title: WT rep2

city: Stanford

first: Gun Woo

last: Byeon

state: CA

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

description: polyA selected RNA

data_processing:
VELCRO-IP RNA-seq Data Analysis: Read Alignment and Quantification
First, for removal of adapter sequences, low quality bases, and short reads, we use cutadapt (Martin, 2011) to trim Illumina adapter sequences and <Q20 bases. Reads <40 nt were removed. Parameters: cutadapt -m 40 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --nextseq-trim=20. Next, for UMI extraction, we used umi_tools (Smith et al., 2017) to extract the UMI region (first 8 bases). Parameters: umi_tools extract --bc-pattern=NNNNNNNN --bc-pattern2=NNNNNNNN. We additionally remove 1 base from 5’ end of the reads, which is the A/T nucleotide overhang from the ligation reaction during library preparation. For splice-aware alignment using STAR (Dobin et al., 2013), we used STAR to align the reads to a reference genome/transcriptome. STAR reference is built using a combination of yeast genome (sacCer3), mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18). Only uniquely mapped reads were retained. Parameters: STAR --sjdbOverhang 66 --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignIntronMin 20 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterType BySJout. While the majority of the reads mapped to yeast mRNAs that we believe reflect background binding from the initial ribosome-IP (~20 million reads), 1-3% mapped to mouse mRNAs which corresponds to ~500,000 reads per sample. For deduplication using UMI, we used umi_tools to deduplicate the alignments. Deduplicated alignments are re-aligned using STAR and the same parameters as before. Parameters: umi_tools dedup --paired --buffer-whole-contig. For read quantification, we used bedtools (Quinlan and Hall, 2010) to count alignments over 200 nt sliding windows with step size of 100 nt across mouse genome.
VELCRO-IP RNA-seq Data Analysis: Enrichment Analysis
For data matrix and normalization, each cell in the data matrix is the read count, where rows are 200 nt genomic windows and columns are the samples. We discarded rows whose sum of counts across the mutant and wild-type samples was < 5. We used the TMM (Robinson and Oshlack, 2010) method to calculate normalization factors. Counts divided by normalization factors were used for plotting tracks along the transcript. Tracks are plotted using wiggleplotR (Alasoo et al., 2015). Each genomic window is annotated as 5’ UTR, ORF, or 3’ UTR based on any overlap with any isoform present in the GENCODE vM18 annotation. For statistical significance of enriched windows, we use voom (Law et al., 2014)-limma (Ritchie et al., 2015) strategy to model mean-variance bias and calculate moderated t-statistics and p-values for the difference in mutant versus wild-type samples. We noted the heavy tailed histogram of the t-statistics suggesting high proportion of non-null windows and used locfdr (Efron, 2010) approach to estimate local false discovery rates. All reported FDR values in the manuscript are locfdr estimates. Locfdr parameters: bre=150, df=25, pct=0, nulltype=1, type=0, mlests=(-0.5, 1.0). For Gene Ontology (GO) term enrichment, GO terms and gene mappings were obtained from Bioconductor annotation package org.Mm.eg.db (version 3.6.0). We used topGO (Alexa et al., 2006) to perform enrichment analysis. We choose the combination of Fisher’s exact test and weight01 algorithm for handling local similarities between GO terms. Genes that have at least one window with FDR <= 0.05 are used as the positive set. All genes that have at least one window tested are used as the background. For the reported list of GO terms in the manuscript, the following criteria are true: observed/expected ratio >= 2, minimum number of genes >= 4, rank by classic Fisher statistic <= 100, and weight01-conditioned Fisher p-value <= 0.05.
Genome_build: yeast genome (sacCer3), mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18)
Supplementary_files_format_and_content: Text file includes the data matrix of read counts where rows are 200 nt sliding genomic windows and columns are the samples

molecule: polyA RNA

source_name: Whole embryo

extract_protocol:
In order to generate a pool of endogenous mouse embryo mRNAs as RNA input for the ribosome-IP, up to 10 stage 11.5 embryos per FVB female were harvested as described in the mouse section, individually collected in 2 ml Eppendorf tubes, washed once with 1x PBS (Gibco, 14190-250), and lyzed in 1 mL TRIzol (Invitrogen, 15596) by pipetting and vortexing, and addition of another 800 µL TRIzol. Embryo lysates were stored at -80°C until total RNA extraction. From each embryo, 150-200 µg total RNA was obtained. From total RNA, poly(A) mRNA was isolated on oligo(dT) beads using the Oligotex mRNA Mini Kit (QIAgen, 70022) or Poly(A) Purist MAG kit (Invitrogen, AM1922) according to the manufacturer’s instructions, which yielded ~5 µg mRNA (2-3%) of 150-200 µg total RNA per embryo. Purified embryo mRNA was fragmented to 100-200 nt RNA fragments using the NEBNext Magnesium RNA Fragmentation Module (NEB, E6150S). Fragmentation was optimized for time and RNA input amount monitoring RNA size using the mRNA Pico Chip (Agilent) on a Bioanalyzer (Agilent), and by 8% denaturing urea-PAGE and SYBR Gold staining. Fragmentation of 1 µg mRNA aliquots for 5 min at 94°C in 1x Fragmentation Buffer (NEB) was optimal to obtain a pool of 100-200 nt fragments. Reactions were quenched on ice and by addition of 1x Stop Solution (NEB). Immediate isopropanol-based precipitation recovered 75-95% of input mRNA as mRNA fragments in water.
For Flag-pulldown of Flag-tagged yeast 40S, powderized yeast lysates of a 250 mL culture per three samples were dissolved in 500 µL lysis buffer and the tube was washed with another 200 µL lysis buffer. Lysates were cleared by centrifugation for 5 min at 17,000 g at 4°C and 2 min at 17,000 g at 4°C, and 800 µL lysate was recovered. RPS2-Flag tagged 40S ribosomes were immuno-precipitated by addition of 50 µL washed anti-Flag M2 affinity agarose gel (Sigma Aldrich, A2220-5mL) and 5 µL RNasin Plus (Promega) per sample to 800 µL lysate and 1.5-2 hours of rotation at 4ºC. Beads were washed 3 times with 500 µL lysis buffer and bound ribosomes were resuspended by addition of 200 µL lysis buffer. 10 µg fragmented mRNA from E11.5 FVB embryos in 40 µL per sample were pooled for 6 samples. 5 µL was saved as an input RNA sample for sequencing. Pooled mRNA was refolded in lysis buffer in a total volume of 600 µL as described in the 4xS1m pulldown section and used as input for 6 samples. 10 µg refolded RNA in 100 µL was added to 100 µL ribosome-coupled 50% beads, 3 µL RNasin (Promega) and 100 µL lysis buffer for a total volume of 300 µL for IP by rotation for 2 hours at 4ºC. Bound ribosome-mRNA fragment complexes were rinsed once with 1 mL lysis buffer and washed 3 times with wash buffer for 5 min tumbling at 4°C. Samples were then eluted off the anti-Flag beads using competitive 500 µg/mL 3xFlag peptide (Sigma-Aldrich, F4799-4mg) elution in 150 µL lysis buffer by rotation for 1 hour at 4°C. 5% of the elution was used for protein analysis by WB, and 95% was subjected to TRIzol total RNA extraction and library preparation.
Library Preparation and Deep Sequencing
5 µg total RNA isolated from Flag elution samples were treated with Yeast RiboZero Gold (Illumina, MRZY1306) according to the manufacturer’s instructions to remove yeast rRNAs from the samples. From the remaining fragmented RNA in water (10 µL, yield 80-160 ng RNA), 30 ng of elution and mRNA fragment input samples were used for library preparation. Library preparation for deep sequencing was performed using the NextFlex Rapid Directional qRNA-Seq Library Prep Kit (Perkin Elmer, Bioo Scientific, NOVA-5130-01D) according to the manufacturer’s instructions using 7 unique barcodes. In brief, the standard protocol was applied with the following changes: the initial fragmentation step was omitted and PCR amplification was performed using 16 cycles. DNA fragments were purified for Illumina sequencing, subjected to analysis using the High Sensitivity DNA Assay (Agilent) on a Bioanalyzer (Agilent) and all DNA libraries were pooled to a final concentration of 4 nM. Sequencing was performed at the Stanford Functional Genomics Facility (SFGF) at Stanford University, on the Illumina NextSeq 550 instrument, using 2x 75 nt paired-end sequencing and the following library design: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNT-insert-NNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACBBBBBBBBATCTCGTATGCCGTCTTCTGCTTG, where N is the 2x 8 nt unique molecular index, and B is the 8 nt sample barcode.

tag: age

value: Wild-type


title: EK43

status: Public on Jan 29 2021

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description:
Neuron from right side of DMV in Naive Rat
BioMark-RTqPCR

data_processing:
Samples were normalized through centering aound the median of the 35 genes with highest expression values across all samples.
Raw Matrix contains raw Ct values for genes and control RNA dilution series

label: EvaGreen

molecule: total RNA

organism: Rattus norvegicus

source_name: DMV neuron

label_protocol: cDNA labeled with SYBR green according to manufacture's protocol.

extract_protocol: Brainstems were extracted and frozen in OCT, sectioned on a cryostat at 10 um, sections were prepared with rapid IHC for DAPI and NeuN in less than 15 minutes, single neurons were captured using Arcturus CapSure system according to manufacture protocols.  Single cells or cell pools (2-5 single cells) were indiviually lysed and PCR performed according to Fluidigm's Biomark preparation protocols.

treatment_protocol: Male sprague dawley rats were subjected to remote ischemia preconditioning (rIPC) through ligation of bilateral femoral arteries or sham operation incluing ketamine/xylazine anesthesia and surgical exposure without ligation. n=3 biological replicates. All samples were collected 2.5 hours after referfusion.

