city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Trachea 72h post-injury by polidocanol, mouse id 65, 1082 cells after all filtering steps

data_processing:
Raw fastq were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):
*_R1_001.fastq.gz   : contains the 3' UTR cDNA read
*_R2_001.fastq.gz   : contains the first half of the cell barcode
*_R3_001.fastq.gz   : contains the library index for demultiplexing libraries
*_R4_001.fastq.gz   : contains the second half of the barcode and the UMI."
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the parameter values specified in the yaml files provided as supplementary material to the published paper (Plasschaert et al.). The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).
For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called ""not_included_in_study_*"" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing."
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, see Supplementary Files 1-3 of the manuscript for details). The reference transcriptome was built using annotations from ENSEMBL (GRCm38 and GRCh37 for mouse and human, respectively). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > N; ii) mitochondrial gene content <M. For mouse samples N = 1500 and M = 20%. For human sample, M = 25%, and  N = 1500,1500, 2000, and 1500 for donors 1-3 and the lentiviral transduction experiment, respectively. In mouse data, cell with strong immune gene expression were also excluded from this study. Counts were normalized as described in methods, and combined into three normalized filtered matrices (genes x cells ): filtered_normalized_counts_mouse.tsv.gz, filtered_normalized_counts_human.tsv.gz, and filtered_normalized_counts_human_viral_transduction.tsv.gz)
genome build: hg19 and mm10
The *.counts.tsv.gz files include raw unique molecular identifier (UMI)-filtered counts for all cell barcodes (prior to filtering). The file filtered_normalized_counts_*.tsv.gz contains filtered normalized counts. The file meta_raw_counts_*.tsv.gz contains meta information for each cell prior to filtering, including raw count file name, cell barcode, and the  index of the cell in the filtered normalized count matrix ('nan' for cells that were filtered out). The file meta_filtered_counts_*.tsv.gz contains meta information about filtered counts, such as library id, mouse id, raw count file name, barcode, and x and y coordinates used for 2-dimensional data representations.

source_name: Trachea

growth_protocol: C57/BL6 mice from the Jackson Laboratory aged 6-8 wk were used for all studies. Animals were handled in accordance with Novartis Institutes for Biomedical Research Animal Care and Use Committee protocols and regulations. Mice were housed in a temperature- and humidity-controlled animal facility with ad libitum access to food and water and acclimated for at least 3 d before experimental manipulation.

extract_protocol:
Polidocanol-induced injury was performed as previously described (Borthwick et al. 2001). Briefly, mice were anesthetized and delivered one dose of 15 ?L 2% Polidacanol or PBS vehicle control by oralpharyngeal aspiration to induce injury. Tracheas were harvested at 1 day (1d), 2d, 3d and 7d following injury for scRNA-seq or for fixation and immunofluorescence.
For single-cell isolation for scRNA-seq, tracheas were dissected and opened longitudinally in Ham?s F12 (Life Technologies, 11765-054) plus 1% Pen-Strep on ice. Each trachea was individually placed in a 15 mL conical tube with 5 mL of 1.5 mg/mL Pronase (Roche, 10165921001) in Ham?s F12 plus 1% Pen-Strep and incubated for 18h at 4°C. 500 mL FBS was added to inactivate pronase and conical tubes were vigorously inverted to dislodge cells. Each trachea was transferred twice to a 15 mL conical tube containing Ham?s F12 plus 1% Pen-Strep plus 10% FBS and then inverted. Media from each of the three tubes was pooled and cells were pelleted at 400g for 10 min at 4°C. Cells were resuspended in 500 µL DNase (Sigma-Aldrich, DN25), incubated on ice for 5 min and then pelleted at 400g for 10 min at 4°C. Cells were then washed twice in Hams F12 1% Pen-Strep 10% FBS and then resuspended in PBS + 0.02% BSA.  Cells were diluted to 90,000 cells/mL in 15% Optiprep + 0.02% BSA in PBS for scRNA-seq.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 10 of this manuscript (Plasschaert et al).

treatment_protocol: Samples come from uninjured adult mice, and from mice following Polidocanol-induced injury. Polidocanol-induced injury was performed as previously described in the paper. Briefly, mice were anesthetized and delivered one dose of 15 μL 2% Polidacanol or PBS vehicle control by oralpharyngeal aspiration to induce injury. Tracheas were harvested at 1 day (1d), 2d, 3d and 7d following injury for scRNA-seq or for fixation and immunofluorescence.

value: 6-8 weeks

value: upper airway epithelial cells


status: Public on Aug 01 2018

type: SRA

description: Trachea 48h post-injury by polidocanol, mouse id 61, 1964 cells after all filtering steps

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

tag: age

tag: cell type


description: Trachea 1wk post-injury by polidocanol, mouse id 67, 1068 cells after all filtering steps


description: Trachea 1wk post-injury by polidocanol, mouse id 68, 1041 cells after all filtering steps


description: Uninjured trachea, mouse id 56, 2659 cells after all filtering steps

extract_protocol:
For single-cell isolation for scRNA-seq, tracheas were dissected and opened longitudinally in Ham?s F12 (Life Technologies, 11765-054) plus 1% Pen-Strep on ice. Each trachea was individually placed in a 15 mL conical tube with 5 mL of 1.5 mg/mL Pronase (Roche, 10165921001) in Ham?s F12 plus 1% Pen-Strep and incubated for 18h at 4°C. 500 mL FBS was added to inactivate pronase and conical tubes were vigorously inverted to dislodge cells. Each trachea was transferred twice to a 15 mL conical tube containing Ham?s F12 plus 1% Pen-Strep plus 10% FBS and then inverted. Media from each of the three tubes was pooled and cells were pelleted at 400g for 10 min at 4°C. Cells were resuspended in 500 µL DNase (Sigma-Aldrich, DN25), incubated on ice for 5 min and then pelleted at 400g for 10 min at 4°C. Cells were then washed twice in Hams F12 1% Pen-Strep 10% FBS and then resuspended in PBS + 0.02% BSA.  Cells were diluted to 90,000 cells/mL in 15% Optiprep + 0.02% BSA in PBS for scRNA-seq.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 10 of this manuscript (Plasschaert et al).


description: Uninjured trachea, mouse id 57, 1971 cells after all filtering steps


title: CTRL 48h.2

city: Pisa

first: Marco

last: Terrigno

address: Via Giuseppe Moruzzi, 1

country: Italy

institute: Scuola Normale Superiore

description: small RNA-deq

data_processing:
FastQ files were extracted with bcl2fastq v1.8.3
Library adaptors were trimmed and reads were mapped to the mouse genome (NCBI37/mm9) with miRExpress (Wang et al., 2009). miRNA reads were annotated using the miRBase mouse reference (mirbase.org, V19). Normalization was performed as counts per million (CPM).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Excel file includes mapped read counts

molecule: total RNA

source_name: Embryonic Stem Cells

growth_protocol: Murine ES cell lines E14Tg2A (passages 25-38) were cultured on gelatin-coated tissue culture dishes at a density of 40000 cells/cm2. ES cell medium, changed daily, contained GMEM (Sigma), 10% Fetal Calf Serum, 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin and 1000 U/ml recombinant mouse LIF (Invitrogen). Chemically defined minimal medium (CDMM) for neural induction consisted of DMEM/F12 (Invitrogen), 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids (NEAA), 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A; Invitrogen). The differentiation protocol is organized in three steps. In Step-I, ES cells were dissociated, washed with DMEM/F12 and seeded on gelatin-coated culture dishes (65000 cells per cm2), then cultured in CDMM plus 2.5μM WNT inhibitor (53AH, Cellagen Technology) and 0.25μM BMP inhibitor (LDN193189, Sigma) for 3 days. In Step-II, ES cells were dissociated and seeded (65000 cells per cm2) on Poly-ornithine (Sigma; 20 μg/ml in sterile water, 24hr coating at 37°C) and natural mouse Laminin (Invitrogen; 2.5 μg/ml in PBS, 24hr coating at 37°C). Cells were maintained for 4 additional days in CDMM Plus WNT/BMP inhibitors, changing the medium daily. Several washes with DMEM/F12 were used to remove the serum employed for Trypsin inactivation. In Step-III, cells were dissociated and seeded (125000 cells per cm2) on Poly-ornithine and Laminin coated wells. Subsequently, WIBI cultures were kept in CDMM plus WNT/BMP inhibitors for four (WiBi 11) additional days.

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (Qiagen).
Libraries were prepared using 1 μg of total RNA per sample and the TruSeq Small RNA Sample Preparation (Illumina) following the manufacturer's instructions and sequenced on Illumina HiSeq 2000 platform, running in 50-bp single-read mode using sequencing chemistry v3.

treatment_protocol: FGF8-treated cells (FGF8) were grown in CDMM supplemented with FGF 100ng/mL (R&D), replaced daily. MEK inhibitor (PD0325901, Calbiochem, 1μM; Barrett et al., 2008) was added daily to block FGF signaling.

