title: Ricky.NLE

data_processing:
Library strategy: WGS
All gibbon genomic shot-gun data were aligned to the gibbon genome reference (Nleu3.0) using BWA
MELT v2.1.3 was used to predict de novo LAVA insertions and deletions (indels) from each of the 23 whole genome shot-gun alignments
We characterized all LAVA inserts based on information such as genomic location, length, and insertion position relative to closest gene [intergenic, exonic, intronic, promoter (<3Kb upstream of gene) or terminator (<3Kb downstream of gene)]
The initial set of LAVA predictions was next filtered to remove: 1) low quality inserts, as assessed by MELT, 2) single copy inserts in the population, 3) inserts shorter than 290bp (the minimum length required to discriminate a composite LAVA from its non-SVA subunits), and 4) inserts found on unplaced Nleu3.0 contigs.
We generated binary LAVA genotype profiles for all gibbon individuals (heterozygous or homozygous LAVA insertion=1, homozygous absence of LAVA= 0)
Genome_build: Nleu3.0
Supplementary_files_format_and_content: an excel spreadsheet containing position, genomic and genotype information for all LAVA insertions across 23 gibbons

source_name: blood

extract_protocol:
Total gDNA was extracted from blood of gibbons and randomly sheared
sheared gDNA was used to generate illumina libraries using the NEBNext Ultra II library contruction kit (NEB)

value: blood


title: Vok.NLE (RNA-Seq)

status: Public on Jul 20 2020

type: SRA

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

country: USA

institute: Oregon Health and Science University

library_source: transcriptomic

data_processing:
Reads were trimmed with Trimmomatic (Bolger et al. 2014)
Trimmed reads were aligned to Nleu3.0 using STAR (Dobin et al. 2013)
We counted high-quality uniquely mapping reads (MAPQ>25) aligning to each gene
We used edgeR (Robinson et al. 2010) to remove genes for which fewer than two individuals had >0.5 read counts per million (CPM)
We used the Conditional Quantile Normalization package (CQN; Hansen et al, 2012) to normalize gene counts based on gene length, GC content and RNA-seq library size
The normalized read counts were regularized log (rlog) transformed using DEseq2 (Love et al. 2014) to stabilize the variance
Lastly, genes located on unassembled contigs in the genome were excluded
Genome_build: Nleu3.0
Supplementary_files_format_and_content: A table in txt format with the normalized gene counts for each individual

molecule: total RNA

organism: Nomascus leucogenys

source_name: EBV-transformed lymphocyte cell line

extract_protocol:
Total RNA was extracted from EBV-transformed lymphocyte cell lines using the RNeasy Mini kit (Qiagen) and RNA integrity scores were assessed on the Bioanalyzer with the RNA 6000 Pico kit (Agilent Genomics)
RNA libraries were prepared for sequencing using the illumina Truseq kit protocol

tag: cell type

value: EBV-transformed lymphocyte cell line


title: D3

city: Hong Kong

first: Qian

last: Yu

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: Hong Kong University

data_processing:
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAIL- ING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the rat reference genome m6 with HISAT2. HTSeq vret0. 6.0 was used to count the reads numbers mapped to each gene.
The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression using a protocol from Mortazavi A et al., Nat Methods, 2008
The statistically significant different expression genes were obtained by an adjusted P-value threshold of <0.05 and |log2(fold change)| > 1 using the DEGseq software.
Genome_build: m6
Supplementary_files_format_and_content: counts, RPKM

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was isolated from the liver using Trizol (Invitrogen).RNA was purified by the removal of ribosomal RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and then subjected to cDNA synthesis followed by adaptor ligation and enrichment according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and paired-end sequenced (PE150, Sequencing reads were 150 bp) using IlluminaHiSeq 3000 platform. The clean reads were aligned to the rat reference genome using HISAT2 and then converted into read counts for each gene model by HTSeq. DEseq was applied to assess the differential expression using read counts as input.

tag: strain

value: Sprague Dawley

tag: tissue

value: liver

tag: treatment

value: Control+SAMC co-administration


title: wt_rep1

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

data_processing:
Raw reads where trimmed (first 10 nucleotides) with FASTX-Toolkit
Adapters were removed using Trimmomatic
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
StringTie and prepDE.py script was used to create gene_count_matrix with count reads
TAIR10
Gene raw counts matrix

organism: Arabidopsis thaliana

source_name: aerial tIssue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 20°C

extract_protocol:
Leaves of 4 weeks old Arabidopsis plants were harvested then flash frozen in Liquid Nitrogen. RNA was isolated using Trizol and Direct-zol RNA Kit from Zymo Research. rRNA from samples was removed with RiboMinus Plant
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

tag: ecotype background

tag: genotype/variation

value: wild-type (WT)


title: RNA fraction from hen2-2 mutant plants rep2

data_processing:
Raw reads where trimmed (first 12 nucleotides) with FASTX-Toolki
Adapters were removed using Trimmomatic
rRNA sequences where removed with Bowtie
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
Transcript-level abundance for RNA clean reads where estimated using Salmon. Multifasta file with Arabidopsis thaliana reference transcripts (cdna and ncrna) for quasi-mapping was additionally supplemented with pri-miRNA transcirpts described in mirEX2 database.
Genome_build: TAIR10
Supplementary_files_format_and_content: transcript abundance, output format from Salmon software .sf extension

source_name: hen2-2 mutant plants_aerial tissue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C

extract_protocol:
Leaves of 4 weeks old Arabidopsis plants were harvested then flash frozen in Liquid Nitrogen. RNA was isolated using Trizol and Direct-zol RNA Kit from Zymo Research. rRNA from samples was removed with RiboMinus Plant Kit for RNA-seq (Thermo Fisher Scientific)
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

tag: age

value: 4 weeks

value: aerial tussue


title: RNAPII-Ser2Phos_EV_1_SetA

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
ChIP-seq (anti Ser2 Phosphorylated RNAPII) performed on A375 cells expressing empty vector. Replicate 1 of 2.
RNAPII_Ser2Phos_EV.bigWig

library_source: genomic

data_processing:
Base Calling. Basecalling, quality scoring and de-multiplexing was performed directly using the NextSeq 550 software (RTAv2). Alignment. For each de-multiplexed sample, multiple fastq files were merged using the ‘cat’ function (four raw files per sample). Merged files were aligned to the human genome (GRCh38 build) using bowtie2 v2.2.6 for single end sequence data (default options) to generate .SAM files. Aligned read data was processed using HOMER v4.8. Using the HOMER suite of tools, SAM files were converted into tag directories and multi-mapping reads were removed using makeTagDirectory -unique -fragLength 150. Mapped regions which, due to fragment processing, extended beyond the end of the chromosomes were removed using removeOutOfBoundsReads.pl with chromosome lengths for GRCh38.  Replicate data, was combined at this stage and genome browser files (.bw) were generated using makeUCSCfile with the following options: -bigWig -fsize 1e20 -strand both -norm 10e7. Supplementary files format and content. Processed files are in bigwig format representing mapped tag densities across the mappable portion of the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition).  .bigWig files are in an indexed binary format.

