title: O sativa, IL, rep2

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: csv, raw abundances

organism: Oryza sativa

source_name: leaf

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: no specific treatment was applied

tag: adapters

value: standard


title: HOS-3 (re-analyzed)

status: Public on Sep 01 2019

type: SRA

city: Boston

first: Rachel

last: Flynn

state: MA

address: 72 East Concord Street, K-712D

department: Department of Pharmacology

country: USA

institute: Boston University School of Medicine

description: ribo-depleted RNA

library_source: transcriptomic

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
Read library quality was assessed using fastqc (FastQC 2016) and multiqc (Ewels 2016) packages.
Illumina adapters were removed (R1: TACACTCTTTCCCTACACGACGCTCTTCCGATCT, R2: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) and leading and trailing low quality bases (below quality 30) were trimmed using Trimmomatic (Bolger 2014).  Reads which were less than 36 bases long after these steps were dropped.
The expression of the genes was quantified using Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, 2017) with index built from the GENCODE v27 transcriptome.
The counts matrix was then normalized using in-house bioinformatics software package de_toolkit’s deseq2 method.
The counts of the genes were extracted and plotted with ggplot2 package (Wickham, 2016).
Genome_build: hg38
Supplementary_files_format_and_content: A table of the normalized counts of ATRX, DAXX, H3F3A, SMARCAL1, SLX4IP, TERT genes in the 60 samples (including all three batches of each cell line and patient derived osteosarcoma xenograft sample) and their correspnding ATL statuc and full source name.

molecule: total RNA

organism: Homo sapiens

source_name: in vitro cells

extract_protocol:
QIAzol, Qiagen Rneasy kit
Kapa RNA HyperPrep kit with Riboerase. Sequenced on a Illumina NextSeq 500.

tag: cell line

value: HOS

tag: alt status

value: ALT-


title: RF-78-2 (re-analyzed)

description: ribo-depleted RNA

value: ALT+


title: HOS-1 (re-analyzed)

description: ribo-depleted RNA


title: FOB-1 (re-analyzed)

description: ribo-depleted RNA

value: FOB


title: naive mice

type: RNA

city: Paris

first: Frédéric

last: Fercoq

address: 61 Rue Buffon

department: AVIV

country: France

institute: MNHN

description: Control

data_processing:
Applied Biosystems 7300 Real-Time PCR System; SDS v1.4.1
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: RT2 Profiler PCR Array Data analysis 3.5 software
For the normalization it uses the average of four housekeeping genes:  Actb, Gapdh, Gusb, Hsp90ab1.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., lungs from infected mice/lungs from naive mice) ratios.

label: SYBR Green

organism: Mus musculus

label_protocol: PCR assays were performed using the SABiosciences PCR Array for Mouse Cytokines and Chemokines following the Manufacturer’s instructions. Reverse transcription was performed  using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (7300 real-time PCR System, Applied biosystem) with with 40 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Midi Kit followed by DNase I treatment.

tag: strain

value: BALB/c

tag: gender

value: female

tag: age

value: 16 weeks

tag: tissue

value: Lung

tag: time post infection

value: uninfected control


title: MG-3 (re-analyzed)

description: ribo-depleted RNA

value: MG


title: G2-3 (re-analyzed)

description: ribo-depleted RNA


title: O sativa, IL, rep1

department: School of Biological Sciences

country: United Kingdom

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light


title: O sativa, HD, rep1

value: HD


title: MG-1 (re-analyzed)

description: ribo-depleted RNA


title: 78-1 (re-analyzed)

description: ribo-depleted RNA


title: NOS-1 (re-analyzed)

description: ribo-depleted RNA

value: NOS


title: MTgal4_shW_H3K9

city: Pasadena

first: Maria

last: Ninova

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

library_source: genomic

data_processing:
Reads were mapped to the Drosophila genome allowing 2 mismatches and 1 mapping position (-v 2 -m 1) using Bowtie.
UCSC genome browser tracks were were generated from aligned reads using BedTools and BigWig tools.  RPKM values for 1kb genomic intervals were calculated using a custom script.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC genome browser tracks (bigWig format) and tables showing RPKM normalized read counts, and raw read counts for 1kb gw.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: adult fly ovaries gDNA (ChIP)

growth_protocol: Fly stocks were maintained at 24C on standard diet

extract_protocol:
Ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1% in PBS  for 10min at RT. Samples were quenched by 125mM glycine for 5 min at RT and washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Lysates were sonicated using Bioruptor (Diagenode, 20 cycles of 30sec ON, 30sec OFF). Supernatants were pre-cleared for 2h at 4C using Dynabeads Protein G (Invitrogen) beads. 5% of samples were saved for inputs. The rest of the lysates were incubated with indicated antibodies pre-conjugated to protein G dynabeads (Invitrogen) for 2h to overnight at 4C. The beads were washed 5 times at 4C with LiCl IP wash buffer (10mM  Tris pH 7.4;  500mM  LiCL;  1%NP40/Igepal;  1%  Sodium  Deoxycholate) and once with TE. Protein was digested with proteinase K for 3hrs at 55C and reverse-crosslinked by incubation at 65C overnight. DNA was extracted by phenol:chloroform standard protocol.
ChIP-seq library construction was carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240) with minor modifications. After adaptor ligation and PCR amplification, size selections were done on a 2% agarose gel to select the 200bp-400bp window size window. Libraries were sequenced on the Illumina HiSeq 2500 platform (SR 50bp).

treatment_protocol: Flies were fed with yeast for 2-3 days prior to dissection

value: adult ovaries

tag: genotype

tag: chip antibody

value: anti-Histone H3K9me3 (Abcam, ab8988)


title: MTgal4_shSov_H3K9


title: G2-1 (re-analyzed)

description: ribo-depleted RNA


title: 78-3 (re-analyzed)

description: ribo-depleted RNA


title: MTgal4_shW_H3K9_repeat


title: MTgal4_shSov_H3K9_repeat


title: FOB-3 (re-analyzed)

description: ribo-depleted RNA


title: 72-3 (re-analyzed)

description: ribo-depleted RNA


title: MTgal4_shSov_input_repeat

source_name: adult fly ovaries gDNA


title: O sativa, HD, rep2


title: RF-72-2 (re-analyzed)

description: ribo-depleted RNA


title: 72-1 (re-analyzed)

description: ribo-depleted RNA


title: NY-1 (re-analyzed)

description: ribo-depleted RNA

value: NY


title: Litomosoides sigmodontis-infected mice

description: Test

value: 70 dpi


title: MTgal4_shSov_input


title: 3N1-3 (re-analyzed)

description: ribo-depleted RNA


title: 3N1-1 (re-analyzed)

description: ribo-depleted RNA


title: RF-OS9-2

description: ribo-depleted RNA

tag: patient age

tag: Sex

value: M

tag: region

value: Right distal femur

tag: status

value: Diagnosis


title: RF-OS33-2

description: ribo-depleted RNA

value: ALT+

value: F

value: Right humerus


title: MTgal4_shW_input


title: RR S2 CDA high rep 2

city: Berkeley

first: David

last: Raulet

address: 485 Life Sciences addition

department: Molecular and Cell Biology

institute: University of California Berkeley

description: Mageck_counts RR S2 CDA.txt

data_processing:
Library strategy: CRISPR screen
Sequencing data was collected as part of the primary run processing using the innate HiSeq control software. Multiplexed sequencing data were demultiplexed using the BCL2Fastq program (version 2.17 and later).
The Python-based ScreenProcessing pipeline (https://github.com/mhorlbeck/ScreenProcessing) was used to analyze the CRISPRi sequencing results.
Illumina 50bp single end sequencing reads for pooled sublibraries one to four and five to seven were trimmed to 29bp and guides were quantified by counting exact matches to the CRISPRi v2 human library guides.
Counts from the ScreenProcessing pipeline were then used as input to the MAGeCK program (0.5.2.) to generate gRNA counts per gene
Genome_build: hg19
Supplementary_files_format_and_content: txt file generated by MaGeck showing CRISPRi v2 gRNA counts per gene

source_name: THP-1 monocyte

growth_protocol: THP-1 cells were cultured at 37°C in humidified atmosphere containing 5% CO2 with RPMI-1640 media supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, 0.2 mg/ml glutamine, 10 μg/ml gentamycin sulfate, 20 mM Hepes and 10% FCS. Cells were transduced with CDN reporter, dCas9-BFP-KRAB and single cell sorted. One clone was maintained in two separate cultures of THP-1 cells, and were transduced with the human genome-wide CRISPRi v2 library. Each culture was divided in two and screened separately after treatment with 2’3’-RR CDA or 2’3’-cGAMP, followed by selection and analysis. Hence, each screen was performed twice, with independent library transductions. For each transduction, the THP-1 clone was expanded to 3.2 x 10E8 cells and transduced with the human genome-wide CRISPRi v2 library, which contains approximately 100,000 gRNAs targeting around 20,000 genes. Sufficient cells were transduced and propagated to maintain at least 5 x 10E7 transduced (BFP+) cells, representing 500x coverage of the gRNA library. The transduction efficiency was around 20% to minimize the chance of multiple lentiviral integrations per cell. Two days after transduction, cells were cultured in the presence of puromycin for two days and one additional day without puromycin.

extract_protocol:
Genomic DNA was isolated from sorted cells using NucleoSpin Blood kits (Macherey-Nagel). PCR was used to amplify gRNA cassettes with Illumina sequencing adapters and indexes as described previously44. Genomic DNA samples were first digested for 18 hours with SbfI-HF (NEB) to liberate a ~500 bp fragment containing the gRNA cassette. The gRNA cassette was isolated by gel electrophoresis using NucleoSpin Gel and PCR Clean-up kits (Macherey-Nagel), and the DNA was then used for PCR.
Indexed samples were pooled and sequenced on an Illumina HiSeq-2500 for the 2’3’RR CDA screen and an Illumna HiSeq-4000 for the 2’3’-cGAMP screen using a 1:1 mix of two custom sequencing primers. Sequencing libraries were pooled proportional to the number of sorted cells in each sample. The target sequencing depth was at least 2,000 reads/gRNA in the library for unsorted “background” samples, and at least 10 reads/cell in sorted samples.

treatment_protocol: 4 x 10^8 cells were seeded to a density of 106 cells/ml and stimulated with 2’3’-RR CDA (2 µg/ml) or 2’3’-cGAMP (15 µg /ml). 20h later, cells were harvested, washed in PBS, and sorted based on BFP expression (presence of gRNAs), GFP expression (presence of reporter) and tdTomato expression using the BD Influx cell sorter and BD FACSaria Fusion cell sorter.

tag: facs sort

value: sorted for high CDN reporter expression

tag: stimulation

value: 2'3'-RR S2 CDA


title: RR S2 CDA high rep 1

description: Mageck_counts RR S2 CDA.txt

value: sorted for low CDN reporter expression


title: MF7

city: Shanghai

first: Sanlan

last: Li

address: 320 Yueyang Road, Xuhui District

country: China

institute: Institute of Neuroscience, Chinese Academy of Sciences

data_processing:
base calling（Illumina 1.8+ Phred+33, raw reads typically (2, 40)）
Filtering low quality bases, adaptor sequences
Read alignments by Cellranger (version 3.0.2, 10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files or matrix file containing features, barcodes, and gene expression matrix

source_name: iNA neurons from MEFS

growth_protocol: Cells are cultured at 37 °C with 5% CO2

extract_protocol:
10x Genomics gel beads and barcoding protocol
Library were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) following the manufacturer’s instructions. Barcodes are the the read1 files.  The 16 nt barcodes locate upstream of 12 nt UMI sequence which is before the polydT sequence.

