title: ChIP-Seq_H3K27_ry-2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the Drosophila reference genome (release 5.22/6.02).
.tdf files were generated from .bam files via IGV tools.
Genome_build: Release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format.

organism: Drosophila melanogaster

source_name: 3rd instar brains and imaginal disks, H3K27me3 ChIP

growth_protocol: All flies were grown at 25°C. 3rd instar larvae were dissected for brains and imaginal discs.

extract_protocol:
Fixed brains and imaginal discs were dissected from 10 third instar larvae. Sonicated chromatin incubated with anti ChIP was performed with 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies.
Input ChIP DNA (30 ng) was blunt-ended and phosphorylated. A single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products were purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA was purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated before cluster generation.

tag: strain/background

value: ry

tag: developmental stage

value: 3rd instar larvae

value: CNS and imaginal disks


title: wildtype male mouse [WM1]

status: Public on Aug 13 2019

type: SRA

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

country: USA

institute: University of Connecticut Health Center

description:
LA1_S1
WM1

library_source: transcriptomic

data_processing:
Read trimming: sickle parameters: -l 45 -q 25
alignment: HiSat2 parameters: default
abundance estimation: htseq-count parameters: default
FPKM
Differential expression analyzed using DESeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: wildtype male mouse atrium

growth_protocol: adult mice, aged 60-90 days

extract_protocol:
Individual atria were extracted in Trizol and processed as per manufacturer's instructions
Illumina TruSeq Stranded mRNA per manufacturer's instructions
RNASeq samples were barcoded and all run in a single NextSeq run with 20 million total paired end 75bp reads per sample.

tag: Sex

value: male

tag: tissue

value: atrium

tag: genotype/variation

value: wildtype


title: 965

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: HippExpressionmatrix.txt

data_processing:
StrandNGS Software was used to align, adaptor trim, and call differential expression.
Aligned Against:Transcriptome and genome together (with novel splices;) Transcriptome used:RefSeq Genes and Transcripts (2013.04.01); Maximum number of Novel Splices allowed : 1; Minimum percent identity : 90; Maximum percent gaps : 5; Minimum aligned read length : 25;Number of matches to output per read : 1; Ignore reads with matches more than : 5 ;Fixed trim on 5' end : 5 ;Fixed trim on 3' end : 2
DeSeq quantitation, normalized to male vehicle control.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Abundance measurements- Expression matrix

source_name: Hippocampus

extract_protocol:
AllPrep DNA/RNA Mini kits (Qiagen, Germantown, MD)
TruSeq RNA Library Prep Kit v2

value: Male

tag: treatment

value: Vehicle (Sunflower Oil)

tag: age

value: 3 Months


title: MK50_5

city: Turku

first: Ubaid Ullah

last: Sheikh

state: Turku

address: Tykistökatu

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description:
activated in Th17 condition
MK50_5_CGTACG_L001

data_processing:
Raw reads quality was assessed using FastQC. Adapters and low quality bases were trimmed by Trimmomatic (v0.32).
Trimmed reads were then aligned to the human reference genome GRCh37.75 (Ensembl release 75) using Tophat2 (v2.0.10).
HTSeq (v0.6) was used to summarize the read counts for each gene
Genome_build: GRCh37.75 (Ensembl release 75)
Supplementary_files_format_and_content: read counts for each gene

organism: Homo sapiens

source_name: CD4+T cells from human cord blood

growth_protocol: Human umbilical cord blood was layered on ficol (GE Healthcare, cat# 17-1440-03) for isolation of white blood cells. CD4+ T cells were then isolated using the bead-based CD4+ isolation kit from Invitrogen (cat# 11331D).

extract_protocol:
The total RNA was purified using RNeasy Mini Kit (QIAGEN, cat# 74106) following the manufacturer's instruction.
Libraries were prepared using the Illumina protocol. The quality of the library was confirmed using Advanced Analytical Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany) or with an Agilent Bioanalyzer, and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies, ThermoFisher). The sequencing was performed using a HiSeq2500 Next-Generation Sequencing platform at the Finnish Functional Genomics Centre (FFGC).
The quality control of raw sequencing reads was performed with FastQC, and adapters and low-quality bases were trimmed by Trimmomatic (Bolger et al., 2014). The trimmed reads were then aligned to the human reference genome GRCh37.75 (Ensembl release 75) using Tophat2 (Kim et al., 2013). Htseq-count (Anders et al., 2015) was used to calculate summarized read counts for each gene. The R/Bioconductor packages edgeR (Robinson et al., 2010) and DESeq2 (Love et al., 2014) were used to identify differentially expressed (DE) genes. Genes with a false discovery rate (FDR) <0.05 and detected using both methods were considered significantly DE.

treatment_protocol: For Th17 cell culture, CD4+ T cells were stimulated in a density of 0.5 × 106 cells/mL of X-vivo 20 serum-free medium (Lonza). The X-vivo 20 medium was supplemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17 cell polarization was initiated with a cytokine cocktail of IL6 (20 ng/mL; Roche, cat# 11138600 001), IL1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) in the presence of neutralizing anti-IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and anti-IL4 (1 μg/mL, R&D Systems, cat# MAB204).

tag: cell type

value: human Th17 cells

tag: time point

tag: sirna

value: NT siRNA


title: ChIP-Seq_H3K27_ry-1

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: MK48_6

description:
activated in Th17 condition
MK48_6_GATCAG_L002

value: CIP2A siRNA


title: 964

description: HippExpressionmatrix.txt


title: GC B cells - immune mother rep2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.80

source_name: draining inguinal lymph nodes

extract_protocol:
inguinal draining lymph nodes were removed at day 18 post HA/CAF01 immunization of neonatal mice born with or without maternal antibodies. Samples from each group were pooled and B cells were enriched by using the EasySep™ Mouse B Cell Isolation Kit. Enriched B cells were then stained with the following antibodies: Alexa Fluor 488 anti- GL7, BV510 anti- B220 , PE-Cy7 anti- CD19, PE anti-Fas, and APC anti- TCR β. DAPI was used to discriminate live from dead cells.  B220+CD19+GL7+CD95+ GC B cells and B220+CD19+GL7negCD95neg non-GC B cells were simultaneously isolated from the enriched B cells by flow-cytometry cell sorting using a MoFlo® Astrios™ flow cytometer.
RNA libraries were prepared for sequencing using standard Illumina protocols; RNA was harvested using the RNeasy Mini Kit (Qiagen), 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled and loaded at 2 nM for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: group

value: immune mother

tag: strain

value: inguinal lymph nodes

tag: time

value: Day 18 post-immunization

value: 25 days

value: CD19+B220+GL7+FAS+ GC B cells sorted by flow cytometry


title: 962

description: HippExpressionmatrix.txt

value: Tamoxifen


title: MK47_5

description:
activated in Th17 condition
MK47_5_GTGGCC_L001


title: MK50_6

description:
activated in Th17 condition
MK50_6_TAGCTT_L002


title: L125_K562_SRSF2_MS023_GSK591_D8

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to hg19 genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the htseq package and edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with gene level counts generated with htseq/edger

source_name: K562 cell line

growth_protocol: K562 cells were grown in IMDM + 10%, K562 SRSF2 P95H knock-in cells are derived as previously described (Cancer cell 34(2):225-241 (2018))

extract_protocol:
RNA was isolated from cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: K562 WT and SRSF2 P95H cells were treated with DMSO/ MS023 250nM/ GSK591 250nM/ MS023 250nM + GSK591 250nM for 8 days before collection

value: chronic myelogenous leukemia cells

tag: cell line


title: 961

description: HippExpressionmatrix.txt


title: MK47_6

description:
activated in Th17 condition
MK47_6_ACTTGA_L002


title: 958

description: HippExpressionmatrix.txt

value: Female


title: 963

description: HippExpressionmatrix.txt


title: L125_K562_SRSF2_MS023_250nM_D8


title: L125_K562_SRSF2_ctrl_D8

value: control


title: 960

description: HippExpressionmatrix.txt


title: L125_K562_SRSF2_GSK591_250nM_D8


title: L125_K562_WT_MS023_GSK591_D8

value: WT


title: 957

description: HippExpressionmatrix.txt


title: 959

description: HippExpressionmatrix.txt


title: 953

description: HippExpressionmatrix.txt


title: 955

description: HippExpressionmatrix.txt


title: L125_K562_WT_GSK591_250nM_D8


title: L125_K562_WT_ctrl_D8


title: L125_K562_WT_MS023_250nM_D8


title: 954

description: HippExpressionmatrix.txt


title: 952

description: HippExpressionmatrix.txt


title: MK48_5

description:
activated in Th17 condition
MK48_5_GTTTCG_L001


title: L124_K562_SRSF2_MS023_GSK591_D8


title: L124_K562_SRSF2_GSK591_250nM_D8


title: 951

description: HippExpressionmatrix.txt


title: L124_K562_SRSF2_MS023_250nM_D8


title: HEK TE single-cell clone 3AD8 9p21 deleted_3

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Reads were mapped on hg38 human transcriptome with gencode.v24 as gene annotation and quantified using RSEM v1.3.1
Read counts were normalized by calculating TPM (Transcripts Per Kilobase Million)
DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene TPM for each Sample

source_name: human embryonic kidney cells

growth_protocol: HEK TE cells were cultured in DMEM (Thermofisher), supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Cells were trypsinized, pelletted, and RNA was harvested using Nucleospin (Macherey). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown to 70-80% confluency before harvesting.