molecule: genomic DNA

organism: Homo sapiens

source_name: Cultured A375 melanoma cells

growth_protocol: A375 cells (ATCC) were cultured in DMEM media supplemented with 2 mM L-glutamine (Life Technologies) and 10% fetal calf serum (Life Technologies) and grown at 37°C in a 5% CO2 humidified incubator. The HA-tagged PRL3 plasmid (Addgene) was linearized and transfected with Attractene transfection reagent according to manufacturer's instructions (Qiagen). Targeted A375 cells were maintained in hygromycin containing media at concentration of 100 μg/ml.

extract_protocol:
Empty vector and PRL3 stable overexpressing cells were cultured to 80% confluency and harvested by dissociation with trypsin in PBS/EDTA. Cells were resuspended in PBS and immediately fixed in 1% formaldehyde in PBS for 10 minutes at room temperature. The fixation was neutralised by the addition of glycine and incubated for an additional 5 minutes. The cells were washed in cold PBS. Cell pellets were resuspended in 150 µl cold lysis buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH8.1, 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT) and supplemented with 1350 µl 1% Triton X IP dilution buffer (1% Triton X, 20mM Tris-HCl pH8.1, 150mM NaCl, 2mM EDTA, 1x protease inhibitor cocktail (Roche), 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT and 1mM PMSF) and incubated on ice for 10 min. Lysed cells were sonicated on ice for 5x30 seconds with a probe sonicator followed by 50-60 cycles (30 sec on / 30 sec off) in a chilled bioruptor (Diagenode) to yield chromatin fragments ranging between 200 – 800 bp in length. For MITF ChIP, lysed cells were sonicated in a chilled SoniPrep150 probe sonicator for 15x30 seconds with a 30 seconds gap between burst. Sheared chromatin was centrifuged at max speed for 10 minutes at 4°C and the soluble supernatant transferred to new tubes. 500 ml chromatin samples were supplemented with 5 ml (5mg/ml) BSA. 10% of the input was stored and the rest was used for the immunoprecipitation. Anti-DDX21 (Proteintech; cat no. 10528-1-AP), RNA-POLII tot, RNA-POLII PS2, PS5 (Novus Biologicals) and MITF (Atlas Antibodies) were pre-bound to proteinG dynabeads (ThermoFisher) in 10% w/v BSA in PBS according to the manufacturer’s instructions (Life Technologies) for approximately 1 h at 4°C with rotation following which free antibody was removed with 3 washes of cold 10% w/v BSA in PBS. Chromatin and proteinG beads were combined and incubated over night at 4°C (at a ratio of 500 ng of bead bound antibody per 1M cell equivalents of chromatin). Samples were washes at 4°C with rortation through the following series: 2 times in 1% Triton X IP dilution buffer, 2 times with ChIP wash A (50mM Hepes ph7.9, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS. 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT) and 2 times with ChIP wash B (20mM Tris pH 8.0, 1mM EDTA, 250mM LiCl, 1% NP-40, 0.1% Na-deoxycholate, 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT). Finally, the samples were washed with TE (1mM EDTA ,10mM Tris pH8.0). The samples were resuspended in TE and supplemented with preheated 37°C Extraction buffer (0.1M NaHCO3 and 1%SDS), vortexed and incubated for 15 minutes at 37°C on a vibrating platform. The pH of the extracted chromatin was adjusted by adding 6ml 2M Tris-HCl pH6.8 following which both the ChIP and input samples were incubated with 20mg RNAseA at 65°C for 1 hour. Cross-links were reversed and the protein degraded by the addition of 20mg Proteinase K and incubation at 65°C for 6-8 h. Following removal of the dynabeads from the ChIP samples, DNA was purified using a Qiagen PCR cleanup kit following manufacturer’s instructions.
DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) following manufacturer’s instructions.

tag: cell line

value: A375 cells expressing empty vector

tag: antibody

value: anti-RNA-POLII PS2  (Novus Biologicals cat no. C15200005-50)


title: RNAPII-Ser2Phos_EV_2_SetA

description:
ChIP-seq (anti Ser2 Phosphorylated RNAPII) performed on A375 cells expressing empty vector. Replicate 2 of 2.
RNAPII_Ser2Phos_EV.bigWig


title: Vok.NLE.H3K4me3

data_processing:
All reads were aligned to Nleu3.0 using BWA with default single-end settings, and low-quality and multi-mapping read alignments (MAPQ<30) were removed
The Pearson correlation of ChIP-seq signal across biological replicates and histone marks was calculated using deepTools
ChromHMM tool (21) was used to identify and characterize 9 chromatin states based on the histone ChIP-seq alignments
Genome_build: Nleu3.0
Supplementary_files_format_and_content: a bedgraph containing genome-wide chromatin state annotations

extract_protocol:
We fixed 5x106 cells per ChIP assay, with 1% formaldehyde for 5min on ice and then quenched fixation by adding glycine to a final concentration of 0.1M. After washing the cells twice with cold 1X PBS, we lysed the fixed cells at a concentration of 3x106cells/100ul in Lysis buffer (0.1% SDS, 0.5% Triton X-100, 20mM Tris-HCl pH=8.0, 150mM NaCl, 1x Proteinase inhibitor (Roche)) for 5min on ice. Using the Bioruptor Pico sonicator (Diagenode), we sheared lysates in 1.5mL tubes with 7 cycles (30sec on/off). We spun the sonicated lysates at max speed for 10min at 4°C to remove cell debris and then rotated them for 2hr at 4°C with 20ul ChIP-grade Protein A/G Magnetic Beads (Pierce) to preclear the lysate. From each chromatin preparation, we set aside a 1% volume aliquot as chromatin input, and the rest we divided equally into each histone mark ChIP reactions. We diluted the reactions to 1.6x106cells/100ul with Lysis buffer and then added the corresponding antibodies in the following amounts: 2ug H3K4me1 (ab8895, Abcam), 1ug H3K4me3 (ab8580, Abcam), 1ug H3K27ac (ab4729, Abcam), 2ug H3K27me3 (39155, Active Motif) and 2ug H3K9me3 (ab9263, Abcam), and let reactions rotate overnight at 4°C. Next, we added 20ul Pierce ChIP-grade Protein A/G Magnetic Beads (Pierce) and let samples rotate for 2hrs at 4°C. We then washed the beads consecutively (rotating at 4°C) with TBST buffer (3 times for 15min), Lysis buffer (once for 1hr), 1xTE pH=8 (once for 1hr, then once for 10min). Following washes, we eluted chromatin in 250ul fresh Elution buffer (1% SDS, 0.1M NaHCO3). We incubated the ChIP and input samples overnight at 65°C in presence of NaCl to reverse crosslinks and then digested them consecutively with 8ug RNAse A (30 minutes at 37°C) and 80ug Proteinase K (2 hour at 55°C). Lastly, we purified the samples using traditional phenol:chloroform extraction and ethanol precipitation. We quantified all samples using the Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific).
All sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) for 1-5ng of starting material and without size selection. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: anti-H3K4me3, (ab8580, Abcam)


title: D2


title: Vok.NLE.input-2


title: RNA fraction from hen2-2 mutant plants rep1


title: Asterisks.NLE


title: D1


title: Asia.NLE.H3K4me3


title: RNAPII-Ser2Phos_PRL3_2_SetA

description:
ChIP-seq (anti Ser2 Phosphorylated RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.
RNAPII_Ser2Phos_PRL3.bigWig

value: A375 cells expressing HA-tagged PRL3


title: Vok.NLE


title: A3

value: Control group (normal diet)


title: Nancy.NLE


title: NGP_ctrl_input_for_ARID1A

city: Hangzhou

first: Ting

last: Tao

state: Zhejiang

address: 3333 Binsheng Road

country: China

institute: Children's Hospital, Zhejiang University School of Medicine

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.9 with configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19 -U. For ARID1A and its corresponding input ChIP-Seq, configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19  was used.
Data were filtered using SAMtools version 1.3.1 with configuration samtools view -bS -q 20
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files represent counts of aligned reads within 20 bp bins with each read being extended 75 (50 for ARID1A and its corresponding input ChIP-Seq) in the direction of alignment. Counts are in reads-per-million.