treatment_protocol: Primary astrocytes or MEFs were transfected with control virus or virus mixture expressing NA transcription factors we screened previously. After an induction period of 28 days, cells were detached from the culture plate by accutase and enriched by FACS.

tag: cell type

value: iNA neurons from MEFS

tag: developmental stage

value: Embryonic day 13.5

tag: induction days

value: 28 days in vitro


title: RR S2 CDA low rep 2

description: Mageck_counts RR S2 CDA.txt

tag: cell line


title: RR S2 CDA low rep 1

description: Mageck_counts RR S2 CDA.txt


title: F7_1

source_name: iNA neurons from astrocytes

value: iNA neurons from astrocytes

tag: strain


title: FUGW_1

source_name: Astrocytes

value: Astrocytes


title: RF-OS2-2

description: ribo-depleted RNA

tag: alt status

value: 14 years 7 months

value: Femur


title: RF-OS17-2

description: ribo-depleted RNA

value: 16 years 5 months


title: MF

source_name: MEFs

value: MEFs


title: RF-OS29-2

description: ribo-depleted RNA

value: M

value: Lung mass

value: Relapse


title: RR S2 CDA background rep 2

description: Mageck_counts RR S2 CDA.txt

value: unsorted control


title: input DNA

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

institute: IRCM-U1194- INSERM

data_processing:
Reads were aligned to hg19 genome using Bowtie2 allowing no more than 2 mismatches and no multiple alignment sites.
Aligned reads were processed with R package PASHA (Fenouil et al., 2013; doi: 10.1093/bioinformatics/btw206) to eliminate PCR artefacts, extend reads to an estimated fragment length and generate WIG files.
R Package PASHA was used to normalize the WIG files to calculate the scores per million reads sequenced and Input DNA signal was subtracted from normalized WIG files.
Wig files from biological replicates were merged.
Peaks were called using Thresholding function of Integrated Genome Browser (https://bioviz.org/) with the following settings :  threshold =50, Max gap = 50, Min run = 50
Genome_build: Hg19
Supplementary_files_format_and_content: wig files

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 cells (ATCC, Rockville, MD, USA) were cultured cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C. Cells freshly amplified and frozen after obtention from the ATCC were used every 3months and were routinely tested for the absence of mycoplasma contamination

extract_protocol:
Lysates were clarified from sonicated nuclei and Fra-1 or Fra-2 complexes were isolated with the appropriate antibodies.
ChIP-seq libraries were prepared  using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France)
ChIP-seq - Instrument model :  Illumina HiSeq 2500 (MGX Platform, Montpellier France)

treatment_protocol: experiments were carried out in 2 independent replicates for Fra-1, Fra-2 and input

value: breast cancer cell line

tag: source tumor type

value: triple negative - basal b


title: RR S2 CDA background rep 1

description: Mageck_counts RR S2 CDA.txt

value: 2'3'-RR S2 CDA


title: RF-OS1-2

description: ribo-depleted RNA

value: ALT+

value: Tibia

value: Diagnosis


title: RF-OS31-2

description: ribo-depleted RNA

value: F

value: Right distal femur


title: Fra-2 ChIP-seq

value: Fra-2 (sc-13017X, lot J2403, Santa Cruz Biotechnology)


title: MTgal4_shW_input_repeat

tag: tissue

value: adult ovaries


title: OS9-3

description: ribo-depleted RNA


title: Fra-1 ChIP-seq

value: Fra-1 (sc-376148X, lot G0814, Santa Cruz Biotechnology)


title: OS9-1

description: ribo-depleted RNA


title: sample2

city: New York

first: Li

last: Wang

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

data_processing:
Cell Ranger pipeline from 10X genomics (Pleasanton, CA) was used to align reads and generate gene-cell matrices.
Genome_build: hg19
Supplementary_files_format_and_content: sample_matrix.mtx: gene read count for each sample as output from Cell Ranger pipeline; sample_genes.tsv: gene annotation; sample_barcodes.tsv: cell barcodes for each sample

source_name: Urothelial Cancer

extract_protocol:
The fresh muscle invasive bladder tumor samples were minced to 1-2 mm chunks via mechanical dissociation. The samples were subsequently undergone mechanical/chemical dissociation using the Mintenyi Biotec Gentlemacs 130-096-427 Octo Dissociator at the h_2 dissociation program. Upon completion of the dissociation, the dissociated tumor and buffer was filtered to single cell suspension, using the 70 μm Gentelmacs filter. The suspension was then spun down and the dissociation buffer was removed, followed by the addition of 1% ACK lysis buffer for RBC lysis for 1 minute. The RBC lysis buffer was then diluted with DBPS and the bladder cancer cells were then spun down at 200-300 G. After a final wash, the supernatant was discarded, and the pellet was resuspended in cold FACS buffer (DPBS containing 2% BSA and 2 mM EDTA). Bladder cancer single cells were analyzed by fluorescence-activated cell sorting (FACS) to determine phenotype. In brief, cells were stained with fixable viability dye blue to ascertain viability (ThermoFisher) and BV510-labeled anti-CD45 (BioLegend). For the sort, cells were gated on live singlets followed by the CD45 makers. All CD45- were collected.
Prior to preparation of single cell sequencing libraries, the cell density was determined using a hemocytometer using a mixture of trypan blue and cell suspension was examined under the microscope at low magnification using the Evos Cell Imaging System-digital inverted microscope.  This assessment of cell viability ensured successful preparation.  The single-cell Chromium chip loading, gel emulsion (GEM) generation & barcoding, post GEM_RT & cDNA amplification, and library construction were performed according to the ChromiumTM Single Cell 3’ Protocol - Chemistry version 2 (10X Genomics).  For GEM generation an input of >10,000 cells total was targeted for each sample, with a target cell recovery goal of 2000+ cells. For the cDNA amplification reaction we used 12 cycles during incubation for a targeted cell recovery of interest (2000-6000 cells).  Quantification of the synthesized cDNA was evaluated using Qubit (Qubit dsDNA HS Assay Kit, Thermo Fisher), and Agilent cDNA High Sensitivity Kit, following the manufacturers’ instructions. During library construction, the sample index PCR incubation was performed according to the protocol’s recommendation. Quantification of the constructed libraries was evaluated using Qubit (Qubit dsDNA HS Assay Kit, Thermo Fisher), Agilent cDNA High Sensitivity Kit, and Kapa DNA Quantification Kit for Illumina platforms, following the manufacturers’ instructions.
Each sample was then sequenced using the Illumina HiSeq 2500 platform leveraging one lane per sample to assure 50,000 reads or more per cell for expression profiling.

value: CD45-negative cells


title: OS33-3

description: ribo-depleted RNA

value: Right humerus


title: sample1


title: OS33-1

description: ribo-depleted RNA


title: OS31-1

description: ribo-depleted RNA


title: OS31-3

description: ribo-depleted RNA


title: H34

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Ecto- and endocervical cells were grown in corresponding media as described in the accompanying publication (materials and methods).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Cells were cultured in 2D (without feeders) or 3D Matrigel cultures in the described media. Differentiated organoids were harvested at 2 weeks after seeding while early organoids were harvested at 3 days post seeding into matrigel.

tag: tissue type

value: Endocervical columnar

tag: media

value: WNT-proficient media

tag: organoid type

tag: patient-id

tag: passage


title: H30

source_name: Ectocervical squamous_Wnt-deficient media_Differentiated Organoid_hc040

value: Ectocervical squamous

value: Wnt-deficient media

value: Differentiated Organoid


title: H28

source_name: Endocervical columnar_WNT-proficient media_Differentiated Organoid_hc045


title: H33


title: TAPBPR yeast display library sorted for binding 2000 ng/ml HLA-A*02:01 in presence of 300 nM Tax peptide

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: plasmid DNA

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script (add 100 to index numbers for read2 when fastq files were generated with a 2x250nt instead of 2x150nt protocol): python Paired_read_fuser.py --path output/ --read1 TAPBPR_R2.fastq.bz2 --read2 TAPBPR_R1.fastq.bz2 --wtseq GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --read1_overlap_start 22 --read1_overlap_end 58 --read2_overlap_start 34 --read2_overlap_end 70 --mode B --paired_mismatch_threshold 250
Aligner script:python Fused_read_aligner.py --path output/ --infile TAPBPR_R2.fast_B_qc1 --referenceDNA GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --referenceAA GAHRGALASSED --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path output/ --infile TAPBPR_R2.fast_B_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path ratios/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size 12
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

growth_protocol: For yeast surface display experiments to look at TAPBPR binding to HLA-A*02:01 tetramers, EBY100 yeast were electroporated with the TAPBPR scoop loop plasmid library, cultured in SDCAA medium at 30 deg C, and then protein expression was induced at a density of OD(600nm) = 0.5 in SGCAA for 3 days at 24 deg C. Induced yeast were incubated with HLA-A*02:01 tetramers (loaded with Goldie-Tax peptide) conjugated to APC, and with anti-myc-FITC to detect surface TAPBPR expression.  After washing, cells were FACS sorted based on expression (collected cells were positive in the FITC channel) and based on HLA-A*02:01 binding (highest 2.5% in the APC channel).

extract_protocol:
For yeast display, plasmid DNA was harvested from unsorted and sorted cells. For experiments in human Expi293F tapasin-KO cells, cDNA was synthesized from total RNA of the sorted cells and compared to the naive plasmid library.  In all cases, the scoop loop region was PCR amplified in 2 steps; in the first, primer overhangs added sequences for annealing to the Illumina sequencing primers, and in the second, primer overhangs added unique barcodes and Illumina adaptors.
Primer pair for 1st round of PCR to amplify TAPBPR scoop loop: Illumina_TAPBPR_111F (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGACTGTTTCCTGGTGAAGG) and Illumina_TAPBPR_229R (TCTTTCCCTACACGACGCTCTTCCGATCTCCTTGGAAATCGGTGAAGTC).
Primer pair to amplify tapasin exon 2: Tapasin_Illumina_FOR (TCTTTCCCTACACGACGCTCTTCCGATCTGGCGACCGCCGTCTCAG) and Tapasin_Illumina_REV (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAACAGCAGTGCACCGGGTC).
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a MiSeq using a 2x150nt PE v2 protocol (HLA-A2 processing experiments), Miseq using a 2x150nt PE NANO v2 protocol (validation of tapasin-kock out line), or HiSeq 2500 using a 2x250 nt paired end protocol.