tag: condition

value: right side of DMV in Naive Rat

tag: Sex

value: Male

tag: strain

value: Sprague Dawley

tag: treatment

value: Naive Rat

tag: animal number

tag: single cells/sample

tag: side of the brainstem

value: Reft Side of DMV


title: ES rep3

type: SRA

description: polyA selected RNA

library_source: transcriptomic

organism: Mus musculus

tag: genotype

value: Human ES9S


title: EK41


title: WT rep3

description: polyA selected RNA


title: EK42

description:
Neuron from left side of DMV in Naive Rat
BioMark-RTqPCR

value: left side of DMV in Naive Rat

value: Left Side of DMV


title: input

description: polyA selected RNA


title: EK44


title: EK47


title: EK40


title: ES rep1

description: polyA selected RNA


title: EK39


title: ES rep2

description: polyA selected RNA


title: primary human islets-IgG CUT&RUN [S178_neg]

first: Romina

middle: J

last: Bevacqua

address: 279 Campus Drive W

department: Developmental Biology

description:
S178-neg
merged_S369_178_A385_peaks.bed

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Trimmomatic (Bolger et al. 2014) was used for trimming.
Bowtie2 (Langmead and Salzberg 2012) was used for alignment.
HOMER (Heinz et al. 2010) was used for peak calling.
The GREAT algorithm was used for gene annotation (McLean et al. 2010).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: *.bed: Peaks files.

molecule: genomic DNA

organism: Homo sapiens

source_name: primary human islets

growth_protocol: Primary human islets were disersed/ transduced with lentiviruses and cultured for 5 days.

extract_protocol:
Lysates were clarified from Protein A-micrococcal nuclease digested DNA. DNA fragments were released for 20 min at 37°C and purified using phenol/chloroform/isoamyl alcohol followed by chloroform extraction and precipitated with glycogen and ethanol. SIX2-Flag-DNA complexes were isolated with anti-Flag antibody.
NEBnext Ultra II library kit.
CUT&RUN (similar to ChIP-seq) and sequenced as 2 × 75 on HiSeq4000.

treatment_protocol: Lentiviruses expressing SIX2-Flag.

tag: cell type

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: SIX2-Flag overexpression

value: pA-MN; EpiCypher

tag: chip antibody

value: IgG (Millipore)


title: EK38


title: EK35


title: EK32


title: EK33


title: EK31-replicate


title: EK31


title: EK46


title: primary human islets-antiFlag CUT&RUN [R388_PostPublication_sample]

description:
R388
merged_peaks_S369_r385_r388_postPubl.bed

value: Flag (Sigma-Millipore F7425)


title: primary human islets-IgG CUT&RUN [R388_PostPublication_sample_neg]

description:
R388_neg_PostPublication
merged_peaks_S369_r385_r388_postPubl.bed


title: primary human islets-IgG CUT&RUN [R385-neg]

description:
A385-IgG
merged_S369_178_A385_peaks.bed


title: EK29


title: EK37


title: EK28


title: S2_α-Ball_ChIP_rep1

city: Lahore

first: Muhammad

last: Tariq

state: Punjab

address: DHA, Lahore Cantt.

department: Biology

country: Pakistan

institute: Lahore University of Management Sciences

data_processing:
Base calling was performed using BGISEQ-500
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were detected by BGI programs. Low-quality reads include three types, and the read which were accord with anyone of the three types were removed: 1) The ratio of N in whole read was over 10%; 2) Removed reads in which unknown bases were more than 10%; 3) The ratio of base whose quality was less than 20 was over 10%. Data filtering parameters： Clean Parameter: SOAPnuke filter -l 10 -q 0.5 -n 0.1 -Q 2 -c 22 -f AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA-r GAACGACATGGCTACGATCCGACTT After filtering, the remaining reads are called "clean reads".
ChIP seq analysis was performed using online tool (https://usegalaxy.org/)
Alignment was performed using Bowtie2 against dm6 Drosophila genome at default parameters. The mapped reads were extended to 200 bp to represent sequenced fragments
Peak calling was done using MACS2 call peak
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph were converted into BigWig using Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1)

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Schneider’s Drosophila medium (Gibco, ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Gibco, ThermoFisher Scientific) and 1% penicillin–streptomycin (Gibco, ThermoFisher Scientific) was used to culture Drosophila S2 cells

extract_protocol: Reverse cross-linking of chromatin was carried out overnight with 5 M NaCl at 65 °C followed by proteinase K treatment for 2 h at 45 °C and reverse cross-linked chromatin was extracted using phenol–chloroform followed by ethanol precipitation. 1. DNA-end repair,3'-dA overhang and ligation of methylated sequencing adaptor.  2. PCR amplification and size selection (usually 100-300bp, including adaptor sequence).

tag: cell line

value: S2 cells

value: Early embryonic stem cells

tag: antibody

value: Anti Ball

value: untreated


title: primary human islets-antiFlag CUT&RUN [R385]

description:
A385-S2
merged_S369_178_A385_peaks.bed


title: S2_input_rep1


title: S2_input_rep2


title: S2_α-Ball_ChIP_rep2


title: EK26-replicate

value: right side of DMV in Naive Rat

value: Male


title: EK27

value: Sprague Dawley

value: Naive Rat


title: Donor_3507_1_Isotype

city: Boston

first: Eric

last: Muise

state: MA

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

data_processing:
Alignment and differential gene expression analysis was performed in Omicsoft Array Studio version10.0.1.118.
Cleaned reads were aligned to the human B38 genome references using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R86 gene models.
Genome_build: Human.B38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample. Each column corresponds to one sample (barcode).

growth_protocol: Human PBMCs from healthy individual donors (2x10^6 cells per well) were co-cultured with tumor cell line SK-MEL-5 (4x10^4 cells per well) in 6-well flat-bottom tissue culture plates in complete cell culture medium in the presence of 20 ng/mL GM-CSF (R & D Systems) at 37°C for 7 days.

extract_protocol:
Total RNA was isolated from cells using Arcturus PicoPure RNA Isolation method, according to the manufacturer's protocol (Thermo Fisher Scientific Inc.).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Illumina, #RS-122-2201) according to the manufacturer’s instructions.  The resulting cDNA libraries were sequenced on an Illumina HiSeqTM 4000 using a 50 base paired-end run.

treatment_protocol: The cells were treated with isotype control hIgG4 or anti-ILT3 antibody c52B8 (1 μg/mL) for 7 days. SK-MEL-5–educated live CD45+ CD14+ CD33+ cells were isolated from tumor cell PBMC co-cultures by FACS.

tag: replicate group

value: Isotype

tag: donor id

value: SK-MEL-5-educated live CD45+ CD14+ CD33+ cells


title: Donor_3507_2_Isotype

source_name: SK-MEL-5–educated live CD45+ CD14+ CD33+ cells


title: EK25

value: left side of DMV in Naive Rat

value: Left Side of DMV


title: EK24

value: Reft Side of DMV


title: EK30


title: EK26


title: Donor_3507_5 anti_ILT3_c52B8


title: Donor_3507_4 anti_ILT3_c52B8


title: primary human islets-antiFlag CUT&RUN [S178]

description:
S178-S2
merged_S369_178_A385_peaks.bed

value: Primary islet cells

value: Adult

value: SIX2-Flag overexpression


title: Donor_3507_6 anti_ILT3_c52B8


title: EK21


title: Donor_3180_2_Isotype


title: EK20


title: EK14


title: EK15


title: Donor_3180_3_Isotype


title: Donor_3180_1_Isotype


title: EK13


title: EJY

description:
Neuron from right side of DMV in Sham surgery rat
BioMark-RTqPCR

value: right side of DMV in Sham surgery rat

value: Sham surgery


title: EJZ

description:
Neuron from left side of DMV in Sham surgery rat
BioMark-RTqPCR

value: left side of DMV in Sham surgery rat


title: Donor_3835_1_Isotype


title: Donor_3180_5 anti_ILT3_c52B8


title: EK23


title: Donor_3835_3_Isotype


title: EJX


title: Donor_3835_4 anti_ILT3_c52B8


title: EK19


title: Donor_3180_6 anti_ILT3_c52B8


title: EJT


title: EK1


title: Donor_3180_4 anti_ILT3_c52B8


title: Donor_3835_6 anti_ILT3_c52B8


title: EJP


title: EJU


title: EJO


title: Donor_3835_5 anti_ILT3_c52B8


title: EJS


title: Donor_3428_1_Isotype


title: EJN


title: Donor_3428_6 anti_ILT3_c52B8


title: Donor_3507_3_Isotype


title: Donor_3428_5 anti_ILT3_c52B8


title: EJD


title: EJJ


title: EJI


title: Donor_3428_2_Isotype


title: 16HBE14o- BRD8 rep2 (ChIP-seq)

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Libraries were sequenced on Illumina HiSeq 4000 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, regionPeak

source_name: 16HBE14o- BRD8 rep2

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibodies.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

value: Human bronchial epithelial cell line 16HBE14o-

value: Active Motif 61007

tag: growth media

value: DMEM + 10% FBS


title: Donor_3428_4 anti_ILT3_c52B8


title: EJB

tag: condition

value: Male


title: 16HBE14o- BRD8 rep1 (ChIP-seq)

source_name: 16HBE14o- BRD8 rep1


title: Calu3 CTCF rep2 (ChIP-seq)

source_name: Calu3 CTCF rep2

value: Human lung adenocarcinoma cell line Calu3

value: Millipore 07‐729


title: Donor_3428_3_Isotype

value: Isotype


title: EJA

tag: Sex

value: Sprague Dawley


title: Donor_3835_2_Isotype

value: SK-MEL-5-educated live CD45+ CD14+ CD33+ cells


title: EJ18

tag: strain


title: EJ3

tag: treatment


title: EJK

tag: animal number

value: Left Side of DMV


title: EJ8

tag: single cells/sample


title: Calu3 CTCF rep1 (ChIP-seq)

source_name: Calu3 CTCF rep1


title: Calu3 BRD8 rep1 (ChIP-seq)

source_name: Calu3 BRD8 rep1


title: Calu3 BRD8 rep2 (ChIP-seq)

source_name: Calu3 BRD8 rep2


title: EJ5

tag: side of the brainstem


title: Calu3 Negative Control rep2 (RNA-Seq)