source_name: Neuroblastoma

growth_protocol: The NGP neuroblastoma cell line was maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO),and 0.5ug/ml puromycin (Sigma #P8833).

extract_protocol:
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: NGP

tag: genotype

value: control

tag: chip antiboy


title: Phyllis.NLE


title: Asia.NLE.input-2


title: A2


title: RNAPII-Ser5Phos_EV_2_SetA

description:
ChIP-seq (anti Ser5 Phosphorylated RNAPII) performed on A375 cells expressing empty vector. Replicate 2 of 2.
RNAPII_Ser5Phos_EV.bigWig

value: anti-RNA-POLII PS5  (Novus Biologicals cat no. C15200007-50)


title: RNAPII-Ser5Phos_PRL3_1_SetA

description:
ChIP-seq (anti Ser5 Phosphorylated RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.
RNAPII_Ser5Phos_PRL3.bigWig


title: NGP_ctrl_ARID1A

value: ARID1A (EMD Millipore, #04-080)


title: Honey.HLA

organism: Hylobates lar

value: blood


title: RNAPII-Ser5Phos_PRL3_2_SetA

description:
ChIP-seq (anti Ser5 Phosphorylated RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.
RNAPII_Ser5Phos_PRL3.bigWig


title: China.NLE


title: RNAPII-Ser2Phos_PRL3_1_SetA

description:
ChIP-seq (anti Ser2 Phosphorylated RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.
RNAPII_Ser2Phos_PRL3.bigWig


title: RNAPII-Ser5Phos_EV_1_SetA

description:
ChIP-seq (anti Ser5 Phosphorylated RNAPII) performed on A375 cells expressing empty vector. Replicate 1 of 2.
RNAPII_Ser5Phos_EV.bigWig


title: Flox

status: Public on Jul 19 2020

city: Göttingen

first: Franziska

middle: Sophie

last: Rathjens

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University Medical Centre Göttingen

data_processing:
cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; 51 cycles with single indexing; 6 GB ca. 30- 35 million reads per sample).
Sequence reads were aligned to the mouse reference assembly (UCSC version mm9) using Bowtie 2.0
For each gene, the number of mapped reads was counted using htseqcount and DESeq2 was used to analyze the differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Excel file contains the output from DESeq2: variance stabilized counts of the raw data (normalization).

organism: Mus musculus

source_name: Cardiac ventricles

growth_protocol: mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
RNA was isolated from mice cardiac tissue using NucleoSpin RNA kit from Macherey-Nagel (Cat no: 740955.10). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12 weeks-old adult mice were administered with TX 30mg/Kg/day for 3 days and were sacrificed 4 weeks-post induction

tag: strain background

value: 16 weeks

value: Cardiac ventricles


title: vTBX5KO

value: Myh6-MerCreMer, Tbx5LDN/LDN


title: A1

value: Sprague Dawley

value: liver


title: 4T1_CD95ko2

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
We used the first end of the sequencing reads for the analyses. The raw reads were filtered to remove low-quality reads using FASTQ Quality Filter from FASTX-Toolkit v0.0.14 (RRID:SCR_005534). High-quality reads were then mapped to the mouse reference genome (mm10) using STAR v2.6.0 (RRID:SCR_015899). The transcriptomic BAM file was used to quantify gene expression using RSEM v1.3.0 (RRID:SCR_013027).
Genome_build: mm10
Supplementary_files_format_and_content: RSEM calculated gene expression values

source_name: 4T1 cell line

growth_protocol: The mouse 4T1 breast cancer cell line was purchased from the ATCC and cultured in RPMI 1640 medium (Mediatech Inc) containing 10% heat-inactivated fetal bovine serum (FBS) (Sigma-Aldrich), 1% L-glutamine (Mediatech Inc) and 1% penicillin/streptomycin (Mediatech Inc).

extract_protocol:
Total RNAs from Ctr, vCas9, FAS54, and FAS69 cells were extracted using TRIzol (Life Technology, 15596018).
mRNAs were enriched using Oligo d(T)25 Magnetic Beads (NEB S1419S) following manufacturer’s protocol. mRNAs were then fragmented at 94 °C in 10mM MgCl2 buffer. Fragmented RNAs were end-repaired by T4 PNK (NEB M0201S) and Poly(A)-tailed by  E. coli Poly(A) Polymerase (NEB M0276S). The poly(A) tailed RNA fragments were reverse transcribed to cDNA using custom-designed oligo(dT) and locked nucleic acid (LNA) based on SMART-seq2 method (Picelly et al. Nature Protocols, 2014). The cDNAs were then PCR amplified using KAPA HiFi HotStart master mix (KK2601). 200-400 bp fragments of the library were cut from gels for Illumina Hiseq sequencing.

treatment_protocol: In order to generate CD95 k.o. 4T1 clones, first stably expressing lentiCas9-Blast-4T1 cell (vCas9-4T1) lines were established. The lentiCas9-Blast virus was obtained from the viral core facility of Northwestern University. 4T1 cells (105/well) were plated in 6 well plates and on the next day cells were infected with the indicated lentiCas9-Blast virus supernatants with polybrene (final concentration: 8 μg/ml). Culture supernatants were replaced with fresh medium containing antibiotics 48 hours after transduction.  Uninfected cells were eliminated by a selection medium RPM1-1640 including 4 g/ml Blasticidin. The two guide RNAs for exon 9 deletion of CD95 gene GCCGGGTTCACATCTGCGCTAGG and CTTGAGGAATCTGATGACCGTGG were designed using the CRISPR design tool available at crispr.mit.edu. The 19-20nt crisprRNA (crRNA) complementary to the target of interest and 67nt transactivating crRNA (tracrRNA), which served as a bridge between the cas9 protein and the crRNA, were ordered from IDT. vCas9-4T1 cells were transfected with crRNA and tracrRNA according the manufactures protocol using TransIT-X2 transfecting reagent (Mirus) in 12 well plates. 3 days after transfection cells were subjected to cell sorting at 1 cell per well directly into 96-well plates. After two to three weeks, single cell clones were expanded and subjected to genotyping and single cell cloning. Deletions in clones were verified by genomic PCR using external and internal primers pairs.

value: Breast cancer cell line


title: 4T1_Ctrl1


title: 4T1_Ctrl2


title: 4T1_CD95ko1


title: Healthy Control Blood Donor BD107704

type: RNA

city: Scottsdale

first: Sangkon

last: Oh

state: AZ

address: 13400 east Shea street

department: immunology

institute: Mayo Clinic

description:
raw data file:
Non-normalized_data_3.txt
BD107704

hyb_protocol: Amplified and labeled RNA was hybridized overnight to beadchips following standard Illumina protocol

scan_protocol: Scanned on Illumina HiScan following standard Illumina protocol

data_processing: Each sample was background subtracted and scaled to the average of all samples. Raw values less than 10 were set to 10 and the data was log2 transformed. Probes were then filtered to select transcripts that were present in at least one sample (PALO) using an alpha of 0.01 for the signal detection, thus eliminating background. The probes were then additionally filtered by removing probes with the lowest variability using a standard deviation of less than 0.344.