treatment_protocol: For HLA-A2 processing experiments in human cells, tapasin-KO Expi293F cells were transfected with a plasmid library encoding variants of chimeric TAPBPR, where the TAPBPR C-terminus is replaced with the equivalent residues of tapasin.  Library DNA was diluted with a large excess of carrier DNA to ensure that cells typically acquired no more than one TAPBPR variant, maintaining a tight genotype-to-phenotype link.  24 h post-transfection, cells with the highest surface HLA-A2 (the top 0.5% of fluorescent cells after staining with PE-conjugated anti-HLA-A2) were collected by FACS.

tag: protein

value: TAPBPR

tag: sort gate

value: Top 2.5% of yeast that both express TAPBPR and bind HLA-A2 tetramers


title: TAPBPR yeast display library sorted for binding 2000 ng/ml HLA-A*02:01 in presence of 3000 nM Tax peptide

description: plasmid DNA


title: H35


title: M. tuberculosis H37Rv, delta mycP1-eccE1, with empty vector, replicate 1

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Reads were adapter- and quality-trimmed with Trimmomatic v0.33 and mapped onto the M. tuberculosis H37Rv reference genome (RefSeq NC_000962.3) using Bowtie2 v2.2.5.
Counting reads over features was done with featureCounts from the Subread package v1.4.6.
Note that the resulting few counts for mycP1 (Rv3883c) and eccE1 (Rv3882c) in the mutants are artefactual as they derive from reads that seemingly overlap a few bases within the deleted region.
DESeq2 was used to infer differentially expressed genes.
Genome_build: NC_000962.3
Supplementary_files_format_and_content: Counts and DESeq2 results

organism: Mycobacterium tuberculosis

source_name: cell culture

growth_protocol: M. tuberculosis strains were grown in 25 ml of Sautons media without detergent to OD600 ~0.5. Then, cultures were harvested by centrifugation and the resulting pellets resuspended in 1mLTRIzol Reagent (ThermoFisher) and stored at -80°C until further processing.

extract_protocol:
Total mRNA was extracted with 300 μl of chloroform : isoamyl alcohol (24:1) and precipitated at −20°C overnight with isopropyl alcohol prior to washing with 70% EtOH, then dried and resuspended in 40 μl DEPC‐treated water. RQ1 RNase‐Free DNase (Promega) and TURBO DNase (Ambion) were used to remove contaminating DNA, as recommended by the manufacturers. DNase treatment was followed by RNA purification using one volume of phenol : chloroform : isoamyl‐alcohol (25:24:1) and precipitation using 0.1 volume of 3 M sodium acetate (pH = 5.2) and 0.7 volume of isopropanol. RNA was resuspended in DEPC‐treated water and stored at −80°C. Total RNA concentration was measured using the Qubit RNA HS Assay Kit. Libraries of ribosomal-depleted RNA were prepared with 300ng of fragmented RNA using the Ribo-zero rRNA removal kit for Gram positive bacteria and the Truseq Stranded mRNA Library Prep kit reagents (Illumina).
RNA-seq libraries were prepared from 1 ug of total RNA. The RNA samples were depleted of r-RNAs with the Illumina Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) then used to generate sequencing libraries with the Illumina TruSeq Stranded mRNA reagents, omitting the polyA selection step (Illumina, San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents.

treatment_protocol: No treatment was perfomed; mutant strains were compared to the wild type.

tag: genotype

value: delta mycP1-eccE1, with empty vector


title: H11


title: H9


title: H31

value: EarlyOrganoids


title: H13


title: H32

source_name: Ectocervical squamous_Wnt-deficient media_Differentiated Organoid_hc047


title: H27

source_name: Endocervical columnar_WNT-proficient media_Differentiated Organoid_hc042


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with mycP1-eccE1, replicate 1


title: H6


title: OS29-1

description: ribo-depleted RNA

value: ALT+

tag: patient age

tag: Sex

value: M

tag: region

value: Lung mass

tag: status

value: Relapse


title: H7

source_name: Ectocervical squamous_Wnt-deficient media_Differentiated Organoid_hc036


title: M. tuberculosis H37Rv, delta mycP1-eccE1, with empty vector, replicate 2


title: OS29-3

description: ribo-depleted RNA

source_name: in vitro cells

tag: cell line


title: OS2-3

description: ribo-depleted RNA

value: 14 years 7 months

value: F

value: Femur

value: Diagnosis


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with eccE1-HA, replicate 2

tag: strain


title: TAPBPR yeast display library sorted for binding 300 ng/ml HLA-A*02:01

description: plasmid DNA


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with mycP1-HA, replicate 2


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with eccE1-HA, replicate 1


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with mycP1-HA, replicate 1


title: TAPBPR naive library for yeast display

description: plasmid DNA


title: TAPBPR yeast display library sorted for binding 100 ng/ml HLA-A*02:01

description: plasmid DNA


title: H1

source_name: Ectocervical squamous_Wnt-deficient media_Differentiated Organoid_hc029


title: H29


title: OS2-1

description: ribo-depleted RNA

tag: alt status


title: M. tuberculosis H37Rv, delta mycP1-eccE1, replicate 1

value: delta mycP1-eccE1


title: M. tuberculosis H37Rv, delta mycP1-eccE1, replicate 2


title: OS17-3

description: ribo-depleted RNA

value: 16 years 5 months


title: H2

source_name: Endocervical columnar_WNT-proficient media_Differentiated Organoid_hc034

value: Endocervical columnar

value: WNT-proficient media


title: M. tuberculosis H37Rv, control, replicate 2

value: control


title: M. tuberculosis H37Rv, control, replicate 1


title: OS17-1

description: ribo-depleted RNA


title: t-MN_3_RNAseq

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt 1.8.1
Reads were aligned against hg19 build of the human genome using TopHat 2.1.0
Counts were generated using HTseq
DESeq2_1.18.1 was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts generated for each Sample ...

source_name: Unsorted Bone Marrow Cells

extract_protocol:
RNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). Ribosomal RNA depletion and library preparation were obtained following manufacturer’s instructions using RiboGone Mammalian Kit (Clonotech Laboratories Inc.) and NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, NEB), respectively.
RNA libraries were prepared for sequencing using manufacturer’s recommended protocol for 50bp stranded single-end read runs (Illumina San Diego, CA)

value: Unsorted Bone Marrow Cells

tag: cytogenetics

tag: mutations

tag: age


title: t-MN_5_RNAseq

tag: tissue


title: t-MN_2_RNAseq


title: OS1-1

description: ribo-depleted RNA

value: Tibia


title: OS1-3

description: ribo-depleted RNA


title: t-MN_4_RNAseq

value: Not Found


title: t-MN_1_RNAseq


title: CTL_5_RNAseq


title: CTL_4_RNAseq


title: CTL_3_RNAseq


title: CTL_2_RNAseq


title: DIC_5_RNAseq


title: DIC_4_RNAseq

value: Not Available


title: PRO-Seq HDGF2KO clone10 rescued by WT

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

description: 05_HDGF2KO2_clone10_WT_myoblast_Pro082318

data_processing:
library strategy: PRO-seq
Adaptors were removed from raw reads by cutadapt 1.14. Reads were trimmed from the 3’ end with removing low quality bases using Trimmomatic 0.33 requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were mapped on human hg19 or fly dm3 genome using Bowtie 1.1.2 with options -m 1 -v 2. The 5’ ends of the reads were taken using bedtools genomecov 2.25 with options -strand -bg -5 and strands of reads were then swapped. Read counts were normalized by spike-in aligned reads. Normalized read counts were divided by total aligned million reads of wild-type sample.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig files are generated as described above. The scores represent the spike-in normalized read counts, divided by total aligned million reads of wild-type sample.

source_name: PRO-Seq HDGF2KO  rescued by WT

growth_protocol: Cells are seeded on 15cm gelatinized plates and grown in Ham’s F-10 media (Gibco/Thermo Fisher) supplemented with 15% fetal bovine serum (Atlanta Biologicals), 1mM sodium pyruvate (Sigma), 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher), 2.5ng/ml basic human fibroblast growth factor (Promega), 1X GlutaMax (Thermo Fisher) and 1uM Dexamethasone.  Cells were grown to 90% confluency prior to harvesting nuclei for PRO-seq.

extract_protocol:
Nuclei were isolated using dounce homogenizer and flash-frozen.
PRO-seq was performed according to the protocol (Mahat et al., Nat Protoc 11, 1455, 2016) with minor modifications. In the nuclear run-on reaction using myoblast with spike-in drosophila S2, all 4 biotinylated nucleotides were used at 25 μM each final concentration. RNA fragmentation was done by adding 0.2 M NaOH for 10 min on ice. Biotin RNA was enriched, and 3’ RNA adaptor (VRA3) was then ligated, followed by the second biotin enrichment step. RppH (NEB) was used to remove the 5’ RNA cap, followed by PNK 5’ phosphorylation. 5’ RNA adaptor (VRA5) was ligated, followed by the third biotin enrichment. Reverse-transcription and PCR amplification were done to generate DNA libraries. After size selection by AMPure XP beads (Beckman Coulter), libraries were sequenced on a NextSeq 500.

tag: cell type

value: myoblast cells

value: HDGF2KO clone10 rescued by WT

tag: molecule subtype

value: short RNA


title: PRO-Seq Wild type

source_name: PRO-Seq Wild type

value: Wild type


title: PRO-Seq HDGF2KO clone2 rescued by WT

description: 04_HDGF2KO2_clone2_WT_myoblast_Pro082318

source_name: PRO-Seq HDGF2KO rescued by WT

value: HDGF2KO clone2 rescued by WT


title: PRO-Seq HDGF2KO clone10

source_name: PRO-Seq HDGF2KO

value: HDGF2KO clone10


title: PRO-Seq HDGF2KO clone2

value: HDGF2KO clone2


title: DIC_3_RNAseq


title: UTD media RNA-Seq sample donor1

city: Philadelphia

first: Paul

middle: Zhiping

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

data_processing:
Low quality reads were trimmed using Trimmomatic (v0.36) and mapped to human genome (hg38) using STAR (v2.6.0c) with default parameters. Gene count was calculated using featureCounts (v1.6.1).
Genome_build: hg38
Supplementary_files_format_and_content: un-normalized read counts for each sample

source_name: UTD, media, donor1

growth_protocol: Selected CD14 monocytes were seeded in Cell Differentiation Bags (Miltenyi) in RPMI with 10% FBS, penicillin, streptomycin, 1x glutamax, 1x HEPES, and 10ng/mL recombinant human GM-CSF (Peprotech, 300-03) for 7 days.

extract_protocol:
RNA was isolated from human macrophages from matched donors, treated as described in each figure and polarized/challenged as above using Ambion RiboPure RNA purification kit (Thermo Fisher Scientific, AM1924).
RNA-seq libraries were generated using TruSeq RNA Library Prep Kit (Illumina, RS-122-2001/2) and validated via BioA by the University of Pennsylvania Next Generation Sequencing Core facility prior to sequencing. The libraries were sequenced on 75bp single-end reads using a NextSeq sequencer (Illumina).

treatment_protocol: Human monocyte derived macrophages (control untransduced or anti-HER2 CAR macrophages) were exposed to 20ng/mL recombinant human IL4 (Peprotech, 200-04) or IL13 (Peprotech, 200-13) for 24 hours prior to RNA collection.