tag: tissue

value: Embryonic Stem Cells

tag: cell line

tag: age group


title: FGF8 48h.1

description: small RNA-deq


title: CTRL 48h.1

description: small RNA-deq


description: Trachea 24h post-injury by polidocanol, mouse id 59, 898 cells after all filtering steps


title: FGF8 48h.2

description: small RNA-deq


title: CTRL 24h.2

description: small RNA-deq


title: PRMT5 olig2cre KO rep3

city: Montreal

first: Stéphane

last: Richard

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute for Medical Research - Jewish General Hospital, McGill University

data_processing:
Quality control: FASTQC v0.11.2
Read trimming: Trimmomatic v0.32
Alignment to reference genome: STAR v2.3.0e
Counting exonic reads mapping to UCSC known genes: featureCounts v1.5.0
Normalization of exonic read counts: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw exonic read counts: compressed .tsv file; Normalized exonic read counts: compressed .tsv file

source_name: mouse brain

extract_protocol:
Brains were removed and RNA was harvested using Trizol reagent. RNA-sequencing (150bp paired-end) was performed using Illumina platform (NGS Core, Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson CCRD, Smithville, Tx).
RNA libraries were prepared for sequencing using Illumina mRNA TruSeq protocol

tag: genotype/variation

value: PRMT5 olig2cre KO


title: PRMT5 olig2cre KO rep2


title: CTRL 24h.1

description: small RNA-deq


title: WT rep3

value: wild-type


title: DRG trap normal [normal trap biosample2]

city: Richardson

first: Theodore

middle: John

last: Price

state: TX

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

country: USA

institute: The University of Texas at Dallas

description:
DRG_normal_TRAP2_TPM
3' sequencing assay : Quantseq assay (Lexogen)

data_processing:
Sequence files generated by the Illumina NextSeq500 sequencer were downloaded from BaseSpace. An  Initial quality check using FastQC 0.11.5 (Babraham Bioinformatics) was done on the sequencing files and then  trimming was performed on the server with the FASTQ Toolkit. Sequences were trimmed with optimized  parameters (13 bases from 3’-end, 17 bases from 5’-end, and any poly-adenine longer than 2 bases from the 3’  side). Trimming parameters were optimized based on FastQC results and mapping rate, as well as manually  checking high reads or abundant chromosomal regions with IGV 2.3.80. The trimmed sequencing samples were  then processed using TopHat 2.1.1 (with Bowtie 2.2.9) and mapped to the mouse reference genome (NCBI  reference assembly GRCm38.p4) and reference transcriptome (Gencode vM10) generating files in .bam format.
We filtered reads such that uniquely mapped reads were processed for further analysis (Supplementary Table 6).  Processed .bam files were then quantified for each gene using Cufflinks 2.2.1 with gencode.vM10 genome  annotation. Since reads only mapped to the 3’UTR of the gene, read counts were not normalized by length by  the using the Cufflinks option -- no–length–correction. Relative abundance for the ith gene was determined by  calculating transcripts per million (TPM) by constraining Cufflinks reported RPKMs to sum to a million for all coding genes in each sample to provide TPMs.
Two samples were pooled in silico to create biosample 7 (biosample7_subsample1 and biosample_subsample2) : the way this was done was to take a weighted average of TPMs based on the number of mapped reads for each sample.
Finally, TPM values were normalized to upper decile for each biological replicate and udTPM  (upper decile TPM) were used for analysis, to provide uniform processing for samples with varying sequencing  depth and because of varying number of genes in the transcriptome and translatome
Details about post processing steps can be found at : https://www.utdallas.edu/bbs/painneurosciencelab/sensoryomics/cipntrap/
Genome_build: GRCm38.p4 (reference annotation GENCODE vM10)
Supplementary_files_format_and_content: Zipped (gzip 1.3.12), tab separated text file (text encoding : Unicode UTF-8 with Unicode Byte Order Mark, end of line : \n) with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes

source_name: Dorsal root ganglia (DRG)

growth_protocol: Rosa26fsTRAP mice were generated (P. Zhou et al, Proc Natl Acad Sci U S A 110, 15395 (Sep 17, 2013)) and purchased from Jackson Laboratory (Stock number: 022367). Transgenic mice expressing Cre recombinase under the control of the Scn10a (Nav1.8) promoter were obtained initially from Professor John Wood (University College London) but are commercially available from Infrafrontier (EMMA ID: 04582). The initial characterization of these mice demonstrated that the introduction of the Cre recombinase in heterozygous animals does not affect pain behavior, and their DRG neurons have normal electrophysiological properties (2). Nav1.8cre mice on a C57BL/6J genetic background were maintained and bred at the University of Texas at Dallas. Upon arrival, Rosa26fstrap mice were crossed to Nav1.8cre to generate the Nav1.8-trap mice that express a fused EGFP-L10a protein in Nav1.8 expressing neurons. All experiments were carried out using male and female littermates aged 8 to 12 weeks old. Mice were group housed (4 maximum) in non-environmentally enriched cages with food and water ad libitum in a 12h light-dark cycle. Room temperature was maintained at 21 ± 2°C.

extract_protocol:
Nav1.8-trap male and female mice were decapitated and dorsal root ganglia (DRG) rapidly dissected in ice-cold dissection buffer (1X HBSS (Invitrogen 14065006), 2.5 mM HEPES, 35 mM Glucose, 4 mM NaHCO3, 100 μg/ml cycloheximide, 0.001V 2 mg/ml emetine). DRGs were transferred to ice-cold polysome buffer (20 mM HEPES, 12 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 100 μg/ml cyclohexamide, 20 μg/ml emetine, 40U/ml SUPERase IN (Promega), 1 μl DNAse and protease inhibitor and homogenized using a dounce homogenizer.  Samples were centrifuged at 3,000 x g for 10 min to prepare post-nuclear fraction (S1). Then, 1% NP-40 and 30 mM DHPC were added to the S1 fraction and then centrifuged at 15,000 x g for 15 min to generate a post-mitochnodrial fraction (S20). A 200 μl sample of S20 was removed for use as Input, and 800 μl of S20 was incubated with protein G-coated Dynabeads (Life Technologies) bound to 50 μg of anti-GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8, Memorial Sloan Kettering Centre) for 3 hrs at 4°C with end-over-end mixing. Anti-GFP beads were washed with high salt buffer (20 mM HEPES, 5 mM MgCl2, 350 mM KCl, 1% NP-40, 0.5 mM DTT and 100 μg/ml cyclohexamide) and RNA was eluted from all samples using a Direct-zol kit (Zymo Research) according to the manufacturer’s instructions. RNA yield was quantified using a Nanodrop system (ThermoFisher Scientific) and RNA quality was determined by a fragment analyzer (Advanced Analytical Technologies Inc.) For RNA-seq, the pulldown step was not performed.
Libraries were generated from 100 ng to 1 ug of total RNA using Quantseq 3ʹ mRNA-Seq library kit (Lexogen) with RiboCop rRNA depletion kit (Lexogen) treatment according to the manufacturer’s protocols. The endpoint PCR amplification cycle number for each sample was determined by quantitative PCR (qPCR) assay with PCR Add-on kit for Illumina (Lexogen). The cycle number was selected when the fluorescence value reached 33% of the maximum for each sample. Purified libraries were quantified by Qubit (Invitrogen) and the average size was determined by fragment analyzer (Advanced Analytical Technologies Inc.) with high sensitivity NGS fragment analysis kit. Libraries were then sequenced on an Illumina NextSeq500 sequencer using 50-bp single-end reads. [library construction protocol]

treatment_protocol: Mice were treated with paclitaxel (4mg/kg in cremaphor vehicle) by intraperitoneal injection every other day for 8 days. They received a total of 4 injections for a cumulative dose of 16 mg/kg.  Vehicle treated animals were dosed in exactly the same way but without paclitaxel.

value: DRG / Scn10a +ve cells

tag: treatment

value: Normal

value: Nav1.8cre mice on C57BL/6J  background

tag: fraction

value: rRNA depleted RNA associated with L10a + eGFP pulldown


title: WT rep1


title: WT rep2


title: Mouse_Li_KPDS

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

description: G4-seq protocol

library_source: genomic

data_processing:
library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes:  http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)

molecule: genomic DNA

source_name: skin

growth_protocol: Organisms were cultured in standard conditions, withouth any treatment.

extract_protocol:
DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were  sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).

treatment_protocol: All samples were untreated, wild type organisms.

tag: strain or cell type

value: C57BL/6J strain

value: skin


title: Mouse_Li_K

description: G4-seq protocol


description: Uninjured trachea, mouse id 55, 1470 cells after all filtering steps


description: Trachea 1wk post-injury by polidocanol, mouse id 69, 212 cells after all filtering steps


title: FGF8 24h.1

description: small RNA-deq


title: RNA-seq_βTC3_r2

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

data_processing:
Reads where aligned to mm9 genome index using TopHat v2 and processed with Samtools v1.6
Subread v1.5 feature counts was used to generate read counts and then FPKM scores calculated for each gene using mm9 RefSeq genes.gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: Table of feature counts output, which contains read distrubution for each replicate over mm9 RefSeq gene and then an additional FPKM calculation for each gene (using total number of aligned of reads and gene length).

source_name: β-TC3 cells

growth_protocol: β-TC3 cells were cultured in Dulbecco’s Modified Eagle Medium (ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin-Streptomycin at 37°C in 5% CO2. Two experimental replicates where generated with two T25 culture flask of β-TC3 cultured to ~70% confluency.

extract_protocol:
Total RNA was prepared using the Qiagen RNeasy mini kit (Qiagen) with an on-column DNase I digestion using the Qiagen RNase-Free DNase set as the manufactures guidelines
Ribosomal RNA was depleted using the RiboMinus Eukaryote Kit for RNA-Seq (Life Technology) and RiboMinus Concentration module as manufactures’ guidelines.
Sequencing libraries where prepared using NEBNext mRNA Library Prep Master Mix Set (NEB), following the manufactures protocol, with all size selection performed using Agencourt AMPure XP beads (Beckman Cutler). Samples where multiplexed using the NEBNext Multiplex Oligos for Illumina kit to barcode each sample and amplified for 11 cycles. Sequnced using an Illumina Hi-Seq 2000 single end 50bp reads


title: RNA-seq_βTC3_r1


title: FGF8 24h.2

description: small RNA-deq


title: shLincenc1_rep2_RNAseq

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm9 reference assembly by the Tophat2 software.
We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
For differential gene expression analysis, we analyzed raw read counts for GENCODE M1 gene models using HTSeq (Anders et al., 2015), and then calculated statistics of differential expression via DESeq2 version 1.8.2 (Love et al., 2014) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Different expressed genes list during nESCs to EpiLSCs

source_name: nESCs

growth_protocol: To maintain ESCs in ground state or naïve state, cells from two mouse ESC lines (E14TG2a and R1) were cultured in 2i /LIF conditions as described (Ying et al., 2008).