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: BRD8_DEGs.csv includes normalized count values for each Sample

source_name: Calu3 Negative Control rep2

extract_protocol:
Confluent HBE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: Samples were treated with negative control siRNA (D-001206-14-05, Dharmacon) or siRNA targetting either BRD8 (M-006377-00-0005) each at 20 nmol using RNAiMax transfection reagent (Life Technologies)

value: siNC

tag: genotype

value: control


title: Calu3 Negative Control rep3 (RNA-Seq)

source_name: Calu3 Negative Control rep3


title: Calu3 Negative Control rep1 (RNA-Seq)

source_name: Calu3 Negative Control rep1


title: EJ11

value: Reft Side of DMV


title: EIZ

description:
Neuron from left side of DMV in Ischemia preconditioning surgery rat
BioMark-RTqPCR

value: Ischemia preconditioning


title: EIY

description:
Neuron from right side of DMV in Ischemia preconditioning surgery rat
BioMark-RTqPCR


title: EJ17


title: Calu3 BRD8 KD rep3 (RNA-Seq)

source_name: Calu3 BRD8 KD rep3

value: BRD8 KD


title: Calu3 BRD8 KD rep2 (RNA-Seq)

source_name: Calu3 BRD8 KD rep2


title: EJ12

value: Sham surgery


title: Calu3 BRD8 KD rep1 (RNA-Seq)

source_name: Calu3 BRD8 KD rep1


title: A549, hypoxia, replicate 2, HIF1A ChIP

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: HIF1A ChIP genomic DNA from A549 cells in hypoxia(1%O2)

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina, v2.7.3).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina, v2.16.0.10).
FASTQC (v0.11.5) was used to assess sequence data quality.
fastq files from 2 separate lanes were merged for each sample to obtain sufficient read depth.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants.
Alignment to the Human reference genome (GRCh37/hg19) was carried out using Bowtie2 (v2.2.9) in --sensitive –-end-to-end mode  with a GRCh37/hg19 index.
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
The Homer suite (version 4.3) (Heinz et al., 2010) was used for identification of peak regions, annotation, quantitation, and motif discovery.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files containing HOMER peak calls and normalized tag counts per peak; bedGraph files with genomic coverage tracks.

source_name: A549 cells

growth_protocol: HCT116, RKO, A549, and H460 cells were cultivated in McCoy's 5A (HCT116), DMEM (RKO, A549) or RPMI media (H460) supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic. All cells were plated the day before treatment and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Chromatin immunoprecipitation. Sub-confluent cultures of each cell line (HCT116, RKO, A549, and H460) were placed in normoxic or hypoxic conditions for 24 hours. After treatment, media was removed and replaced with 1% formaldehyde in PBS (equilibrated by bubbling for 20 min with a mix of 1% O2, 5% CO2, and 94% N2 for hypoxia samples). To avoid rapid degradation of HIF1A, a crosslinking time of 5 min was used for all samples and terminated by addition of glycine to 0.125 M final concentration. Following 5 min of formaldehyde quenching, plates were placed on ice and washed three times with ice-cold PBS. Subsequently, cells were lysed in RIPA buffer and sonicated to generate DNA fragments of ~200-300 bp (Qsonica Q800R, 70% amplitude, 30 sec on/30 sec off cycle, 20 cycles for H460 lysates, 25 cycles for HCT116 and RKO lysates, and 30 cycles for A549 lysates). Samples were centrifuged at 20000 g for 20 min at 4°C and protein concentration in collected supernatants was measured with a BCA Protein Assay Kit. At this step, input samples (50 µg of total protein per cell line) were set aside. For each sample, four 1 ml aliquots each containing 1 mg of total protein were used for immunoprecipitation. Samples were pre-cleared with 15 µl of RIPA-washed Dynabeads Protein G (Invitrogen, Thermo Fisher Scientific) by rocking for 1 hour at 4°C. The supernatant was then collected and incubated with 30 µl of Dynabeads and 5 µl of anti-HIF1A antibody (Novus Biologicals, NB100-134) incubated overnight on a rocker at 4°C. Next, beads were washed twice with RIPA buffer, twice with IP wash buffer (500 mM LiCl, 100 mM Tris pH 8.5, 1% v/v NP-40, 1% w/v sodium deoxycholate), and twice with RIPA (2 min on rocker at 4°C for each washing step). Immunocomplexes were eluted by resuspending beads in 100 µl TE buffer and 200 µl of elution buffer (70 mM Tris pH 8, 1 mM EDTA and 1.5% w/v SDS) and incubating for 10 min at 65°C. Both eluted immunocomplexes and input samples were combined with NaCl solution to a final concentration of 200 mM and incubated overnight at 65°C to reverse formaldehyde crosslinks, followed by treatment with 20 µg proteinase K. DNA fragments recovered using phenol/chloroform extraction followed by ethanol precipitation and re-dissolved in TE buffer.
Library preparation. DNA fragments were size-selected (80-600 bp) by agarose gel electrophoresis (2% gel, BluePippin) and used for barcoded library preparation with the NEBNext Ultra II DNA kit, according to the manufacturer’s instructions (New England Biolabs). Final libraries were size-selected (200-600 bp, BluePippin) and analyzed on Bioanalyzer High Sensitivity DNA chips (Agilent) to confirm fragments ranging from 200 to 400 bp. Single-end 150 bp sequencing of pooled barcoded libraries was carried out on the Illumina HiSeq 4000 platform by the Genomics Core facility at the University of Colorado Anschutz.

treatment_protocol: Cells were maintained in normoxia (as above) or exposed to hypoxic conditions by incubation in a humidified atmosphere containing 1% O2, 5% CO2, and 94% N2 for 24hrs.

tag: cell type

value: lung adenocarcinoma

value: Hypoxia (1% O2 24hrs)

tag: library type

value: unstranded

value: Novus Biologicals, NB100-134


title: H460, hypoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from H460 cells in hypoxia(1%O2)

source_name: H460 cells

value: lung large cell carcinoma


title: WT rep1

description: polyA selected RNA

source_name: Whole embryo

tag: age

value: Wild-type


title: EIR

source_name: DMV neuron

value: right side of DMV in Ischemia preconditioning surgery rat

value: Male


title: A549, normoxia, replicate 1, HIF1A ChIP

description: HIF1A ChIP genomic DNA from A549 cells

value: Normoxia

tag: chip antibody


title: H460, hypoxia, replicate 1, HIF1A ChIP

tag: cell line


title: EHX

value: left side of DMV in Sham surgery rat

value: Sprague Dawley


title: EI13

value: left side of DMV in Ischemia preconditioning surgery rat

value: Left Side of DMV


title: EI18

value: Reft Side of DMV


title: H460, normoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from H460 cells


title: EIQ

value: Ischemia preconditioning


title: H460, normoxia, replicate 1, HIF1A ChIP

description: HIF1A ChIP genomic DNA from H460 cells


title: RKO, hypoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from RKO cells in hypoxia(1%O2)

source_name: RKO cells

value: RKO

value: colon carcinoma


title: EI19


title: EI9


title: A549, hypoxia, replicate 1, HIF1A ChIP

value: lung adenocarcinoma


title: EI8


title: EI5


title: EI4


title: A549, normoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from A549 cells


title: EHT

value: Sham surgery


title: EHS

value: right side of DMV in Sham surgery rat


title: EIX


title: EI3


title: RKO, hypoxia, replicate 1, HIF1A ChIP

value: Hypoxia (1% O2 24hrs)

value: unstranded

value: Novus Biologicals, NB100-134


title: HCT116, hypoxia, replicate 1, HIF1A ChIP

description: HIF1A ChIP genomic DNA from HCT116 cells in hypoxia(1%O2)

source_name: HCT116 cells

value: colorectal carcinoma


title: RKO, normoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from RKO cells


title: H460, input

description: ChIP input genomic DNA from H460 cells

value: lung large cell carcinoma


title: RKO, input

description: ChIP input genomic DNA from A549 cells

value: Normoxia


title: A549, input

description: ChIP input genomic DNA from RKO cells


title: RKO, normoxia, replicate 1, HIF1A ChIP

description: HIF1A ChIP genomic DNA from RKO cells


title: EHW

value: left side of DMV in Sham surgery rat

value: Male


title: EHF

value: Sprague Dawley


title: EHG


title: HCT116, hypoxia, replicate 2, HIF1A ChIP


title: EHA


title: EHR

value: Left Side of DMV


title: H460, hypoxia, replicate 2

description: poly(A)+ RNA from H460 cells in hypoxia (1% O2)

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
fastq files from 2 separate lanes were merged for each sample to obtain sufficient read depth.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

growth_protocol: RKO, A549, and H460 cells were cultivated in DMEM (RKO, A549) or RPMI media (H460) supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic. All cells were plated the day before treatment and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
TRI reagent
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

value: hypoxia (1% O2 24hrs)

value: strand-specific


title: HCT116, normoxia, replicate 2, HIF1A ChIP

description: HIF1A ChIP genomic DNA from HCT116 cells


title: EH2


title: EGZ

value: right side of DMV in Ischemia preconditioning surgery rat

value: Ischemia preconditioning

value: Reft Side of DMV


title: EGX

value: left side of DMV in Ischemia preconditioning surgery rat


title: H460, normoxia, replicate 1

description: poly(A)+ RNA from H460 cells in normoxia

value: normoxia


title: A549, normoxia, replicate 2

description: poly(A)+ RNA from A549 cells in normoxia

value: lung adenocarcinoma


title: EHN

value: right side of DMV in Sham surgery rat

value: Sham surgery


title: H460, normoxia, replicate 2


title: HCT116, normoxia, replicate 1, HIF1A ChIP

value: colorectal carcinoma

value: unstranded

value: Novus Biologicals, NB100-134


title: A549, hypoxia, replicate 1

description: poly(A)+ RNA from A549 cells in hypoxia (1% O2)


title: EHB

value: left side of DMV in Sham surgery rat


title: H460, hypoxia, replicate 1

value: lung large cell carcinoma


title: RKO, hypoxia, replicate 2

description: poly(A)+ RNA from RKO cells in hypoxia (1% O2)

value: RKO

value: colon carcinoma


title: A549, hypoxia, replicate 2

value: hypoxia (1% O2 24hrs)


title: EHL

value: Male

value: Sprague Dawley

value: Left Side of DMV


title: HCT116, input

description: ChIP input genomic DNA from HCT116 cells

value: Normoxia


title: EGU

value: left side of DMV in Ischemia preconditioning surgery rat

value: Ischemia preconditioning


title: EGT

value: right side of DMV in Ischemia preconditioning surgery rat

value: Reft Side of DMV


title: EGS


title: EGN


title: RKO, normoxia, replicate 1

description: poly(A)+ RNA from RKO cells in normoxia

value: normoxia

value: strand-specific


title: EGG


title: RKO, normoxia, replicate 2

description: poly(A)+ RNA from RKO cells in normoxia


title: A549, normoxia, replicate 1

value: lung adenocarcinoma


title: EGO


title: RKO, hypoxia, replicate 1


title: EG9-replicate


title: EG9


title: EGH


title: EG7


title: EG4


title: EG3


title: EG33


title: Animal number R602-1, DVC tissue punch

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: Samples were normalized where each count x was normalized by log2((100000*(x/sample.cts.end))), where sample.cts.end represents the sum of all counts for endogenous miRs in that sample.  MicroRNAs with low counts were then filtered out where at least 20% of the samples had expression above the threshold of 5 normalized counts (above all negative controls), leaving 146 miRs and 4 housekeeping genes.