label: biotin

source_name: Whole blood

label_protocol: 1500ng of RNA from each sample that passed quality control was amplified and labled using Illumina TotalPrep RNA Amplification kit following manufacturer's protocol

extract_protocol: Total RNA was isolated utilizing MagMax Nucleic Acid Isolation kit (Ambion) according to manufacturer's protocol. Globin mRNA was removed with using Globin Clear kit (Ambion).

value: Whole blood

tag: diagnosis

value: healthy control

tag: Sex

value: Male


title: Healthy Control Blood Donor BD158304

description:
raw data file:
Non-normalized_data_2.txt
BD158304

value: Female


title: Healthy Control Blood Donor BD106485

description:
raw data file:
Non-normalized_data_2.txt
BD106485


title: Healthy Control Blood Donor BD106691 Replicate 2

description:
raw data file:
Non-normalized_data_2.txt
BD106691-2


title: Healthy Control Blood Donor BD106691 Replicate 1

description:
raw data file:
Non-normalized_data_2.txt
BD106691-1


title: Healthy Control Blood Donor BD155612 Replicate 2

description:
raw data file:
Non-normalized_data_3.txt
BD155612-2


title: Healthy Control Blood Donor BD110992 Replicate 2

description:
raw data file:
Non-normalized_data_2.txt
BD110992-2


title: Healthy Control Blood Donor BD105933 Replicate 2

description:
raw data file:
Non-normalized_data_3.txt
BD105933-2


title: Healthy Control Blood Donor BD158224

description:
raw data file:
Non-normalized_data_3.txt
BD158224


title: Healthy Control Blood Donor BD155612 Replicate 1

description:
raw data file:
Non-normalized_data_1.txt
BD155612-1


title: Healthy Control Blood Donor BD158567

description:
raw data file:
Non-normalized_data_1.txt
BD158567


title: Healthy Control Blood Donor BD155622

description:
raw data file:
Non-normalized_data_3.txt
BD155622


title: Healthy Control Blood Donor BD107589

description:
raw data file:
Non-normalized_data_1.txt
BD107589


title: Healthy Control Blood Donor BD135083

description:
raw data file:
Non-normalized_data_1.txt
BD135083


title: Healthy Control Blood Donor BD110992 Replicate 1

description:
raw data file:
Non-normalized_data_1.txt
BD110992-1


title: Healthy Control Blood Donor BD152919

description:
raw data file:
Non-normalized_data_3.txt
BD152919


title: Patient X49 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X49W26
ACT Score 15, FEV1 73

value: asthma

tag: omalizumab responder status

value: Non-responder


title: Healthy Control Blood Donor BD105933 Replicate 1

description:
raw data file:
Non-normalized_data_2.txt
BD105933-1


title: Patient X50 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X50W0
ACT Score 20, FEV1 83, Serum IgE 325, former smoker


title: Healthy Control Blood Donor BD106692

description:
raw data file:
Non-normalized_data_2.txt
BD106692


title: Patient X49 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X49W6
ACT Score 15


title: Healthy Control Blood Donor BD103375

description:
raw data file:
Non-normalized_data_1.txt
BD103375


title: Patient X50 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X50W26
ACT Score 22, FEV1 78, former smoker


title: Healthy Control Blood Donor BD138614

description:
raw data file:
Non-normalized_data_3.txt
BD138614


title: Patient X50 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X50W14
ACT Score 21, former smoker


title: Patient X49 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X49W0
ACT Score 12, FEV1 76, Serum IgE 87


title: Healthy Control Blood Donor BD153031

description:
raw data file:
Non-normalized_data_1.txt
BD153031


title: Patient X49 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X49W14
ACT Score 14


title: Patient X48 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X48W14
ACT Score 20, FEV1 80

value: Responder


title: Patient X50 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X50W6
ACT Score 24, former smoker


title: Patient X49 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X49W-1


title: Patient X48 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X48W26
ACT Score 23, FEV1 82


title: Patient X48 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X48W-1


title: Patient X48 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X48W6
ACT Score 16


title: Patient X48 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X48W0
ACT Score 7, FEV1 62, Serum IgE 23


title: Patient X50 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X50W-1
Former smoker


title: Patient X47 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X47W6
ACT Score 25


title: Patient X47 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X47W14
ACT Score 24, FEV1 63


title: Patient X47 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X47W0
ACT Score 12, FEV1 70, Serum IgE 53


title: Patient X47 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X47W26
ACT Score 24, FEV1 78


title: Patient X46 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X46W14
ACT Score 13, smoker


title: Patient X47 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X47W-1


title: Patient X46 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X46W26
ACT Score 23, FEV1 73, smoker


title: Patient X46 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X46W6
ACT Score 11, smoker


title: Patient X45 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X45W26
ACT Score 23, FEV1 64


title: Patient X46 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X46W-1
Smoker


title: Patient X46 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X46W0
ACT Score 8, FEV1 64, Serum IgE 1000, smoker


title: Patient X45 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X45W6
ACT Score 22


title: Patient X44 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X44W26
ACT Score 22, FEV1 76


title: Patient X45 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X45W14
ACT Score 22


title: Patient X45 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X45W-1


title: Patient X44 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X44W14
ACT Score 21


title: Patient X45 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X45W0
ACT Score 15, FEV1 70, Serum IgE 245


title: Patient X43 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X43W26
ACT Score 15, FEV1 79


title: Patient X44 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X44W0
ACT Score 24, FEV1 67, Serum IgE 283


title: Patient X43 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X43W14
ACT Score 20, FEV1 80


title: Patient X44 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X44W-1


title: Patient X42 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X42W26
ACT Score 25, FEV1 93, former smoker


title: Patient X43 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X43W0
ACT Score 11, FEV1 78, Serum IgE 372


title: Patient X43 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X43W-1


title: Patient X42 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X42W6
ACT Score 25, former smoker


title: Patient X42 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X42W0
ACT Score 8, FEV1 53, Serum IgE 606.1, former smoker


title: Patient X43 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X43W6
ACT Score 21, FEV1 79


title: Patient X42 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X42W14
ACT Score 25, former smoker


title: Patient X41 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X41W26
ACT Score 21, former smoker


title: Patient X42 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X42W-1
Former smoker


title: Patient X41 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X41W0
ACT Score 9, FEV1 103, Serum IgE 99.7, former smoker


title: Patient X41 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X41W6
ACT Score 21, former smoker


title: Patient X41 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X41W-1
Former smoker


title: Patient X44 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X44W6
ACT Score 23, FEV1 70


title: Patient X41 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X41W14
ACT Score 24, former smoker


title: Patient X40 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X40W14
ACT Score 22


title: Patient X40 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X40W26
ACT Score 18, FEV1 62


title: Patient X40 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X40W-1


title: Patient X40 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X40W6
ACT Score 6


title: Patient X39 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X39W26
ACT Score 19, FEV1 68


title: Patient X40 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X40W0
ACT Score 9, FEV1 52, Serum IgE 185