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).

treatment_protocol: For shRNA-based knockdown, two hairpins were designed to target each lncRNA gene. The shRNAs were synthesized and cloned into the plko.1 lentiviral vector, and the lentiviruses were then prepared as previously described (Fu et al., 2015). Then, 3×105 mESCs were infected with viruses and selected by 1ng/ml of puromycin for two days.

tag: lentivirus


title: shCtrl_rep2_RNAseq

value: shCtrl


title: E14_naive_RNAseq

treatment_protocol: The nESC-to-EpiLC transition was conducted as described (Hayashi et al., 2011) with minor modifications. Briefly, mouse nESCs cells were plated at a density of 1×104 per cm2 in gelatin-coated plates with N2B27 medium containing activin A (20 ng/ml) and bFGF (12 ng/ml). The medium was changed every day. The converted EpiLCs were collected on day 3. For spontaneous differentiation, nESC cells were plated at a density of 1×104 per cm2 in gelatin-coated plates in N2B27 medium without 2i/LIF for four days.


title: R1_naive_RNAseq


title: shLincenc1_rep1_RNAseq


title: E14_Epi_RNAseq

source_name: EpiLSCs


title: OK3: OK_seq_aB_72h_NT_rep3

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Library strategy: OK-seq
mouse OK-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done as described previosuly (Petryk et al., 2016)
Analysis done as described previosuly (Petryk et al., 2016)
Genome_build: GRCm38p2/mm10 for mouse
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Activated primary B cells

extract_protocol:
OK-seq was performed in asynchronous mouse B cells activated for 48 hours, as previously described in a detailed protocol (Petryk et al., 2016).
libraries were prepared and sequenced following standard Illumina protocols

value: Activated primary B cells

tag: genotype

value: WT


title: shCtrl_rep1_RNAseq


title: PRMT5 olig2cre KO rep1


title: OK2: OK_seq_aB_72h_NT_rep2


title: RS1: Repli_seq_rB_0h_NT_rep1

data_processing:
Library strategy: Repli-seq
mouse Repli-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
Log2 ratio was calculated in 100kb bins. Early and late replicating regions were identified based on the bins having positive and negative values respectively
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Resting primary B cells

extract_protocol:
Replication timing profiles were determined using TimEX as described (Bartholdy et al., PMID: 25987481) with minor modifications.  Briefly, The S/G1 TimEX ratio, proportional to the replication time during S phase, was measured in mature splenic B cells from wild-type C57BL/6NCr mice.  The G1 population was obtained from mature resting B cells (100% G0/G1 arrested), which were isolated using anti-CD43 MicroBeads (Miltenyi Biotech) for negative selection. To obtain the S-phase population, the resting B cells were activated with LPS (25 mg/ml; Sigma), IL-4 (5 ng/ml; Sigma) and RP105 (0.5 mg/ml; BD) for 48 hours (~70% S-phase).   5 million cells were collected for both populations, and whole genome sequencing was performed using standard Illumina library prep and sequenced on HiSeq 2000.
libraries were prepared and sequenced following standard Illumina protocols

value: Resting primary B cells


title: R1_Epi_RNAseq


title: III-4 healthy t6

type: RNA

city: Milan

first: Ana Maria

last: Osiceanu

address: via Olgettina 58

department: INSPE

institute: IRCCS San Raffaele Scientific Institute

description:
after 6 months
7677153009_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantification was performed at the probe level with quantile normalization and background subtraction as implemented by Illumina GenomeStudio software v2010.3

organism: Homo sapiens

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep kit for Illumina arrays

extract_protocol: whole blood was collected in PaxGene tubes (PreAnalytix) and total RNA was extracted using the PaxGene Blood miRNA kit (PreAnalytix) according to manufacturer instructions.

tag: disease course

value: healthy

tag: gender

value: female

value: untreated


title: II-6 affected t6

description:
after 6 months
7677153009_C

value: secondary progressive MS

value: Interferon-β


title: III-12 healthy t6

description:
after 6 months
7677153009_H


title: II-3 healthy t0

description:
baseline
7677153015_H


title: III-7 healthy t0

description:
baseline
7677153009_K

value: male


title: II-15 affected t0

description:
baseline
7677153015_G


title: II-4 healthy t0

description:
baseline
7677153015_E


title: III-7 healthy t6

description:
after 6 months
7677153009_G


title: III-12 healthy t0

description:
baseline
7677153009_L


title: II-11 affected t6

description:
after 6 months
7677153009_D

value: chronic steroid treatment


title: II-13 healthy t6

description:
after 6 months
7677153009_F


title: III-5 affected t6

description:
after 6 months
7677153009_A

value: relapsing-remitting MS

value: Glatiramer Acetate


title: II-3 healthy t6

description:
after 6 months
7677153009_J


title: II-15 affected t6

description:
after 6 months
7677153009_I


title: II-13 healthy t0

description:
baseline
7677153015_F


title: II-11 affected t0

description:
baseline
7677153015_D


title: VCX3A/B-2R -GFP rep3

city: macau

first: gang

last: li

state: macau

address: N22  Research Building, Faculty of Health Sciences (FHS),  University of Macau,  Avenida de Universidade, Taipa, Macau, China

department: faculty of health and science

institute: university of macau

description:
replicate 3
SAMPLE 15

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.28.0). It was vst transformed and quantile normalized.

label: biotin

source_name: Pediatric glioblastoma cell

label_protocol: Total RNA was amplified and labeled using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, #TAN091096). Labeled cRNA was purified with the RNeasy mini kit (QIAGEN, #74106) and hybridized on HumanHT-12 v4 Expression BeadChip microarrays (Illumina) according to the manufacturer's protocol.

growth_protocol: Res259 pediatric glioma cells were cultured in high glucose Dulbecco's Modified Eagle Medium growth media (Gibco #11965) supplemented with 10% fetal bovine serum. All cell lines were tested negative for mycoplasma contamination.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen), and genomic DNA was digested by RNase-Free DNase Set (QIAGEN, #79254), the RNA was furthered purified using the RNeasy Mini Kit (Qiagen, #74106) following manufacturer’s instructions. Quality and concentration of RNA were determined by the Bioanalyzer 2100 (Agilent technologies).

treatment_protocol: Human H3F3A (C-terminal Myc-DDK-tagged) cloned into the pCMV6-Entry was purchased from OriGene. The H3.3K27M (c.83A>T) mutation was introduced by the QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent Technologies) according to the manufacturer’s protocol. Different forms of VCX3A/B (encoding two, seven or ten copies of tandem repeats respectively) were amplified using cDNA derived from ResES259 cells as a template and cloned into pcDNA3 GFP LIC cloning vector (6D), which was a gift from Scott Gradia (Addgene plasmid # 30127). The vectors mentioned above were stably transfected into Res259 cells.

tag: tag

value: GFP

value: Brain


title: GFP-control rep3

description:
replicate 3
SAMPLE 13


title: II-4 healthy t6

description:
after 6 months
7677153009_E


title: VCX3A/B-7R-GFP rep2

description:
replicate 2
SAMPLE 12


title: II-6 affected t0

description:
baseline
7677153015_C


title: VCX3A/B-7R-GFP rep3

description:
replicate 3
SAMPLE 16


title: III-5 affected t0

description:
baseline
7677153015_A


title: VCX3A/B-10R -GFP rep3

description:
replicate 3
SAMPLE 14


title: VCX3A/B-7R-GFP rep1

description:
replicate 1
SAMPLE 8


title: III-4 healthy t0

description:
baseline
7677153015_B


title: GFP-control rep2

description:
replicate 2
SAMPLE 9


title: VCX3A/B-10R -GFP rep1

description:
replicate 1
SAMPLE 6


title: VCX3A/B-10R -GFP rep2

description:
replicate 2
SAMPLE 10


title: H3.3K27M rep2

description:
replicate 2
SAMPLE 4

value: Flag


title: GFP-control rep1

description:
replicate 1
SAMPLE 5


title: VCX3A/B-2R -GFP rep2

description:
replicate 2
SAMPLE 11


title: VCX3A/B-2R -GFP rep1

description:
replicate 1
SAMPLE 7


title: H3.3K27M rep1

description:
replicate 1
SAMPLE 3


title: Vector-control rep2

description:
replicate 2
SAMPLE 2


title: Vector-control rep1

description:
replicate 1
SAMPLE 1


title: D2-0h

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing: Only Gene probes with Detection P value below 0.05 in at least one samples were kept for further processing including normalization. Signals were normalized against the median in each sample.

source_name: P493-6 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: P493-6 cells were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted using the RNeasy kit (Qiagen).

treatment_protocol: P493-6 cells were infected with lentiviruses expressing control (scramble) or Dpy30 shRNAs #2 or #5, followed by puromycin (2 μg/ml) selection for 2–3 days starting from 2 days after infection. control and Dpy30 KD P493-6 cells were treated with tetracycline for 3 days (to turn off Myc). Tetracycline was thoroughly washed and cells were incubated in Tet-free medium for 4 hours. RNAs from cells before Tet treatment, after Tet treatment and right before washing Tet away, and 4h after washing Tet away, were subjected to Illumina microarray analyses.

value: Dpy30 shRNA #2, after Tet treatment, right before Tet withdrawl


title: Scr-4h

value: scramble shRNA, 4h after Tet withdrawl


title: D2-4h

value: Dpy30 shRNA #2, 4h after Tet withdrawl


title: D5

value: Dpy30 shRNA #5


title: Scr

value: scramble shRNA


title: HIV- healthy donor 9

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

hyb_protocol: Illumina standard iSCAN protocol

scan_protocol: Illumina standard iSCAN protocol

data_processing: Quantile Normalized, Background Corrected (BeadStudio).