tag: individual

value: monocyte derived macrophage

tag: treatment

value: UTD, media


title: UTD media RNA-Seq sample donor2

source_name: UTD, media, donor2


title: CAR media RNA-Seq sample donor2

source_name: CAR, media, donor2

value: CAR, media


title: DIC_2_RNAseq

value: GGPS1 (R74H); ANKS1B (T247I)


title: upf1-1_6d_3: lba1-1/upf1-1 callus _6 d-culture on shoot-inducing medium_rep3

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Quality control (RMA normalization), statistical analysis, and filtering were then carried out using the R packages affy (Irizarry et al., 2003) and RankProd (Hong et al., 2006).

label: biotin

organism: Arabidopsis thaliana

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 6 d, rep3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Hypoctyls from 12-d-old seedlings grown in the MS medium were cultured on callus-inducing medirum for 6 d, and then the resultant callus were transferred to shoot-inducing medium.

extract_protocol: Total RNA was extracted using TRIzol Reagent with a PureLink RNA Mini kit (Thermo Fisher Scientific) following instruction.

treatment_protocol: Callus derived from hypocotyls were transferred to shoot-inducing medium, and cultured for 0, 3, and 6 d.

tag: ecotype

value: Columbia (Col-0)

value: Callus derived from hypocotyls


title: upf3-1_3d_2: upf3-1 callus _3 d-culture on shoot-inducing medium_rep2

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 3 d, rep2

tag: genotype


title: upf1-1_3d_2: lba1-1/upf1-1 callus _3 d-culture on shoot-inducing medium_rep2

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 3 d, rep2


title: D1_YPAC(-)

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

description: Gene expression

hyb_protocol: For each hybridization, 100 ng of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID: 39494).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing:
Intensity values of each scanned feature were quantified using Agilent feature extraction software, which performs background subtractions.
Normalization was performed using Agilent GeneSpring software (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples).

source_name: PHHs (lot HC5-25) cultured for 1 day in YPAC(-) medium

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA)

extract_protocol: RNA was extracted using the miRNAeasy mini kit (QIAGEN).

treatment_protocol: Cryopreserved PHHs were cultured in hepatocyte culture medium (HCM, Lonza) supplemented with or without YPAC (10 uM Y-27632, 1uM PD0325901, 0.5 uM A-83-01 and 3 uM CHIR99021) with medium change every 2-3 days. On day 1 and 40, total RNA was extracted from each group.

tag: gender

value: Male

value: 56 years

value: primary human hepatocytes

tag: culture condition

value: for 1 day in YPAC(-) medium


title: D40_YPAC(-)

description: Gene expression

source_name: PHHs (lot HC5-25) cultured for 40 days in YPAC(-) medium

value: for 40 days in YPAC(-) medium


title: upf3-1_3d_3: upf3-1 callus _3 d-culture on shoot-inducing medium_rep3

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 3 d, rep3


title: upf3-1_6d_1: upf3-1 callus _6 d-culture on shoot-inducing medium_rep1

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 6 d, rep1


title: upf3-1_0d_2: upf3-1 callus _0 d-culture on shoot-inducing medium_rep2

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 0 d, rep2


title: upf1-1_3d_3: lba1-1/upf1-1 callus _3 d-culture on shoot-inducing medium_rep3

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 3 d, rep3


title: upf1-1_6d_2: lba1-1/upf1-1 callus _6 d-culture on shoot-inducing medium_rep2

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 6 d, rep2


title: upf1-1_6d_1: lba1-1/upf1-1 callus _6 d-culture on shoot-inducing medium_rep1

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 6 d, rep1


title: upf3-1_6d_3: upf3-1 callus _6 d-culture on shoot-inducing medium_rep3

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 6 d, rep3


title: upf3-1_0d_3: upf3-1 callus _0 d-culture on shoot-inducing medium_rep3

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 0 d, rep3


title: upf3-1_6d_2: upf3-1 callus _6 d-culture on shoot-inducing medium_rep2

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 6 d, rep2


title: D1_YPAC(+)

description: Gene expression

source_name: PHHs (lot HC5-25) cultured for 1 day in YPAC(+) medium

value: for 1 day in YPAC(+) medium


title: CAR media RNA-Seq sample donor1

source_name: CAR, media, donor1


title: upf1-1_3d_1: lba1-1/upf1-1 callus _3 d-culture on shoot-inducing medium_rep1

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 3 d, rep1


title: DIC_1_RNAseq

source_name: Unsorted Bone Marrow Cells

value: Unsorted Bone Marrow Cells

value: Not Available


title: upf3-1_0d_1: upf3-1 callus _0 d-culture on shoot-inducing medium_rep1

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 0 d, rep1


title: upf3-1_3d_1: upf3-1 callus _3 d-culture on shoot-inducing medium_rep1

source_name: Callus of the upf3-1 mutant were cultured on shoot-inducing medium for 3 d, rep1


title: D40_YPAC(+)

description: Gene expression

source_name: PHHs (lot HC5-25) cultured for 40 days in YPAC(+) medium

value: for 40 days in YPAC(+) medium


title: UTD IL4 RNA-Seq sample donor2

source_name: UTD, IL4, donor2

value: UTD, IL4


title: upf1-1_0d_1: Wild-type callus _0 d-culture on shoot-inducing medium_rep1

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 0 d, rep1


title: upf1-1_0d_3: lba1-1/upf1-1 callus _0 d-culture on shoot-inducing medium_rep3

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 0 d, rep3


title: upf1-1_0d_2: lba1-1/upf1-1 callus _0 d-culture on shoot-inducing medium_rep2

source_name: Callus of the lba1-1/upf1-1 mutant were cultured on shoot-inducing medium for 0 d, rep2


title: t-MN_4_mERRBS

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt 1.8.1
Reads were aligned against a bisulfite-converted human genome using Bowtie and Bismark
Downstream analysis  was performed on MethylSig using beta-binomial regression (FDR less than 0.1) with a minimum cutoff of 25% methylation difference to identify Differential Methylated Cytosines (DMCs). Differentially Methylated Regions (DMRs) were identified by first summarizing the methylation status of the genomic regions into 25-bp tiles and then identifying regions with an absolute methylation difference more than 25% and an FDR less than 0.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with CpGs for each sample. mERRBS gives us base pair resolution info of the sequenced DNA (chr position of the detected base,  first column), the chromosome of the detected base (second column), the position of the detected base on the specific chromosome (third column),sequencing info was assessed from which strand (forward, reverse, fourth column), read coverage (fifth column), frequency of methylated cytosine (sixth column), frequency of unmethylated cytosine (last column).

extract_protocol:
DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). 75ng of high quality genomic DNA were digested with 200U of methylation-insensitive endonuclease enzyme MspI (New England Biolabs, NEB),end repaired, A-tailed and ligated to RNA TruSeq Illumina indexed adapters (Illumina, RS-122-2001). Library fragments were gel isolated from a 1.8% agarose gel (Low range Ultra aga-rose, Biorad) using Qiaquick Gel Extraction kit and bisulfite converted using EZ DNA Methylation kit (Zymo Research). Products were amplified by PCR and final libraries were purified using AMPure XP beads (Agencort).
mERRBS libraries were prepared for sequencing using manufacturer’s recommended protocol for 50bp stranded single-end read runs (Illumina San Diego, CA)

value: Not Found


title: UTD IL4 RNA-Seq sample donor1

source_name: UTD, IL4, donor1

value: monocyte derived macrophage


title: t-MN_2_mERRBS


title: CAR IL4 RNA-Seq sample donor2

source_name: CAR, IL4, donor2

value: CAR, IL4


title: t-MN_1_mERRBS


title: CAR IL4 RNA-Seq sample donor1

source_name: CAR, IL4, donor1


title: CTL_4_mERRBS


title: Col-0_6d_3: Wild-type callus _6 d-culture on shoot-inducing medium_rep3

source_name: Callus of the wild type were cultured on shoot-inducing medium for 6 d, rep3

value: wild type


title: Col-0_6d_1: Wild-type callus _6 d-culture on shoot-inducing medium_rep1

source_name: Callus of the wild type were cultured on shoot-inducing medium for 6 d, rep1


title: CTL_3_mERRBS


title: CTL_2_mERRBS


title: UTD IL13 RNA-Seq sample donor1

source_name: UTD, IL13, donor1

value: UTD, IL13


title: CAR IL13 RNA-Seq sample donor2

source_name: CAR, IL13, donor2

value: CAR, IL13


title: M. tuberculosis H37Rv, delta mycP1-eccE1, complemented with mycP1-eccE1, replicate 2

source_name: cell culture


title: Col-0_0d_2: Wild-type callus _0 d-culture on shoot-inducing medium_rep2

source_name: Callus of the wild type were cultured on shoot-inducing medium for 0 d, rep2

value: Columbia (Col-0)

value: Callus derived from hypocotyls


title: CTL_1_mERRBS

source_name: Unsorted Bone Marrow Cells


title: Col-0_3d_3: Wild-type callus _3 d-culture on shoot-inducing medium_rep3

source_name: Callus of the wild type were cultured on shoot-inducing medium for 3 d, rep3


title: CAR IL13 RNA-Seq sample donor1

source_name: CAR, IL13, donor1


title: Col-0_0d_1: Wild-type callus _0 d-culture on shoot-inducing medium_rep1

source_name: Callus of the wild type were cultured on shoot-inducing medium for 0 d, rep1


title: DIC_5_mERRBS


title: control media RNA-seq sample rep4

source_name: control media

treatment_protocol: For M1 or classically-activated macrophage polarization, human monocyte derived macrophages were exposed to 20ng/mL recombinant interferon-g (Peprotech, 300-02) and 100ng/mL lipopolysaccharide (LPS-EK, Invivogen, tlrl-eklps) in RPMI with 10% FBS for 24 hour. Ad5f35 (empty or CAR-HER2) was added at an MOI of 1000 for 48 hours.

value: untreated


title: Columbia_0 strain_7 days after seedling rep3

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

institute: Tokyo University of Agriculture

description: twenty plants were mixed and extracted the total RNA

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: After normalization of the signals with the DFW algorism using the statistical language R, the expression levels in nine samples were compared by the Rankproducts function.

source_name: whole plant of Arabidopsis thaliana

label_protocol: Biotinylated cRNA from the samples were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix) from 1 ug total RNA.

growth_protocol: Arabidopsis thaliana Col-0 strain and each three lines of AtSPP over expression and knock down were soaked in 1% hypochlorous acid, and then rinsed in water. The seeds were then placed on a half strength of MS medium containing 0.8% agar for 7 days.

extract_protocol: Total RNA of was extracted with Qiagen RNeasy Plant Mini kit (Qiagen, Tokyo, Japan) according to the manufacturer's instructions. DNA was removed with DNase I, and the RNA was purified using the same kit. RNA quality and quantity were verified with an agarose gel electrophorasis and an NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: After 7-days, twenty of whole plants in each line were collected, and stored at −80°C until use.