title: Patient X38 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X38W6
ACT Score 17, former smoker


title: Patient X39 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X39W0
ACT Score 17, FEV1 57, Serum IgE 121


title: Patient X38 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X38W26
ACT Score 15, FEV1 81, former smoker


title: Patient X38 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X38W14
ACT Score 18, former smoker


title: Patient X39 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X39W6
ACT Score 21


title: Patient X39 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X39W14
ACT Score 20, FEV1 65


title: Patient X39 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X39W-1


title: Patient X38 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X38W-1
Former smoker


title: Patient X37 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X37W-1


title: Patient X37 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X37W0
ACT Score 10, FEV1 53, Serum IgE 459


title: Patient X35 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X35W26
ACT Score 22, FEV1 75


title: Patient X36 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X36W6
ACT Score 18, former smoker


title: Patient X36 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X36W0
ACT Score 5, FEV1 72, Serum IgE 148, former smoker


title: Patient X38 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X38W0
ACT Score 8, FEV1 73, Serum IgE 371, former smoker


title: Patient X35 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X35W0
ACT Score 18, FEV1 104, Serum IgE 54


title: Patient X36 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X36W-1
Fomer smoker


title: Patient X36 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X36W14
ACT Score 20, former smoker


title: Patient X37 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X37W14
ACT Score 10


title: Patient X34 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X34W26
ACT Score 9, FEV1 61, former smoker


title: Patient X35 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X35W-1


title: Patient X33 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X33W26
ACT Score 6, FEV1 49, former smoker


title: Patient X35 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X35W14
ACT Score 23, FEV1 102


title: Patient X35 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X35W6
ACT Score 13


title: Patient X33 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X33W0
ACT Score 7, FEV1 46, Serum IgE 140, former smoker


title: Patient X33 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X33W-1
Former smoker


title: Patient X33 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X33W6
ACT Score 7, FEV1 45, former smoker


title: Patient X33 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X33W14
ACT Score 7, former smoker


title: Patient X34 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X34W6
ACT Score 14, FEV1 64, former smoker


title: Patient X32 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X32W26
ACT score 22, FEV1 108


title: Patient X32 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X32W0
ACT Score 18, FEV1 89, Serum IgE 24


title: Patient X32 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X32W6
ACT Score 21 FEV1 87


title: Patient X34 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X34W14
ACT Score 18, former smoker


title: Patient X32 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X32W14
ACT score 25, FEV1 86


title: Patient X32 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X32W-1


title: Patient X30 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X30W14
ACT Score 11, FEV1 52


title: Patient X30 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X30W0
ACT Score 13, FEV1 49, Serum IgE 183


title: Patient X31 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X31W14
ACT Score 25, FEV1 63


title: Patient X31 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X31W-1


title: Patient X31 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X31W0
ACT Score 18, FEV1 50, Serum IgE 2292


title: Patient X30 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X30W-1


title: Patient X29 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X29W26
ACT Score 18, FEV1 64


title: Patient X30 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X30W6
ACT Score 12, FEV1 49


title: Patient X30 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X30W26
ACT Score 20, FEV1 42


title: Patient X29 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X29W0
ACT Score 15, FEV1 66, Serum IgE 469


title: Patient X29 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X29W-1


title: Patient X31 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X31W26
ACT Score 25, FEV1 61


title: Patient X31 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X31W6
ACT Score 22


title: Patient X28 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X28W14
ACT Score 20


title: Patient X29 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X29W6
ACT Score 16


title: Patient X28 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X28W-1


title: Patient X29 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X29W14
ACT Score 17, FEV1 71


title: Patient X27 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X27W14
ACT Score 21


title: Patient X28 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X28W6
ACT Score 18


title: Patient X27 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X27W26
ACT Score 22, FEV1 63


title: Patient X37 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X37W6
ACT Score 18, FEV1 71


title: Patient X27 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X27W6
ACT Score 20, FEV1 69


title: Patient X34 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X34W-1
Former smoker


title: Patient X27 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X27W0
ACT Score 13, FEV1 65, Serum IgE 136


title: Patient X28 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X28W0
ACT Score 12, FEV1 84, Serum IgE 603


title: Patient X28 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X28W26
ACT Score 21, FEV1 85


title: Patient X27 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X27W-1


title: Patient X26 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X26W0
ACT Score 9, FEV1 72


title: Patient X26 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X26W26
ACT Score 22, FEV1 76


title: Patient X23 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X23W6
ACT Score 17


title: Patient X26 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X26W14
ACT Score 17, FEV1 78


title: Patient X25 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X25W14
ACT Score 21, former smoker


title: Patient X25 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X25W-1
Former smoker


title: Patient X22 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X22W26
ACT Score 19, FEV1 69


title: Patient X25 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X25W0
ACT Score 14, FEV1 96, Serum IgE 54, former smoker


title: Patient X23 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X23W26
ACT Score 18, FEV1 90


title: Patient X22 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X22W6
ACT Score 10


title: Patient X25 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X25W26
ACT Score 22, FEV1 78, former smoker


title: Patient X23 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X23W0
ACT Score 12, FEV1 88, Serum IgE 3


title: Patient X37 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X37W26
ACT Score 20, FEV1 82


title: Patient X23 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X23W-1


title: Patient X25 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X25W6
ACT Score 18, former smoker


title: Patient X21 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X21W14
ACT Score 18


title: Patient X20 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X20W26
ACT Score 20, FEV1 78


title: Patient X26 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X26W-1


title: Patient X23 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X23W14
ACT Score 13, FEV1 90


title: Patient X22 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X22W0
ACT Score 11, FEV1 74, Serum IgE 130


title: Patient X26 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X26W6
ACT Score 13, FEV1 80


title: Patient X21 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X21W0
ACT Score 20, FEV1 109, Serum IgE 256


title: Patient X22 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X22W-1


title: Patient X22 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X22W14
ACT Score 13


title: Patient X21 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X21W26
ACT Score 19, FEV1 109


title: Patient X20 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X20W14
ACT Score 23


title: Patient X21 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X21W-1


title: dve-1+atp-2 RNAi rep2

city: Beijing

first: Liwa

last: Shao

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Reads were aligned to the C. elegans genome (ce11) using TopHat2 (v2.1.1, --read-mismatches 6 --read-edit-dist 6 --min-anchor 8 --segment-length 26).
Uniquely mapped reads were used for further analysis.
Gene expression level and differentially expressed genes were generated by Cufflinks.
Genome_build: C. elegans genome (ce11)
Supplementary_files_format_and_content: Excel file contains gene FPKM.

organism: Caenorhabditis elegans

source_name: the whole organism

growth_protocol: Synchronized worms were raised on RNAi at 20°C. Synchronized from L1 to Day of adulthood stage

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: atp-2 RNAi bacterial culture solution was seeded 30 hours later after worms cultured on the empty vector RNAi, hda-1 RNAi or dve-1 RNAi clones.