source_name: Dorsal Vagal Complex

label_protocol: Nanostring protocol

extract_protocol: Brainstems were extracted and frozen in OCT, sectioned on a cryostat at 200 um, and the dorsal vagal complex (DVC) was extracted using a tissue punch.  Total RNA was extracted using the Direct-zol micro kit from zymo.  RNA was then run put through the Nanostring protocol to assay for miRNAs as per the manufacturer's instructions

treatment_protocol: Male Sprague-Dawley rats were subjected to remote ischemia preconditioning (rIPC), ligation of the left anterior descending artery (LAD), or rIPC with LAD following two hours later (rIPC 2h/LAD). All samples were collected 24 hours after LAD.

value: male

value: LAD

value: Sprague Dawley-RGD_737909


title: Animal number R608-2, DVC tissue punch

value: Sprague Dawley-RGD_737908


title: Animal number R602-4, DVC tissue punch

value: Sprague Dawley-RGD_737910


title: Animal number R601-2, DVC tissue punch

value: rIPC 2h/LAD

value: Sprague Dawley-RGD_737912


title: Animal number R601-1, DVC tissue punch

value: Sprague Dawley-RGD_737911


title: EGP

value: Male

value: Sprague Dawley

value: Left Side of DMV


title: EG29

value: Ischemia preconditioning


title: Animal number R609-2, DVC tissue punch

value: Age Matched Control

value: Sprague Dawley-RGD_737905


title: Animal number R597-1, DVC tissue punch

value: rIPC

value: Sprague Dawley-RGD_737906


title: Animal number R609-1, DVC tissue punch

value: Sprague Dawley-RGD_737904


title: EG27

value: right side of DMV in Ischemia preconditioning surgery rat

value: Reft Side of DMV


title: EG20

value: left side of DMV in Ischemia preconditioning surgery rat


title: Animal number R598-2, DVC tissue punch

value: male

value: Sprague Dawley-RGD_737903


title: EG27-replicate


title: EG13


title: Myeloid Malignancy Sample H49

city: Baltimore

first: Ying

last: Zou

state: MD

address: 1812 Ashland Ave, Suite 221

department: Department of Pathology

institute: Johns Hopkins University

data_processing:
Binary Cluster files (raw data) from Hiseq or Novarseq instruments are used to generate fastq data using Illumina bcl2fastq software
Genome_build: hg19

source_name: Patient sample

extract_protocol:
DNA was extracted from blood, or bone marrow specimens by conventional methods (Maxwell system; Promega Corporation, Madison, WI)
DNA was captured with Kapa Roche reagents, Integrated DNA Technologies probes,

tag: tissue

value: Bone marrow/Peripheral blood

tag: case

value: 20q deletions


title: Myeloid Malignancy Sample H56


title: Myeloid Malignancy Sample H57


title: Myeloid Malignancy Sample H47

value: trisomy / tetrasomy 8


title: EFX

value: right side of DMV in Sham surgery rat

value: Male

value: Sham surgery


title: EFW

value: left side of DMV in Sham surgery rat

value: Sprague Dawley

value: Left Side of DMV


title: Myeloid Malignancy Sample H45

value: monosomy 5 / 5q deletions


title: EG28

value: Ischemia preconditioning


title: EFU


title: Myeloid Malignancy Sample H44


title: Myeloid Malignancy Sample H43


title: Animal number R603-1, DVC tissue punch

value: rIPC

value: Sprague Dawley-RGD_737907


title: Myeloid Malignancy Sample H39


title: EFP

value: Reft Side of DMV


title: EFF


title: EG18

value: left side of DMV in Ischemia preconditioning surgery rat


title: Myeloid Malignancy Sample H37


title: Myeloid Malignancy Sample H53


title: EFO


title: Myeloid Malignancy Sample H35


title: EFK


title: Myeloid Malignancy Sample H30

value: 7q deletions


title: EFE


title: Myeloid Malignancy Sample H22


title: Myeloid Malignancy Sample H24


title: EFD


title: Myeloid Malignancy Sample H21

value: monosomy 7


title: Myeloid Malignancy Sample H27

value: Bone marrow/Peripheral blood


title: EF2


title: EF6


title: Myeloid Malignancy Sample H16


title: Myeloid Malignancy Sample H34


title: Myeloid Malignancy Sample H20


title: EF11


title: EF8


title: EEV

description:
Neuron from right side of DMV in Naive Rat
BioMark-RTqPCR

value: right side of DMV in Naive Rat

value: Naive Rat


title: EEX

description:
Neuron from left side of DMV in Naive Rat
BioMark-RTqPCR

value: left side of DMV in Naive Rat


title: EEU

value: Male


title: EF7

description:
Neuron from right side of DMV in Sham surgery rat
BioMark-RTqPCR

value: right side of DMV in Sham surgery rat

value: Sham surgery


title: EES

value: Sprague Dawley


title: Myeloid Malignancy Sample H25


title: EEQ


title: Myeloid Malignancy Sample H4


title: EEH

value: Left Side of DMV


title: EF12

description:
Neuron from left side of DMV in Sham surgery rat
BioMark-RTqPCR

value: left side of DMV in Sham surgery rat


title: EFJ


title: Myeloid Malignancy Sample H15


title: EF1


title: Myeloid Malignancy Sample H13


title: Myeloid Malignancy Sample H10


title: EEE


title: N Rep58

city: Columbus

first: Huiling

last: He

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

data_processing:
Quality trimming and adapter sequence removal using AdapterRemoval ver. 2.2.0 with parameters "--minlength 28 --trimqualities --minquality 20"
Sequence alignment against human decontaminome using Hisat2 ver. 2.0.6 with parameters "--no-discordant --no-mixed"
Sequence alignment of unaligned reads from decontaminome against human reference using Hisat2 ver. 2.0.6 with parameters "--no-discordant --no-mixed"
Transcriptome quantification using Subreads featureCounts ver. 1.5.1 with parameters "-O -s 1 -p -B -C --primary"
Genome_build: GRCh38p7
Supplementary_files_format_and_content: Tab-separated values of unfiltered gene expression counts

source_name: Thyroid tissue

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The purity of extracted RNA was measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and the concentration was assessed with Qubit 2.0 Fluorometer (Agilent Technologies, Santa Clara, CA) using an RNA HS Assay Kit. Samples with RNA Integrity Number (RIN) greater than 4 as assessed by a BioAnalyzer (Agilent) with no visible sign of genomic DNA contamination from the HS Nanochip tracings were used for total RNA library generation.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (catalog #RS-122-2201) according to the manufacturer protocol. The sequencing was performed in paired end manner, generating 2 X 100 bp paired-end reads using the Illumina HiSeq 2500 system.  Pre-alignment data QC were assessed with FastQC. Post-alignment data quality was assessed with an in-house quality control pipeline/database for RNA-seq database (14). RNA-seq data were trimmed for any adapter sequences using Adapter Removal (15).

tag: disease state

value: laryngeal cancer without thyroid lesions

value: Thyroid

tag: tissue type

value: Normal

tag: gender

value: M

tag: lymphocytic thyroiditis status

value: LT-


title: N Rep56


title: N Rep54


title: EEAN

tag: condition

tag: Sex

tag: strain

value: Reft Side of DMV


title: Myeloid Malignancy Sample H7

value: monosomy 5 / 5q deletions


title: Myeloid Malignancy Sample H3

value: Bone marrow/Peripheral blood

value: 20q deletions


title: N Rep53


title: EER

value: right side of DMV in Naive Rat

tag: treatment

value: Naive Rat

tag: animal number

tag: single cells/sample


title: N Rep52


title: EEAM

value: Male

tag: side of the brainstem


title: EEAL

value: left side of DMV in Naive Rat


title: N Rep57


title: N Rep55


title: EEF


title: EEB


title: EEAT


title: EEAC


title: N Rep49


title: N Rep50


title: EDY

value: right side of DMV in Sham surgery rat

value: Sham surgery


title: N Rep51


title: N Rep47


title: Myeloid Malignancy Sample H2


title: N Rep48


title: EDX

value: Sprague Dawley

value: Left Side of DMV


title: EEAD


title: EDQ


title: NAT Rep44

value: Papillary thyroid carcinoma (PTC)

value: Normal appearing thyroid tissue adjacent to PTC tumor

value: F

value: LT+


title: NAT Rep46

value: Thyroid

value: M


title: NAT Rep43


title: EEAA


title: NAT Rep45


title: EDI

value: Reft Side of DMV


title: EDL


title: EDR


title: NAT Rep42


title: NAT Rep41


title: NAT Rep39


title: NAT Rep40


title: NAT Rep38


title: NAT Rep36


title: EDD


title: EDB


title: ED4

value: left side of DMV in Sham surgery rat


title: ED6


title: ED3


title: NAT Rep33

value: LT-


title: EDE


title: NAT Rep34


title: ED17


title: NAT Rep32


title: ED21


title: ED16


title: ED10


title: NAT Rep29


title: NAT Rep28


title: ED12


title: EBS

description:
Neuron from left side of DMV in Ischemia preconditioning surgery rat
BioMark-RTqPCR

value: Ischemia preconditioning


title: NAT Rep37


title: NAT Rep31


title: ED13


title: EBX

value: left side of DMV in Ischemia preconditioning surgery rat


title: NAT Rep27


title: NAT Rep26


title: NAT Rep35


title: EBR

value: Male


title: ED22


title: EBP

description:
Neuron from right side of DMV in Ischemia preconditioning surgery rat
BioMark-RTqPCR