source_name: HIV- healthy donor

label_protocol: Illumina Whole Genome DASL assay per manufacturer protocol

extract_protocol: mirVana™ RNA Isolation Kit, Ambion

treatment_protocol: No treatment of ex vivo sorted cells

tag: infection status

value: HIV- donor

value: NO Treatment

tag: cluster

value: CD8 T cell


title: HIV- healthy donor 6


title: Scr-0h

value: scramble shRNA, after Tet treatment, right before Tet withdrawl


title: D2

value: Dpy30 shRNA #2


title: HIV- healthy donor 3


title: HIV- healthy donor 5


title: HIV- healthy donor 10


title: HAART patient 30

source_name: HAART patient

value: Chronic Treated

value: HAART


title: HIV- healthy donor 1


title: HIV- healthy donor 4


title: HIV- healthy donor 8


title: HIV- healthy donor 7


title: HIV- healthy donor 2


title: HAART patient 32


title: HAART patient 31


title: HAART patient 20


title: HAART patient 26


title: HAART patient 25


title: HAART patient 28


title: HAART patient 27


title: HAART patient 15


title: HAART patient 21


title: HAART patient 17


title: HAART patient 14


title: HAART patient 12


title: HAART patient 29


title: HAART patient 8


title: HAART patient 24


title: HAART patient 9


title: HAART patient 11


title: HAART patient 16


title: HAART patient 22


title: HAART patient 23


title: HAART patient 18


title: HAART patient 19


title: HAART patient 7


title: HAART patient 6


title: HAART patient 10


title: HAART patient 5


title: HAART patient 4


title: HAART patient 13


title: Wild type minus P_Exp2

city: Haifa

first: Sigal

last: Savaldi-Goldstein

address: Technion City

country: Israel

institute: Technion

data_processing:
These reads were aligned to the TAIR10 assembly of the Arabidopsis thaliana genome, using Tophat2 v2.0.11.  Transcript coordinates from the TAIR10 reference set were used to guide the alignment process.
After alignment, the numbers of reads per gene were estimated using HTSeq v0.6.1.
DESeq2 v1.2.8 was used to normalize read counts
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: Wild type minus P_Exp2

growth_protocol: Arabidopsis (Arabidopsis thaliana) lines in the Columbia-0 (Col-0) background, wild type and bzr1-D mutant, were germinated on one-half-strength Murashige and Skoog medium supplemented with 0.2% (w/v) sucrose for 7 days,  in 16h light (approximately 70 mol m-2 s-1)/ 8h dark cycles, at 22°C.

extract_protocol:
RNA was isolated from the root tissues of 7-day-old seedlings using RNA extraction kit (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-day-old seedlings were transfered for 24h to medium with either adequate (0.625 mM) or deficient (1µM) Pi levels (as described in Singh et al, Plant Phys, 2014). 8 samples of mRNA from two biological replicates were collected (i.e. from roots of 7-day-old seedlings). Samples were sequenced on an Illumina HiSeq 2500, to obtain 50 bp single end reads.

tag: strain

value: Root

value: 7-day-old seedlings

value: wild type


title: bzr1-D minus P_Exp 2

source_name: bzr1-D minus P_Exp 2

tag: age


title: HAART patient 3

tag: cell type


title: HAART patient 1


title: bzr1-D plus P_Exp 2

source_name: bzr1-D plus P_Exp 2

tag: tissue


title: Wild type plus P_Exp 2

source_name: Wild type plus P_Exp 2


title: bzr1-D minus P_Exp 1

source_name: bzr1-D minus P_Exp 1


title: Wild type minus P_Exp 1

source_name: Wild type minus P_Exp 1


title: Elite Controller group5 patient 2

source_name: Elite Controller group5 patient

value: Elite Controller


title: bzr1-D- plus P_Exp 1

source_name: bzr1-D- plus P_Exp 1


title: Wild type plus P_Exp 1

source_name: Wild type plus P_Exp 1


title: X17_indel_day5

city: Seattle

first: Lea

middle: M

last: Starita

state: WA

department: Genome Sciences

institute: University of Washington

description: amplicon

data_processing:
Illumina bcl2fastq v2.16 for base calling and demultiplex
SeqPrep (available at https://github.com/jstjohn/SeqPrep) to align R1 and R2, trim adaptors;https://github.com/shendurelab/saturationGenomeEditing_pipeline:run_seqprep_BRCA1_pipeline.py
N bases are removed;https://github.com/shendurelab/saturationGenomeEditing_pipeline:run_remove_n_bases.py
convert cDNA to gDNA;https://github.com/shendurelab/saturationGenomeEditing_pipeline:run_cDNA_to_gDNA_SGE_pipeline.py
align to WT BRCA1 exons;sam output;https://github.com/shendurelab/saturationGenomeEditing_pipeline:run_needle_to_sam_BRCA1_pipeline.py
identify programmed edits;https://github.com/shendurelab/saturationGenomeEditing_pipeline:sam_to_edits_wRNA_pipeline_20170517.py
call SNVs; https://github.com/shendurelab/saturationGenomeEditing_pipeline:annotate_variants_BRCA1_pipeline_20170622.py
count SNVs;calculate frequencies;normalize within exons;https://github.com/shendurelab/saturationGenomeEditing_pipeline:BRCA1_SGE1_X_all_ggplot_removed_20171012.Rmd
model positional effects of CRISPR editing;https://github.com/shendurelab/saturationGenomeEditing_pipeline:positional_modeling_SGE1_v6_20171013_noggplot.Rmd
normalize between exons;https://github.com/shendurelab/saturationGenomeEditing_pipeline:BRCA1_SGE1_global_20171119_noggplot.Rmd
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated file,counts,frequencies,scores for all variants in the HAP1∆LIG4 and HAP1 cells

source_name: cell line: HAP1

growth_protocol: Quality-controlled WT HAP1 cells were purchased (Haplogen/Horizon Discovery) and cultured in media comprising Iscove’s Modified Dulbecco’s Medium (IMDM) with L-glutamine and 25 mM HEPES (GIBCO) supplemented with 10% fetal bovine serum (Rocky Mountain Biologicals) and 1% penicillin-streptomycin (GIBCO).

extract_protocol:
Qiagen All Prep
amplicon, see supplementary table 3 for primer sequences

treatment_protocol: For all experiments, HAP1 cells were transfected using TurboFectin 8.0 (Origene) according to manufacturer’s protocol. A 2.5x volume of Turbofectin was added to the transfection mix for each ug of plasmid DNA in Opti-Mem (Life Technologies). For each SGE transfection, 10 million cells were passaged to a 10 cm dish. The next day (day 0), cells were co-transfected with 12 ug of the Cas9/gRNA plasmid (pX459) and 3 ug of the SGE library corresponding to a single exon. For negative control transfections, a pX459 vector targeting HPRT1 was used instead. On day 1, cells were passaged into a supplemented with puromycin (1 ug/ml) to select for successfully transfected 757 cells. On day 4, cells were washed twice and passaged to 6 cm plates in regular media. Cell populations were sampled on day 5 and day 11 for all SGE experiments. On day 5, half of the cells were pelleted and frozen and the other half passaged. The cells were passaged on day 8 into 15 cm dishes and then harvested on day 11. Negative control transfections were harvested on day 5.

tag: cell line

value: cell line:HAP1

tag: library

value: Day 5 gDNA sample

tag: sample name


title: Elite Controller group5 patient 3

tag: treatment


title: Elite Controller group4 patient 15

source_name: Elite Controller group4 patient


title: Elite Controller group5 patient 1


title: X17_indel_day11

description: amplicon

value: Day 11 gDNA sample


title: Arabidopsis_Li_K

description: G4-seq protocol

source_name: whole organism

value: whole organism


title: BRCA1_WT_Exon23_Rep2_Day5

description: amplicon


title: Arabidopsis_Li_KPDS

description: G4-seq protocol


title: BRCA1_WT_Exon23_Rep2_Day11

description: amplicon


title: HAART patient 2


title: BRCA1_WT_Exon23_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon22_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon23_Rep1_Day11

description: amplicon


title: Elite Controller group4 patient 9


title: Elite Controller group4 patient 14


title: Elite Controller group4 patient 13


title: BRCA1_WT_Exon22_Rep2_Day11

description: amplicon


title: Elite Controller group4 patient 4


title: Elite Controller group4 patient 10


title: BRCA1_WT_Exon22_Rep1_Day11

description: amplicon


title: Elite Controller group4 patient 7


title: BRCA1_WT_Exon22_Rep1_Day5

description: amplicon


title: Elite Controller group4 patient 8


title: Elite Controller group4 patient 6


title: Elite Controller group4 patient 12


title: Elite Controller group4 patient 11


title: Elite Controller group4 patient 2


title: BRCA1_WT_Exon21_Rep3_Day11

description: amplicon


title: BRCA1_WT_Exon20_Rep3_Day5

description: amplicon


title: BRCA1_WT_Exon20_Rep3_Day11

description: amplicon


title: Elite Controller group3 patient 10

source_name: Elite Controller group3 patient


title: BRCA1_WT_Exon20_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon21_Rep4_Day5

description: amplicon


title: BRCA1_WT_Exon21_Rep4_Day11

description: amplicon


title: Elite Controller group4 patient 1


title: BRCA1_WT_Exon20_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon21_Rep3_Day5

description: amplicon


title: BRCA1_WT_Exon19_Rep2_Day5

description: amplicon


title: Elite Controller group3 patient 9


title: Elite Controller group4 patient 3


title: Elite Controller group3 patient 6


title: BRCA1_WT_Exon19_Rep2_Day11

description: amplicon


title: Elite Controller group3 patient 7


title: Elite Controller group3 patient 5


title: Elite Controller group3 patient 8


title: Elite Controller group3 patient 4


title: BRCA1_WT_Exon19_Rep1_Day5

description: amplicon


title: Elite Controller group3 patient 1


title: Elite Controller group3 patient 2


title: BRCA1_WT_Exon18_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon18_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon18_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon18_Rep1_Day11

description: amplicon


title: BRCA1_WT_Exon17_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon17_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon19_Rep1_Day11

description: amplicon


title: BRCA1_WT_Exon17_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon17_Rep1_Day11

description: amplicon


title: BRCA1_WT_Exon17_RepN2_Day5

description: amplicon


title: BRCA1_WT_Exon17_RepN2_Day11

description: amplicon


title: Elite Controller group2 patient 5

source_name: Elite Controller group2 patient


title: Elite Controller group2 patient 6


title: BRCA1_WT_Exon17_RepN1_Day5

description: amplicon


title: BRCA1_WT_Exon17_RepN1_Day11

description: amplicon


title: Elite Controller group2 patient 1


title: BRCA1_Exon17_plasmid_SNV_library2_WT

description: amplicon

source_name: plasmid

value: plasmid

value: library


title: Elite Controller group2 patient 3


title: Elite Controller group2 patient 4


title: Elite Controller group2 patient 8


title: Elite Controller group2 patient 2


title: Elite Controller group1 patient 10

source_name: Elite Controller group1 patient


title: Elite Controller group1 patient 11


title: Elite Controller group1 patient 12


title: Elite Controller group1 patient 7


title: BRCA1_WT_Exon16_Rep2_Day5

description: amplicon


title: Elite Controller group2 patient 7


title: Elite Controller group3 patient 3


title: BRCA1_WT_Exon16_Rep2_Day11

description: amplicon


title: Elite Controller group1 patient 8


title: Elite Controller group1 patient 6


title: Elite Controller group1 patient 13


title: Elite Controller group1 patient 5


title: BRCA1_WT_Exon16_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon16_Rep1_Day11