tag: mutagenesis

value: nothing


title: Col-0_0d_3: Wild-type callus _0 d-culture on shoot-inducing medium_rep3

source_name: Callus of the wild type were cultured on shoot-inducing medium for 0 d, rep3


title: Col-0_6d_2: Wild-type callus _6 d-culture on shoot-inducing medium_rep2

source_name: Callus of the wild type were cultured on shoot-inducing medium for 6 d, rep2


title: UTD IL13 RNA-Seq sample donor2

source_name: UTD, IL13, donor2


title: Columbia_0 strain_7 days after seedling rep2


title: DIC_4_mERRBS


title: Col-0_3d_1: Wild-type callus _3 d-culture on shoot-inducing medium_rep1

source_name: Callus of the wild type were cultured on shoot-inducing medium for 3 d, rep1


title: DIC_3_mERRBS


title: Columbia_0 strain_7 days after seedling rep1


title: AtSPP over expressed line_7 days after seedling rep3

value: inserted full length of AtSPP between CaMV 35S and Nos-T in a pZH4B binary vector


title: control media RNA-seq sample rep2


title: AtSPP knock down line_7 days after seedling rep2

value: inserted the 400 bp fragment containing Asp198 and Asp239, the both of the active sites in AtSPP, into pBI-sense, anti sense-GW vector


title: AtSPP knock down line_7 days after seedling rep1

value: inserted the 600 bp fragment containing Asp198, one of the active sites in AtSPP, into pBI-sense, anti sense-GW vector


title: AtSPP knock down line_7 days after seedling rep3


title: control media RNA-seq sample rep1


title: DIC_1_mERRBS

value: Unsorted Bone Marrow Cells


title: Col-0_3d_2: Wild-type callus _3 d-culture on shoot-inducing medium_rep2

source_name: Callus of the wild type were cultured on shoot-inducing medium for 3 d, rep2


title: IL4 RNA-seq sample rep4

value: Treated with  IL4


title: ccpAko_2

city: chongqing

first: huagang

last: peng

address: Gaotanyan

department: Department of Microbiology

institute: Army Medical University

data_processing:
The sequenced libraries were mapped against predicted transcripts from the Staphylococcus aureus XN108 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_017331.1
Supplementary_files_format_and_content: FPKMs

organism: Staphylococcus aureus

growth_protocol: XN108 was grown in Tryptone Soya Broth(TSB) broth medium aerobically.

extract_protocol:
Total RNA was isolated using Tripure isolation reagent(Roche) according to the manufacturer’s instructions and   checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer   2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further   purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and   RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).
Barcoded sequencing libraries
Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: XN108 with ccpA gene knock out (as control).

value: ccpA gene knock out


title: IL4 RNA-seq sample rep3


title: IL4 RNA-seq sample rep2


title: DIC_2_mERRBS

value: GGPS1 (R74H); ANKS1B (T247I)


title: ccpAko_1


title: AtSPP over expressed line_7 days after seedling rep1

value: inserted full length of AtSPP between CaMV 35S and Nos-T in a pZH2B binary vector


title: XN108_3

value: control


title: IL4 RNA-seq sample rep1

value: monocyte derived macrophage


title: ccpAko_3


title: AtSPP over expressed line_7 days after seedling rep2

value: inserted full length of AtSPP between CaMV 35S and Nos-T in a pZH3B binary vector


title: IFNy/LPS RNA-seq sample rep2

source_name: IFNy/LPS

value: Treated with  IFNy.LPS


title: IFNy/LPS RNA-seq sample rep3


title: XN108_1


title: XN108_2


title: IFNy/LPS RNA-seq sample rep1


title: WT3_t45

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
The original samples contained R2 to read inner barcodes and unique molelcular identifiers.
Base calling was performed with bcl2fastq (2.17).
Samples were demultiplexed using internal barcodes.
Reads were mapped to the yeast (sacCer3) genome using  bowtie2 default parameters.
Duplicated reads were filtered using UMI, to remove PCR bias.
To estimate the expression level of each gene we counted the number of reads that  mapped to the 3’ end of the gene (from 350bp upstream to 200bp downstream of  TTS).
Reads of HSP12 gene were counted separately after mapping of the raw data to the HSP12-GFP cassette.
The read counts in each sample were normalized to PPM.
Genome_build: sacCer3
Supplementary_files_format_and_content: A table containing the normalized read counts for each yeast gene in each one of the 144 samples.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in SC media at 30°C with constant shaking to OD<1.

extract_protocol:
RNA was purified using a high-throughput RNA isolation protocol (Dye et al. 2005). Briefly, cells were washed in ddw and incubated with Proteinase K (Epicentre MPRK092) and 1% SDS at 70℃ to release the RNA. Cell debris were precipitated by centrifugation in the presence of KOAc precipitation solution. Finally the RNA was purified from the supernatant using nucleic acid binding plates (UNIFILTER plates, catalog #7700-2810) and was stored with RNAse-inhibitor (Murine #M0314L) at -80°C.
RNA-libraries were prepared as previously described (Klein-Brill et al. 2019). Briefly, RNA was reverse transcribed using  SmartScribe enzyme (TaKaRa) and in the presence of  oligo-dT RT primers with a 7bp barcode and a 8bp UMI (a gift from Ido Amit). Barcoded samples were then pooled and purified using SPRI beads X1.2 (AMPure XP). DNA-RNA molecules were tagmented using Tn5 transposase (loaded with oligo Tn5MEDS-A) and 0.2% SDS was used to strip off the Tn5 from the DNA (Picelli et al. 2014). followed by a SPRI X2 clean up. NGS sequences were added to the tagmented DNA by PCR (KAPA HiFi HotStart ReadyMix 2X - KAPA 33 Biosystems KM2605, 12 cycles). Finally, DNA was purified using double SPRI (X0.65  SPRI to clean large fragments followed by X0.8 SPRI beads).

treatment_protocol: Cells were  exposed to osmotic stress (final concentration of 0.4M KCL) and fixed in cold methanol (-80°C) at 0, 5, 10, 15, 20, 30, 45 and 60 minutes after stress addition.

tag: genotype/variation

tag: time-point


title: WT3_t60


title: EP7W whole blood 16p11.2del variant genomic DNA

type: genomic

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Using an Illumina HiScan

data_processing: Background subtraction and normalization to internal array controls were performed on raw intensity data using Illumina GenomeStudio v2011.1 Methylation Module 1.9 software. Probes containing single nucleotide polymorphisms (SNPs), cross-reactive probes with sequences aligned to multiple positions with ≥ 90% identity, and non-specific chromosome probes were removed.

label: Cy5 and Cy3

source_name: whole blood genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: All genomic DNA were extracted from whole blood using standard procedures. One microgram of genomic DNA was sodium bisulfite modified using the Qiagen EZ DNA Methylation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Modified genomic DNA was then processed and analyzed on the Infinium HumanMethylation450 BeadChip from Illumina according to the manufacturer’s protocol.

tag: Sex

value: M

tag: disease state

value: Control

tag: sample type

value: genomic

value: whole blood


title: control media RNA-seq sample rep3

value: untreated


title: EP22W whole blood 16p11.2del variant genomic DNA


title: EP3W whole blood 16p11.2del variant genomic DNA

value: F


title: EP16W whole blood 16p11.2del variant genomic DNA


title: EP1W whole blood 16p11.2del variant genomic DNA


title: EP8W whole blood 16p11.2del variant genomic DNA


title: WT3_t30


title: EP5W whole blood 16p11.2del variant genomic DNA


title: EP9W whole blood 16p11.2del variant genomic DNA


title: EP4W whole blood 16p11.2del variant genomic DNA


title: Empty vector RNA-seq sample rep3

source_name: Empty vector

value: treated with  Empty Ad5f35


title: EP17W whole blood 16p11.2del variant genomic DNA


title: EP15W whole blood 16p11.2del variant genomic DNA


title: EP42W whole blood 16p11.2del variant genomic DNA


title: Empty vector RNA-seq sample rep1


title: anti-HER2 CAR RNA-seq sample rep4

source_name: anti-HER2 CAR

value: treated with CAR-HER2 Ad5f35


title: WT3_t15


title: MM-119/1567 whole blood 16p11.2del variant genomic DNA


title: WT3_t10


title: WT3_t20


title: Empty vector RNA-seq sample rep4


title: anti-HER2 CAR RNA-seq sample rep3


title: MK-311/1601 whole blood 16p11.2del variant genomic DNA


title: EP39W whole blood 16p11.2del variant genomic DNA


title: EM-440/1993 whole blood 16p11.2del variant genomic DNA


title: EP6W whole blood 16p11.2del variant genomic DNA


title: FH-225 whole blood 16p11.2del variant genomic DNA


title: anti-HER2 CAR RNA-seq sample rep2


title: CT0009-003 whole blood 16p11.2del variant genomic DNA


title: KA-352/1734 whole blood 16p11.2del variant genomic DNA


title: WT3_t05


title: anti-HER2 CAR RNA-seq sample rep1


title: Empty vector RNA-seq sample rep2


title: WT3_t00


title: mRNA_WT-Myotube-rep2

data_processing:
Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.6
RNA-seq data were aligned with Tophat v2.0.9 allowing 3 mismatches.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

source_name: Myotube

growth_protocol: E14Tga2 (ATCC, CRL-1821) ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).  For embryoid body differentiation, 600K mESCs were plated in suspension plates with medium containing DMEM (Life Technologies), 20% FBS, 1% NEAA, 1% Pen/Strep, 2 mM L-Glutamine, 100 mM Ascorbic acid (Sigma).  After 5 days, EB colonies were collected for downstream applications. Human myoblasts are seeded on gelatinized plates and grown in Ham’s F-10 media (Gibco/Thermo Fisher) supplemented with 15% fetal bovine serum (Atlanta Biologicals), 1mM sodium pyruvate (Sigma), 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher), 2.5ng/ml basic human fibroblast growth factor (Promega), 1X GlutaMax (Thermo Fisher) and 1uM Dexamethasone.  Once 90% confluent the myoblasts are differentiated to myotubes by changing the media to DMEM (Gibco/Thermo Fisher) supplemented with 2% Horse Serum (Hyclone) and 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher).  Differentiation proceeds for 6 days and the efficiency can be monitored with microscopy as myotubes are easily visually detected.

extract_protocol:
For ChIP-seq, nuclei was isolated from cells fixed with 1% Formaldehyde. Next, chromatin was fragmented into ~250bp.  Chromatin immunoprecipitation was performed with the indicated antibodies. For RNA-seq, total RNA was isolated with RNAeasy (Qiagen) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L).
For ChIP-seq and RNA-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate  blunt 5' P ends  using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third,  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled.