title: NAT Rep25


title: NAT Rep30


title: EBL


title: NAT Rep23


title: EBJ

value: right side of DMV in Ischemia preconditioning surgery rat


title: NAT Rep24


title: NAT Rep22


title: EBD


title: EB6


title: NAT Rep21


title: EBB


title: NAT Rep19


title: EBE


title: EB3


title: NAT Rep17


title: NAT Rep18


title: EB23


title: EB4


title: T Rep16

value: PTC tumor tissue


title: NAT Rep16


title: EB17


title: NAT Rep15


title: T Rep14


title: T Rep15


title: EB22


title: EB13


title: NAT Rep20


title: EAU

value: right side of DMV in Naive Rat

value: Naive


title: NAT Rep14


title: NAT Rep13


title: EAQ

value: Sprague Dawley


title: EAP

value: left side of DMV in Naive Rat

value: Left Side of DMV


title: T Rep12

value: Papillary thyroid carcinoma (PTC)

value: F


title: EAG


title: NAT Rep12

value: Thyroid

value: Normal appearing thyroid tissue adjacent to PTC tumor


title: T Rep13

value: LT+


title: NAT Rep11


title: T Rep11


title: MFC-2 [RNA-seq G]

city: Guang zhou

first: kong

last: guannan

address: 100 Martyrs Central Road

country: China

institute: Guangdong Institute of Microbiology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, removing reads aligned to the barcode adapter using FASTP (https://github.com/OpenGene/fastp) and mapped to the reference genome using Bowtie2 (version 2.2.8) with parameters‘-l 28 -n 2 -e 250 -M 1–best
The clean data were mapped on the annotated genomic objects identified in the genome of Lysinibacillus varians GY32 using TopHat (v2.0.11) and SAMtools (v0.1.18.0), yielding BAM files. Sorted and indexed BAM files were analyzed by Cufflinks (v2.0.0) to calculate the number of fragments per kilobase of transcript per million mapped reads (FPKM) for all genes.
Genome_build: ASM60010v1
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include counts.

organism: Lysinibacillus varians

source_name: microbial fuel cell sample

extract_protocol:
The cells were collected, frozen in liquid nitrogen, and RNA was extracted by TRIzol-based method. Illumina TruSeq RNA Sample Prep Kit v2 (San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: electron donor

value: Yeast extract

tag: electron acceptor

value: Electrode in microbial fuel cell


title: CK-2 [RNA-seq G]

source_name: aerobic sample

value: Oxygen


title: CK-3 [RNA-seq G]


title: CK-1 [RNA-seq G]


title: T Rep9

tag: age


title: MFC-3 [RNA-seq K]

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC (version 0.11.2) were used to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. Sequenced reads were trimmed for adaptor sequence with Trimmomatic (version 0.36), then mapped to the reference genome using Bowtie2 (version 2.3.2) with parameters‘-l 28 -n 2 -e 250 -M 1–best
The clean data were mapped on the annotated genomic objects identified in the genome of Lysinibacillus varians GY32 using TopHat (v2.0.11) and SAMtools (v0.1.18.0), yielding BAM files. Sorted and indexed BAM files were analyzed by Cufflinks (v2.0.0) to calculate the number of fragments per kilobase of transcript per million mapped reads (FPKM) and Transcripts Per Million (TPM) for all genes.
Genome_build: ASM60010v1
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM and FPKM values.

value: Acetate


title: EB12

value: left side of DMV in Ischemia preconditioning surgery rat

value: Male

value: Ischemia preconditioning


title: MFC-1 [RNA-seq K]


title: T Rep8

value: PTC tumor tissue


title: NAT Rep9


title: O2-3 [RNA-seq K]


title: MFC-1 [RNA-seq G]


title: NAT Rep10

value: LT-


title: MFC-3 [RNA-seq G]


title: T Rep7

value: M


title: O2-2 [RNA-seq K]


title: T Rep10


title: NAT Rep7


title: T Rep6


title: NAT Rep6


title: MFC-2 [RNA-seq K]


title: T Rep4


title: NAT Rep4


title: NAT Rep2


title: NAT Rep3


title: NAT Rep8


title: T Rep2


title: T Rep3


title: T Rep1


title: T Rep5


title: NAT Rep1


title: O2-1 [RNA-seq K]


title: 1_monthHFHI_6

city: Washington

first: Bevan

last: Main

state: District of Columbia

address: 3970 Reservoir Rd NW

department: Neuroscience

institute: Georgetown University

data_processing:
RNA-Seq reads (fastq files) were aligned to the mouse reference genome (mm10) using STAR and expression counts per transcript quantified using eXpress.
DESEQ2 pipelines were used  to normalize data and estimate differential expression between groups, and generate datasets containing contrasts for HF-HI treatment compared to Sham
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with contrasts for every gene and every sample (1m)

source_name: HFHI 1m_brain

extract_protocol:
Brains were removed, cortex were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Illumina cat. no. RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols - (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedtotalrna/truseq-stranded-total-rna-sample-prep-ls-euc-ltf-15031060-e.pdf).

value: 12 weeks

value: male

tag: treatment/time-point

value: HFHI 1m

value: brain; cortex


title: fl_2.h3k36me3.batch2

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

description:
fl_merged.batch2.h3k36me3.rpm.bw
fl_merged.batch2.h3k36me3.spikein.bw

data_processing:
Raw reads are demultiplexed into fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
For ChIP-seq samples, reads are aligned to hg38 genome using Bowtie2 (version 2.3.4.1). For samples with spike-in controls, reads are first aligned to spiked-in dm6 genome, and unmapped reads are then aligned to hg38 genome.
Bigwig files are normalized using reads per million (RPM) and extended to fragment length for individual IP samples. For merged bigwig files, reads are extended to 150bp and signals are RPM normalized. The merged bigwig files for spike-in samples are also normalized to the spiked-in dm6 counts.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq in bigwig files

source_name: HEK293T cells

growth_protocol: HEK293T from were maintained as adherent cells in DMEM supplemented with 10% FBS and 2 mM L-glutamine at 37 °C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions.

tag: transfection

value: SETD2 FL

tag: antibody

value: H3K36me3 antibody

tag: cell line


title: flwosri_1.h3k36me3.batch2

description:
flwosri_merged.batch2.h3k36me3.rpm.bw
flwosri_merged.batch2.h3k36me3.spikein.bw

value: FLwoSRI


title: 1_monthHFHI_8

tag: tissue


title: GD18_M_C1_1

city: Hadano

first: Tomoki

last: Takeda

address: Hirasawa 2445

country: Japan

institute: Japan Bioassay Research center

description: SAMPLE 1

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Rat Genome Microarray 4x44K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Pituitaries of male and female fetal Wistar rats at gestational day 18

extract_protocol: Total RNA was extracted using RNeasy kits (QIAGEN).

treatment_protocol: The tissues were immediately immersed in RNAlater stabilization reagent (QIAGEN).

value: Wistar

value: fetal rat; gestational day 18

value: control

value: pituitaries


title: GD18_F_T1_1

description: SAMPLE 10

value: female

value: TCDD-exposed


title: GD18_F_C3_1

description: SAMPLE 9


title: fl_1.h3k36me3.batch2


title: flwoshi_2.h3k36me3.batch1

value: FLwoSHI


title: GD18_M_C3_1

description: SAMPLE 3


title: GD18_M_C2_1

description: SAMPLE 2


title: GD18_M_T2_1

description: SAMPLE 5


title: GD18_F_T2_1

description: SAMPLE 11


title: 1_monthHFHI_3


title: GD18_M_T3_1

description: SAMPLE 6


title: GD18_F_C2_1

description: SAMPLE 8


title: 1_monthHFHI_2


title: flwoshi_1.h3k36me3.batch1


title: fl_2.h3k36me3.batch1


title: 1_monthHFHI_1


title: GD18_F_T3_1

description: SAMPLE 12


title: 1_monthHFHI_4


title: GD18_F_C1_1

description: SAMPLE 7


title: GD18_M_T1_1

description: SAMPLE 4


title: 1_monthHFHI_7


title: 1_monthSham_7

source_name: Sham 1m_brain

value: Sham 1m


title: fl_1.h3k36me3.batch1


title: 1_monthHFHI_5


title: 1_monthSham_5


title: NAT Rep5

tag: disease state

value: Papillary thyroid carcinoma (PTC)

value: Thyroid

tag: tissue type

value: Normal appearing thyroid tissue adjacent to PTC tumor

tag: gender

value: LT+


title: 1_monthSham_4

value: 12 weeks

tag: Sex

value: male


title: 1_monthSham_3

tag: strain

value: brain; cortex


title: flwosri_2.h3k36me3.batch2

value: H3K36me3 antibody


title: 1_monthSham_2


title: P46_Tumor

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

description: 3' RNA

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v2.0.1) and with for and (v3.0.2) for P57, P58, P60 and P61.
EmptyDrops R package (Lun et al. 2019) was used to call droplets for the samples processed without Cellranger v2.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are raw count UMI matrices which are given by Cellranger pipeline and integrated Seurat objects with the original uncorrected matrix, in the "RNA" assay, and the batch-corrected matrix in the "integrated" assay

source_name: NSCLC tumor tissue

extract_protocol:
RNA from P34, P35, P42, P43 and P46 was extracted according to the Single Cell 3' Reagent Kits V2. RNA from P47, P55, P57, P58 and P61 was extracted according to the Single Cell VDJ 5' Reagent Kits
3' single cell RNA-seq; 5' for paired single cell RNA/TCR-seq

treatment_protocol: Tumor and adjacent normal lung tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25μg/ml, Sigma-Aldrich). The tissue pieces were gently triturated with a 20 ml syringe plunger on a 40 μ m cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco) until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g and resuspended in PBS 1X buffer with 1% FBS and 2mM EDTA (Gibco). Isolation of tumor infiltrating lymphocytes and peripheral blood mononuclear cells was performed using Ficoll-paque PLUS solution (Sigma-Aldrich). CD3+ T cell isolationwas performed using CD3 microbeads and MACS separation (Miltenyi). Susequently dead cells and debris was removed following SOP (Dead cell removal kit; Debris removal kit; Miltenyi Biotec). Purified CD3+ T cells were resuspended in 1X PBS buffer with 0.04% BSA.