description: amplicon


title: BRCA1_WT_Exon15_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon15_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon15_Rep3_Day11

description: amplicon


title: BRCA1_WT_Exon15_Rep3_Day5

description: amplicon


title: Elite Controller group1 patient 4


title: Elite Controller group1 patient 9


title: BRCA1_WT_Exon5_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon5_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon5_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon5_Rep1_Day11

description: amplicon


title: BRCA1_WT_Exon4_Rep2_Day5

description: amplicon


title: Elite Controller not in any group patient 1


title: Elite Controller group1 patient 1


title: Elite Controller group1 patient 2


title: BRCA1_WT_Exon4_Rep1_Day5

description: amplicon


title: Elite Controller not in any group patient 2


title: BRCA1_WT_Exon4_Rep1_Day11

description: amplicon


title: Elite Controller group4 patient 5


title: BRCA1_WT_Exon3_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon3_Rep1_Day5

description: amplicon


title: BRCA1_WT_Exon2_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon3_Rep1_Day11

description: amplicon


title: VEC_127

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

description: Primary feto-placental endothelial cells from control vein (VEC)

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing: Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Primary arterial (AEC) and venous endothelial cells (VEC) were isolated from third trimester human placentas after healthy and GDM (dAEC, dVEC) complicated pregnancies following a standard protocol (Lang I et. al,  Differentiation. 76:1031-1043, 2008)

extract_protocol: RNA isolation with TRI REAGENT according to manufacturer

tag: fetal sex

value: female


title: AEC_117

description: Primary feto-placental endothelial cells from control artery (AEC)

value: male


title: VEC_105

value: Primary feto-placental endothelial cells from control vein (VEC)


title: VEC_100

source_name: Primary feto-placental endothelial cells


title: VEC_135


title: AEC_135

value: Primary feto-placental endothelial cells from control artery (AEC)


title: AEC_100


title: VEC_117


title: AEC_105


title: AEC_127


title: AEC_92


title: VEC_98


title: BRCA1_lig4_Exon23_Rep2_Day5_cDNA

description: amplicon

source_name: cell line: HAP1_∆LIG4

value: Day 5 cDNA sample


title: BRCA1_WT_Exon4_Rep2_Day11

description: amplicon


title: AEC_98


title: AEC_97d

description: Primary feto-placental endothelial cells from control artery (dAEC)

value: Primary feto-placental endothelial cells from diabetic artery (AEC)


title: BRCA1_WT_Exon2_Rep2_Day11

description: amplicon


title: VEC_92


title: BRCA1_WT_Exon2_Rep1_Day5

description: amplicon


title: AEC_84f


title: BRCA1_lig4_Exon23_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon23_Rep2_Day5

description: amplicon


title: BRCA1_WT_Exon3_Rep2_Day11

description: amplicon


title: BRCA1_WT_Exon2_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon23_Rep1_Day5

description: amplicon


title: BRCA1_lig4_Exon23_Rep1_Day11

description: amplicon


title: VEC_84f


title: BRCA1_lig4_Exon23_Rep1_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon23_negControl_sgRNA

description: amplicon

value: negative control


title: AEC_24d

description: Primary feto-placental endothelial cells from diabetic artery (dAEC)


title: BRCA1_lig4_Exon22_Rep2_Day5

description: amplicon


title: BRCA1_lig4_Exon22_Rep2_Day5_cDNA

description: amplicon


title: BRCA1_Exon23_plasmid_SNV_library

description: amplicon


title: VEC_25d

description: Primary feto-placental endothelial cells from diabetic vein (dVEC)


title: AEC_23d

value: Primary feto-placental endothelial cells from diabetic artery (dAEC)


title: BRCA1_lig4_Exon22_Rep2_Day11

description: amplicon


title: VEC_21d

value: Primary feto-placental endothelial cells from diabetic vein (dVEC)


title: VEC_22d


title: VEC_23d


title: VEC_20d


title: BRCA1_lig4_Exon22_Rep1_Day5

description: amplicon


title: AEC_20d


title: AEC_16d


title: BRCA1_lig4_Exon22_negControl_sgRNA

description: amplicon


title: BRCA1_lig4_Exon22_Rep1_Day5_cDNA

description: amplicon


title: BRCA1_Exon22_plasmid_SNV_library

description: amplicon


title: AEC_22d


title: VEC_17d


title: VEC_14d


title: BRCA1_lig4_Exon22_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon21_Rep2_Day5

description: amplicon


title: BRCA1_lig4_Exon21_Rep2_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon21_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon21_Rep1_Day5_cDNA

description: amplicon


title: AEC_12d


title: BRCA1_Exon21_plasmid_SNV_library

description: amplicon


title: VEC_11d


title: AEC_11d


title: VEC_9d


title: AEC_18d


title: BRCA1_lig4_Exon21_negControl_sgRNA

description: amplicon


title: AEC_5d


title: BRCA1_lig4_Exon20_Rep2_Day5_cDNA

description: amplicon


title: AEC_2d


title: BRCA1_lig4_Exon21_Rep1_Day5

description: amplicon


title: VEC_1d


title: BRCA1_lig4_Exon20_Rep2_Day5

description: amplicon


title: BRCA1_lig4_Exon21_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon20_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon20_Rep3_Day5_cDNA

description: amplicon


title: Sample 21 - PP rhIL-2 Treated Day 4 - mAdbID:130570

city: Baltimore

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

description: mAdb experiment ID: 130570

hyb_protocol: Affymetrix Hybridization Protocol Other: cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: Affymetrix Scanning Protocol Other: The arrays were scanned by GeneChip Scanner 3000 (Affymetrix, Santa Clara,CA, USA).

data_processing:
Data Processing Protocol
Calculation Method: The global gene expression profiling was analyzed using Partek Genomics Suite (St Louis, MO). RMA (Robust Multiarray Average) normalization was used for intensity calculations.

source_name: PP rhIL-2 Treated Day 4

label_protocol:
Sample Labeling Protocol
Other: RNA quality and quantity was estimated using Nanodrop (Thermo Scientific, Waltham, MA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). First- and second-strands cDNA were synthesized from 10 ng of total RNA by using Nugen Ovation Pico WTA System V2 (Nugen technologies, San Carlos, CA, USA) and following manufacturer's instructions. cDNAs were fragmented and biotinylated by using Nugen Encore Biotin Module (Nugen technologies, San Carlos, CA, USA).

extract_protocol:
miRNeasy Minikit
Other: Total RNA was extracted using miRNeasy minikit (Qiagen, Germantown, MD,USA) according to the manufacture's protocol.

treatment_protocol:
Treatment type: compound
Agent: rhIL-2
Treatment dose: 200 U/mL
Treatment time: 4 days
In-vitro treatment: Peripheral purified NK cells were activated for 4 days in vitro culture with rhIL-2 (200 U/mL; Proleukin; Chiron Corp.).

value: blood

value: Natural Killer (NK) cell

tag: disease state

value: HIV Infection; HIV patients controlling replication after progression and antiretroviral treatment (PP)


title: Sample 19 - PP rhIL-2 Treated Day 4 - mAdbID:130568

description: mAdb experiment ID: 130568


title: BRCA1_lig4_Exon20_Rep3_Day5

description: amplicon

value: Day 5 gDNA sample


title: Sample 22 - PP Untreated Day 0 - mAdbID:130571

description: mAdb experiment ID: 130571

source_name: PP Untreated Day 0


title: BRCA1_lig4_Exon20_Rep3_Day11

description: amplicon

value: Day 11 gDNA sample


title: Sample 15 - PP Untreated Day 0 - mAdbID:130565

description: mAdb experiment ID: 130565


title: Sample 20 - PP Untreated Day 0 - mAdbID:130569

description: mAdb experiment ID: 130569


title: BRCA1_lig4_Exon20_negControl_sgRNA

description: amplicon


title: Sample 16 - PP rhIL-2 Treated Day 4 - mAdbID:130566

description: mAdb experiment ID: 130566


title: BRCA1_lig4_Exon19_Rep2_Day5

description: amplicon


title: Sample 10 - HIC rhIL-2 Treated Day 4 - mAdbID:130562

description: mAdb experiment ID: 130562

source_name: HIC rhIL-2 Treated Day 4

value: HIV Infection; HIV patients controlling replication spontaneously (HIC)


title: BRCA1_lig4_Exon19_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon19_Rep2_Day5_cDNA

description: amplicon


title: Sample 12 - HIC Untreated Day 0 - mAdbID:130563

description: mAdb experiment ID: 130563

source_name: HIC Untreated Day 0


title: BRCA1_lig4_Exon19_Rep1_Day5_cDNA

description: amplicon


title: Sample 7 - HIC rhIL-2 Treated Day 4 - mAdbID:130560

description: mAdb experiment ID: 130560


title: Sample 9 - HIC Untreated Day 0 - mAdbID:130561

description: mAdb experiment ID: 130561


title: BRCA1_lig4_Exon19_Rep1_Day5

description: amplicon


title: Sample 17 - PP Untreated Day 0 - mAdbID:130567

description: mAdb experiment ID: 130567


title: Sample 14 - HIC rhIL-2 Treated Day 4 - mAdbID:130564

description: mAdb experiment ID: 130564


title: Sample 3 - HIC rhIL-2 Treated Day 4 - mAdbID:130558

description: mAdb experiment ID: 130558


title: BRCA1_Exon20_plasmid_SNV_library

description: amplicon

value: plasmid


title: BRCA1_lig4_Exon18_Rep2_Day5

description: amplicon


title: BRCA1_lig4_Exon18_Rep2_Day5_cDNA

description: amplicon


title: HCT116  ABCB5-positive cells

city: Boston

first: Natasha

middle: Y

last: Frank

state: MA

address: 320 Longwood Avenue

department: Medicine

institute: Children's Hospital Boston

description: Gene expression data from  ABCB5-positive HCT116 cells

hyb_protocol: Terminal labeling RNA labeling and hybridization (cat # 702808) was done onto Affymetrix Human Gene 1.0ST arrays.The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain (cat # 900720).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: The CHP files were generated from the CEL files using Affymetrix Expression Console Software.