value: Wild type

value: Myotube


title: WT2_t45


title: WT2_t30


title: EP59W whole blood 16p11.2del variant genomic DNA


title: EP2W whole blood 16p11.2del variant genomic DNA


title: AD-350/ 1728 whole blood 16p11.2del variant genomic DNA


title: mRNA_WT-Myoblast-rep2

data_processing:
Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.4
RNA-seq data were aligned with Tophat v2.0.9 allowing 3 mismatches.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

source_name: Myoblast

value: Myoblast


title: mRNA_WT-Myotube-rep1

data_processing:
Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.5
RNA-seq data were aligned with Tophat v2.0.9 allowing 3 mismatches.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig


title: EP45W whole blood 16p11.2del variant genomic DNA


title: CT0011-003 whole blood 16p11.2del variant genomic DNA


title: JB-042 whole blood 16p11.2del variant genomic DNA


title: WT2_t20


title: mRNA_WT-Myoblast-rep1

data_processing:
Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.3
RNA-seq data were aligned with Tophat v2.0.9 allowing 3 mismatches.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig


title: JL-137/1362 whole blood 16p11.2del variant genomic DNA


title: WT2_t15


title: WT2_t10


title: WT2_t05


title: EP43W whole blood 16p11.2del variant genomic DNA


title: EP32W whole blood 16p11.2del variant genomic DNA


title: CG-092 whole blood 16p11.2del variant genomic DNA


title: WT2_t00


title: EP56W whole blood 16p11.2del variant genomic DNA


title: WT2_t60


title: TB-342/1706 whole blood 16p11.2del variant genomic DNA


title: TG-278W whole blood 16p11.2del variant genomic DNA


title: WT_t60


title: WT_t45


title: JS-265W whole blood 16p11.2del variant genomic DNA


title: 460/2048 whole blood 16p11.2del variant genomic DNA


title: MT_SPT16

data_processing:
Quality of sequencing was assed with FastQC v0.11.4 & adapters were removed by the sequencing facility.
Human hg19 and mouse mm10 from Illumina igenomes UCSC collection were used as reference genomes. Chip-seq data were aligned with Bowtie v1.0.0 allowing 3 mismatches and keeping uniquely aligned reads.
Sam ouputs were converted to Bam with Samtools v1.0.6 and sorted with Picard tools v1.88
Data were further processed with Pasha to obtain wiggle files that were converted to bigwigs.
Some chip-seq tracks were further spike-in normalized using drosophila dna.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

tag: chip antibody

value: SPT16, Cell Signaling, #12191


title: EP34W whole blood 16p11.2del variant genomic DNA


title: WT_t30


title: WT_t20


title: BB-236 whole blood 16p11.2del variant genomic DNA


title: EP60W whole blood 16p11.2del variant genomic DNA


title: WT_t15


title: CB-314/1610 whole blood 16p11.2del variant genomic DNA


title: MT_Input


title: mRNA_HDGF2_KO_2-Myotube-rep2

value: HDGF2 knockout


title: EP58W whole blood 16p11.2del variant genomic DNA


title: 13844.p1 whole blood 16p11.2del variant genomic DNA

value: CHD8 pathogenic


title: 14233.p1 whole blood 16p11.2del variant genomic DNA


title: mRNA_HDGF2_KO_2-Myotube-rep1


title: WT_t10


title: EP51  whole blood 16p11.2del variant genomic DNA


title: 14016.p1 whole blood 16p11.2del variant genomic DNA


title: 12991.p1 whole blood 16p11.2del variant genomic DNA


title: EH-268W whole blood 16p11.2del variant genomic DNA


title: EP41W whole blood 16p11.2del variant genomic DNA


title: 12752.p1 whole blood 16p11.2del variant genomic DNA


title: RJ-258W whole blood 16p11.2del variant genomic DNA


title: 11654.p1 whole blood 16p11.2del variant genomic DNA


title: 12714.p1 whole blood 16p11.2del variant genomic DNA


title: EP57W whole blood 16p11.2del variant genomic DNA


title: mRNA_HDGF2_KO_2-Myoblast-rep2


title: WT_t05


title: MB_Input


title: WT_t00


title: 7-0229-003 whole blood 16p11.2del variant genomic DNA


title: mRNA_HDGF2_KO_2-Myoblast-rep1


title: EP48W whole blood 16p11.2del variant genomic DNA


title: Tor1_t45


title: Tor1_t60


title: EP47W whole blood 16p11.2del variant genomic DNA


title: Tor1_t30


title: Tor1_t20


title: 3-0269-000 whole blood 16p11.2del variant genomic DNA


title: 1-0019-004 whole blood 16p11.2del variant genomic DNA


title: GP-112 whole blood 16p11.2del variant genomic DNA


title: Tor1_t15


title: Tor1_t10


title: Tor1_t05


title: Tor1_t00


title: 639 whole blood 16p11.2del variant genomic DNA


title: Sok2_t60


title: 871 whole blood 16p11.2del variant genomic DNA


title: 435 whole blood 16p11.2del variant genomic DNA


title: mRNA-WT

value: 293-TRex cell line


title: 1-0748-003 whole blood 16p11.2del variant genomic DNA

value: ASD


title: Sok2_t45


title: 516 whole blood 16p11.2del variant genomic DNA


title: input_native


title: 1-0763-003 whole blood 16p11.2del variant genomic DNA


title: Sok2_t30


title: 1-0780-003 whole blood 16p11.2del variant genomic DNA


title: 1-0754-003 whole blood 16p11.2del variant genomic DNA


title: 293 whole blood 16p11.2del variant genomic DNA


title: 1-0722-003 whole blood 16p11.2del variant genomic DNA


title: input


title: Sok2_t20


title: 797 whole blood 16p11.2del variant genomic DNA


title: 11-0027-003 whole blood 16p11.2del variant genomic DNA


title: 1-0749-003 whole blood 16p11.2del variant genomic DNA


title: 11-0009-003 whole blood 16p11.2del variant genomic DNA


title: Sok2_t15


title: 1-0784-003 whole blood 16p11.2del variant genomic DNA


title: Sok2_t10


title: 1-0710-003 whole blood 16p11.2del variant genomic DNA


title: 1-0665-003 whole blood 16p11.2del variant genomic DNA


title: 1-0675-003 whole blood 16p11.2del variant genomic DNA


title: 1-0614-003 whole blood 16p11.2del variant genomic DNA


title: Sok2_t05


title: 1-0667-003 whole blood 16p11.2del variant genomic DNA


title: 1-0700-003 whole blood 16p11.2del variant genomic DNA


title: 1-0612-003 whole blood 16p11.2del variant genomic DNA


title: 1-0610-003 whole blood 16p11.2del variant genomic DNA


title: 2-0272-003 whole blood 16p11.2del variant genomic DNA


title: 1-0681-003 whole blood 16p11.2del variant genomic DNA


title: Sok2_t00


title: Snf1_t60


title: 1-0761-003 whole blood 16p11.2del variant genomic DNA


title: Snf1_t30


title: 1-0703-003 whole blood 16p11.2del variant genomic DNA


title: 1-0682-003 whole blood 16p11.2del variant genomic DNA


title: 1-0607-003 whole blood 16p11.2del variant genomic DNA


title: Snf1_t45


title: 1-0219-003 whole blood 16p11.2del variant genomic DNA


title: Snf1_t20


title: 1-0618-003 whole blood 16p11.2del variant genomic DNA


title: 1-0678-003 whole blood 16p11.2del variant genomic DNA


title: 1-0716-003 whole blood 16p11.2del variant genomic DNA


title: medial (M) facial subnucleus at_E16.5_replicate 2

city: Boston

first: Alan

middle: Peter

last: Tenney

address: 3 Blackfan Circle

department: Kirby Center for Neuroscience

institute: Boston Children's Hospital

description: pooled M tissue from 3 different embryos

hyb_protocol: µg of biotinylated cRNA from three independent samples for each motor neuron group isolated by LCM was hybridized to on Affymetrix Mouse Genome 430 2.0 Arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition

data_processing: GeneSpring and BioconductorLIMMA package was used for statistical analysis

source_name: facial motor nucleus

label_protocol: biotinylation. At least 1.5 ng of purified RNA was the starting material used in the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos,CA) with the FL-Ovation cDNA Biotin Module V2 (Nugen) to generate labeled probe.

growth_protocol: Mice were obtained from Jackson Labs and were housed under standerd condicition as per IACUC protocol.

extract_protocol: hindbrains were rapidly removed from E16.5 mice and frozen directly into optical cutting compound (OCT). Subnuclei were isolated from hindbrain cryosections using laser capture microdissection, samples were pooled from 3 embryos, and total RNA was extracted using an Absolutely RNA nanoprep kit

tag: strain

value: ICR

value: male and female

tag: age

value: facial motor neurons, medial subnucleus


title: medial (M) facial subnucleus at_E16.5_replicate 3

tag: cell type


title: Snf1_t15


title: medial (M) facial subnucleus at_E16.5_replicate 1


title: 1-0628-003 whole blood 16p11.2del variant genomic DNA

value: M

value: genomic

tag: tissue


title: lateral (L) facial subnucleus_at_E16.5_replicate 3

description: pooled L tissue from 3 different embryos

value: motor neurons, lateral subnucleus


title: Snf1_t10


title: 1-0627-003 whole blood 16p11.2del variant genomic DNA

value: whole blood


title: Snf1_t00


title: 1-0680-003 whole blood 16p11.2del variant genomic DNA


title: 1-0630-003 whole blood 16p11.2del variant genomic DNA


title: Sch9_t60


title: 1-0228-003 whole blood 16p11.2del variant genomic DNA


title: 11282.p1 whole blood 16p11.2del variant genomic DNA


title: 1-0601-003 whole blood 16p11.2del variant genomic DNA

value: F


title: 1-0465-003 whole blood 16p11.2del variant genomic DNA


title: lateral (L) facial subnucleus_at_E16.5_replicate 1


title: Sch9_t45


title: 1-0232-004 whole blood 16p11.2del variant genomic DNA


title: 1-0584-003 whole blood 16p11.2del variant genomic DNA


title: 1-0644-003 whole blood 16p11.2del variant genomic DNA


title: 12130.p1 whole blood 16p11.2del variant genomic DNA


title: 1-0458-003 whole blood 16p11.2del variant genomic DNA


title: 1-0186-004 whole blood 16p11.2del variant genomic DNA


title: 1-0613-003 whole blood 16p11.2del variant genomic DNA


title: 1-0186-005 whole blood 16p11.2del variant genomic DNA


title: intermediate (I) facial subnucleus_at_E16.5_replicate 3

description: pooled I tissue from 3 different embryos

value: facial motor neurons, intermediate subnucleus


title: 1-0578-003 whole blood 16p11.2del variant genomic DNA


title: intermediate (I) facial subnucleus_at_E16.5_replicate 2


title: Sch9_t30


title: 1-0631-003 whole blood 16p11.2del variant genomic DNA


title: lateral (L) facial subnucleus_at_E16.5_replicate 2


title: Sch9_t20


title: Snf1_t05


title: 1-0633-003 whole blood 16p11.2del variant genomic DNA


title: 1-0643-003 whole blood 16p11.2del variant genomic DNA


title: Sch9_t15


title: dorsolateral (DL) facial subnucleus_E16.5_replicate 3

description: pooled DL tissue from 3 different embryos

value: facial motor neurons, dorsolateral subnucleus


title: intermediate (I) facial subnucleus_at_E16.5_replicate 1


title: Sch9_t05


title: CHD8-V2 (father of CHD8-V1) whole blood 16p11.2del variant genomic DNA

value: CHD8 sequence variant


title: 1-0617-003 whole blood 16p11.2del variant genomic DNA


title: Sch9_t00


title: dorsolateral (DL) facial subnucleus_E16.5_replicate 2


title: Sch9_t10


title: 11033.p1 whole blood 16p11.2del variant genomic DNA


title: 1-0620-003 whole blood 16p11.2del variant genomic DNA


title: dorsolateral (DL) facial subnucleus_E16.5_replicate 1


title: Reg1_t60


title: Lactation_Npr1-/-_rep4

city: Suita

first: Kentaro

last: Otani

address: 5-7-1 Fujishiro-dai

department: Department of Regenerative Medicine and Tissue Engineering

institute: National Cerebral and Cardiovascular Center Research Institute

description: Gene expression in cardiac tissues from lactating-Npr1-deficient mice