value: HEK TE

value: human embryonic kidney cells

value: 9p21 deletion


title: HEK TE single-cell clone 3AD8 9p21 deleted_4


title: HEK TE single-cell clone 3AD8 9p21 deleted_2


title: L124_K562_SRSF2_ctrl_D8


title: L124_K562_WT_MS023_GSK591_D8


title: L124_K562_WT_GSK591_250nM_D8


title: HEK TE single-cell clone 3AD8 9p21 deleted_1


title: HEK TE single-cell clone 3DE4 9p21 wt_3

value: wild type


title: HITS-CLIP

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
The CLIP reads had a 4-nt sample multiplexing index and a 8-nt random barcode at the 5′ end. The libraries generated with BrdU-CLIP adaptors were first filtered according to their quality scores. We required a minimum average quality score of 20 for the read. As NPM is known to bind to rRNAs and rRNA would confound the alignment due to its repetitive nature in the genome, we computationally subtracted all sequences that aligned to the 5S, 5.8S, 18S and 28S rRNAs. The remaining read sequences (actual RNA tags without index and barcodes) were mapped to the reference genomes (mm9) using Novoalign program (http://www.novocraft.com) with no more than two mismatches (substitutions, insertions, or deletions) allowed per read. We only kept reads that mapped uniquely to the genome. To remove PCR duplicates, we analyzed barcode sequences of all reads that mapped to the same genomic position. Initially, we collapsed all reads with identical barcodes into one read.  Next we compared all different barcodes at the same position and only kept reads for which at least two out of eight of the barcode nucleotides were different from all other barcode sequences of reads at that position. These steps remove PCR duplicates while retaining genuinely unique reads representing independent events. Next, we calculated peaks, which were defined as regions that contain overlapping reads. The peak intensity refers to the number of independent reads that falls within the boundary of the peak. Statistical significance was calculated using the program Piranha.
Genome_build: mm9
Supplementary_files_format_and_content: Text file (txt)

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Npm1+/+Trp53-/- MEFs or Npm1-/-Trp53-/- MEFs were UV-Crosslinked in a hybridization oven at setting 400 mJ/cm2, followed by an additional 200 mJ/cm2 after one minute of recovery. Cross-linked cells were washed once with ice-cold PBS, collected and pelleted for 5 min at 4°C. PBS was aspirated and cells were snap-frozen on dry ice and stored in -80°C until further processing. Cross-linked cells were lysed in 1xPXL buffer (1xPBS, 0.1% SDS, 0.5% DOC, 0.5% NP-40) for 5 min on ice, followed by the addition of RQ1 DNAse, which was incubated at 37°C for 10 minutes. To partially digest the crosslinked RNAs, RNAseA was added to the lysates at a 1:10000 dilution and incubated at 37°C for 5 min. Next, the lysates were spun at 14000 rpm in a table top centrifuge for 20 min at 4°C.
HITS-CLIP was performed as described in the accompanying paper.

tag: genotype


title: L124_K562_WT_ctrl_D8


title: HEK TE single-cell clone 3DE4 9p21 wt_2


title: L124_K562_WT_MS023_250nM_D8


title: X721_05_L

city: Huddinge

first: Maria

last: Eriksson

address: Karolinska Institutet, Biosciences and Nutrition, NEO Halsovagen 7

department: BioNut

country: Sweden

institute: Karolinska Institutet

data_processing:
RNAseq: Strand specific RNA-Seq libraries were pooled and paired-end sequenced on an Illumina Hiseq 2000 sequencing system. The generated sequence reads were mapped to the mouse genome (mm10) using Galaxy software. Sequences were aligned to the reference genome using TopHat (Trapnell et al., 2009) and differential expression analysis was done using Cufflinks (Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each tissue source, basal wt vs basal bt and suprabasal wt vs suprabasal bt

source_name: Suprabasal

extract_protocol:
Primary keratinocytes were isolated and processed for FACS. After sorting, cells were pelleted by centrifugation and re-suspended in Trizol (Invitrogen) followed by chloroform extraction. The aqueous phase was applied to RNeasy minElute column (Qiagen) and the RNA was purified according to manufacturer instructions.
10 ng of purified RNA were processed with Nugen Ovation RNA-Seq System (NuGen) for mouse, to make strand specific RNA-Seq libraries.

value: FVB/N

value: Skin

value: post natal day 4

value: bitransgenic HGPS (BT)


title: X682_11_L

value: Wild type


title: X682_05_L


title: X721_05_H

source_name: basal


title: L123_K562_SRSF2_MS023_GSK591_D8


title: X667_05_H


title: X667_06_L


title: X721_08_H


title: L123_K562_SRSF2_GSK591_250nM_D8


title: X682_11_H


title: X667_06_H


title: LoVo-shLGR5-1-replicate1

type: RNA

city: Houston

first: Kendra

last: Carmon

state: TX

address: 1825 Pressler St., Rm 530H

department: The Brown Foundation Institute of Molecular Medicine

institute: UT Health Science Center at Houston

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with GenomeStudio software (Illumina, Inc.).

label: Biotin

label_protocol: Standard Illumina labeling protocol

growth_protocol: LoVo cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 2 µg/ml puromycin, and penicillin/streptomycin at 37°C with 95% humidity and 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified using the Qiagen RNeasy kit.

treatment_protocol: The cells were infected via lentivirus with short hairpin RNA targeting LGR5 mRNA (shLGR5) or pLKO.1 as non-targeting control.

value: LoVo

value: colorectal adenocarcinoma cell line

value: LGR5 knockdown cell line with LGR5-targeting shRNA-1


title: L123_K562_SRSF2_MS023_250nM_D8


title: LoVo-shLGR5-2-replicate1

value: LGR5 knockdown cell line with LGR5-targeting shRNA-2


title: LoVo-shLGR5-2-replicate2


title: LoVo-shCTL-replicate1

source_name: LoVo-shCTL

value: control cell line with non-targeting shRNA


title: LoVo-shCTL-replicate2


title: LoVo-shLGR5-1-replicate2


title: X721_08_L


title: L123_K562_WT_MS023_GSK591_D8

value: chronic myelogenous leukemia cells


title: Con-beta-catenin-input

city: guangzhou

first: Feng

last: Lu

address: 601 huangpu avenue west

country: China

institute: Jinan university

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: hepatocellular carcinoma cells

growth_protocol: HepG2i cells were grown in DMEM medium containing 10% FBS,50 units/mL penicillin and supplemented with 100 µg/mL streptomycin

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

treatment_protocol: HepG2i cells cultured with DMEM containing 10% FBS medium and incubated at 37°C in 5% CO2 grown to 80-90% confluence before treated w/o DOX (1µg/mL) for 48 hours.

value: liver

value: HCC-derived liver cancer cells

value: Control


title: HEK TE single-cell clone 3DE4 9p21 wt_1

value: HEK TE

value: human embryonic kidney cells


title: Dox-beta-catenin-input

value: Dox


title: L123_K562_SRSF2_ctrl_D8

value: control


title: Dox-GATA4

value: FLAG(Abcam)


title: L123_K562_WT_MS023_250nM_D8

value: WT


title: Dox-beta-catenin

value: β-catenin (CST)


title: 10dpa_replicate3

city: LYON

first: Pauline

last: NAUROY

address: 46 Allée d'Italie

department: Institute of Functional Genomics of Lyon

country: France

institute: CNRS - ENS of Lyon

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam

data_processing:
SOLiD Wildfire sequencer (Thermo Fisher Scientific)
Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow
Genome_build: zv9
Supplementary_files_format_and_content: Data (raw counts) are provided as a table where each line corresponds to a gene and each column to a sample

organism: Danio rerio

source_name: caudal fin tissue_10 days post amputation

growth_protocol: Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.

extract_protocol:
RNAs were extracted using the Macherey-Nagel RNA XS kit (ref. 740902) and according to manufacturer's instructions exept that the carrier RNA was not used.
Libraries were built using the SENSE mRNA-Seq Library Prep Kit (Lexogen) dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.

treatment_protocol: Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey-Nagel RNA XS kit (ref. 740902) lysis buffer and stored at -80°C before RNA extraction.

value: caudal fin

value: AB-Tu

value: adults between 8 and 18 months old


title: L123_K562_WT_ctrl_D8


title: L123_K562_WT_GSK591_250nM_D8


title: Con-beta-catenin


title: Dox-GATA4-input


title: 3dpa_replicate3

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam

source_name: caudal fin tissue_3 days post amputation


title: HHV-6B_RNA_72hpi

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human and HHV-6A and HHV-6B genomes.
All remaining reads were aligned to viral genes (canonical known genes and novel).
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
The genomic location of removed polyA sequences was registered and summed in wig files
Genome_build: hg19 + KC465951.1 (HHV-6A) or hg19 + AF157706.1 (HHV-6B)
Supplementary_files_format_and_content: Wiggle files, generated as described in the above data processing steps; bed files, describing the genomic elements identified in our work

organism:
Homo sapiens
Human herpesvirus 6 strain Z29

source_name: Molt-3 cells infected with HHV-6B 72hpi

extract_protocol:
cells were harvested with Tri-Reagent (Sigma) and total RNA was extracted following manufacturer protocol
RNA-seq library generation was performed as previously described (Ingolia et al., 2011)

value: HHV-6B Z29

tag: hours post infection


title: HHV-6B_RNA_24hpi

source_name: Molt-3 cells infected with HHV-6B 24hpi


title: HHV-6B_RNA_05hpi

source_name: Molt-3 cells infected with HHV-6B 05hpi


title: HHV-6B_CHX_72hpi

data_processing:
library strategy: Ribo-seq
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human and HHV-6A and HHV-6B genomes.
All remaining reads were aligned to viral genes (canonical known genes and novel).
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
The genomic location of removed polyA sequences was registered and summed in wig files
Genome_build: hg19 + KC465951.1 (HHV-6A) or hg19 + AF157706.1 (HHV-6B)
Supplementary_files_format_and_content: Wiggle files, generated as described in the above data processing steps; bed files, describing the genomic elements identified in our work

extract_protocol:
cells were treated with 100µg/mL cycloheximide for 1 minute.  Subsequenct isolation of ribosome protected fragments was performed as previously described (Ignolia et al. 2011)
Ribo-seq library generation was performed as previously described (Ingolia et al., 2011)


title: MEF-WT-PolysomeRNA

description:
Ribosome-bound RNA
Npm1+/+

hyb_protocol: The resulting biotin-labeled cRNA was fragmented and hybridized to the microarray chip for 16 hr at 45C.

scan_protocol: Following hybridization, the probe array was washed and stained on a fluidics station and immediately scanned on a Hewlett Packard GeneArray Scanner.

data_processing: Microarray CEL files were analyzed with the affy package (v1.56.0) in R (v3.4.3) using RMA normalization with standard parameters.

label: biotin

label_protocol: Linear amplification with T7-RNA polymerase (Ambion) and biotin labeling (ENZO) were performed by in vitro transcription by according to manufactures’ instructions.