tag: developmental stage

value: Day1 of adulthood

tag: knockdown

value: dve-1+atp-2 RNAi


title: dve-1+atp-2 RNAi rep1


title: dve-1 RNAi rep1

value: dve-1 RNAi


title: hda-1+atp-2 RNAi rep2

value: hda-1+atp-2 RNAi


title: Patient X19 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X19W14
ACT Score 20


title: Patient X20 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X20W6
ACT Score 25, FEV1 79


title: Patient X19 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X19W0
ACT Score 20, FEV1 68, Serum IgE 323


title: Patient X20 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X20W-1


title: hda-1+atp-2 RNAi rep1


title: Patient X19 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X19W6
ACT Score 25


title: Patient X19 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X19W-1


title: Patient X18 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X18W26
ACT Score 21 FEV1 61


title: hda-1 RNAi rep1

value: hda-1 RNAi


title: Patient X18 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X18W14
ACT Score 21


title: Patient X20 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X20W0
ACT Score 9, FEV1 78, Serum IgE 2026


title: Patient X19 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X19W26
ACT Score 19, FEV1 89


title: Patient X18 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X18W6
ACT Score 18


title: Patient X18 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X18W0
ACT Score 8, FEV1 70, Serum IgE 30


title: hda-1 RNAi rep2


title: Patient X34 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X34W0
ACT Score 10, FEV1 64, Serum IgE 298, former smoker


title: Patient X36 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X36W26
ACT Score 18, FEV1 95, former smoker


title: L4440+atp-2 RNAi rep1

value: L4440+atp-2 RNAi


title: L4440+atp-2 RNAi rep2


title: dve-1 RNAi rep2


title: L4440 RNAi rep2

value: L4440 RNAi


title: L4440 RNAi rep1


title: Patient X18 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X18W-1


title: WT embryos

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

country: South Korea

institute: KRIBB

data_processing:
Raw paired-end seqeuncing read were trimmed using 'Trim_galore' with '--paired' to remove adapters sequences and low quality bases.
Then, trimmed reads were mapped on mouse reference genome (mm9) using 'bwa' with dafault parameters.
For quantification, reads in 500 bp genomic bins were counted and normalized (counts per million, CPM) using 'bedtools intersect'.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: embryos

extract_protocol:
A pair of single-guide RNAs (sgRNAs) were designed to target exon-32 of mouse Dnmt1 gene and were synthesized (see Supplementary_Data_File_S1 for sgRNA information; Macrogen, Korea). Both sgRNAs (40 ng each) and Cas9 recombinant protein (40 ng; Toolgen, Korea) were mixed and incubated  in a microinjection buffer (0.1 mM EDTA, 10 mM Tris-Cl, pH 7.4) for 15 min at 37°C (1). Microinjection was performed 24 hrs after human chorionic gonadotropin injection. To visualize the pronuclei, cumulus-free zygotes were centrifuged at 13,000 rpm for 5 min, injected with the cocktail of sgRNA and Cas9, and cultured in M16 media for 48 hrs. Microinjection was performed under an inverted microscope equipped with micromanipulator and a microinjector (Leica). The resulting 4- and 8-cell stage embryos were treated with Tyrode’s solution (Sigma) for 2 minutes to remove zona pellucida, washed 3 times with 0.1% PVA-PBS, and collected for either genotyping or MBD-sequencing.
MBD-seq libraries were prepared using MethylMiner Methylated DNA Enrichment Kit (Thermo) according to manufacturer’s protocol

value: wild-type

value: 4/8-cell stage embryos


title: Patient X17 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X17W26
ACT Score 25, FEV1 96


title: Patient X17 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X17W6
ACT Score 21


title: Dnmt1 CR embryo group 2

value: Dnmr1 KO


title: Patient X17 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X17W14
ACT Score 22

value: Whole blood


title: Dnmt1 CR embryo group 1


title: Ly6cloF4/80hi subsets from 15Day T-ALL Spleen

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

data_processing:
Base calling was done by Illumina HiSeqTM 4000
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5)
FPKM values of each gene for each sample was measured via RSEM (version v1.2.12)
Supplementary_files_format_and_content: FPKMs

source_name: Macrophage

extract_protocol:
Sorted Ly6chiF4/80lo, Ly6cloF4/80lo and Ly6cloF4/80hi macrophages were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103).
RNA libraries were prepared for sequencing using Illumina HiSeqTM 4000 protocols

treatment_protocol: GFP+ leukemia cells were isolated from leukemia mice and transplanted into 6-8 weeks old C57BL/6 mice (1×10^6 cells/mouse) without irradiation. All mice suffered T-ALL with a survival time of 35 to 40 days. Ly6chiF4/80lo, Ly6cloF4/80lo and Ly6cloF4/80hi macrophages were sorted from  spleen of leukemia mice at 0d and 15d.

tag: disease state

value: T-ALL

value: Spleen

tag: cell type

value: Ly6cloF4/80hi macrophage subpopulation


title: siDnmt1-RNAseq

description: processed data file: DESeq2_counts_normalized.csv

data_processing:
Raw RNA-seq reads were trimmed using Trim_galore.
Trimmed reads were mapped on mm9 using HISAT2.
Gene expression levels were calculated by HTSeq.
Differential expression analysis was performed using DESeq2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: DESeq2_counts_normalized.csv: DESeq2 normalized expression of si-Dnmt1 or si-Scrb injected embryos.

extract_protocol:
Due to the limited starting amount of materials, we adopted pico-profiling method as described in previous reports to enrich the transcriptomic materials. First, mRNAs were isolated from a pool of si-Dnmt1 or si-Control injected 4/8-cell embryos using Dynabeads mRNA DIRECT Kit (Invitrogen). Using the extracted mRNAs as templates, pico-profiling specific adapter-tagged ds-cDNA fragments were generated by reacting mRNA and pico-profiling primers with SuperScript III (Invitrogen) followed by T4 DNA polymerase (NEB). Then, the adapter-tagged ds-cDNAs were amplified by 20 cycles of PCR using the anchor primers for the tagged adapters. The amplicons were digested by MlyI (NEB) to remove the pico-profiling adapters, and then the products were purified using AMPure XP beads (Beckman).
RNA-seq libraries were generated using the pico-profiling products according to the protocol suggested by NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and home-brew method previously reported. If not indicated otherwise, all materials were purchased from NEB. Two hundred-ng pico-profiling products were treated with T4 DNA polymerase, T4 polynucleotide kinase, and Klenow enzymes to repair the ends of amplified DNA fragments. The reaction products were purified using AMPure XP Beads (Beckman Coulter) according to manufacturer’s instructions. To adenylate 3’-ends of the end-repaired products, DNAs were reacted with Klenow Fragment (3'→5' exo) and 10 mM dATP for 2 hours at 30°C. After purification with AMPure XP Beads, NEBNext adapters with unique bar-codes were ligated overnight at 16°C in the presence of diluted T4 DNA ligase. The next day, ligation mixtures were purified twice with AMPure XP Beads and were enriched by PCR. Paired-end sequencing was performed using NextSeq 550 (Illumina) to generate raw sequencing data.