tag: tumor stage

value: NSCLC tumor tissue

tag: smoking status

value: smoker

tag: tumor type

value: ADK

value: M


title: P43_Tumor

description: 3' RNA


title: P35_Tumor

description: 3' RNA

value: non smoker

value: F


title: P42_Tumor

description: 3' RNA


title: P47_Tumor

description: 5' RNA


title: P34_Tumor

description: 3' RNA


title: 1_monthSham_1


title: 24h_HFHI_10

data_processing:
RNA-Seq reads (fastq files) were aligned to the mouse reference genome (mm10) using STAR and expression counts per transcript quantified using eXpress.
DESEQ2 pipelines were used  to normalize data and estimate differential expression between groups, and generate datasets containing contrasts for HF-HI treatment compared to Sham
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with contrasts for every gene and every sample

source_name: HF-HI 24h_brain

value: HF-HI 24h


title: 24h_HFHI_11


title: Case 62

city: Melbourne

first: Clyde

last: Dapat

state: Victoria

address: 792 Elizabeth Street

country: Australia

institute: WHO Collaborating Centre for Reference and Research on Influenza

data_processing:
Image analysis and base calling was performed using the Illumina's Real Time Analysis v1.18.61.
Reads were trimmed for adapter sequence using Skewer v0.2.2.
Reads were mapped to the reference human genome using STAR v2.5.
Counts were generated using RSEM v1.2.25 software.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample determined by RSEM.

source_name: whole blood

extract_protocol:
Whole blood samples (1 mL) were collected in PAXgene Blood RNA tubes. Total RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit (ThermoFisher Scientific). Total RNA integrity was checked using Agilent RNA 6000 Pico Kit (Agilent Technologies).
Library preparation was performed using TruSeq Stranded Total RNA (Illumina) with Ribo-Zero Globin Kit (Illumina) to reduce the level of alpha and beta globin transcripts.

value: whole blood

value: Male

tag: age (months)

tag: pathogen

value: RSV

tag: batch (hospital)

tag: batch (year enrollment)


title: Case 63

value: Female

value: RSV,HRV


title: 24h_HFHI_9

tag: age

tag: treatment/time-point


title: 24h_HFHI_8


title: 24h_HFHI_7


title: Case 59


title: Case 58

value: HRV


title: Case 64


title: 1_monthSham_6

value: 12 weeks

value: Sham 1m


title: 24h_HFHI_5

value: male

value: brain; cortex


title: 24h_HFHI_6


title: 24h_HFHI_4


title: Case 57


title: Case 56


title: 24h_HFHI_3


title: Case 55


title: 24h_HFHI_2


title: Case 54


title: Case 52

value: negative


title: Case 53


title: 24h_sham_10

source_name: Sham 24h_brain

value: Sham 24h


title: Case 61

value: FLU


title: 24h_sham_9


title: 24h_sham_8


title: Case 60

value: HMPV


title: Case 50


title: Case 51


title: 24h_sham_5


title: Case 49


title: Case 48


title: 24h_sham_6


title: 24h_sham_7


title: Case 45

value: Adenovirus


title: Case 43


title: Case 44


title: Case 47


title: Case 46


title: 24h_sham_1


title: 24h_sham_3


title: Case 41


title: 24h_sham_2


title: 24h_HFHI_1


title: Case 40


title: Case 39


title: mRNA in vehicle-treated poly I:C mouse rep3

city: Fujusawa

first: Satoru

last: Matsuda

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

institute: Takeda Pharmaceutical Company Limited

description: count.all.txt.gz

data_processing:
Mapping to Genome by TopHat
Count data was generated by featureCounts 1.4.6
Genome_build: rn5 or mm10
Supplementary_files_format_and_content: Count data in matrix format

source_name: Brain cortex

extract_protocol:
Brain cortex tissues were removed, flash frozen on dry ice, and RNA was harvested using an RNeasy Mini QIAcube Kit (74116, Qiagen).
RNA libraries were prepared for sequencing by Takara Bio Inc.

value: prenatal poly I:C injection

tag: treatment

value: vehicle


title: mRNA in TAK-418-treated poly I:C mouse rep2

description: count.all.txt.gz


title: mRNA in TAK-418-treated poly I:C mouse rep3

description: count.all.txt.gz


title: mRNA in TAK-418-treated poly I:C mouse rep1

description: count.all.txt.gz


title: Case 38

value: whole blood


title: 24h_sham_4


title: mRNA in vehicle-treated poly I:C mouse rep1

description: count.all.txt.gz


title: Case 37

value: Male


title: mRNA in vehicle-treated control mouse rep2

description: count.all.txt.gz

value: healthy


title: Case 36


title: Case 42


title: mRNA in vehicle-treated control mouse rep3

description: count.all.txt.gz


title: mRNA in vehicle-treated control mouse rep1

description: count.all.txt.gz


title: Case 35

value: Female

value: RSV


title: Case 34


title: Case 33


title: SS replicate 2

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Raw reads are trimmed by Trimmomatics to filter out adapters and low-quality reads
FASTQ files were aligned to BAM by HISAT2
BAM files were quantified by HTSEQ
Genome_build: mm10
Supplementary_files_format_and_content: HTSEQ raw count

source_name: LIVER

extract_protocol:
Qubit Fluorometric Quantitation and TapeStation BioAnalyzer
Qubit Fluorometric Quantitation and TapeStation bioanalyzer

value: Hbatm1(HBA)Tow,  Hbbtm2(HBG1,HBB*)Tow

value: 7 months

tag: genotype

value: SS


title: SS replicate 3


title: Case 32

tag: tissue


title: mRNA in vehicle-treated poly I:C mouse rep2

description: count.all.txt.gz

tag: disease state


title: pristane-treated WT rep3

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2-transformed and normalized using the robust spline normalization method implemented in the lumi Bioconductor package.

label: Biotin

source_name: peritoneal macrophage from pristane-treated BALB/c mouse

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Freshly isolated peritoneal macrophages sorted from the peritoneal lavage .

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit according to manufacturer's instructions

treatment_protocol: Peritoneal macrophages were obtained from WT (BALB/c) and Sparc-/- mice intraperitoneally injected with 0.5 ml of Pristane.  (Day 130 post injection).

tag: cell type

value: peritoneal macrophages

value: WT (BALB/c)


title: pristane-treated Sparc-/- rep5

source_name: peritoneal macrophage from pristane-treated Sparc-/- mouse

value: Sparc-/-


title: SD-LPS

city: Blacksburg

first: Song

last: Li

state: VA

address: 185 Ag-Quad Lane

institute: Virginia Tech

description:
lps1_S3_L008
Fresh LPS was added to the cell cultures every 2 days, and the cells were harvested on day 5 to simulate in vitro chronic low-grade inflammation.

data_processing:
Raw single-cell RNA-seq fastq files were processed by 10X Chromium Cell Ranger pipeline v3.0.2 including mapping sequenced reads, and quantifying gene expression.
Filtered UMI count data sets were used for downstream analysis
Genome_build: Cell Ranger reference version 3.3.0, mm10, Ensembl 93
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5 or H5) includes matrices of feature, barcode, and matrix.

source_name: monocyte

growth_protocol: Crude bone marrow cells were isolated from of 6-8 weeks old C57BL/6 mice, and cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 2 mM L-glutamine, 1% penicillin/streptomycin and with monocyte colony stimulating factor (M-CSF, 10 ng/ml)

extract_protocol:
In brief, 500K cells of each sample were sorted and then centrifuged at 300g x 5 minutes, 4 °C. The supernatant was aspirated, and cells were re-suspended in 100 μl of ice cold 1× PBS containing 0.04% BSA. The cells were then counted with trypan blue to make sure high viability above 98%. Cell concentration was adjusted to exactly 700 cells/μl by ice cold 1× PBS containing 0.04% BSA, and cells were kept on ice.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3′ v3 Library and Gel Bead Kit. Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15ul of 5 nM for each sample. Pooled library sample was sent to Novogen for sequencing. Pair-end sequencing was performed on Illumina® HiSeq platform, with the read length of paired-end 150 bp at each end plus 8-bp i7 index.
10X Genomics Chromium Single Cell RNA-seq

treatment_protocol: Cultured monocytes were treated as described and briefly listed as follows. (1) PBS: phosphate-buffered saline as a control; (2) SDL-LPS: super-low dose lipopolysaccharide (100 pg/ml); (3) 4-PBA (1 mM): 4-phenylbutyrate known as a potential therapeutic agent to reduce pro-inflammatory responses; and (4) 4-PBA and LPS: a mixed treatment with both SLD-LPS (100 pg/ml) and 4-PBA (1 mM). Fresh LPS and 4-PBA were added to the cell cultures every 2 days, and the cells were harvested on day 5 to simulate in vitro chronic low-grade inflammation.

value: 6-8 weeks old

value: monocyte

value: SDL-LPS:super-low dose lipopolysaccharide (100 pg/ml)


title: PBS

description:
pbs1_S6_L008
PBS was added to the cell cultures every 2 days, and the cells were harvested on day 5 to simulate in vitro chronic low-grade inflammation.

value: PBS:phosphate-buffered saline as a control


title: SD-LPS + 4-PBA

description:
lps4pba1_S5_L008
Fresh LPS and 4-PBA were added to the cell cultures every 2 days, and the cells were harvested on day 5 to simulate in vitro chronic low-grade inflammation.

value: 4-PBA and LPS:a mixed treatment with both SLD-LPS (100 pg/ml) and 4-PBA (1 mM)


title: 4-PBA

description:
A4pba1_S1_L008
Fresh 4-PBA was added to the cell cultures every 2 days, and the cells were harvested on day 5

value: 4-PBA:4-phenylbutyrate (1 mM)


title: pristane-treated WT rep5


title: pristane-treated WT rep4


title: pristane-treated Sparc-/- rep4


title: pristane-treated Sparc-/- rep2


title: pristane-treated WT rep2


title: pristane-treated Sparc-/- rep1


title: pristane-treated Sparc-/- rep3


title: P58 Blood

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v2.0.1) and with for and (v3.0.2) for P57, P58, P60 and P61.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are filtered contigs annotations files which are given by Cellranger pipeline.