extract_protocol: RNA was extracted from each sucrose fraction using Trizol and the RNeasy Mini Kit (QIAGEN). Double-stranded cDNA was synthesized from total or polysomal RNA (1 to 10 μg).


title: 34_34_minus_Nplus

city: Amsterdam

first: Mattia

last: Falcone

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: NKI

data_processing:
Sequences were aligned to hg19 reference genome using the STAR alignment software with Gencode v19 as the transcriptome annotation
DESeq2 was used to generate a normalised read counts table and a list of differentially expressed protein-coding genes between NKG2DLneg and NKG2DLpos samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalised read counts for each Sample

source_name: bone marrow

extract_protocol:
total RNA isolation from 50,000 sorted cells was performed using an Arcturus PicoPure RNA isolation kit (Life Technologies, Invitrogen) according to the manufacturer’s instructions
cDNA libraries were generated with 10 ng of total RNA using the SMARTer Ultra Low RNA kit for Illumina sequencing (Clontech Laboratories) according to the manufacturer’s indications

tag: patient

value: Patient #34

tag: nkg2dl expression

value: pos


title: 34_34_minus_Nminus

value: neg


title: 33_34_minus_Nminus

value: Patient #33


title: HHV-6B_CHX_24hpi


title: MEF-WT-TotalRNA

description:
Total RNA
Npm1+/+


title: 0dpa_replicate3

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam

source_name: caudal fin tissue_0 days post amputation


title: MEF-Het-TotalRNA

description:
Total RNA
Npm1+/-


title: 10dpa_replicate2

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam


title: 33_34_minus_Nplus


title: MEF-Het-PolysomeRNA

description:
Ribosome-bound RNA
Npm1+/-


title: HHV-6B_CHX_05hpi


title: suprabasal keratinocytes bitransgenic (bt_low) [X682_05_L]

hyb_protocol: according to Affymetrix protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Scanning of arrays was performed using an Affymetrix GeneChip Scanner 3000 7G, and the generated image (DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC, v.3.2) software to generate cell intensity (CEL) files. The CEL files were imported to the Affymetrix Expression Console (EC, v.1.2) software and analyzed using the Robust Multichip Average (RMA) method including quantile normalization and median polish summarization.
MTA-1_0.r1.pgf
MTA-1_0.na35.3.mm10.probeset.csv

label_protocol: according to Affymetrix protocol

extract_protocol: Primary keratinocytes were isolated and processed for FACS. After sorting, cells were pelleted by centrifugation and re-suspended in Trizol (Invitrogen) followed by chloroform extraction. The aqueous phase was applied to RNeasy minElute column (Qiagen) and the RNA was purified according to manufacturer instructions.

value: FVB/N

value: post natal day 4

value: Skin

value: BT


title: 11_34_minus_Nminus

value: Patient #11


title: 11_34_minus_Nplus


title: HHV-6B_RNA


title: 2dpa_replicate3

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam

source_name: caudal fin tissue_2 days post amputation


title: 3dpa_replicate2

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam


title: HHV-6B_Harr

extract_protocol:
cells were treated with 2µg/mL Harringtonine for 5 minutes abd subsequently treated with 100µg/mL cycloheximide for 1 minute.  Subsequenct isolation of ribosome protected fragments was performed as previously described (Ignolia et al. 2011)
Ribo-seq library generation was performed as previously described (Ingolia et al., 2011)


title: 2dpa_replicate2

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam


title: 10_34_minus_Nminus

value: Patient #10


title: 0dpa_replicate2

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam


title: 10_34_minus_Nplus


title: 10dpa_replicate1

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam


title: suprabasal keratinocytes wild-type (wt_low) [X682_11_L]

value: Wild type


title: 9_34_minus_Nminus

value: Patient #9


title: 3dpa_replicate1

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam


title: HHV-6A_RNA

organism:
Homo sapiens
Human herpesvirus 6 (strain GS)

source_name: HSB2 infected with HHV-6A 72hpi

value: HHV-6A GS


title: suprabasal keratinocytes wild-type (wt_low) [X667_06_L]


title: suprabasal keratinocytes wild-type (wt_low) [X721_08_L]


title: 2dpa_replicate1

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam

value: caudal fin


title: suprabasal keratinocytes bitransgenic (bt_low) [X667_05_L]


title: suprabasal keratinocytes bitransgenic (bt_low) [X721_05_L]


title: basal keratinocytes bitransgenic (bt_high) [X667_05_H]


title: basal keratinocytes bitransgenic (bt_high) [X721_05_H]


title: HHV-6A_Harr


title: ΔnarK ΔNarS + pPL-NarS

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

data_processing:
SOAP v2.21 (-m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3) to filter the reads.
HISAT v2.0.1 (beta (-p 8 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 --rna-strandness RF) for reads mapping.
Bowtie2 v2.2.5 (q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --：) for reads mapping.
RSEM：v1.2.12 forward-prob=0.0) to calculate the gene expression levels.
possionDis：(abs log2(FoldChange) >= 1 && FDR <= 0.005) to call for genes with significant difference expression among two samples.
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium SL1344 (NC_016810.1)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Bacterial cells

growth_protocol: Overnight cultures were grown from a single colony, diluted 1:100 in fresh LB medium, and grown to the OD600 ~ 0.3 at 37°C with shaking at 220 rpm.

extract_protocol:
Bacterial cultures were mixed with 0.2 (v/v) of stop solution (95% ethanol and 5% phenol) and immediately frozen within liquid nitrogen. Total RNA was isolated using the hot phenol method. Briefly, 2.0 OD600 cell pellet was resuspended with 300 μL lysozyme (#L3790, Sigma-Aldrich) at 0.5 mg/mL, 30 μL 10% SDS and 33 μL 3M sodium acetate (pH5.2). Cleared lysate was mixed with 375 μL saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. The aqueous phase was collected after centrifuge and mixed with 375 μL chloroform in Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech). RNA was precipitated at -80 °C overnight by mixing the aqueous phase (~350 μL) with 700 μL 30:1 ethanol: sodium acetate (pH 6.5) mix. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and was quantified using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. Purified and fragmentated RNA was then treated by Illumina TruSeq Standard Kit: Fragmented RNA was reverse transcribed to first chain cDNA random oligo and reverse transcriptase. Second chain cDNA was generated with DNA polymerase I and RNase H. dTTP was replaced by dUTP when Second chain cDNA was generated to increase the chain-specificity. Double chain cDNA was then poly A tailed and ligated with adaptor. After PCR application, samples were sequenced in Illumina Hi-seq platform.

treatment_protocol: Cells were aerobically cultured to an OD 600 of 0.3, filled in 50 ml closed Falcon tubes, and incubated without agitation at 37°C for the indicated times.

value: SL1344 strain with NarS-narK deletion

tag: plasmid

value: NarS-overexpressed plasmid pPL-NarS


title: HHV-6A_LTM

extract_protocol:
cells were treated with 50µM LTM for 30 minutes and subsequently treated with 100µg/mL cycloheximide for 1 minute.  Subsequenct isolation of ribosome protected fragments was performed as previously described (Ignolia et al. 2011)
Ribo-seq library generation was performed as previously described (Ingolia et al., 2011)


title: 9_34_minus_Nplus


title: 0dpa_replicate1

description:
Each sample corresponds to a batch of 6 fish
sample name in processed data file: Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam

tag: tissue

value: AB-Tu

value: adults between 8 and 18 months old


title: ΔnarK ΔNarS + pJV300

tag: genotype/variation

value: Empty plasmid pJV300


title: basal keratinocytes wild-type (wt_high) [X682_11_H]


title: HHV-6A_CHX


title: sc-N7_83_pooling_before

status: Public on Aug 12 2019

city: La Jolla

first: Daria

last: Merkurjev

state: CA

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

description:
Induced  differentiation from hiPSCs
83a_S83_L007

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph

molecule: polyA RNA

growth_protocol: hiPSCs were seeded onto PA6 cells in PA differentiation medium for 12 days. Between days 12-14, when rosettes were visible, after dissociation, were  FACS-sorted based on the  CD184+/CD271-/CD44-/CD24+ cell-surface signature. Sorted NPCs were cultured on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated plates in NPC medium until confluency was reached. To generate neurons, NPCs grown in 10 cm-plates at confluency were switched to NPC medium without FGF (day 1), and cultured afterwards for 3 weeks. Around day 21, neurons were sorted based on the CD184-/CD44-/CD24+ signature. For our experiments 1x10^6 CD24+ sorted neurons were plated on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated 24-well plates in NPC media supplemented with 0.5mM dbcAMP from Sigma, and 20ng/µL BDNF and 20 ng/µL GDNF.  After 10 days recovery, neuronal cultures were sorted for single cell isolation and individual cells were processed for scRNA-seq.

extract_protocol:
Total RNA was extracted and processed following the SMART-seq protocol from Takada and NEXTERA from Illumina, following in both cases the Takada's protocol that allows full-length coverage of gene expression at the level of single cell.
Samples were processed using the SMART-seq protocol from Takada and NEXTERA from Illumina, following in both cases the Takada's protocol that allows full-length coverage of gene expression at the level of single cell.RNA quality. DNA quality and size was examined for every individual cells using Bioanalyzer (Agilent Technologies). Only samples with detectable DNA and size in accord with not prior RNA degradation were selected for sequencing. Libraries were pooled before cleaning up and final DNA concentration measuring (these samples represent "pooling_before," or [a] files; while the same libraries were pooled after. cleaning and final DNA concentration measuring (these samples represent "pooling_after," or [b] files; in short, therefore, each single cell  library was sequenced twice,  in onec case the exact concentration of each library in the pool was not adjusted individually, while in the other case it was adjusted before pooling; these two options are suggested in the Takada's protocol and we aimed to test both).

treatment_protocol: No particular treatment was applied after differentiation.