tag: strain/background

tag: tissue

value: embryos

tag: sirna


title: Ly6cloF4/80lo subsets from 15Day T-ALL Spleen

tag: strain

value: Ly6cloF4/80lo macrophage subpopulation


title: Patient X17 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X17W-1

value: asthma

value: Female

tag: age

value: Responder


title: Ly6chiF4/80lo subsets from 15Day T-ALL Spleen

value: Ly6chiF4/80lo macrophage subpopulation


title: Ly6cloF4/80hi subsets from Normal Spleen

value: control


title: Patient X16 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X16W6
ACT Score 19, former smoker


title: Patient X16 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X16W26
ACT Score 25, FEV1 79, former smoker


title: Ly6cloF4/80lo subsets from Normal Spleen


title: Ly6chiF4/80lo subsets from Normal Spleen


title: Patient X17 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X17W0
ACT Score 13, FEV 107, Serum IgE 530


title: DamControl-DamID

description: DamControl-DamID

data_processing:
Library strategy: DamID-seq
Basecalls performed using CASAVA.
Sequencing reads were aligned to the mm9 genome assembly using BWA with the default option.
Peaks were called by SISSRs.
Genome_build: mm9
Supplementary_files_format_and_content: Peak information file

source_name: 4/8-cell embryos

growth_protocol: Mouse zygotes were collected from superovulated BCF1 (C57BL/6 x CBA/CA) females. Briefly, female BCF1 mice at 5 weeks of age were injected with 5 IU of pregnant mare serum gonadotrophin, followed by 5 IU of human chorionic gonadotropins 48 h apart, and mated with male mice. Successful mating was determined the following morning by detection of a vaginal plug. Mouse zygotes were collected from mouse oviduct and transferred to M2 medium (Sigma) containing 0.1% (w/v) hyaluronidase to remove cumulus cells and cultured in M16 medium (Sigma) at 37°C, 5% CO2 in air.

extract_protocol:
gDNAs were extracted from 4/8-cell embryos and purified using phenol:chlroform.
DNAs were incubated for 30 min with DNA polymerase to repair-ends and 3' adenylation, and then Illumina adapters were ligated. Ligates were amplified by 15 cycles of PCR. DNA fragments around 300 bp were size-selected and used for GenomeAnalyzer.

value: BCF1 (C57BL/6 x CBA/CA)

value: 4/8-cell embryos


title: Patient X16 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X16W14
ACT Score 25, FEV1 77, former smoker


title: Patient X16 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X16W-1
Former smoker


title: DnmtDam-DamID

description: DnmtDam-DamID


title: Patient X16 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X16W0
ACT Score 10, FEV1 72, Serum IgE 249, former smoker


title: Patient X15 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X15W26
ACT Score 19, FEV1 87

value: Non-responder


title: Patient X15 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X15W0
ACT Score 11, FEV1 81, Serum IgE 92


title: Patient X15 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X15W-1


title: Patient X15 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X15W14
ACT Score 11, FEV1 88


title: Patient X14 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X14W26
ACT Score 21, FEV1 91, former smoker


title: Patient X15 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X15W6
ACT Score 18, FEV1 85


title: Patient X14 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X14W6
ACT Score 23, former smoker


title: siScrb-RNAseq

value: scrambled


title: Patient X14 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X14W-1
Former smoker


title: Patient X14 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X14W0
ACT Score 8, FEV1 88, Serum IgE 183, former smoker


title: Patient X14 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X14W14
ACT Score 20, former smoker


title: 15X+0X (3)

first: Shuai

last: Li

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

data_processing:
Paired-end reads from the original DNA fragments were merged using FLASH, a very fast and accurate analysis tool which was designed to merge paired-end reads when there are overlaps between reads 1 and reads 2.
Paired-end reads were assigned to each sample according to the unique barcodes. Nucleotide sequences generated by ldsDNA-based AND-gate genetic circuits were extracted by in-house Perl scripts. PCR primers used for library amplification are: Forward, [Barcode]TCAGATCCGCTAGCGCTACC; Reverse, [Barcode]GAACTTCAGGGTCAGCTTGC. the barcodes information in the "Supplementary Table 1 barcode.xlsx".
Reads were filtered by QIIME quality filters.
The fna file contains the nucleotide sequence of the peptide library (these sequences are not aligned with any reference sequence).
Genome_build: NA
Supplementary_files_format_and_content: fna files were generated for each sample.

growth_protocol: The HEK293T cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Hudson, NH, USA) containing 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin solution at 37 degree with 5% CO2.

extract_protocol:
Forty-eight hours after transfection, total RNAs were extracted by RNAiso Plus (TaKaRa, Beijing, China) reagent. cDNAs were synthesized using the PrimeScript TM RT reagent Kit with gDNA Eraser (TaKaRa) following standard protocol. KOD-Plus-Ver.2 DNA polymerase (Toyobo) was used to amplify the corresponding cDNA sequences surrounding ldsDNA junctions.
Library construction and high-throughput sequencing were conduct by Novogene (Beijing, China). Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations and index codes were added.
The library quality was assessed on the Qubit Fluorometer and Agilent Bioanalyzer 2100 system. At last, the libraries were sequenced on an Illumina HiSeq 2500 platform and 250 bp paired-end reads were generated.

treatment_protocol: HEK293T cells were seeded into 6-well plates the day before transfection (60% - 70% confluency). 500 ng/well of each input amplicons (total 1000 ng/well) were transfected into cells with Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) reagent following standard protocol.

tag: cell line

tag: ldsdnas subgroup combination

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>15 and <NNK>0-GFP-SV40 PAS

tag: molecule subtype

value: PCR amplicon


title: 15X+0X (1)


title: 10X+0X (1)

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>10 and <NNK>0-GFP-SV40 PAS


title: 5X+0X (2)

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>5 and <NNK>0-GFP-SV40 PAS


title: 10X+0X (3)


title: 10X+0X (2)


title: 15X+0X (2)


title: 5X+0X (3)


title: Patient X13 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X13W26
ACT Score 22, FEV1 60

value: Whole blood


title: Patient X13 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X13W14
ACT Score 23, FEV1 61


title: Patient X13 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X13W0
ACT Score 7, FEV1 46, Serum IgE 51


title: 15X+5X (3)

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>15 and <NNK>5-GFP-SV40 PAS


title: 5X+0X (1)


title: Patient X13 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X13W-1


title: Patient X12 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X12W14
ACT Score 14, FEV1 62


title: 15X+5X (2)


title: Patient X12 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X12W6
ACT Score 10


title: Patient X12 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X12W0
ACT Score 9, FEV1 56 , Serum IgE 45


title: Patient X12 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X12W26
ACT Score 15, FEV1 62


title: 10X+5X (3)

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>10 and <NNK>5-GFP-SV40 PAS


title: 10X+5X (2)


title: Patient X12 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X12W-1


title: Patient X13 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X13W6
ACT Score 20


title: 10X+5X (1)


title: Patient X11 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X11W14
ACT Score 14, FEV1 62


title: Patient X11 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X11W26
ACT Score 12, FEV1 87


title: 5X+5X (3)

value: Peptide library generated by ldsDNA CMV-Kozak-<NNK>5 and <NNK>5-GFP-SV40 PAS


title: 5X+5X (2)


title: 5X+5X (1)


title: M90-c

city: New York

first: Rebecca

last: Haeusler

state: NY

address: 1150 Saint Nicholas Ave Room 303A

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Data processing was done by the Columbia Genome Center. RTA (Illumina) was used for base calling.
bcl2fastq (version 2.17) used for converting BCL to fastq format, coupled with adaptor trimming.
STAR (2.5.2b) and featureCounts (v1.5.0-p3) used to map reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files containing number of raw counts for each gene.

source_name: Primary ileal organoids

growth_protocol: Intestinal crypts were isolated from mouse ileum and cultured in 3D matrigel mounds and IntestiCult Mouse Organoid Growth Medium. Medium was replaced every 3-4 days. Organoids were split after 10 days in culture, and vehicle/bile acid treatments were carried on day 14.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit following manufacturer's instructions. RNA quality control was done using Qubit Bioanalyzer.
Standard RNA-seq pipeline at Columbia Genome Center: poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1µg per sample, RIN>8), library preparation using Illumina TruSeq RNA prep kit.