source_name: Blood sample

extract_protocol:
TCR libraries from P47, P55, P57, P58 and P61 was extracted according to the Single Cell VDJ 5' Reagent Kits
TCR enrichment from amplified cDNA
5' for paired single cell TCR-seq

value: Blood sample

value: smoker

value: ADK

value: F


title: Case 31

value: whole blood

value: Female

value: RSV


title: pristane-treated WT rep1


title: AS replicate 3

value: 7 months

value: AS


title: AS replicate 2


title: P57 Blood

value: pT3 N0

value: M


title: Case 29

value: Male

value: HRV


title: P57 Tumor

value: NSCLC tumor tissue


title: Case 30


title: P47 Tumor

value: non smoker


title: Case 28


title: SS replicate 1

value: Hbatm1(HBA)Tow,  Hbbtm2(HBG1,HBB*)Tow

value: SS


title: P58 Tumor


title: D2_1

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner (Dobin and Gingeras, 2015) with default settings and to virus PR8M sequence as published in Blazejewska et al., 2011, Virology, 412, 36-45.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts from mouse and virus reads were combined and then then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL mm10 release 98, Genome: Mus_musculus.GRCm38.98; virus PR8M sequence: Blazejewska et al., 2011, Virology, 412, 36-45.
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
Whole lung RNA was extracted using Rneasy Midi kit from Qiagen. Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
500ng of total RNA was used to prepare libraries for sequencing using the Lexogen SENSE mRNA-seq library kit for Ion Torrent. Barcode quantification data from the PGM were used to balance the barcodes for final pooling before sequencing. Following this final pooling, the library pools were sized to a target size of 260bp on a Pippin Prep instrument using the 2% Pippin Agarose gel.
The sized libraries were used to prepare spheres using a One-Touch 2 device. These spheres were then sequenced on an Ion Torrent Proton sequencer with a P1 chip. On average, 55 million reads were obtained per sample.

treatment_protocol: Lungs were collected from mice


title: AS replicate 1


title: BXD102_1


title: P55 Tumor

value: pT2b N0

value: CE


title: BXD101_1


title: EBO4-mus3m-WT4

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using CASAVA 1.8 and convered into fastq files with bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCm38, GRCh37 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated by countOverlaps from GenomicRanges_1.20.5 with minoverlap 10
Genome_build: GRCm38, GRCh37
Supplementary_files_format_and_content: count file was generated by "countOverlaps" from GenomicRanges package. The numbers are raw counts.

source_name: muscle

growth_protocol: HEK293 cells stably transfected with MRPS5 wild-type or MRPS5 V336Y mutant expressing constructs were cultured in Dulbecco's MEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA from cell culture samples was isolated using RNeasy Mini Kit (Qiagen). Total RNA from muscle samples was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MRPS5 WT

tag: mouse background strain

value: muscle

value: 3 months


title: EBO4-mus3m-WT3


title: BXD091_2


title: Case 26

value: whole blood

tag: Sex


title: Case 25

value: Female

value: RSV


title: BXD090_2

tag: strain


title: Case 27

value: HMPV


title: BXD089_1


title: BXD087_1


title: EBO4-mus3m-WT1


title: Case 24

value: RSV,HRV


title: EBO4-mus3m-Kl4

value: MRPS5 V338Y


title: Case 23

value: Male


title: BXD085_1


title: EBO4-mus3m-WT2


title: BXD084_2


title: BXD079_2


title: EBO4-mus3m-Kl3


title: BXD083_3


title: BXD077_2


title: Case 22


title: EBO4-mus3m-Kl2


title: Case 21


title: BXD099_1


title: EBO4-mus3m-Kl1


title: BXD075_2


title: BXD074_1


title: BXD073b_1


title: Case 20

value: HRV


title: BXD095_1


title: BXD086_2


title: EBO4-mus19m-WT5

value: 19 months


title: EBO4-mus19m-WT4


title: EBO4-mus19m-WT2


title: BXD069_2


title: Case 19


title: BXD070_2


title: BXD068_2


title: Case 18


title: BXD067_2


title: BXD065b_2


title: BXD066_2


title: Case 17


title: Case 16


title: EBO4-mus19m-Kl5


title: BXD064_1


title: BXD065a_1


title: EBO4-mus19m-Kl3


title: BXD062_1


title: EBO4-mus19m-Kl4


title: BXD061_2


title: BXD056_2


title: Case 15


title: Case 14


title: BXD055_2


title: BXD073_2


title: EBO4-mus19m-Kl2


title: BXD053_1


title: Case 13


title: Case 12


title: BXD051_2


title: mterf2_3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 6-d-old seedlings

growth_protocol: Wild-type (Col-0) and mutant seeds were sterilized with 70% [v/v] ethanol and the surface sterilized seeds were stratified for at least 2 days at 4°C. Seedlings were grown on autoclaved half MS medium containing 1% (w/v) sucrose, 0.05% MES, pH 5.8, and 0.8 % plant agar (Duchefa, Haarlem, Netherlands) at 22°C under illumination provided by white fluorescent lamps (100 μmol photons m-2 sec-1)

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: long-day conditions

value: amiR-mterf2 mutant


title: BXD050_3


title: BXD049_2


title: mterf2_2


title: Case 11


title: mterf2_1


title: Case 10


title: BXD048_1


title: BXD029_1


title: BXD040_3


title: Case 9

value: negative


title: BXD045_1


title: BXD024_1


title: BXD022_1


title: Case 8


title: BXD006_5


title: Col-0_2

value: wild type


title: Col-0_1


title: B6_2


title: Case 7


title: Cells treated with Guanine and MPA

city: Hinxton

first: Jimmy

middle: Tsz Hang

last: Lee

state: Cambridgeshire

address: Wellcome Genome Campus

department: Cellular Genetics

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
Paired end reads were combined after trimming of adapters and subjected to fastq quality control and trimming
Cell barcodes were extracted from reads and attached to read name.
Reads were aligned to S. cerevisiae genome
Feature count was performed to create raw count matrix
Samples were combined for quality control and downstream analysis using the R package SC3
Genome_build: S. cerevisiae genome (R64-1-1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: Cells were grown for 18 hrs in CSM 2% glucose in MPA, Guanine, DMSO, or Guanine+MPA for MPA experiments.

extract_protocol:
DropSeq
Libraries were prepared for sequencing using Nextera XT standard illumina protocol

treatment_protocol: Treated with 10 uM DMSO, MPA, Guanine, of Guanine and MPA.

value: WT

tag: growth period

value: 18 hrs

value: Treated with 10 uM Guanine and MPA


title: Cells treated with MPA

value: Treated with 10 uM MPA


title: Case 6


title: Cells treated with Guanine

value: Treated with 10 uM Guanine


title: neurons_ S2_corr_rep1

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

institute: Max Delbrück Center for Molecular Medicine

description:
single cells
neur_S2_corr_rep1

data_processing:
We processed raw paired-end scRNA-seq data using Dropseq tools v. 2.3.0 with default parameters
We performed alignment to the hg19 reference genome using STAR v. 2.6.0. We discarded non-uniquely mapped reads.
We selected the top 1’000 barcodes for DNs, the top 8’000 for organoids from S2 and S2_Corr1, and the top 3’500 for organoids from C1
Genome_build: hg19
Supplementary_files_format_and_content: Digital Gene Expression (DGE) Matrix

source_name: iPSC derived neurons 4weeks old

growth_protocol: cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013), We obtained NPCs and DNs using a previously published protocol (Reinhardt et al., 2013)

extract_protocol:
Organoid/neurons were dissociated for scRNAseq using Worthington papainesystem according to manufacturers instruction.RNA samples for total RNAseq were extracted with Trizol and ribodepleted using RNase H-based protocol.
Total RNAseq libraries were generated according to Illumina sequencing protocol, using  ribo-depleted RNA samples as a starting material. We carried out single-cell RNAseq using Nadia instrument Dolomite bio (neurons) or Drop-seq instruments (organoids), libraries were prepared according to published protocol (Alles et al., 2017)
For scRNAseq we have applied Nextseq, for totalRNAseq we have applied Multiplexed 2x76+8In, Truseq

treatment_protocol: patient-derived samples (organoid, neurons) and isogenic gene corrected controls were analyzed

value: isogenic corrected control

tag: sample id

value: iPSC derived neurons


title: Cells treated with DMSO

value: Treated with 10 uM DMSO


title: neurons_ S2_corr_rep2

description:
single cells
neur_S2_corr_rep2


title: mRNA in TAK-418-treated VPA rat (15-week old) rep3

description: count.all.txt.gz

value: Sprague-Dawley

value: prenatal VPA injection


title: mRNA in TAK-418-treated VPA rat (15-week old) rep2

description: count.all.txt.gz


title: Case 5

value: whole blood

value: Female


title: Case 4

value: Male

value: HRV


title: Col-0_3


title: neurons_ S2_rep2

description:
single cells
neur_S2_rep2

value: LS-patient-derived


title: neurons_C1_rep1

description:
single cells
neur_C1_rep1

value: WT healthy control


title: Case 3

value: RSV


title: mRNA in vehicle-treated control rat (15-week-old) rep3

description: count.all.txt.gz

value: healthy

value: vehicle


title: mRNA in vehicle-treated VPA rat (15-week old) rep3

description: count.all.txt.gz


title: mRNA in vehicle-treated VPA rat (15-week old) rep2

description: count.all.txt.gz


title: cerebral organoids 90days old CTRL rep2

description:
single cells
co_C1_rep2

source_name: iPSC-derived brain organoids

value: wild-type

value: iPSC-derived brain organoids


title: wt 2.h3k36me3

description:
wt_merged.h3k36me3.rpm.bw
wt_merged.h3k36me3.spikein.bw

data_processing:
Raw reads are demultiplexed into fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
For RNA-seq samples, reads are aligned to UCSC genome hg38 with STAR aligner (version STAR_2.6.1c ), using Ensembl 96 gene models.
Transcript per million (TPM) values are generated by RSEM (version 1.3.0).
For ChIP-seq samples, reads are aligned to hg38 genome using Bowtie2 (version 2.3.4.1). For WT and KO ChIP-seq samples, reads are first aligned to spiked-in dm6 genome, and unmapped reads are then aligned to hg38 genome.
Bigwig files are normalized using reads per million (RPM) and extended to fragment length for individual IP samples. For merged bigwig files, reads are extended to 150bp and signals are RPM normalized. WT (except batch2) and KO merged bigwig files are also normalized to the spiked-in dm6 counts.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq TPM in tab delimited text file, ChIP-seq in bigwig files

source_name: HEK293T cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Included as additional column in the SAMPLES section.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions. For RNA-Seq, ribodepletion and polyA enrichment was performed before library preparation.