value: Craig Venter-B (CVB) hiPSC subline (hiPSC7)

value: hiPSC-derived single-cell neuron


title: sc-N7_85_pooling_after

description:
Induced  differentiation from hiPSCs
85a_S85_L008


title: sc-N7_82_pooling_before

description:
Induced  differentiation from hiPSCs
82a_S82_L007


title: sc-N7_81_pooling_after

description:
Induced  differentiation from hiPSCs
81a_S81_L008


title: sc-N7_85_pooling_before

description:
Induced  differentiation from hiPSCs
85a_S85_L007


title: sc-N7_87_pooling_after

description:
Induced  differentiation from hiPSCs
87a_S87_L008


title: sc-N7_81_pooling_before

description:
Induced  differentiation from hiPSCs
81a_S81_L007


title: sc-N7_86_pooling_after

description:
Induced  differentiation from hiPSCs
86a_S86_L008


title: basal keratinocytes wild-type (wt_high) [X721_08_H]

value: FVB/N


title: sc-N7_86_pooling_before

description:
Induced  differentiation from hiPSCs
86a_S86_L007


title: sc-N7_87_pooling_before

description:
Induced  differentiation from hiPSCs
87a_S87_L007


title: sc-N7_78_pooling_after

description:
Induced  differentiation from hiPSCs
78a_S78_L008


title: sc-N7_83_pooling_after

description:
Induced  differentiation from hiPSCs
83a_S83_L008


title: sc-N7_79_pooling_after

description:
Induced  differentiation from hiPSCs
79a_S79_L008


title: sc-N7_78_pooling_before

description:
Induced  differentiation from hiPSCs
78a_S78_L007


title: sc-N7_76_pooling_after

description:
Induced  differentiation from hiPSCs
76a_S76_L008


title: sc-N7_79_pooling_before

description:
Induced  differentiation from hiPSCs
79a_S79_L007


title: sc-N7_76_pooling_before

description:
Induced  differentiation from hiPSCs
76a_S76_L007


title: sc-N7_74_pooling_after

description:
Induced  differentiation from hiPSCs
74a_S74_L008


title: basal keratinocytes wild-type (wt_high) [X667_06_H]

value: post natal day 4


title: sc-N7_82_pooling_after

description:
Induced  differentiation from hiPSCs
82a_S82_L008


title: sc-N7_73_pooling_after

description:
Induced  differentiation from hiPSCs
73a_S73_L008


title: sc-N7_72_pooling_after

description:
Induced  differentiation from hiPSCs
72a_S72_L008


title: sc-N7_72_pooling_before

description:
Induced  differentiation from hiPSCs
72a_S72_L007


title: sc-N6_96_pooling_after

description:
Induced  differentiation from hiPSCs
96a_S96_L008

value: Craig Venter-B (CVB) hiPSC subline (hiPSC6)


title: sc-N6_92_pooling_before

description:
Induced  differentiation from hiPSCs
92a_S92_L007


title: sc-N6_94_pooling_after

description:
Induced  differentiation from hiPSCs
94a_S94_L008


title: sc-N6_88_pooling_after

description:
Induced  differentiation from hiPSCs
88a_S88_L008


title: sc-N6_92_pooling_after

description:
Induced  differentiation from hiPSCs
92a_S92_L008


title: sc-N6_96_pooling_before

description:
Induced  differentiation from hiPSCs
96a_S96_L007


title: sc-N7_73_pooling_before

description:
Induced  differentiation from hiPSCs
73a_S73_L007


title: sc-N6_93_pooling_after

description:
Induced  differentiation from hiPSCs
93a_S93_L008


title: sc-N6_95_pooling_after

description:
Induced  differentiation from hiPSCs
95a_S95_L008


title: sc-N6_89_pooling_before

description:
Induced  differentiation from hiPSCs
89a_S89_L007


title: sc-N6_93_pooling_before

description:
Induced  differentiation from hiPSCs
93a_S93_L007


title: sc-N7_74_pooling_before

description:
Induced  differentiation from hiPSCs
74a_S74_L007


title: sc-N6_88_pooling_before

description:
Induced  differentiation from hiPSCs
88a_S88_L007


title: sc-N6_91_pooling_before

description:
Induced  differentiation from hiPSCs
91a_S91_L007


title: sc-N6_89_pooling_after

description:
Induced  differentiation from hiPSCs
89a_S89_L008


title: sc-N6_90_pooling_after

description:
Induced  differentiation from hiPSCs
90a_S90_L008


title: sc-N2_49_pooling_before

description:
Induced  differentiation from hiPSCs
49a_S49_L007

value: Craig Venter-B (CVB) hiPSC subline (hiPSC2)