source_name: HCT116  ABCB5-positive cells

label_protocol: Total RNA was processed using the Ambion WT Expression Kit (cat # 4425209) followed by labeling with Affymetrix GeneChip WT.

growth_protocol: Cells were cultured in RPMI 1640 medium (Lonza Bio-Whittaker) supplemented with 10% (v/v) FBS (Invitrogen GIBCO) and 1% (v/v) penicillin/streptomycin (Lonza Bio-Whittaker).

extract_protocol: Total RNA was isolated using RNAeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: ABCB5-positive cells and ABCB5-negative cell populations were isolated by  FACS cell sorting using anti-ABCB5 mAb described (Ksander et al., Nature, 2014).

value: colon carcinoma


title: BRCA1_lig4_Exon18_Rep1_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon18_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon18_Rep1_Day5

description: amplicon


title: BRCA1_lig4_Exon18_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon19_Rep1_Day11

description: amplicon


title: HCT116  ABCB5-negative cells

description: Gene expression data from  ABCB5-negative HCT116 cells

source_name: HCT116  ABCB5-negative cells


title: BRCA1_Exon18_plasmid_SNV_library

description: amplicon

value: library


title: BRCA1_lig4_Exon19_negControl_sgRNA

description: amplicon


title: Sample 5 - HIC Untreated Day 0 - mAdbID:130559

description: mAdb experiment ID: 130559


title: BRCA1_Exon19_plasmid_SNV_library

description: amplicon


title: BRCA1_lig4_Exon17_Rep2_Day5

description: amplicon


title: SW620  ABCB5-positive cells

description: Gene expression data from  ABCB5-positive SW620 cells

source_name: SW620  ABCB5-positive cells

value: colon carcinoma lymph node metastasis


title: Elite Controller group1 patient 3

value: Elite Controller

value: NO Treatment

value: CD8 T cell


title: Sample 1 - HIC Untreated Day 0 - mAdbID:130557

description: mAdb experiment ID: 130557


title: BRCA1_lig4_Exon17_Rep2_Day11

description: amplicon


title: HT29  ABCB5-positive cells

description: Gene expression data from  ABCB5-positive HT29 cells

source_name: HT29  ABCB5-positive cells

value: colon adenocarcinoma


title: COLO741 ABCB5-negative cells

description: Gene expression data from  ABCB5-negative COLO741 cells

source_name: COLO741  ABCB5-negative cells


title: HT29  ABCB5-negative cells

description: Gene expression data from  ABCB5-negative HT29 cells

source_name: HT29  ABCB5-negative cells


title: COLO741  ABCB5-positive cells

description: Gene expression data from  ABCB5-positive COLO741 cells

source_name: COLO741  ABCB5-positive cells


title: BRCA1_lig4_Exon17_Rep1_Day5_cDNA

description: amplicon

value: Day 5 cDNA sample


title: SW620  ABCB5-negative cells

description: Gene expression data from  ABCB5-negative SW620 cells

source_name: SW620  ABCB5-negative cells


title: BRCA1_lig4_Exon18_negControl_sgRNA

description: amplicon

value: negative control


title: BRCA1_lig4_Exon17_Rep1_Day5

description: amplicon


title: BRCA1_lig4_Exon17_Rep2_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon17_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon17_negControl_sgRNA

description: amplicon


title: BRCA1_Exon17_plasmid_SNV_library

description: amplicon


title: CD44 Low WT_1

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented cRNAs were hybridized to the standard arrays for 17 hours at 45°C, the arrays were then washed and stained using the fluidics station according to genechip array manufacturer's protocol

scan_protocol: The chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was analyzed with RMA/quantile normalization in r v 3.1.3 in bioconductor using the oligo package

source_name: Primary isolate from Lamina Propria_CD44 Low WT

label_protocol: cDNA were prepared according to the Ambion® WT Expression Kit's protocol from 100ng Total RNA. 5.5ug of cDNA were fragmented and labelled according to Affymetrix GeneChip® WT Terminal Labeling and Hybridization kit's protocol.

growth_protocol: Mice were bred in the specific pathogen-free BRC animal facility

extract_protocol: Total RNA was extracted using miRNeasy Mini Kits (Qiagen). RNA Integrity Number (RIN) was assessed by Agilent Bioanalyzer (Agilent Technologies). All RNA samples were RIN≥9.2.

tag: genotype/variation

value: control WT; CD4neg/Cnb1flox

value: Lamina Propria (LP)-colon CD45+CD3+CD4+CD44low cells

tag: cd44 level

value: low


title: CD44 Low WT-2


title: 200598350080_R03C01

type: genomic

city: Atlanta

first: Sarah

middle: Whelan

last: Curtis

state: GA

address: 101 Woodruff Circle NE, Ste 42

institute: Emory University

description: HumanMethylationEPIC BeadChip - standard protocol

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing:
non-normalized, background subtracted
beta-values

label: Cy3, Cy5

source_name: Peripheral Blood

label_protocol: not provided

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

value: Peripheral Blood

value: Female

tag: ln(totalpbb)


title: 200594740075_R08C01

tag: gender


title: BRCA1_lig4_Exon16_Rep2_Day5_cDNA

description: amplicon


title: CD44 Low flox_2A

source_name: Primary isolate from Lamina Propria_CD44 Low flox

value: conditional (CD4cre/Cnb1flox)


title: CD44 Low flox_3A


title: 200598360007_R07C01

value: Male


title: 200598350015_R06C01


title: CD44 Low flox_1


title: ALDH2-overexpression rep1

first: Gang

last: Liu

address: 320 Yueyang Rd, Shanghai

institute: Shanghai Institutes for Biological Sciences

description: ALDH2 over expression

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The raw data were normalized with GeneSpring Software GX 12.6.1 using quartile

source_name: cell line

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: HCC cell line MHCCLM3 were over expressed with ALDH2 and GFP

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity 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).

value: liver


title: ALDH2-overexpression rep2

description: ALDH2 over expression


title: BRCA1_lig4_Exon16_Rep2_Day11

description: amplicon

source_name: cell line: HAP1_∆LIG4

value: Day 11 gDNA sample


title: BRCA1_lig4_Exon16_Rep2_Day5

description: amplicon

value: Day 5 gDNA sample


title: ALDH2-overexpression rep3

description: ALDH2 over expression


title: 200598360005_R03C01


title: GFP-overexpression rep2 (2)

description: GFP over expression


title: GFP-overexpression rep1 (2)

description: GFP over expression


title: 200598350080_R07C01


title: 200550980034_R08C01


title: BRCA1_lig4_Exon16_Rep1_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon16_Rep1_Day5

description: amplicon


title: BRCA1_lig4_Exon16_Rep1_Day11

description: amplicon


title: 200598350080_R05C01


title: BRCA1_lig4_Exon16_negControl_sgRNA

description: amplicon


title: BRCA1_Exon16_plasmid_SNV_library

description: amplicon

source_name: plasmid

value: plasmid

value: library


title: 200598350080_R02C01


title: 200598350076_R03C01


title: 200598350076_R06C01


title: GFP-overexpression rep4

description: GFP over expression


title: BRCA1_lig4_Exon15_Rep2_Day5_cDNA

description: amplicon


title: 200598350031_R07C01


title: 200598350031_R05C01


title: BRCA1_lig4_Exon15_Rep2_Day11

description: amplicon


title: 200598350076_R02C01


title: BRCA1_lig4_Exon15_Rep1_Day5_cDNA

description: amplicon


title: 200598350031_R04C01


title: BRCA1_lig4_Exon15_Rep1_Day5

description: amplicon


title: 200598350031_R02C01


title: 200598350005_R08C01


title: BRCA1_Exon15_plasmid_SNV_library

description: amplicon


title: 200598350005_R03C01


title: BRCA1_lig4_Exon15_negControl_sgRNA

description: amplicon


title: BRCA1_lig4_Exon5_Rep2_Day5_cDNA

description: amplicon


title: 200598350005_R02C01


title: 200598360027_R08C01


title: BRCA1_lig4_Exon5_Rep2_Day5

description: amplicon


title: 200598360027_R07C01


title: BRCA1_lig4_Exon5_Rep1_Day5_cDNA

description: amplicon


title: BRCA1_lig4_Exon5_Rep1_Day5

description: amplicon


title: 200598360027_R06C01


title: BRCA1_lig4_Exon5_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon5_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon15_Rep2_Day5

description: amplicon


title: BRCA1_Exon5_plasmid_SNV_library

description: amplicon


title: 200598360027_R05C01


title: 200598360027_R04C01


title: 200598360027_R03C01


title: BRCA1_lig4_Exon5_negControl_sgRNA

description: amplicon


title: 200598360027_R01C01


title: BRCA1_lig4_Exon4_Rep2_Day5_cDNA

description: amplicon


title: 200598360027_R02C01


title: 200598350005_R06C01


title: BRCA1_lig4_Exon4_Rep2_Day5

description: amplicon


title: 200598360026_R06C01


title: 200598360026_R07C01


title: BRCA1_lig4_Exon4_Rep1_Day5

description: amplicon


title: BRCA1_lig4_Exon4_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon15_Rep1_Day11

description: amplicon


title: BRCA1_lig4_Exon4_Rep1_Day11

description: amplicon


title: 200598360026_R05C01


title: 200598360026_R03C01


title: BRCA1_lig4_Exon4_negControl_sgRNA

description: amplicon


title: BRCA1_Exon4_plasmid_SNV_library

description: amplicon


title: BRCA1_lig4_Exon3_Rep2_Day5_cDNA

description: amplicon


title: 200598360026_R02C01


title: 200598360026_R01C01


title: BRCA1_lig4_Exon3_Rep2_Day5

description: amplicon


title: Sample 24 - PP rhIL-2 Treated Day 4 - mAdbID:130572

description: mAdb experiment ID: 130572

source_name: PP rhIL-2 Treated Day 4

value: blood

value: Natural Killer (NK) cell

value: HIV Infection; HIV patients controlling replication after progression and antiretroviral treatment (PP)