treatment_protocol: Cells were treated with siRNA  as per manufacturer's instruction (Dharmacon) for 72 hours.

tag: antibody

tag: cell line

tag: genotype/variation

value: wild type


title: mRNA in TAK-418-treated VPA rat (5-week-old) rep2

description: count.all.txt.gz


title: mRNA in TAK-418-treated VPA rat (5-week-old) rep3

description: count.all.txt.gz


title: Case 2

tag: age (months)

tag: pathogen

tag: batch (hospital)


title: cerebral organoids 90days old CTRL rep1

description:
single cells
co_C1_rep1


title: mRNA in vehicle-treated control rat (15-week-old) rep1

description: count.all.txt.gz


title: wt 1.h3k36me3


title: mRNA in vehicle-treated VPA rat (5-week-old) rep2

description: count.all.txt.gz


title: Case 1

value: negative

tag: batch (year enrollment)


title: mRNA in TAK-418-treated VPA rat (15-week old) rep1

description: count.all.txt.gz

tag: treatment


title: cerebral organoids_90days old S2_rep2

description:
single cells
co_S2_rep2


title: mRNA in TAK-418-treated VPA rat (5-week-old) rep1

description: count.all.txt.gz


title: SOX10 OE repeat 3 dox

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

description:
Brooks_InVitro_RAW.csv
G144_p36_Dox

data_processing:
Raw reads were aligned and feature counts extracted using the STAR aligner.
reference genome build:hg38
Supplementary_files_format_and_content: csv files containing unfiltered raw counts drom the STAR aligner

source_name: SOX10 over expression G144 cells passage 36

extract_protocol:
RNA was isolated using the RNAeasy Plus Mini Kit (Qiagen)
For RNA-seq of in vitro GSCs, oligo dT-based mRNA isolation was performed using the NEBNext Poly(A) mRNA magnetic isolation module. dsDNA libraries were prepared using NEB Ultra II directional RNA library prep kit and indexed using NEBNext® Multiplex Oligos.

value: Patient-derived Glioma stem cell line (G144)

tag: host strain

value: Patient derived line G144 expressing luciferase-GFP

tag: patient derived xenograft

tag: facs sorting of tumour cells

tag: culture conditions

value: In vitro cell were cultured in defined media containing 10ng/ml of EGF and 10ng/ml of FGF

value: In vitro cells were exposed to 3mg/ml Doxycyline or untreated for 2 days prior to RNA extraction


title: mRNA in vehicle-treated VPA rat (5-week-old) rep1

description: count.all.txt.gz

value: Sprague-Dawley

tag: disease state

value: prenatal VPA injection


title: cerebral organoids_90days old S2_rep1

description:
single cells
co_S2_rep1

tag: tissue


title: mRNA in vehicle-treated control rat (5-week-old) rep3

description: count.all.txt.gz

tag: strain


title: SOX10 OE repeat 3 control

description:
Brooks_InVitro_RAW.csv
G144_p36_Ctl

source_name: Control G144 cells (no dox) passage 36

tag: cell type


title: mRNA in vehicle-treated VPA rat (15-week old) rep1

description: count.all.txt.gz


title: mRNA in vehicle-treated control rat (5-week-old) rep1

description: count.all.txt.gz


title: cerebral organoids_90days old S2_corr_rep2

description:
single cells
co_S2_corr_rep2

value: isogenic corrected control

tag: sample id


title: neurons_C1_rep2

description:
single cells
neur_C1_rep2

value: iPSC derived neurons


title: mRNA in vehicle-treated control rat (5-week-old) rep2

description: count.all.txt.gz


title: cerebral organoids_90days old S2_corr_rep1

description:
single cells
co_S2_corr_rep1


title: mRNA in vehicle-treated control rat (15-week-old) rep2

description: count.all.txt.gz


title: neurons_ S2_rep1

description:
single cells
neur_S2_rep1

value: LS-patient-derived


title: SOX10 OE repeat 2 dox

description:
Brooks_InVitro_RAW.csv
G144_p35_Dox

source_name: SOX10 over expression G144 cells passage 35


title: DNA methylation in TAK-418-treated VPA rat rep2

data_processing:
The reads are mapped to the genome using RRBSMAP using default settings (12bp seed length, max number of mismatches = 0.08 x read length); only unique alignments are kept (if a fragment maps to more than one location, it is discarded)
The methylation ratio values were calculated by the methyratio function in RRBSMAP
Genome_build: rn6 or mm10
Supplementary_files_format_and_content: standard BED file containing methylation ratios of individual CpGs.

extract_protocol:
Brain cortex tissues were removed, and flash frozen on dry ice
Libraries were prepared by Active Motif


title: DNA methylation in TAK-418-treated VPA rat rep3


title: WT sihnRNPL 1

extract_protocol:
Total RNA was isolated from exponentially growing 293T cells and treated with DNaseI.
Included as additional column in the SAMPLES section.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions. For RNA-Seq, ribodepletion and polyA enrichment was performed before library preparation.

value: hnRNPL siRNA knock down


title: SOX10 OE repeat 1 dox

description:
Brooks_InVitro_RAW.csv
G144_p34_Dox

source_name: SOX10 over expression G144 cells passage 34


title: SOX10 OE repeat 2 control

description:
Brooks_InVitro_RAW.csv
G144_p35_Ctl

source_name: Control G144 cells (no dox) passage 35


title: SOX10 OE repeat 1 control

description:
Brooks_InVitro_RAW.csv
G144_p34_Ctl

source_name: Control G144 cells (no dox) passage 34


title: DNA methylation in vehicle-treated VPA rat rep3

source_name: Brain cortex


title: DNA methylation in vehicle-treated VPA rat rep2


title: DNA methylation in vehicle-treated VPA rat rep1


title: DNA methylation in TAK-418-treated VPA rat rep1


title: WT sihnRNPL 2


title: mRNA in vehicle-treated VPA rat (5-week-old) rep3

description: count.all.txt.gz


title: WT siSETD2 3

value: SETD2 siRNA knock down


title: Mouse 4 Striatum

description:
Brooks_InVivo_RAW.csv
M4_4

source_name: Invasive cells from Striatum of mouse 4

extract_protocol:
RNA was isolated using the RNAeasy Plus Micro Kit (Qiagen)
For RNA-seq of FACS-sorted tumour cells, dsDNA libraries were prepared according to the Smart-seq2 protocol from FAC-sorted GFP+ cells (RIN >8) (Picelli et al., 2014). Next-generation sequencing libraries were prepared from 1ng dsDNA using the Nextera XT DNA library preparation kit (Illumina) and indexed using the Nextera XT index Kit (illumina).

value: CD-1 Nude (mouse)

value: 6-8 week old female CD-1 nude mice underwent stereotactic implantation of 1x105 GFP-luciferase expressing GSCs (anteroposterior 0, mediolateral -2.5, dorsoventral -3.5). Tumour growth was monitored using an IVIS Spectrum in vivo imaging system (Perkin Elmer). 10 minutes following i.p. D-luciferin (120 mg/kg, Intrace medical) bioluminescent images were acquired under isoflurane anaesthesia. Tumour size was quantified by calculating total flux (photons/s/cm2) using Living Image software (Xenogen, Caliper Life Sciences). Animals were sacrificed when they showed signs of distress or weight loss.

value: Brains were harvested and tumour regions corresponding to tumour bulk, invaded striatum and corpus callosum were micro-dissected under fluorescent guidance in ice cold HEPES buffered HBSS. Micro-dissected regions were dissociated by incubating with papain (20 units/ml) DNase (0.005%) for 30min at 37°C (Worthington). Samples were triturated in HEPES buffered EBSS to fully dissociate the tissue and centrifuged (3 min, 300xg). Digestion was terminated by trituration in EBSS ovomucoid inhibitor (10mg/ml), albumin (10mg/ml) and DNase (0.005%). Following centrifugation (3 min, 300xg), cells were resuspended in 400 μL FACs sorting buffer containing 2.5% RNAsin and 1/10000 DAPI.


title: WT siSETD2 2


title: DNA methylation in vehicle-treated control rat rep1

value: healthy

value: vehicle


title: DNA methylation in vehicle-treated control rat rep3


title: DNA methylation in vehicle-treated control rat rep2


title: Mouse 4 CC

description:
Brooks_InVivo_RAW.csv
M4_2

source_name: Invasive cells from Corpus callosum of mouse 4


title: Mouse 4 Bulk

description:
Brooks_InVivo_RAW.csv
M4_1

source_name: Tumour bulk cells from Mouse 4


title: WT scramble 2

value: wild type


title: WT scramble 1


title: Mouse 3 Striatum

description:
Brooks_InVivo_RAW.csv
M3_4

source_name: Invasive cells from Striatum of mouse 3

value: Patient-derived Glioma stem cell line (G144)


title: H3K9me3 in TAK-418-treated VPA rat rep1

description:
34_Model-CpdH-1_H3K9me3_rn-dm_i89
HistonePath_rn.txt.gz

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) or rat genome (rn5) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: rn5 or mm10
Supplementary_files_format_and_content: Peak metrics, peak locations and gene annotations in text format

extract_protocol:
Brain cortex tissues were removed, and flash frozen on dry ice. Tissues were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

tag: chip antibody


title: H3K9me3 in TAK-418-treated VPA rat rep3

description:
36_Model-CpdH-3_H3K9me3_rn-dm_i91
HistonePath_rn.txt.gz


title: H3K9me3 in vehicle-treated VPA rat rep3

description:
33_Model-Veh-3_H3K9me3_rn-dm_i88
HistonePath_rn.txt.gz


title: Pooled input of rat samples

value: pooled


title: H3K9me3 in vehicle-treated VPA rat rep2

description:
32_Model-Veh-2_H3K9me3_rn-dm_i87
HistonePath_rn.txt.gz


title: Mouse 2 Striatum

description:
Brooks_InVivo_RAW.csv
M2_4

source_name: Invasive cells from Striatum of mouse 2

tag: cell line

value: Patient derived line G144 expressing luciferase-GFP


title: H3K9me3 in vehicle-treated VPA rat rep1

description:
31_Model-Veh-1_H3K9me3_rn-dm_i86
HistonePath_rn.txt.gz