title: sc-N6_94_pooling_before

description:
Induced  differentiation from hiPSCs
94a_S94_L007


title: sc-N2_50_pooling_after

description:
Induced  differentiation from hiPSCs
50a_S50_L008


title: sc-N2_48_pooling_after

description:
Induced  differentiation from hiPSCs
48a_S48_L008


title: sc-N2_51_pooling_after

description:
Induced  differentiation from hiPSCs
51a_S51_L008


title: sc-N6_95_pooling_before

description:
Induced  differentiation from hiPSCs
95a_S95_L007


title: sc-N6_91_pooling_after

description:
Induced  differentiation from hiPSCs
91a_S91_L008


title: sc-N2_47_pooling_after

description:
Induced  differentiation from hiPSCs
47a_S47_L008


title: sc-N6_90_pooling_before

description:
Induced  differentiation from hiPSCs
90a_S90_L007


title: sc-N2_47_pooling_before

description:
Induced  differentiation from hiPSCs
47a_S47_L007


title: sc-N2_46_pooling_after

description:
Induced  differentiation from hiPSCs
46a_S46_L008


title: sc-N2_46_pooling_before

description:
Induced  differentiation from hiPSCs
46a_S46_L007


title: sc-N2_44_pooling_before

description:
Induced  differentiation from hiPSCs
44a_S44_L007


title: sc-N2_44_pooling_after

description:
Induced  differentiation from hiPSCs
44a_S44_L008


title: sc-N2_43_pooling_after

description:
Induced  differentiation from hiPSCs
43a_S43_L008


title: sc-N2_42_pooling_before

description:
Induced  differentiation from hiPSCs
42a_S42_L007


title: sc-N2_39_pooling_after

description:
Induced  differentiation from hiPSCs
39a_S39_L008


title: sc-N2_42_pooling_after

description:
Induced  differentiation from hiPSCs
42a_S42_L008


title: sc-N2_38_pooling_after

description:
Induced  differentiation from hiPSCs
38a_S38_L008


title: sc-N2_38_pooling_before

description:
Induced  differentiation from hiPSCs
38a_S38_L007


title: sc-N2_45_pooling_after

description:
Induced  differentiation from hiPSCs
45a_S45_L008


title: sc-N2_45_pooling_before

description:
Induced  differentiation from hiPSCs
45a_S45_L007


title: sc-N2_39_pooling_before

description:
Induced  differentiation from hiPSCs
39a_S39_L007


title: sc-N2_48_pooling_before

description:
Induced  differentiation from hiPSCs
48a_S48_L007


title: sc-N2_40_pooling_before

description:
Induced  differentiation from hiPSCs
40a_S40_L007


title: sc-N2_37_pooling_after

description:
Induced  differentiation from hiPSCs
37a_S37_L008


title: sc-N2_37_pooling_before

description:
Induced  differentiation from hiPSCs
37a_S37_L007


title: sc-N2_36_pooling_before

description:
Induced  differentiation from hiPSCs
36a_S36_L007


title: sc-N2_40_pooling_after

description:
Induced  differentiation from hiPSCs
40a_S40_L008


title: sc-N2_36_pooling_after

description:
Induced  differentiation from hiPSCs
36a_S36_L008


title: sc-N2_34_pooling_after

description:
Induced  differentiation from hiPSCs
34a_S34_L008


title: sc-N2_35_pooling_before

description:
Induced  differentiation from hiPSCs
35a_S35_L007


title: sc-N2_33_pooling_after

description:
Induced  differentiation from hiPSCs
33a_S33_L008


title: sc-N2_34_pooling_before

description:
Induced  differentiation from hiPSCs
34a_S34_L007


title: sc-N2_32_pooling_after

description:
Induced  differentiation from hiPSCs
32a_S32_L008


title: sc-N2_43_pooling_before

description:
Induced  differentiation from hiPSCs
43a_S43_L007


title: sc-N2_31_pooling_after

description:
Induced  differentiation from hiPSCs
31a_S31_L008


title: sc-N2_29_pooling_after

description:
Induced  differentiation from hiPSCs
29a_S29_L008


title: sc-N2_35_pooling_after

description:
Induced  differentiation from hiPSCs
35a_S35_L008


title: sc-N2_31_pooling_before

description:
Induced  differentiation from hiPSCs
31a_S31_L007


title: sc-N2_29_pooling_before

description:
Induced  differentiation from hiPSCs
29a_S29_L007


title: sc-N2_25_pooling_before

description:
Induced  differentiation from hiPSCs
25a_S25_L007


title: sc-N2_25_pooling_after

description:
Induced  differentiation from hiPSCs
25a_S25_L008


title: sc-N2_27_pooling_after

description:
Induced  differentiation from hiPSCs
27a_S27_L008


title: sc-N2_24_pooling_after

description:
Induced  differentiation from hiPSCs
24a_S24_L008


title: sc-N2_27_pooling_before

description:
Induced  differentiation from hiPSCs
27a_S27_L007


title: sc-N2_28_pooling_before

description:
Induced  differentiation from hiPSCs
28a_S28_L007


title: sc-N2_24_pooling_before

description:
Induced  differentiation from hiPSCs
24a_S24_L007


title: sc-N2_28_pooling_after

description:
Induced  differentiation from hiPSCs
28a_S28_L008


title: sc-N2_23_pooling_after

description:
Induced  differentiation from hiPSCs
23a_S23_L008


title: sc-N2_23_pooling_before

description:
Induced  differentiation from hiPSCs
23a_S23_L007


title: sc-N2_22_pooling_before

description:
Induced  differentiation from hiPSCs
22a_S22_L007


title: sc-N2_20_pooling_before

description:
Induced  differentiation from hiPSCs
20a_S20_L007


title: sc-N2_20_pooling_after

description:
Induced  differentiation from hiPSCs
20a_S20_L008


title: sc-N2_33_pooling_before

description:
Induced  differentiation from hiPSCs
33a_S33_L007


title: sc-N2_22_pooling_after

description:
Induced  differentiation from hiPSCs
22a_S22_L008


title: sc-N2_19_pooling_after

description:
Induced  differentiation from hiPSCs
19a_S19_L008


title: sc-N2_19_pooling_before

description:
Induced  differentiation from hiPSCs
19a_S19_L007


title: sc-N2_15_pooling_after

description:
Induced  differentiation from hiPSCs
15a_S15_L008


title: sc-N2_16_pooling_after

description:
Induced  differentiation from hiPSCs
16a_S16_L008


title: sc-N2_16_pooling_before

description:
Induced  differentiation from hiPSCs
16a_S16_L007


title: sc-N2_32_pooling_before

description:
Induced  differentiation from hiPSCs
32a_S32_L007


title: sc-N2_15_pooling_before

description:
Induced  differentiation from hiPSCs
15a_S15_L007


title: sc-N2_14_pooling_after

description:
Induced  differentiation from hiPSCs
14a_S14_L008


title: sc-N2_12_pooling_after

description:
Induced  differentiation from hiPSCs
12a_S12_L008


title: sc-N2_14_pooling_before

description:
Induced  differentiation from hiPSCs
14a_S14_L007


title: sc-N2_11_pooling_before

description:
Induced  differentiation from hiPSCs
11a_S11_L007


title: sc-N2_10_pooling_after

description:
Induced  differentiation from hiPSCs
10a_S10_L008


title: sc-N2_10_pooling_before

description:
Induced  differentiation from hiPSCs
10a_S10_L007


title: sc-N2_7_pooling_after

description:
Induced  differentiation from hiPSCs
7a_S7_L008


title: sc-N2_7_pooling_before

description:
Induced  differentiation from hiPSCs
7a_S7_L007


title: sc-N2_4_pooling_after

description:
Induced  differentiation from hiPSCs
4a_S4_L008


title: sc-N2_5_pooling_before

description:
Induced  differentiation from hiPSCs
5a_S5_L007


title: sc-N2_1_pooling_after

description:
Induced  differentiation from hiPSCs
1a_S1_L008


title: sc-N2_4_pooling_before

description:
Induced  differentiation from hiPSCs
4a_S4_L007


title: sc-N2_3_pooling_after

description:
Induced  differentiation from hiPSCs
3a_S3_L008


title: sc-N2_5_pooling_after

description:
Induced  differentiation from hiPSCs
5a_S5_L008


title: sc-N2_12_pooling_before

description:
Induced  differentiation from hiPSCs
12a_S12_L007


title: sc-N2_3_pooling_before

description:
Induced  differentiation from hiPSCs
3a_S3_L007


title: sc-N2_2_pooling_before

description:
Induced  differentiation from hiPSCs
2a_S2_L007


title: sc-N2_1_pooling_before

description:
Induced  differentiation from hiPSCs
1a_S1_L007


title: sc-N1_71_pooling_before

description:
Induced  differentiation from hiPSCs
71a_S71_L007

value: Craig Venter-B (CVB) hiPSC subline (hiPSC1)


title: sc-N2_2_pooling_after

description:
Induced  differentiation from hiPSCs
2a_S2_L008


title: sc-N1_70_pooling_after

description:
Induced  differentiation from hiPSCs
70a_S70_L008


title: sc-N1_69_pooling_after

description:
Induced  differentiation from hiPSCs
69a_S69_L008


title: sc-N1_70_pooling_before

description:
Induced  differentiation from hiPSCs
70a_S70_L007


title: sc-N1_69_pooling_before

description:
Induced  differentiation from hiPSCs
69a_S69_L007


title: sc-N1_68_pooling_after

description:
Induced  differentiation from hiPSCs
68a_S68_L008


title: sc-N1_71_pooling_after

description:
Induced  differentiation from hiPSCs
71a_S71_L008


title: sc-N1_68_pooling_before

description:
Induced  differentiation from hiPSCs
68a_S68_L007


title: sc-N2_11_pooling_after

description:
Induced  differentiation from hiPSCs
11a_S11_L008


title: sc-N1_67_pooling_before

description:
Induced  differentiation from hiPSCs
67a_S67_L007


title: sc-N1_67_pooling_after

description:
Induced  differentiation from hiPSCs
67a_S67_L008


title: HHV-6B_CHX

value: HHV-6B Z29


title: sc-N1_66_pooling_after

description:
Induced  differentiation from hiPSCs
66a_S66_L008


title: HHV-6B_LTM


title: sc-N1_66_pooling_before

description:
Induced  differentiation from hiPSCs
66a_S66_L007


title: sc-N1_65_pooling_after

description:
Induced  differentiation from hiPSCs
65a_S65_L008


title: sc-N1_63_pooling_after

description:
Induced  differentiation from hiPSCs
63a_S63_L008


title: sc-N1_65_pooling_before

description:
Induced  differentiation from hiPSCs
65a_S65_L007


title: sc-N1_62_pooling_after

description:
Induced  differentiation from hiPSCs
62a_S62_L008


title: sc-N1_61_pooling_before

description:
Induced  differentiation from hiPSCs
61a_S61_L007


title: sc-N1_61_pooling_after

description:
Induced  differentiation from hiPSCs
61a_S61_L008


title: sc-N1_60_pooling_after

description:
Induced  differentiation from hiPSCs
60a_S60_L008


title: sc-N1_62_pooling_before

description:
Induced  differentiation from hiPSCs
62a_S62_L007


title: sc-N1_60_pooling_before

description:
Induced  differentiation from hiPSCs
60a_S60_L007


title: sc-N1_59_pooling_after

description:
Induced  differentiation from hiPSCs
59a_S59_L008


title: Sample WTAP sg2 replicate 2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: CRISPR KO of WTAP with sg2 replicate 2

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
All data was combined and normalized using a CPM method from the R/Bioconductor package, edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each Sample.

source_name: cell line

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: sample WTAP


title: Sample WTAP sg2 replicate 1

description: CRISPR KO of WTAP with sg2  replicate 1


title: Sample WTAP sg1 replicate 2

description: CRISPR KO of WTAP with sg1 replicate 2


title: sc-N1_57_pooling_after

description:
Induced  differentiation from hiPSCs
57a_S57_L008


title: sc-N1_58_pooling_before

description:
Induced  differentiation from hiPSCs
58a_S58_L007


title: Sample METTL3 sg2 replicate 2

description: CRISPR KO of METTL3 with sg1  replicate 1

value: sample METTL3


title: Sample WTAP sg1 replicate 1

description: CRISPR KO of WTAP  with sg1  replicate 1


title: sc-N1_57_pooling_before

description:
Induced  differentiation from hiPSCs
57a_S57_L007


title: sc-N1_63_pooling_before

description:
Induced  differentiation from hiPSCs
63a_S63_L007


title: sc-N1_56_pooling_after

description:
Induced  differentiation from hiPSCs
56a_S56_L008


title: sc-N1_56_pooling_before

description:
Induced  differentiation from hiPSCs
56a_S56_L007


title: Sample METTL3 sg1 replicate 1


title: Sample METTL3 sg1 replicate 2


title: sc-N1_55_pooling_after

description:
Induced  differentiation from hiPSCs
55a_S55_L008


title: E6 chicken lung rep1

city: Princeton

first: Celeste

middle: M

last: Nelson

state: NJ

address: 303 Hoyt Laboratory

department: Chemical & Biological Engineering

institute: Princeton University

data_processing:
1. Basecalls performed by Illumina RTA version 1.18.64.0
2. PhiX removal using alignment with Bowtie version 1.1.1
3. Demulitiplexing performed by Galaxy's Enhanced Barcode Splitter v 1.1
4. Illumina TruSeq Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) trimmed with Cutadapt (Galaxy version 1.6) with default parameters
5. Alignment to mm10 genome using Tophat (Galaxy version 0.9) with the following settings: --library_type (first-strand), --GTF (UCSC mm10 GTF file), --no-novel-juncs
6. Gene counts generated using htseq-count (Galaxy version 0.6.1galaxy1) with default parameters
7. Differential expression analysis performed using DESeq2  (Galaxy Version 2.1.8.3)
* Step 3 produced the raw data files below
* Step 6 produced the raw count files that were fed into the differential expression analysis with DESeq2 via Galaxy (DESeq2 Galaxy Wrapper version 2.1.8.3) which uses DESeq2 version 1.8.2 ( R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut", DESeq2 version 1.8.2)
* Step 7 produced the lists of fold change and p-values (another possible "processed data file")
Genome_build: Galgal4

organism: Gallus gallus

source_name: embryonic chick lung

growth_protocol: embryonic chicken lungs were isolated from embryos at E5 and E6 for RNA extraction

extract_protocol:
RNA was isolated from a pool of 6 embryonic chicken lungs isolated from E5 and E6 chcicken embryos using QIAGEN Rneasy fibrous tissue kit.
PrepX RNA-Seq for Illumina Library Kit, from WaferGen

tag: breed

value: White Leghorn

value: wildtype

tag: age

value: embryonic E6


title: E6 chicken lung rep2


title: E6 chicken lung rep3


title: sc-N1_59_pooling_before

description:
Induced  differentiation from hiPSCs
59a_S59_L007

tag: cell type


title: WTAP_K4-2

description: WTAP KO CRISPR CUT&RUN sample

data_processing:
Library strategy: CUT&RUN
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
Raw fastq files were aligned with Bowtie to genome (hg19) and spike in genome(sacCer3), spike in calibration was performed Picard was used to remove duplicate reads , aligned framents were extracted from bam file to a bed file, Bed file was used to call peaks following protocol described at https://github.com/Henikoff/Cut-and-Run/
Genome_build: hg19
Supplementary_files_format_and_content: called peaks are submitted as processed data file

source_name: HEL

growth_protocol: Cells were cultured in RPMI+10% FBS at 37C 5% CO2

extract_protocol:
Genomic DNA was MNase digested in vivo and the fragments precipitated from the supernatant per the CUT&RUN protocol (PMID: 29651053)
Libraries were prepared for sequencing using standard Illumina protocols as recommended in the CUT&RUN protocol (PMID: 29651053)

value: human erythroleukemia (HEL) cells

value: HEL

tag: genotype variation

value: WTAP KO


title: E5 chicken lung rep3

value: embryonic E5


title: sc-N1_58_pooling_after

description:
Induced  differentiation from hiPSCs
58a_S58_L008


title: sc-N1_54_pooling_before

description:
Induced  differentiation from hiPSCs
54a_S54_L007


title: WTAP_K4-1

description: WTAP KO CRISPR CUT&RUN sample


title: E5 chicken lung rep2


title: NTC_K4-3

description: NTC CRISPR CUT&RUN sample

value: NTC


title: Genomic DNA.Sample 148

type: genomic

city: Toronto

first: Cynthia

last: Hawkins

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium® HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Raw data was processed  with minfi package, with Noob (normal-exponential out-of-band) normalisation and  probes with a SNP at or near the CpG, plus those on the X and Y chromosomes were removed. All bioinformatics was completed using R studio.
Noob-normalized average beta in processed data file.