title: BRCA1_lig4_Exon3_Rep2_Day11

description: amplicon


title: 200598360025_R08C01


title: 200598360025_R07C01


title: BRCA1_lig4_Exon3_Rep1_Day5

description: amplicon


title: 200598360026_R08C01


title: 200598360025_R05C01


title: BRCA1_lig4_Exon3_Rep1_Day11

description: amplicon


title: 200598360025_R06C01


title: BRCA1_lig4_Exon3_negControl_sgRNA

description: amplicon


title: BRCA1_lig4_Exon4_Rep1_Day5_cDNA

description: amplicon

value: Day 5 cDNA sample


title: 200598360025_R03C01


title: 200598360025_R04C01


title: BRCA1_lig4_Exon2_Rep2_Day5_cDNA

description: amplicon


title: BRCA1_Exon3_plasmid_SNV_library

description: amplicon


title: BRCA1_lig4_Exon2_Rep2_Day5

description: amplicon


title: 200598360014_R08C01


title: BRCA1_lig4_Exon2_Rep2_Day11

description: amplicon


title: BRCA1_lig4_Exon2_Rep1_Day5_cDNA

description: amplicon


title: 200598360025_R02C01


title: 200598360026_R04C01


title: 200598360014_R06C01


title: 200598360025_R01C01


title: BRCA1_lig4_Exon3_Rep1_Day5_cDNA

description: amplicon


title: 200598360014_R04C01


title: BRCA1_lig4_Exon2_Rep1_Day11

description: amplicon


title: BRCA1_Exon2_plasmid_SNV_library

description: amplicon


title: 200598360014_R05C01


title: BRCA1_lig4_Exon2_Rep1_Day5

description: amplicon


title: 200598360014_R03C01


title: BRCA1_lig4_Exon2_negControl_sgRNA

description: amplicon

value: negative control


title: 200598360014_R01C01


title: 200598360008_R08C01


title: HBECs donor 3, 1186 cells

city: Vilnius

first: Rapolas

last: Zilionis

address: Sauletekis av 7

institute: Vilnius University

description: HBECs donor 3, 1186 cells after all filtering steps

data_processing:
Raw fastq were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):
*_R1_001.fastq.gz   : contains the 3' UTR cDNA read
*_R2_001.fastq.gz   : contains the first half of the cell barcode
*_R3_001.fastq.gz   : contains the library index for demultiplexing libraries
*_R4_001.fastq.gz   : contains the second half of the barcode and the UMI."
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the parameter values specified in the yaml files provided as supplementary material to the published paper (Plasschaert et al.). The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).
For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called ""not_included_in_study_*"" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing."
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, see Supplementary Files 1-3 of the manuscript for details). The reference transcriptome was built using annotations from ENSEMBL (GRCm38 and GRCh37 for mouse and human, respectively). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > N; ii) mitochondrial gene content <M. For mouse samples N = 1500 and M = 20%. For human sample, M = 25%, and  N = 1500,1500, 2000, and 1500 for donors 1-3 and the lentiviral transduction experiment, respectively. In mouse data, cell with strong immune gene expression were also excluded from this study. Counts were normalized as described in methods, and combined into three normalized filtered matrices (genes x cells ): filtered_normalized_counts_mouse.tsv.gz, filtered_normalized_counts_human.tsv.gz, and filtered_normalized_counts_human_viral_transduction.tsv.gz)
genome build: hg19 and mm10
The *.counts.tsv.gz files include raw unique molecular identifier (UMI)-filtered counts for all cell barcodes (prior to filtering). The file filtered_normalized_counts_*.tsv.gz contains filtered normalized counts. The file meta_raw_counts_*.tsv.gz contains meta information for each cell prior to filtering, including raw count file name, cell barcode, and the  index of the cell in the filtered normalized count matrix ('nan' for cells that were filtered out). The file meta_filtered_counts_*.tsv.gz contains meta information about filtered counts, such as library id, mouse id, raw count file name, barcode, and x and y coordinates used for 2-dimensional data representations.

source_name: Air-liquid interface culture of primary Human bronchial epithelial cells (HBECs)

growth_protocol: Primary human bronchial epithelial cells (HBECs) from normal donors aged 3-60 were obtained from Lonza (CC-2540; Donor 1 #221175; Donor 2 #323353; Donor 3 #429581) and were expanded twice with growth medium (500ml of BEGM medium (Lonza, CC-3171), 1 SingleQuots kit (Lonza, CC-4175)) in T75 flasks. After expansion, HBECs were seeded on 12-well Transwell® plates (Corning, 3460) at a density of 83,000 cells/Transwell®. The cells were cultured in differentiation medium (250ml of BEGM medium, 250 ml of DMEM medium (ThermoFisher, 11965092), 1 SingleQuots kit) on both apical and basal sides of transwells for the first 7 days. Then, medium was removed from apical side, and cells were cultured for another two weeks at an air-liquid-interface condition. Cells were used for analysis after culture at ALI for 14 days (14d) and no more than 28d.

extract_protocol:
HBECs were harvested at 15d ALI using 0.05% Trypsin-EDTA (ThermoFisher, 25300054). Cells were then pelleted at 300g for 5 min, resuspended in PBS and filtered through a 20 ?m strainer (PluriSelect, 43-50020-03). Cells were counted on a hemocytometer and Optiprep (Sigma-Aldrich, D1556) was added to achieve a final concentration of 15% and 75,000-100,000 cells/mL.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 10 of this manuscript (Plasschaert et al).

value: bronchial epithelial cells


title: HBECs donor 2, 572 cells

description: HBECs donor 2, 572 cells after all filtering steps


title: 200598360008_R06C01


title: HBECs donor 1, 1212 cells

description: HBECs donor 1, 1212 cells after all filtering steps


title: 200598360008_R07C01


title: HBECs transduced with GFP

description:
(PROCESSED COUNTS ONLY), 9436 cells after all filtering steps
meta_filtered_counts_human_viral_transduction.tsv.gz
filtered_normalized_counts_human_viral_transduction.tsv.gz
meta_raw_counts_human_viral_transduction.tsv.gz

data_processing:
Raw fastq were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):   *_R1_001.fastq.gz   : contains the 3' UTR cDNA read  *_R2_001.fastq.gz   : contains the first half of the cell barcode  *_R3_001.fastq.gz   : contains the library index for demultiplexing libraries  *_R4_001.fastq.gz   : contains the second half of the barcode and the UMI.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the parameter values specified in the yaml files provided as supplementary material to the published paper (Plasschaert et al.). The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, see Supplementary Files 1-3 of the manuscript for details). The reference transcriptome was built using annotations from ENSEMBL (GRCm38 and GRCh37 for mouse and human, respectively). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Subsequent steps are performed using the output of inDrops.py to generate the final normalized counts files provided here. Individual cell barcodes were filtered for: i) total counts > N; ii) mitochondrial gene content <M. For mouse samples N = 1500 and M = 20%. For human sample, M = 25%, and  N = 1500,1500, 2000, and 1500 for donors 1-3 and the lentiviral transduction experiment, respectively. In mouse data, cell with strong immune gene expression were also excluded from this study. Counts were normalized as described in methods, and combined into three normalized filtered matrices (genes x cells ): filtered_normalized_counts_mouse.tsv.gz, filtered_normalized_counts_human.tsv.gz, and filtered_normalized_counts_human_viral_transduction.tsv.gz)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: The *.counts.tsv.gz files include raw unique molecular identifier (UMI)-filtered counts for all cell barcodes (prior to filtering). The file filtered_normalized_counts_*.tsv.gz contains filtered normalized counts. The file meta_raw_counts_*.tsv.gz contains meta information for each cell prior to filtering, including raw count file name, cell barcode, and the  index of the cell in the filtered normalized count matrix ('nan' for cells that were filtered out). The file meta_filtered_counts_*.tsv.gz contains meta information about filtered counts, such as library id, mouse id, raw count file name, barcode, and x and y coordinates used for 2-dimensional data representations.

extract_protocol:
For overexpression, FOXI1 (GeneID 2299) was cloned into the plenti6/V5-DEST.NGFP Gateway® vector, which was generated by transferring the N-EmGFP ORF from pcDNA6.2/N-EmGFP-DEST (ThermoFisher, Cat# V35620) into pLenti6/V5-DEST (ThermoFisher, V49610). Lentiviral packaging was performed in 293T. Packaged virus was added to HBEC cultures 1 hour after cell seeding and then removed at feeding the following day.
HBECs were harvested at 15d ALI using 0.05% Trypsin-EDTA (ThermoFisher, 25300054). Cells were then pelleted at 300g for 5 min, resuspended in PBS and filtered through a 20 μm strainer (PluriSelect, 43-50020-03). Cells were counted on a hemocytometer and Optiprep (Sigma-Aldrich, D1556) was added to achieve a final concentration of 15% and 75,000-100,000 cells/mL.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 10 of this manuscript (Plasschaert et al).

tag: transduced

value: GFP


title: 200598360008_R03C01


title: 200598360008_R01C01


title: HBECs transduced with GFP:FOXI1

description:
(PROCESSED COUNTS ONLY), 10330 cells after all filtering steps
meta_filtered_counts_human_viral_transduction.tsv.gz
filtered_normalized_counts_human_viral_transduction.tsv.gz
meta_raw_counts_human_viral_transduction.tsv.gz


title: 200598360008_R04C01


title: 200598360007_R08C01


title: 200598360014_R07C01


title: 200598360007_R06C01


title: 200598360007_R05C01


title: 200598360007_R03C01


title: 200598360007_R04C01


title: 200598360014_R02C01


title: 200598360007_R02C01


title: 200598360007_R01C01


title: 200598360006_R08C01


title: 200598360006_R07C01


title: 200598360006_R06C01


title: 200598360008_R05C01


title: 200598360006_R05C01


title: 200598360006_R03C01


title: 200598360006_R04C01


title: 200598350027_R03C01


title: 200598360006_R01C01


title: 200598360005_R06C01


title: 200598360005_R07C01


title: 200598360005_R08C01


title: 200598360005_R05C01


title: Peyer's Patches of C3H/Hej mouse, male OVA 5

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Peyer's Patches of male OVA-indeced allergic mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Six-week old male and female C3H/Hej mice were gavaged with OVA or normal saline for 28 consecutive days.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Mice of treatment groups were gavaged with OVA at 40 mg/kg body weight per day  for 28 consecutive days. The control groups were treated with the solvent vehicle (normal saline).