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA  (specific activity > 10 pmol Cy3-CTP/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridazation buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE Microarray 8x60K (G4858A#28005) for 17 hours at 65 ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute at 37 ºC with GE Wash Buffer 2.

scan_protocol: Immediately after washing, the microarrays were scanned with an Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Intensities were extracted with Agilent Feature Extraction software (ver.10.7.3.1). Data analyses were conducted with Agilent GeneSpring GX software (ver.12.6). Microarray data were normalized with the 75th percentile shift method. Processing of input data was concluded by baseline transformation to the mean of control samples.

source_name: Heart tissue, Lactation, replicate 4

label_protocol: Cy3-CTP-labeled cRNA was produced from 200ng of total RNA using an Agilent Low Input Quick Amp Labeling Kit. cRNA and dye incorporation was quantified using NanoDrop 1000.

extract_protocol: Total RNA was extracted from ventricular tissues of nulliparous and 2wks-lactating Npr1+/+ or Npr1-/- using Trisol RNA isolation reagents (Thermo Fisher Scientific).

value: knockout

value: female


title: 1-0559-003 whole blood 16p11.2del variant genomic DNA


title: 7-0167-003 whole blood 16p11.2del variant genomic DNA


title: 1-0507-003 whole blood 16p11.2del variant genomic DNA


title: Lactation_Npr1-/-_rep3

source_name: Heart tissue, Lactation, replicate 3


title: 7-0002-003 whole blood 16p11.2del variant genomic DNA


title: Reg1_t45


title: 1-0602-003 whole blood 16p11.2del variant genomic DNA


title: Reg1_t30


title: CHD8-V1 whole blood 16p11.2del variant genomic DNA


title: Reg1_t20


title: 2-1228-003 whole blood 16p11.2del variant genomic DNA


title: 14406.p1 whole blood 16p11.2del variant genomic DNA


title: 6-0196-03 whole blood 16p11.2del variant genomic DNA

value: 16p11.2del variant


title: 1-0277-003 whole blood 16p11.2del variant genomic DNA


title: Reg1_t15


title: 1-0494-003 whole blood 16p11.2del variant genomic DNA


title: NP_Npr1-/-_rep4

description: Gene expression in cardiac tissues from nulliparous Npr1-deficient mice

source_name: Heart tissue, Nulliparous, replicate 4


title: Lactation_Npr1-/-_rep1

source_name: Heart tissue, Lactation, replicate 1


title: 1-0616-003 whole blood 16p11.2del variant genomic DNA


title: 228 whole blood 16p11.2del variant genomic DNA


title: NP_Npr1-/-_rep3

source_name: Heart tissue, Nulliparous, replicate 3


title: 348 whole blood 16p11.2del variant genomic DNA


title: 172 whole blood 16p11.2del variant genomic DNA


title: 3-0406-000 whole blood 16p11.2del variant genomic DNA


title: Lactation_Npr1-/-_rep2

source_name: Heart tissue, Lactation, replicate 2


title: 2-0088-003 whole blood 16p11.2del variant genomic DNA


title: NP_Npr1-/-_rep2

source_name: Heart tissue, Nulliparous, replicate 2


title: Reg1_t05


title: Reg1_t00


title: siSUN1/2 replicate 2

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

description: Gene expression of THP-1 macrophage after transfection with SUN1/2 siRNA

hyb_protocol: Each slide was hybridized with 1.65 ug Cy3-labeled cRNA using Gene Expression Hybridization kit (Agilent) in Hybridization Oven (Agilent), according to the manufacturer's instructions. After 17 h hybridization, slides were washed in staining dishes (Thermo Shandon) with Gene Expression Wash Buffer Kit (Agilent), following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) with default setting, Dye channel: Green, Scan resolution 5 um, PMT 100%, 10%, 16 bit.

data_processing:
Data were extracted with Feature Extraction Software 10.7 (Agilent).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: THP-1, siSUN1/2

label_protocol: The total RNA was labeled by Low input Quick Amp Labeling kit, one-Color (Agilent). Labeled cRNA were purified by Rneasy mini kit (QIAGEN).

growth_protocol: THP-1-derived macrophages were cultured in RMPI1640 medium supplemented with 10%  fetal bovine serums at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: The total RNA was extracted using Trizol Reagent (Life technologies) following the manufacturer's instructions and checked for a RIN mumber to inspet RNA integrity b an Agilent Bioanalyzer 2100 (Agilent). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: After transfection with siSUN1/2 for 48 h, macrophages were then treated with 10ng/ml lipopolysaccharide for 24h

tag: cell line

value: Male

value: SUN1/2 knockdown


title: 875 whole blood 16p11.2del variant genomic DNA


title: Msn5_t60


title: Msn5_t45


title: NP_Npr1-/-_rep1

source_name: Heart tissue, Nulliparous, replicate 1


title: Msn5_t30


title: nc replicate 1

description: Gene expression of THP-1 macrophage after transfection with negative control siRNA

source_name: THP-1, nc

value: control


title: 202065-positive_bisulfite

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Beachips were scanned using iScan software on a Hiscan

data_processing:
Raw intesities were imported into Champ R package to preprocess the data.We filtered 8877 probes with a detection p-value above 0.01 in one or more samples, 281 probes with beadcount <3 in at least 5% of samples, 26935 probes with overlapped SNPs, 8405 probes with multiple aligned locations, and 11066 probes on the X and Y chromosomes. Channel Quantile plus BMIQ normalization method was conducted
Raw data are available in the .idat files on the sample records and in the text file unmethylated_and_methylated_signal_intensities.txt on the series record.

source_name: Whole blood

extract_protocol: genomic DNA was extracted and purified from PAXgene DNA Blood tubes

value: Whole blood

tag: ptsd diagnosis

value: positive


title: LEC Endothel t3r2

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

hyb_protocol: Hybridization was performed with MouseWG-6 v2.0 Expression BeadChip kit (Illumina) according to manufacturer's protocol.

scan_protocol: Scanning was performed according to manufacturer's protocol.

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All microarrays were preprocessed and normalized together. Their intensity distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using manufacturer’s annotations. For genes having multiple beadsets the one with the highest variance (over all samples) was selected to focus on differences between cell types.

source_name: skin-draining lymph nodes, lymphatic endothelial cells

label_protocol: RNA was reverse transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol.

growth_protocol: Cervical, axillary, brachial and inguinal lymph nodes were dissected and enzymatically digested in RPMI1640 medium containing 0.8 mg/ml Dispase II, 0.2 mg/ml Collagenase P and 0.1 mg/ml DNase1 for approximately 50 min at 37°C under frequent agitation. The stromal cell fraction was enriched by leukocyte depletion using anti-CD45 MACS beads according to the manufacturer's instructions. Lymph node stromal cell subpopulations (BEC, LEC, FRC, DN) from Wt control and from animals challenged with Eu-Myc lymphoma B cells were further purified to high purity (>95%) by fluorescence-activated cell sorting. Cells were labeled with anti-CD45, anti-Ter119, anti-gp38 and anti-CD31 to differentiate between blood endothelial  (BEC, CD31+gp38-), lymphatic endothelial (LEC, CD31+gp38+), fibroblastic reticular cells (FRC, CD31-gp38+), and a double negative fraction. Dead cells were excluded using 7AAD. All cell fractions were directly sorted into continuously cooled RNA lysis buffer and stored at -80°C  prior to further analysis.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Qiagen) according to manufacturer's protocol. For each microarray sample, 80 ng of RNA were pooled from 4-6 independent sorting and isolation experiments.

treatment_protocol: Adoptive Eu-Myc tumor cell transfer was performed by i.v. injection of 2-4x10^5 cells per mouse in RPMI-1640 medium. The average tumor load in lymph nodes was in the range of 4-10% of all lymphocytes.

tag: role

value: tumor

value: Lymph node stromal cells

tag: biological replicate

tag: technical replicate


title: Msn5_t20

source_name: Saccharomyces cerevisiae


title: Lactation_Npr1+/+_rep2

description: Gene expression in cardiac tissues from lactating-wild-type mice

tag: genotype

value: wild-type

tag: gender


title: nc replicate 2

city: Shanghai

tag: genotype/variation


title: Lactation_Npr1+/+_rep3


title: LEC Endothel t2r2


title: Lactation_Npr1+/+_rep4


title: siSUN1/2 replicate 1


title: 201186-negative_bisulfite

value: negative


title: LEC Endothel n3r2

value: naive


title: Msn5_t15

tag: time-point


title: 201080-negative_bisulfite


title: LEC Endothel t1r2


title: 201377-negative_bisulfite


title: 202096-positive_bisulfite


title: NP_Npr1+/+_rep3

description: Gene expression in cardiac tissues from nulliparous wild-type mice


title: 202145-positive_bisulfite


title: 292 whole blood 16p11.2del variant genomic DNA

source_name: whole blood genomic DNA

tag: Sex

value: M

value: genomic

value: whole blood


title: Msn5_t10


title: Msn5_t05


title: Reg1_t10


title: Msn5_t00


title: HCT116_2uM_Omomyc_24_hrs_3

first: Mark

last: Demma

address: 33 Avenue Louis Pasteur

institute: Merck Research Laboratories

description:
HCT116_2uM_Omomyc_24_hrs_3
US-10010349

data_processing:
The RNA-seq raw reads were processed using the customized RNA-seq data analysis pipeline in OmicSoft® ArraySuite®. Specially, the raw reads were first filtered based on quality control (QC) and then were aligned to the reference genome B38 using OSA. After alignment, gene expression levels (RPKMs) were quantified by the RSEM algorithm with the gene model Ensembl.R86.
Genome_build: Human.B38, Ensembl.R86
Supplementary_files_format_and_content: txt file, RPKM table