label: Cy5 and Cy3

source_name: Glioma Tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the Qiagen QIAamp DNA FFPE Tissue Kit under manufacturer specification.

value: pediatric low-grade glioma


title: Genomic DNA.Sample 150


title: NTC_K4-2

description: NTC CRISPR CUT&RUN sample


title: Genomic DNA.Sample 149


title: Re-primed_HUES9_1.8_hESC

description:
re-primed cells
IIA12-cortical_S9_L008

source_name: single-cell derived HUES9 1.8 hESC subline

growth_protocol: hiPSCs were seeded onto PA6 cells in PA differentiation medium for 12 days. Between days 12-14, when rosettes were visible, after dissociation, were  FACS-sorted based on the  CD184+/CD271-/CD44-/CD24+ cell-surface signature. Sorted NPCs were cultured on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated plates in NPC medium until confluency was reached. To generate neurons, NPCs grown in 10 cm-plates at confluency were switched to NPC medium without FGF (day 1), and cultured afterwards for 3 weeks. Around day 21, neurons were sorted based on the CD184-/CD44-/CD24+ signature. For RNAseq experiments 1x106 CD24+ sorted neurons were plated on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated 24-well plates in NPC media supplemented with 0.5mM dbcAMP from Sigma, and 20ng/µL BDNF and 20 ng/µL GDNF.

extract_protocol:
Total RNA was extracted using RNeasy Assay (Qiagen) and converted into cDNA using SuperScript First-Strand Synthesis System (Invitrogen) following manufacture’s protocols.
RNA quality was calculated on TapeStation (Agilent Technologies). Most of samples showed a RIN >7.0 and 7 out of 24 had an RIN between 6 and 7. PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

value: HUES9 subline

value: re-primed cells


title: Primed_HUES9_1.8_hESC

description:
primed cells
IID4-cortical_S11_L008

value: primed cells


title: NTC_K4-1

description: NTC CRISPR CUT&RUN sample


title: Sample METTL3 sg2 replicate 1


title: Naive_HUES9_1.8_hESC

description:
naïve cells
ID12-cortical_S10_L008

value: naive cells


title: Genomic DNA.Sample 146


title: CVB_hiPSC-cortical organoid (10 month-old)

description:
Organoids from hiPSCs
CVB_organoids_S15_L008

source_name: CVB line

value: Craig Venter-B (CVB) hiPSC line

value: organoid cultures


title: Genomic DNA.Sample 145


title: METTL3_K4-2

description: METTL3 KO CRISPR CUT&RUN sample

value: METTL3 KO


title: METTL3_K4-1

description: METTL3 KO CRISPR CUT&RUN sample


title: Genomic DNA.Sample 144


title: Genomic DNA.Sample 142


title: Genomic DNA.Sample 141


title: Genomic DNA.Sample 152


title: Cortical_N3

description:
Induced cortical differentiation from hiPSCs
Hues9_1_8_primed_S12_L008

source_name: single-cell CVB derived hiPSC3 subline

value: Craig Venter-B (CVB) hiPSC subline

value: cortical neuronal differentiation


title: Genomic DNA.Sample 151


title: METTL14_K4-2

description: METTL14 KO CRISPR CUT&RUN sample

value: METTL14 KO


title: E5 chicken lung rep1

value: White Leghorn

value: wildtype


title: Cortical_N1

description:
Induced cortical differentiation from hiPSCs
Hues9_1_8_naive_S13_L008

source_name: single-cell CVB derived hiPSC1 subline


title: METTL14_K4-1

description: METTL14 KO CRISPR CUT&RUN sample

value: human erythroleukemia (HEL) cells

value: HEL


title: Genomic DNA.Sample 140


title: Genomic DNA.Sample 139


title: Genomic DNA.Sample 138


title: HEL_150ug_2_IP

description: HEL poly-A m6A IP RNAseq sample from 150ug total RNA

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2
Custom R scripts were written for identification of peaks based on Meyer et al(https://www.ncbi.nlm.nih.gov/pubmed/22608085) and for visualization of peaks. The Human transcriptome (from hg19) was broken into 25nt wide discrete non-overlapping reads. Using bedtools 84 the 50bp reads were mapped to 25nt windows and windows with fewer than 5 aligned reads were dropped. We used one sided Fisher’s exact test to compare the number of reads that mapped to a given window for the MeRIP sample and the non-IP sample to the total number of reads in each. The Benjamini-Hochberg procedure was used to adjust the p-values from the Fisher's exact test to reduce our false discovery rate to 5%. To find a final p-value for each window, Fisher's Method was used to combine p-values across replicates. To find distinct m6A peaks, we combined consecutive significant 25nt windows across the transcriptome. Consecutive significant windows less than 100bp were discarded. Gene region annotations for the peaks were found from UCSC RefSeq Table for Hg19
Genome_build: hg19
Supplementary_files_format_and_content: Peaks identified for each IP and input pair are reported.

source_name: m6A IP

extract_protocol:
RNA was extracted from bulk HEL cells using the Qiagen RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEL cells

value: ip sample


title: Genomic DNA.Sample 137

value: pediatric low-grade glioma


title: Naïve_CVB_hiPSC6_H3K4me3_R2

description:
AGTTCC
IIDV8_NAIVE_HOX_S28_L008

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: bedGraph

source_name: hiPSC6 subline

growth_protocol: hiPSC/hESC lines and sublines were cultured on a feeder layer of gamma-irradiated mouse embryonic fibroblasts (MEFs), and maintained in hESC media made with knockout (KO) Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Plasmanate from Talecris Biotherapeutics; 10% Knockout serum replacement (KOSR) from Gibco; 20 mM GlutaMax, 20 mM nonessential amino acids (NEAA) and 20 mM Pen/Strep from Invitrogen; and, 20 ng/µL FGF from Millipore. Mouse ESCs were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF.

extract_protocol:
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

treatment_protocol: No particular treatments were applied.

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: H3K4me3 (Millipore, 07-473)


title: HEL_150ug_1_IP

tag: group


title: Genomic DNA.Sample 134


title: Genomic DNA.Sample 147


title: Genomic DNA.Sample 135


title: Naïve_CVB_hiPSC6_H3K4me3_R1

description:
AGTCAA
IIDV8_NAIVE_S27_L008


title: Naïve_CVB_hiPSC8_H3K4me3

description:
CGTACG
IB7_naive_S27_L005

source_name: hiPSC8 subline


title: Genomic DNA.Sample 136


title: Genomic DNA.Sample 143


title: HEL_150ug_2

description: HEL input poly-A enriched RNAseq sample from 150ug total RNA

source_name: input control

value: non-ip sample


title: Genomic DNA.Sample 133


title: Cortical_N5

description:
Induced cortical differentiation from hiPSCs
Hues9_1_8_reprimed_S14_L008

source_name: single-cell CVB derived hiPSC5 subline


title: Genomic DNA.Sample 130


title: Re-primed_HUES9_hESC 1.8-1.8_H3K4me3

description:
TTAGGC
HUES9_1_8_RP_SC14_S4_L004

source_name: hiPSC1 1.8-1.8 subline

value: HUES9 hESC subline


title: Re-primed_HUES9_hESC 1.8-1.7_H3K4me3

description:
ATCACG
HUES9_1_8_RP_SC13_S3_L004

source_name: hiPSC1 1.8-1.7 subline


title: WTAPtot_3

description: sample WTAP

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: Total RNA library from WTAP sgRNA HEL cells

extract_protocol:
RNA/protein were extracted following the protocol in the TruSeq Ribo Profile kit from Illumina
RNA libraries were prepared for sequencing following the protocol in the TruSeq Ribo Profile kit from Illumina

treatment_protocol: Cells were treated with puromycin to kill untransduced cells at the start of the experiement

tag: fraction

value: total RNA


title: Genomic DNA.Sample 131


title: WTAPtot_2

description: sample WTAP


title: Genomic DNA.Sample 127


title: Re-primed_HUES9_hESC 1.8-1.6_H3K4me3

description:
GATCAG
RP_clone11_S14_L004

source_name: hiPSC1 1.8-1.6 subline


title: Genomic DNA.Sample 129


title: Genomic DNA.Sample 128


title: Genomic DNA.Sample 126


title: HEL_150ug_1


title: Genomic DNA.Sample 125


title: Re-primed_HUES9_hESC 1.8-1.5_H3K4me3

description:
ATGTCA
RP_clone12_S26_L005

source_name: hiPSC1 1.8-1.5 subline


title: Genomic DNA.Sample 124


title: WTAPribo_3

description: sample WTAP

data_processing:
Library strategy: Ribo-Seq
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: Ribosome protected RNA library from WTAP sgRNA HEL cells