value: male

value: Peyer's Patches

tag: sample type

value: OVA-induced allergic mouse


title: 200598360005_R02C01

value: Peripheral Blood

value: Female


title: 200598360005_R01C01

value: Male


title: MCF10A_ERAS

city: Madrid

first: Manuel

last: Navarro

address: Av. Complutense 40

department: Molecular Oncology

country: Spain

institute: CIEMAT

hyb_protocol: Standard Affymetrix protocol performed at the Cancer Research Center, Salamanca, Spain

data_processing:
Data were normalized using Expression Profiler (Affymetrix) and differential expression was tested using TAC (Affymetrix)
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

source_name: cultured cells, ERAS expressing

growth_protocol: MCF10A cells grown according to ATCC conditions

extract_protocol: Trizol followed by Qiagen RNeasy column

treatment_protocol: Cells cultured at 90% confluence, no treatment

tag: genotype

value: ERAS-expressing


title: Peyer's Patches of C3H/Hej mouse, male OVA 8


title: 200598360005_R04C01


title: Peyer's Patches of C3H/Hej mouse, male OVA 1


title: Peyer's Patches of C3H/Hej mouse, male OVA 13


title: MCF10A_WT

scan_protocol: Standard Affymetrix protocol performed at the Cancer Research Center, Salamanca, Spain

source_name: cultured cells, wt

value: wild type


title: Peyer's Patches of C3H/Hej mouse, female OVA 12

source_name: Peyer's Patches of female OVA-indeced allergic mouse

value: female


title: Peyer's Patches of C3H/Hej mouse, male control 8

source_name: Peyer's Patches of male control

value: control


title: 200598360004_R08C01


title: primary chondrocytes in culture, day 15

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

hyb_protocol: GeneChip arrays were hybridized overnight in the Affymetrix hybridization oven at 42oC. Washing and scanning was performed using the Affymetrix GeneChip Fluidics Station 450.

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

source_name: primary rib chondrocytes E18.5 after 15 days in culture

label_protocol: Biotin-labeled samples were generated using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay.

growth_protocol: Cells were plated on 35mm dishes coated with 0.1% gelatin at a final concentration of 1 X 106 cells/well in DMEM/F12, high glucose, 10% fetal bovine serum and 1% pen/strep antibiotic. The media was supplemented with 50mg/ml Ascorbic acid, 10mM b-glycerolphosphate. Media was changed every other day.

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

treatment_protocol: Rib cages were dissected from E18.5 embryos and washed in PBS. Cells were dissociated by enzymatic digestion with 0.25% Collagenase and 0.25% Trypsin/EDTA for 1h at 37oC. The rib cages were washed, and fresh 0.25% Collagenase in PBS was added for 1h at 37oC. Enzymatic reaction was stopped by adding an equal volume of tissue culture medium containing 10% FCS. The cells were filtered through a 70 micrometer cell strainer and pelleted (1200rpm for 5min). Pellets were washed with PBS, cells were counted and adjusted for desired cell density.  After 2, 6, 9, 12, 15 days of culture cells were scraped in 0.5ml of Trizol reagent.

tag: strain

value: FVB

tag: days in culture

value: 15 days


title: primary chondrocytes in culture, day 9

source_name: primary rib chondrocytes E18.5 after 9 days in culture

tag: age

value: 9 days


title: 200598360004_R07C01

tag: tissue


title: primary chondrocytes in culture, day 12

source_name: primary rib chondrocytes E18.5 after 12 days in culture

value: 12 days


title: primary chondrocytes in culture, day 6

source_name: primary rib chondrocytes E18.5 after 6 days in culture

value: 6 days


title: primary chondrocytes in culture, day 2

source_name: primary rib chondrocytes E18.5 after 2 days in culture

value: 2 days


title: Peyer's Patches of C3H/Hej mouse, female control 7

source_name: Peyer's Patches of female control


title: 200598360004_R04C01

source_name: Peripheral Blood


title: 200598360004_R05C01


title: 200598360004_R03C01


title: 200598360004_R02C01


title: 200598360004_R01C01


title: 200598360003_R08C01


title: 200598360003_R07C01


title: AxD.1161

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
14598_AxD-1161_GTCCGC_L999
RNA-Seq data, Sample AxD.1161, from juvenile NIH Neurobiobank post-mortem brain tissue, with AxD status

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq 1.8 software was used for base calling (for samples split between flowcells and later merged per run)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse"
Genome_build: hg19
Supplementary_files_format_and_content: Read counts (calculated using htseq-count).

source_name: Sample AxD.1161, NIH Neurobiobank post-mortem brain tissue, with AxD status

growth_protocol: For brain tissue, AxD status was determined by clinical observation. Astrocytes were maintained using DMEM/F12 medium supplemented with 1X N2, 1X B27, 10ng/ml EGF, and 10 ng/ml FGF, and were matured for 5-7 days by 10ng/ml CNTF treatment before RNA extraction. The AxD GFAP status was defined by genomic DNA sequencing of the GFAP gene.

extract_protocol:
Astrocytes: RecoverAll Total Nucleic Acid Isolation kit, with added RNase inhibitor  Tissue: Ambion Trizol kit
KAPA stranded mRNA kit

treatment_protocol: For iPSC-induced astroctyes, AxD mutant GFAP was determined by genomic DNA sequencing of the GFAP gene. GFAP+ sorted astrocytes were used for RNA-Seq analsyis.

tag: subject status

value: Alexander disease (AxD) patient

tag: axd status

value: with AxD status

tag: tissue/cell type

value: post-mortem brain tissue

tag: batch

value: Batch 1


title: WT.4907

description:
14595_WT-4907_AGTTCC_L999
RNA-Seq data, Sample WT.4907, from juvenile NIH Neurobiobank post-mortem brain tissue, with WT status

source_name: Sample WT.4907,  NIH Neurobiobank post-mortem brain tissue, without AxD status

value: healthy control

value: without AxD status


title: AxD.885

description:
14597_AxD-885_CCGTCC_L999
RNA-Seq data, Sample AxD.885, from juvenile NIH Neurobiobank post-mortem brain tissue, with AxD status

source_name: Sample AxD.885, NIH Neurobiobank post-mortem brain tissue, with AxD status


title: WT.1671

description:
14594_WT-1671_AGTCAA_L999
RNA-Seq data, Sample WT.1671, from juvenile NIH Neurobiobank post-mortem brain tissue, with WT status

source_name: Sample WT.1671, NIH Neurobiobank post-mortem brain tissue, without AxD status


title: WT.4321

description:
14600_WT-4321_GTGGCC_L999
RNA-Seq data, Sample WT.4321, from juvenile NIH Neurobiobank post-mortem brain tissue, with WT status

source_name: Sample WT.4321, NIH Neurobiobank post-mortem brain tissue, without AxD status


title: 200598360003_R03C01

value: Peripheral Blood

value: Male


title: AxD.5488

description:
14596_AxD-5488_ATGTCA_L999
RNA-Seq data, Sample AxD.5488, from juvenile NIH Neurobiobank post-mortem brain tissue, with AxD status

source_name: Sample AxD.5488, NIH Neurobiobank post-mortem brain tissue, with AxD status


title: 200598360003_R06C01


title: AxD.1070

description:
14593_AxD-1070_CTTGTA_L999
RNA-Seq data, Sample AxD.1070, from juvenile NIH Neurobiobank post-mortem brain tissue, with AxD status

source_name: Sample AxD.1070, NIH Neurobiobank post-mortem brain tissue, with AxD status


title: 200598360003_R05C01

value: Female


title: 200598360003_R04C01


title: 200598360003_R02C01


title: Peyer's Patches of C3H/Hej mouse, female OVA 2

value: female

value: Peyer's Patches

value: OVA-induced allergic mouse


title: 200598360002_R08C01


title: AxD.1482

description:
14599_AxD-1482_TGACCA_L999
RNA-Seq data, Sample AxD.1482, from juvenile NIH Neurobiobank post-mortem brain tissue, with AxD status

source_name: Sample AxD.1482, NIH Neurobiobank post-mortem brain tissue, with AxD status

value: Batch 2


title: 200598360003_R01C01


title: 200598360002_R07C01


title: AxD997.AS

description:
14592_AxD997-AS_GGCTAC_L999
RNA-Seq data, Sample AxD997.AS, from Astrocyte from induced pluripotent stem cell, with AxD status

source_name: Sample AxD997.AS, astrocyte derived from AxD patient iPSCs, with AxD mutant GFAP

value: AxD mutant GFAP

value: iPSC-derived astrocytes


title: C3.AS

description:
14591_C3-AS_TAGCTT_L999
RNA-Seq data, Sample C3.AS, from Astrocyte from induced pluripotent stem cell, with WT status

source_name: Sample C3.AS, astrocytes derived from healthy control iPSCs, with WT GFAP

value: WT GFAP


title: 200598360002_R06C01


title: 200598360002_R04C01


title: AxD999.AS

description:
14590_AxD999-AS_GATCAG_L999
RNA-Seq data, Sample AxD999.AS, from Astrocyte from induced pluripotent stem cell, with AxD status

source_name: Sample AxD999.AS, astrocyte derived from AxD patient iPSCs, with AxD mutant GFAP


title: 200598360002_R03C01

description: HumanMethylationEPIC BeadChip - standard protocol


title: I90.AS

description:
14589_I90-AS_ACTTGA_L999
RNA-Seq data, Sample I90.AS, from Astrocyte from induced pluripotent stem cell, with WT status

source_name: Sample I90.AS, astrocytes derived from healthy control iPSCs, with WT GFAP


title: 200598360002_R02C01


title: 200598360001_R07C01


title: 200598360001_R06C01


title: 200598360001_R05C01


title: 200598360001_R04C01


title: 200598360001_R03C01