse) via STAR version 2.4.2a. We used reference transcriptome annotations Gencode21 (Human) and Refseq mm10 (Mouse).
For DropSeq, reads with low-quality base in either cell or molecular barcode were filtered and reads were trimmed for contaminating primer or poly-A sequence. Sequencing errors in barcodes were inferred and corrected, as implemented by Drop-seq_tools-1.0.1. Uniquely mapped reads, with <= 1 insertion or deletion, were used in quantification. To account for differences in molecule recovery, cell measurements were normalized to UMI per million (UPM).
Fluidigm sequence data were demultiplexed using mRNASeqHT_demultiplex.pl ( https://www.fluidigm.com/c1openapp/scripthub/script/2015-08/mrna-seq-ht-1440105180550-2) .
Demultiplexed data were processed in the same manner as Drop-seq data, with a few modifications: 5’ ends of reads were not trimmed, and reads (rather than UMI) were used for quantification. To account for differences in molecule recovery and sequencing depth, cell measurements were normalized to reads per million (RPM).
Genome_build: hg38 (Human) and mm10 (Mouse)
Supplementary_files_format_and_content: .txt files represent either raw count data or count data normalized to UMI per million (in the case of DropSeq) or read per million (in the case of Fluidigm)

source_name: Melanoma cells

growth_protocol: WM989-A6G3 cells were routinely passaged on Tu2% media.

extract_protocol:
DropSeq libraries were built according to Macoscko et. al, protocol v3.1 (http://mccarrolllab.com/dropseq/). Fluidigm libraries were constructed according to the manufacturer's instructions.
DropSeq libraries were built according to Macoscko et. al, protocol v3.1 (http://mccarrolllab.com/dropseq/). Fluidigm libraries were constructed according to the manufacturer's instructions.
single cell RNA-seq

value: melanoma


title: dTg_7

description: Frontal cortex RNA of mouse


title: WM989-A6G3_Fluidigm COL20_ROW36_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW37_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW34_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW39_sample20

description: fluidigmRPM


title: dTg_6

description: Frontal cortex RNA of mouse


title: WM989-A6G3_Fluidigm COL20_ROW30_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW29_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW31_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW27_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW25_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW28_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW24_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW23_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW40_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW21_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW20_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW22_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW19_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW18_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW16_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW35_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW15_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW33_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW17_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW11_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW13_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW32_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW08_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW07_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW26_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW12_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW04_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW09_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW06_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW03_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW05_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW01_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW40_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW02_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW38_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW39_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW37_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW36_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW35_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW34_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW14_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW33_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL20_ROW10_sample20

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW29_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW30_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW28_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW32_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW31_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW27_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW25_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW23_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW24_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW22_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW26_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW21_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW20_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW19_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW16_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW18_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW13_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW14_sample19

description: fluidigmRPM