value: RPF RNA


title: Genomic DNA.Sample 121


title: WTAPtot_1

description: sample WTAP


title: Naïve_CVB_hiPSC2_H3K4me3

description:
ACTTGA
IIA11_NAIVE_HOX_S10_L007

source_name: hiPSC2 subline


title: Genomic DNA.Sample 120

source_name: Glioma Tissue


title: Genomic DNA.Sample 119


title: Genomic DNA.Sample 132


title: WTAPribo_2

description: sample WTAP


title: Re-primed_HUES9_hESC 1.8-1.3_H3K4me3

description:
GCCAAT
HUES_9_1_8_RP_R3_SC10_S20_L008

source_name: hiPSC1 1.8-1.3 subline


title: WTAPribo_1

description: sample WTAP


title: Genomic DNA.Sample 118


title: Re-primed_HUES9_hESC 1.8-1.4_H3K4me3

description:
ACTTGA
RP_clone8_S25_L005

source_name: hiPSC1 1.8-1.4 subline


title: Re-primed_HUES9_hESC 1.8-1.2_H3K4me3

description:
ACAGTG
HUES_9_1_8_RP_R3_SC9_S19_L008

source_name: hiPSC1 1.8-1.2 subline


title: Genomic DNA.Sample 116


title: NTCtot_3

description: sample NTC

source_name: Total RNA library from NTC sgRNA HEL cells


title: Re-primed_HUES9_hESC 1.8-1.1_H3K4me3

description:
TGACCA
HUES_9_1_8_RP_R3_SC3_S18_L008

source_name: hiPSC1 1.8-1.1 subline


title: Genomic DNA.Sample 115


title: Genomic DNA.Sample 114


title: Re-primed_HUES9_hESC 1.8 _H3K4me3_R3

description:
TAGCTT
HUES_9_1_8_RP_R5_HOX_S24_L008

source_name: HUES9 hESC 1.8 subline


title: NTCtot_2

description: sample NTC


title: NTCtot_1

description: sample NTC


title: Genomic DNA.Sample 113


title: Genomic DNA.Sample 123


title: Genomic DNA.Sample 122


title: Genomic DNA.Sample 112


title: Genomic DNA.Sample 110


title: Genomic DNA.Sample 111


title: Genomic DNA.Sample 108


title: Genomic DNA.Sample 107


title: NTCribo_2

description: sample NTC

source_name: Ribosome protected RNA library from NTC sgRNA HEL cells


title: Genomic DNA.Sample 109


title: Naive_HUES9_hESC 1.8 _H3K4me3_R2

description:
CAGATC
HUES_9_1_8_NAIVE_R5_S21_L008


title: NTCribo_1

description: sample NTC


title: Naive_HUES9_hESC 1.8 _H3K4me3_R3

description:
GATCAG
HUES_9_1_8_NAIVE_R5_HOX_S23_L008


title: Re-primed_HUES9_hESC 1.8 _H3K4me3_R1

description:
TTAGGC
HUES_9_1_8__RP_R3_S17_L008


title: Genomic DNA.Sample 105


title: Crispr Sample Day12_Depleted_7

description: sgRNA

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Reads were aligned to the guide library  using Bowie and counted for gene associations against the guide library used.
Raw counts for each guide are supplied for every sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

source_name: Day 12 CRISPR screen samples containing CD235 low cells in the culture

extract_protocol:
Followed the standard protocol for the Qiagen QIAamp DNA Blood Mini Kit
Nested PCR was used to amplify integrated sgRNAs out of gDNA.  Illumina adapters were added on as part of the primers for the second round PCR.

tag: time

value: Day 12


title: Genomic DNA.Sample 106


title: Genomic DNA.Sample 103


title: Crispr Sample Day12_Depleted_6

description: sgRNA


title: Naive_HUES9_hESC 1.8 _H3K4me3_R1

description:
CGATGT
HUES_9_1_8_NAIVE_R3_S16_L008

tag: cell line


title: Primed_HUES9_hESC 1.8 _H3K4me3

description:
TGACCA
HUES9-1_8_S8_L007


title: Genomic DNA.Sample 101


title: Genomic DNA.Sample 102


title: CVB_hiPSC1 1.6_H3K4me3

description:
GTGGCC
ADAM_35_S17_L005

source_name: hiPSC1 1.6 subline


title: Crispr Sample Day12_Depleted_5

description: sgRNA


title: NTCribo_3

description: sample NTC


title: Genomic DNA.Sample 100


title: Crispr Sample Day12_Depleted_4

description: sgRNA


title: Re-primed_HUES9_hESC 1.8 _H3K4me3_R2

description:
ACTTGA
HUES_9_1_8_RP_R5_S22_L008


title: Genomic DNA.Sample 99


title: CVB_hiPSC1 1.5_H3K4me3

description:
GTGAAA
ADAM_98_S16_L005

source_name: hiPSC1 1.5 subline


title: Genomic DNA.Sample 98


title: Genomic DNA.Sample 97


title: Crispr Sample Day12_Depleted_3

description: sgRNA


title: CVB_hiPSC1 1.4_H3K4me3

description:
GTCCGC
ADAM_19_S15_L005

source_name: hiPSC1 1.4 subline


title: Genomic DNA.Sample 95


title: Genomic DNA.Sample 94


title: Genomic DNA.Sample 92


title: CVB_hiPSC1 1.3_H3K4me3

description:
CGTACG
ABCA7_108_S7_L004

source_name: hiPSC1 1.3 subline


title: Crispr Sample Day12_Depleted_2

description: sgRNA


title: Crispr Sample Day12_Depleted_1

description: sgRNA


title: CVB_hiPSC1 1.2_H3K4me3

description:
CCGTCC
ADAM_58_S2_L004

source_name: hiPSC1 1.2 subline


title: Genomic DNA.Sample 104


title: Genomic DNA.Sample 93


title: Genomic DNA.Sample 91


title: Crispr Sample Day12_all_7

description: sgRNA

source_name: Day 12 CRISPR screen samples containing all cells in the culture


title: CVB_hiPSC1 1.1_H3K4me3

description:
ATGTCA
ADAM_49_S1_L004

source_name: hiPSC1 1.1 subline


title: Crispr Sample Day12_all_6

description: sgRNA


title: Genomic DNA.Sample 88


title: Genomic DNA.Sample 89


title: Crispr Sample Day12_all_5

description: sgRNA


title: Genomic DNA.Sample 117


title: Genomic DNA.Sample 96


title: Genomic DNA.Sample 86


title: Crispr Sample Day12_all_4

description: sgRNA


title: Genomic DNA.Sample 85


title: LuCaP_167_s8 PDX tumor

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 167 PDX tumor

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human and mm10 mouse genomes using TopHat v2.1.0. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 167 PDX tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from flash frozen LuCaP xenograft tissue or cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: prostate cancer


title: LuCaP_176_s5_ET1489 PDX tumor

description: LuCaP 176 PDX tumor

source_name: LuCaP 176 PDX tumor


title: LuCaP_176_s5_ET1374 PDX tumor

description: LuCaP 176 PDX tumor


title: Crispr Sample Day12_all_3

description: sgRNA


title: Genomic DNA.Sample 82

source_name: Glioma Tissue


title: LuCaP_167_s16_ET1911 PDX tumor

description: LuCaP 167 PDX tumor


title: Genomic DNA.Sample 80


title: Genomic DNA.Sample 81


title: Genomic DNA.Sample 79


title: Genomic DNA.Sample 90


title: Genomic DNA.Sample 78


title: Crispr Sample Day12_all_1

description: sgRNA


title: Crispr Sample Day12_all_2

description: sgRNA


title: LuCaP_147CR_s3 PDX tumor

description: LuCaP 147CR PDX tumor

source_name: LuCaP 147CR PDX tumor


title: Genomic DNA.Sample 77


title: Genomic DNA.Sample 87


title: LuCaP_136CR_s4_2 PDX tumor

description: LuCaP 136CR PDX tumor

source_name: LuCaP 136CR PDX tumor


title: Crispr Sample Day0_3

description: sgRNA

source_name: Day 0 CRISPR library control

value: Day 0


title: Genomic DNA.Sample 74


title: Genomic DNA.Sample 76


title: Crispr Sample Day0_2

description: sgRNA


title: Genomic DNA.Sample 84


title: LuCaP_136CR_s4_1 PDX tumor

description: LuCaP 136CR PDX tumor


title: Genomic DNA.Sample 73


title: Crispr Sample Day0_1

description: sgRNA


title: Genomic DNA.Sample 72


title: LuCaP_105CR_s7 PDX tumor

description: LuCaP 105CR PDX tumor

source_name: LuCaP 105CR PDX tumor


title: Sample NTC replicate 3

description: CRISPR NTC in HEL cells replicate 3

source_name: cell line

tag: treatment

value: CRISPR NTC in HEL cells


title: LuCaP_105CR_s11_ET78 PDX tumor

description: LuCaP 105CR PDX tumor


title: LuCaP_147CR_s23n2_ET2390 PDX tumor

description: LuCaP 147CR PDX tumor


title: Genomic DNA.Sample 68


title: Genomic DNA.Sample 66


title: Sample NTC replicate 2

description: CRISPR NTC in HEL cells replicate 2


title: Genomic DNA.Sample 64


title: LuCaP_96CR_s36n1 PDX tumor

description: LuCaP 96CR PDX tumor

source_name: LuCaP 96CR PDX tumor


title: Genomic DNA.Sample 65


title: Sample LMO2 replicate 3

description: CRISPR KO of LMO2 in HEL cells replicate 3

value: CRISPR KO of LMO2 in HEL cells


title: LuCaP_86.2CR_s3n1 PDX tumor

description: LuCaP 86.2CR PDX tumor

source_name: LuCaP 86.2CR PDX tumor


title: Genomic DNA.Sample 75


title: basal keratinocytes bitransgenic (bt_high) [X722_07_H]