source_name: HCT116 cells

extract_protocol: Illumina TruSeq Stranded Total RNA Ribozero

value: MYC stabilized

value: colon carcinoma

tag: replicate

tag: agent

tag: time point


title: 202125-negative_bisulfite


title: HCT116_2uM_Omomyc_24hrs_2

description:
HCT116_2uM_Omomyc_24hrs_2
US-10010342


title: NP_Npr1+/+_rep4

value: female


title: Msn2Msn4_t60


title: NP_Npr1+/+_rep2


title: NP_Npr1+/+_rep1


title: HCT116_2uM_Omomyc_24_hrs_1

description:
HCT116_2uM_Omomyc_24_hrs_1
US-10010335


title: 202046-positive_bisulfite


title: LEC Endothel n1r2


title: 201108-negative_bisulfite


title: Lactation_Npr1+/+_rep1


title: 202180-positive_bisulfite


title: Msn2Msn4_t45


title: DN Endothel t2r2

source_name: skin-draining lymph nodes, double negative cells


title: 202035-negative_bisulfite


title: Msn2Msn4_t30


title: HCT116_10_uM_Omomyc_6_hrs_2

description:
HCT116_10_uM_Omomyc_6_hrs_2
US-10010321


title: DN Endothel t3r2


title: HCT116_10_uM_Omomyc_6_hrs_3

description:
HCT116_10_uM_Omomyc_6_hrs_3
US-10010328


title: Msn2Msn4_t20


title: 201410-positive_bisulfite


title: HCT116_10_uM_Omomyc_6_hrs_1

description:
HCT116_10_uM_Omomyc_6_hrs_1
US-10010314


title: Msn2Msn4_t10


title: DN Endothel t1r2


title: HCT116_10_uM_Omomyc_24_hrs_2

description:
HCT116_10_uM_Omomyc_24_hrs_2
US-10010313


title: HCT116_2uM_Omomyc_6_hrs_2

description:
HCT116_2uM_Omomyc_6_hrs_2
US-10010307


title: 201180-negative_bisulfite


title: DN Endothel n3r2


title: DN Endothel n2r2


title: Msn2Msn4_t05


title: HCT116_10_uM_Omomyc_24_hrs_3

description:
HCT116_10_uM_Omomyc_24_hrs_3
US-10010320


title: DN Endothel n1r2


title: Msn2Msn4_t00


title: BEC Endothel t3r2

source_name: skin-draining lymph nodes, blood endothelial cells


title: Msn2_t60


title: HCT116_10_uM_Omomyc_24_hrs_1

description:
HCT116_10_uM_Omomyc_24_hrs_1
US-10010306


title: BEC Endothel t2r2


title: 201372-negative_bisulfite


title: HCT116_untreated_1

description:
HCT116_untreated_1
US-10010285

value: untreated


title: 201100-negative_bisulfite

value: Male


title: HCT116_untreated_2

description:
HCT116_untreated_2
US-10010284


title: BEC Endothel n3r2


title: Msn2_t30


title: 201233-negative_bisulfite


title: BEC Endothel n2r2


title: 201218-negative_bisulfite


title: 201012-positive_bisulfite


title: HCT116_untreated_3

description:
HCT116_untreated_3
US-10010283


title: Msn2Msn4_t15


title: HCT116_2uM_Omomyc_6_hrs_1

description:
HCT116_2uM_Omomyc_6_hrs_1
US-10010282


title: BEC Endothel t1r2


title: Msn2_t15


title: Msn2_t20


title: 202215-positive_bisulfite


title: BEC Endothel n1r2


title: FRC Endothel t3r2

source_name: skin-draining lymph nodes, fibroblastic reticular cells


title: 201357-positive_bisulfite


title: HCT116_2uM_Omomyc_6_hrs_3

description:
HCT116_2uM_Omomyc_6_hrs_3
US-10010281


title: Msn2_t10


title: Ramos_2.5uM_Omomyc_24hrs_3

description:
Ramos_2.5uM_Omomyc_24hrs_3
US-10010274

source_name: Ramos cells

value: MYC translocation

value: Burkitt's lymphoma

value: Ramos


title: Msn2_t05


title: 202155-negative_bisulfite

value: Whole blood


title: 202111-negative_bisulfite


title: 201349-positive_bisulfite

value: positive


title: FRC Endothel t1r2

value: tumor

value: Lymph node stromal cells


title: FRC Endothel n3r2


title: FRC Endothel t2r2


title: 202041-positive_bisulfite


title: Ramos_2.5uM_Omomyc_24_hrs_1

description:
Ramos_2.5uM_Omomyc_24_hrs_1
US-10010272


title: Msn2_t00


title: Msc1_t45


title: Msc1_t60


title: FRC Endothel n2r2


title: 202008-positive_bisulfite


title: 201256-positive_bisulfite


title: Ramos_500nM_Omomyc_24_hrs_2

description:
Ramos_500nM_Omomyc_24_hrs_2
US-10010270


title: FRC Endothel n1r2


title: Msc1_t30


title: Ramos_500nM_Omomyc_24_hrs_1

description:
Ramos_500nM_Omomyc_24_hrs_1
US-10010269


title: LEC Endothel t3r1


title: Msc1_t20


title: 201043-negative_bisulfite

value: negative


title: Ramos_2.5uM_Omomyc_6hrs_3

description:
Ramos_2.5uM_Omomyc_6hrs_3
US-10010262


title: Msc1_t15


title: Ramos_2.5uM_Omomyc_6hrs_2

description:
Ramos_2.5uM_Omomyc_6hrs_2
US-10010261


title: 202061-positive_bisulfite


title: 202175-positive_bisulfite


title: Msn2_t45


title: Ramos_2.5uM_Omomyc_6hrs_1

description:
Ramos_2.5uM_Omomyc_6hrs_1
US-10010260


title: Msc1_t10


title: LEC Endothel t1r1


title: 201225-negative_bisulfite


title: LEC Endothel n3r1

value: naive


title: LEC Endothel t2r1


title: Msc1_t05


title: Ramos_500nM_Omomyc_6hrs_3

description:
Ramos_500nM_Omomyc_6hrs_3
US-10010259


title: LEC Endothel n2r1


title: Mck1_t60


title: Msc1_t00


title: Ramos_500nM_Omomyc_6hrs_1

description:
Ramos_500nM_Omomyc_6hrs_1
US-10010257


title: Ramos_500nM_Omomyc_6hrs_2

description:
Ramos_500nM_Omomyc_6hrs_2
US-10010258


title: Mck1_t45


title: Ramos_cells_untreated_3

description:
Ramos_cells_untreated_3
US-10010253


title: LEC Endothel n1r1


title: Ramos_500nM_Omomyc_24_hrs_3

description:
Ramos_500nM_Omomyc_24_hrs_3
US-10010271


title: 202079-positive_bisulfite


title: 201389-negative_bisulfite


title: DN Endothel t3r1


title: LEC Endothel n2r2


title: 201054-negative_bisulfite


title: Mck1_t30


title: DN Endothel t1r1


title: Mck1_t20


title: DN Endothel t2r1


title: 202044-positive_bisulfite


title: Ramos_cells_untreated_2

description:
Ramos_cells_untreated_2
US-10010252


title: Ramos_cells_untreated_1

description:
Ramos_cells_untreated_1
US-10010251


title: 202216-negative_bisulfite


title: Mck1_t10


title: 201015-negative_bisulfite


title: Untreated_FAIRE

city: Leiden

first: Daniel

middle: M.

last: Borras

address: Einthovenweg 20

department: CI

country: Netherlands

institute: LUMC

data_processing:
Fastq read quality trimming and filtering
Alginment to GRCh37 reference genome using GSNAP
Genome binarization quantification and identification of overexpressed bins based on bin counts.
Conversion of qualitative overexpressed bin to bed alignment regions delimited by its signal.
Genome_build: GRCh37
Supplementary_files_format_and_content: BED files contain the region boundaries where FAIRE or yH2AX overexpressed signal occur.

extract_protocol:
For ChIP: Cells were lysed, nuclei were isolated and sonicated, yH2AX bound DNA was isolated with antibody. For FAIRE: Cells were lysed, nuclei were isolated and sonicated, protein free DNA was isolated by phenol/Chlorophorm extraction.
DNA libraries were prepared using standard protocols for sequencing on the Illumina HiSeq2000 platform.

tag: treated with

value: none (untreated) for 4hrs


title: Mck1_t05


title: DN Endothel n3r1


title: Mck1_t15


title: DN Endothel n1r1


title: Untreated_yH2AX

tag: chip antibody

value: yH2AX (Millipore, 05-636, clone JBW301)


title: 202068-positive_bisulfite


title: Epirubicin_yH2AX

value: Epirubicin (10uM) for 4hrs


title: DN Endothel n2r1

tag: cell type


title: Epirubicin_FAIRE


title: BEC Endothel t3r1


title: BEC Endothel t2r1


title: 201409-negative_bisulfite

tag: tissue


title: 201128-positive_bisulfite


title: Daunorubicin_yH2AX

tag: cell line

value: Daunorubicin (10uM) for 4hrs


title: Ira2_t45


title: Ira2_t60


title: Mck1_t00


title: Daunorubicin_FAIRE


title: Ramos_2.5uM_Omomyc_24_hrs_2

description:
Ramos_2.5uM_Omomyc_24_hrs_2
US-10010273


title: Ira2_t30


title: 201087-negative_bisulfite

tag: ptsd diagnosis


title: BEC Endothel n3r1

tag: role


title: BEC Endothel t1r1

tag: biological replicate


title: 201136-negative_bisulfite


title: Aclarubicin_FAIRE

value: Aclarubicin (20uM) for 4hrs


title: Ira2_t20


title: diMethyldoxo_FAIRE

value: N,N-dimethyldoxorubicin (10uM) for 4hrs


title: 201013-positive_bisulfite


title: BEC Endothel n2r1

tag: technical replicate


title: 201164-negative_bisulfite


title: Hyp6_OX-+/+

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Mus_musculus genome GRCm38 using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Ensembl annotation 75.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: hypothalamus, Hcrt/Orexin wildtype, replicate 3

extract_protocol:
Total RNA from mice cortex, hypothalamus and brainstem was isolated with the RNeasy Lipid Tissue Midi kit (Quiagen).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

tag: strain

value: hypothalamus

value: Hcrt/Orexin wildtype

tag: mouse model reference


title: 202072-positive_bisulfite

tag: gender

value: Male


title: 201368-negative_bisulfite


title: Hyp5_OX-+/+

source_name: hypothalamus, Hcrt/Orexin wildtype, replicate 2

tag: genotype/variation


title: FRC Endothel t2r1


title: Ira2_t05

tag: time-point


title: Ira2_t15


title: FRC Endothel t3r1


title: BEC Endothel n1r1


title: Hyp6_OX-At-+/+

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 wildtype, replicate 3

value: Hcrt/Orexin-ataxin-3 wildtype


title: Ira2_t10


title: Hyp5_OX-At-+/+

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 wildtype, replicate 2


title: FRC Endothel n3r1


title: 202195-negative_bisulfite


title: FRC Endothel t1r1


title: Hog1_t60


title: 201189-negative_bisulfite


title: 201383-negative_bisulfite


title: FRC Endothel n2r1


title: Hyp4_OX-+/+

source_name: hypothalamus, Hcrt/Orexin wildtype, replicate 1


title: Ira2_t00


title: Hyp4_OX-At-+/+

source_name: hypothalamus, Hcrt/Orexin-ataxin-3 wildtype, replicate 1


title: Hog1_t45


title: Hog1_t30


title: Hyp3_OX-KO

source_name: hypothalamus, Hcrt/Orexin knockout, replicate 3

value: Hcrt/Orexin knockout


title: 201356-positive_bisulfite

value: Whole blood


title: FRC Endothel n1r1


title: Hog1_t20