source_name: basal

tag: strain

value: FVB/N

value: post natal day 4

value: Skin

tag: genotype

value: BT


title: Sample LMO2 replicate 2

description: CRISPR KO of LMO2 in HEL cells replicate 2


title: LuCaP_96CR_s11 PDX tumor

description: LuCaP 96CR PDX tumor


title: Genomic DNA.Sample 62


title: Genomic DNA.Sample 71


title: Genomic DNA.Sample 61


title: Sample LMO2 replicate 1

description: CRISPR KO of LMO2 in HEL cells replicate 1


title: Genomic DNA.Sample 60


title: Genomic DNA.Sample 58


title: Sample GYPA replicate 3

description: CRISPR KO of GYPA in HEL cells replicate 3

value: CRISPR KO of GYPA in HEL cells


title: Genomic DNA.Sample 69

value: pediatric low-grade glioma


title: Genomic DNA.Sample 67


title: Genomic DNA.Sample 57


title: Genomic DNA.Sample 59


title: LuCaP_78CR_s2 PDX tumor

description: LuCaP 78CR PDX tumor

source_name: LuCaP 78CR PDX tumor


title: Sample GYPA replicate 2

description: CRISPR KO of GYPA in HEL cells replicate 2


title: LuCaP_86.2CR_s1 PDX tumor

description: LuCaP 86.2CR PDX tumor


title: LuCaP_78CR_s5 PDX tumor

description: LuCaP 78CR PDX tumor


title: LuCaP_77CR_s18n2_ET414 PDX tumor

description: LuCaP 77CR PDX tumor

source_name: LuCaP 77CR PDX tumor


title: Genomic DNA.Sample 63


title: Genomic DNA.Sample 54


title: Sample GYPA replicate 1

description: CRISPR KO of GYPA in HEL cells replicate 1


title: LuCaP_77CR_s18n2_ET232 PDX tumor

description: LuCaP 77CR PDX tumor


title: Genomic DNA.Sample 51


title: LuCaP_73CR_s9n1_ET2068 PDX tumor

description: LuCaP 73CR PDX tumor

source_name: LuCaP 73CR PDX tumor


title: Sample GATA1 replicate 3

description: CRISPR KO of GATA1 in HEL cells replicate 3

value: CRISPR KO of GATA1 in HEL cells


title: Genomic DNA.Sample 52


title: Genomic DNA.Sample 56


title: Sample GATA1 replicate 2

description: CRISPR KO of GATA1 in HEL cells replicate 2


title: Genomic DNA.Sample 53


title: Genomic DNA.Sample 50


title: LuCaP_73CR_s4n1_020713 PDX tumor

description: LuCaP 73CR PDX tumor


title: Sample GATA1 replicate 1

description: CRISPR KO of GATA1 in HEL cells replicate 1


title: Genomic DNA.Sample 49


title: Genomic DNA.Sample 48


title: T1-23 MethylC-seq

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Library strategy: MethylC-seq
MethylC-seq reads were trimmed (removing sequencing adapter and low-quality reads) by Trimmomatic.  MethylC-seq reads were aligned to the MSUv7 genome using BS Seeker2.
Genome_build: MSU Rice Genome Annotation, Release 7
Supplementary_files_format_and_content: CGmap file

organism: Oryza sativa Japonica Group

source_name: OsNRPD1 Knock-down T1 generation, line 23; leaf sample

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Genomic RNA was extracted by CTAB-based method as described in Debladis et al. 2017 BMC Genomics v.18 p.537
MethylC-seq libraries were constructed as previously described with some variation (Urich et al. 2015. Nat. Protocol v.10 p.475)

tag: cultivar

value: Nipponbare

value: leaf

value: one month

value: OsNRPD1 Knock-down


title: Genomic DNA.Sample 55

tag: tissue


title: T1-15 MethylC-seq

source_name: OsNRPD1 Knock-down T1 generation, line 15; leaf sample

tag: genotype/variation


title: Genomic DNA.Sample 47


title: Genomic DNA.Sample 46


title: Genomic DNA.Sample 45


title: WT MethylC-seq

source_name: wildtype plants; leaf sample

value: wildtype


title: T0 MethylC-seq

source_name: OsNRPD1 Knock-down T0 regenerant; leaf sample


title: Genomic DNA.Sample 44


title: LuCaP_35CR_s54 PDX tumor

description: LuCaP 35CR PDX tumor

source_name: LuCaP 35CR PDX tumor

value: male


title: Genomic DNA.Sample 43

source_name: Glioma Tissue


title: LuCaP_23.1CR_s1 PDX tumor

description: LuCaP 23.1CR PDX tumor

source_name: LuCaP 23.1CR PDX tumor

value: prostate cancer


title: LuCaP_35CR_s37 PDX tumor

description: LuCaP 35CR PDX tumor


title: Genomic DNA.Sample 42


title: LuCaP_70CR_s6 PDX tumor

description: LuCaP 70CR PDX tumor

source_name: LuCaP 70CR PDX tumor


title: LuCaP_70CR_s3 PDX tumor

description: LuCaP 70CR PDX tumor


title: 903 IL4

city: Grand Rapids

first: Sonia

last: George

state: MI

address: 333 Bostwick Ave

institute: Van Andel Research Institute

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Following sequencing, paired-end fastq files were aligned to the GRCm38 primary assembly with STAR v2.5
Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of mm10: GRCm38.95.chr.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse” (supplemental material). This set included exon locations for 54,752 genomic entities including pseudogenes, lncRNAs, and 21,949 protein coding genes. The resulting gene_id counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom in R (v3.3.1)
Prior to statistical testing, genes without more than 0.1 counts per million (CPM) in at least 3 samples were excluded (giving 24,227 genes). Three contrasts were made comparing each pairwise combination of LPS, IL-4, and PBS treatment groups for differential gene expression. A significance threshold of FDR = 0.05 was used with a secondary abs(log2FC) > 1 filter was used to define the highest magnitude changes.
After the PBS group was excluded from further analysis an additional minimum average expression filter of log2CPM > 0 in either the LPS or IL-4 groups was imposed. Expression values (log2CPM) for each sample are included as supplemental data. Some expression data was later converted to FPKM or z-scores for later visualization and comparison.  Z-scores were calculated based on the mean and standard deviation of the IL-4 treatment group only.
Gene ontology enrichment analysis was done using String v.111.0 {Szklarczyk:2015cn} against a background of the 15,938 minimally expressed genes. Genes set enrichment (GSEA, Broad, V3.0) [ https://doi.org/10.1073/pnas.0506580102] was also used to identify affected pathways with both unranked (log2CPM) and preranked (FDR) analysis. Included as supplemental figure are the highest results based on the unranked GSEA. Grouping of enriched biological pathways was done using the Cytoscape (V3.7.1) with the add-on Autoannotate [PMID: 27830058] and c5.bp.v6.2.symbols.gmt. Finally, a subset of biological process gene sets were downloaded from Amigo2 (v2.5.12) for Fig. 6e.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with raw counts and statistical analysis

source_name: brain-striatum

extract_protocol:
Total RNA was extracted from brain homogenates from the ipsilateral striatum from control, LPS and IL-4 injected mice using the QIAshredder and RNeasy micro kit with on-column DNAse treatment, (QIAGEN) according to manufacturer’s protocol. The samples used for RNA-seq were from the biochemistry cohort of animals, separate from the set of mice used for immunohistochemistry and confocal analysis. Quality was assessed by Bioanalyzer (Agilent Technologies) and samples with an RIN >8 were used for library construction.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex dual adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an SP 100 cycle kit (Illumina Inc).

value: ipsilateral striatum

value: 10-14 weeks old

value: AAV over expression, neural graft, inflammatory injection

tag: injected with


title: ZNF850 ChIPexo

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads). For ChIPexo –very-sensitive-local was used.
For ChIP-seq, reads with mapping quality lower than 10 were removed from the analysis.
Peaks were called using MACS v1.4 with default parameters. For ChIP-exo, the “--keep-dup all” was added.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.bed: Bed files as output by MACS.

source_name: transduced 293T cell line

growth_protocol: Human embryonic kidney-derived 293T cells were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Chromatin was prepared by resuspending 3x10e7 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follows: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
NextSeq v2 (with Illumina protocol #15048776).

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/mL) for 7 days and induced using doxycycline (1 ug/mL) for a few days before fixation with formaldehyde (1% for 10 min).

tag: host cell line

value: HEK 293T

tag: transduced kzfp

tag: chip antibody

value: Anti-HA (clone 16B12, Covance)


title: ZNF812 ChIPexo


title: Genomic DNA.Sample 41


title: 901 IL4

tag: age


title: 830 IL4


title: ZNF772 ChIPexo


title: Genomic DNA.Sample 40


title: Liver_TTP_Rep 3

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: Gene expression of liver from LDLR knockout mice transplanted with bone marrow cells isolated from TTP knock out mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.5 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from TTP knock out mice, Replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: Seven week-old female LDLR−/− mice were obtained from Jackson Laboratories (Bar Harbor, Maine). All mice were kept under specific pathogen-free conditions in a temperature controlled environment at the University of South Carolina according to National Institutes of Health (NIH) guidelines. Animal care and experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of South Carolina

extract_protocol: Total RNAs were isolated from liver tissue using RNeasy Mini kit (Qiagen, Germantown, MD) following the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer.

treatment_protocol: 8 week-old female LDLR−/− mice on C57BL/6J background were lethally irradiated  and reconstituted with a wild type (TTP+/+) or TTP knockout (TTP−/−) bone marrow cells. Four weeks after bone marrow transplantation, the mice started to be fed a Western diet for 12 weeks.

value: LDLR knockout

value: Liver

value: female

value: 24 weeks of age


title: Liver_TTP_Rep 1

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from TTP knock out mice, Replicate 1


title: Liver_TTP_Rep 2

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from TTP knock out mice, Replicate 2


title: 50 hpf WT hearts

city: Bad Nauheim

first: Ryuichi

last: Fukuda

state: Select...

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies)  is used following the manufacture's protocol. For example, 600 ng cRNA is hybridised on a  8x60K microarray at 65  C for 17 h using Agilent`s recommended hybridisation chamber and  oven. Finally the microarray is washed once with the Agilent Gene Expression Wash Bu er 1  for one minute at ambient temperature followed by a second wash with preheated (37  C)  Gene Expression Wash Bu er 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent  Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and  5 micron for HD Microarray formats, generating a 20 bit TIFF  le respectively.

data_processing: Data of all samples are quantile normalised using the ranked median quantiles according to  Bolstad et al. \A comparison of normalisation methods for high density oligonucleotide array  data based on variance and bias, Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets.

source_name: 50 hpf zebrafish hearts

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of    uorescent cRNA (complementary RNA) following the manufacture's protocol. For 1st strand  synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer)  is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled  with cyanine 3-CTP is performed.

extract_protocol: Qiagen RNA extraction kit

value: heart

value: wild type

tag: developmental stage

value: 50 hpf


title: LuCaP_23.1CR_s3 PDX tumor

description: LuCaP 23.1CR PDX tumor

tag: cell type


title: Liver_TTP_Rep 4

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from TTP knock out mice, Replicate 4


title: 1003 IL4