treatment_protocol: Organoids were collected by dissolving the Matrigel mounds in ice-cold PBS and passed through a P200 pipette tip to expose the internal lumen. Organoids were washed in PBS, then incubated in vehicle- or bile acid-supplemented medium (DMEM with 0.2% BSA) for 24 hours, at 37 degrees C, 5% CO2. Organoids were harvested by centrifugation.

value: Primary ileal organoids

tag: passages

tag: treatment

value: Bile acid mix, mouse, 90% 12HBA


title: Patient X11 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X11W-1

tag: diagnosis

value: asthma

value: Female

value: Responder


title: 15X+5X (1)


title: Patient X11 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X11W6
ACT Score 13

tag: Sex


title: HDA-1_ChIP (dve-1) rep3

data_processing:
Adaptor in reads were filtered using in-house script then Trim Galore was used to do the quality control with following parameters: -q 20 --fastqc --illumina --stringency 6 -e 0 --length 50 --trim-n –paired.
Processed reads were mapped to the C. elegans genome (ce11) using bwa (v0.7.13-r1126) with default parameters.
Only proper paired uniquely mapping reads with mapping quality ≥20 and mismatches <8 were retained. PCR duplicates were removed by picard-2.17.6 (http://broadinstitute.github.io/picard) MarkDuplicates command.
MACS2 (v2.1.1) was used to obtain peak regions with following parameter: -g ce -f BAMPE --broad --SPMR.
ChIP-seq signals were calculated using deeptools (v2.4.2) by normalizing the read coverage to 10 million reads then subtracting input coverage from the ChIP samples to get final ChIP-seq signals.
Genome_build: C. elegans genome (ce11)
Supplementary_files_format_and_content: Bed3 files contain called peaks of each sample.

source_name: HDA-1_ChIP (dve-1)

extract_protocol:
Worms were cross-linked by formaldehyde and homogenized by a glass homogenizer.Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared by DNA Sample Kit (NEB, E7370).

treatment_protocol: atp-2 RNAi bacterial culture solution was seeded after worms cultured on the first RNAi clones.

value: Day1 of adulthood

tag: chip antibody

value: GFP agarose (ChromoTek, gta-20)


title: HDA-1_ChIP (dve-1+atp-2) rep3

source_name: HDA-1_ChIP (dve-1+atp-2)

tag: developmental stage


title: HDA-1_ChIP (dve-1+atp-2) rep1


title: HDA-1_input (dve-1+atp-2) rep3

source_name: HDA-1_input (dve-1+atp-2)


title: Patient X11 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X11W0
ACT Score 11, FEV1 55, Serum IgE 518

tag: omalizumab responder status


title: HDA-1_ChIP (dve-1+atp-2) rep2


title: Patient X10 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X10W14
ACT Score 16, FEV1 75


title: HDA-1_ChIP (dve-1) rep2


title: Patient X10 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X10W6
ACT Score 21, FEV1 59


title: M90-a


title: HDA-1_input (dve-1+atp-2) rep2


title: HDA-1_ChIP (dve-1) rep1


title: M10-a

value: Bile acid mix, mouse, 10% 12HBA


title: Patient X9 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X9W14
ACT Score 15, FEV1 73

value: Non-responder


title: M10-c


title: M10-b


title: M90-b


title: Patient X10 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X10W0
ACT Score 16, FEV1 67, Serum IgE 580


title: HDA-1_input (dve-1+atp-2) rep1


title: HDA-1_input (dve-1) rep3

source_name: HDA-1_input (dve-1)


title: H90-c

value: Bile acid mix, human, 90% 12HBA


title: HDA-1_input (dve-1) rep2


title: Patient X9 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X9W26
ACT Score 11, FEV1 97


title: Patient X9 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X9W0
ACT Score 8, FEV1 98, Serum IgE 165


title: Patient X7 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X7W26
ACT Score 20, FEV1 76, Former Smoker


title: Patient X10 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X10W26
ACT Score 22, FEV1 81


title: H90-b


title: Patient X9 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X9W6
ACT Score 19


title: HDA-1_input (dve-1) rep1


title: H90-a


title: DVE-1_ChIP (hda-1+atp-2) rep1

source_name: DVE-1_ChIP (hda-1+atp-2)


title: H10-c

value: Bile acid mix, human, 10% 12HBA


title: H10-b


title: DVE-1_ChIP (hda-1) rep2

source_name: DVE-1_ChIP (hda-1)


title: Patient X7 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X7W14
ACT Score 17, Former Smoker


title: Patient X7 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X7W6
Former Smoker


title: DVE-1_ChIP (hda-1) rep1


title: Vehicle-c

value: Vehicle


title: DVE-1_input (hda-1+atp-2) rep2

source_name: DVE-1_input (hda-1+atp-2)


title: Patient X6 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X6W26
ACT Score 22

value: Male


title: Vehicle-b


title: DVE-1_input (hda-1+atp-2) rep1


title: DVE-1_ChIP (hda-1+atp-2) rep2


title: DVE-1_input (hda-1) rep2

source_name: DVE-1_input (hda-1)


title: adult mouse cardiac ventricles_IgG

data_processing:
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and files were generated using MACS2. Narrowpeaks and Broadpeaks were called on TBX5 bound regions respectively.

source_name: adult mouse cardiac ventricles

growth_protocol: 15 weeks-old adult murine cardiac ventricles; mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
Adult murine ventricles were fixed with 2 % formaldehyde and nuclei were isolated and the chromatin was fragmented by sonication. After Chromatin-Immunoprecipitation for TBX5 and IgG-control DNA was isolated with NucleoSpin PCR and Gel Clean-Up with Buffer NTB (Macherey Nagel).
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions

tag: strain background

tag: genotype/variation

value: wild type

value: 15 weeks-old adult

value: cardiac ventricles

tag: chip-seq antibody

value: ChIP grade rb IgG (12-370, Millipore)


title: DVE-1_CHIP (L4440+atp-2) rep2

data_processing:
Adaptor in reads were filtered using in-house script then Trim Galore was used to do the quality control with following parameters: -q 20 --fastqc --illumina --stringency 6 -e 0 --length 50 --trim-n –paired.
Processed reads were mapped to the C. elegans genome (ce11) using bwa (v0.7.13-r1126) with default parameters.
Only proper paired uniquely mapping reads with mapping quality ≥20 and mismatches <8 were retained. PCR duplicates were removed by picard-2.17.6 (http://broadinstitute.github.io/picard) MarkDuplicates command.
MACS2 (v2.1.1) was used to obtain peak regions with following parameter: -g ce -f BAMPE --broad --SPMR.
ChIP-seq signals were calculated using deeptools (v2.4.2) by normalizing the read coverage to 10 million reads then subtracting input coverage from the ChIP samples to get final ChIP-seq signals.
Genome_build: C. elegans genome (ce11)
Supplementary_files_format_and_content: Bed files contain rep overalap called peaks.

treatment_protocol: atp-2 RNAi bacterial culture solution was seeded after worms cultured on the empty vector RNAi clones.

tag: knockdown

value: L4440 and atp-2 RNAi


title: Patient X6 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X6W14
ACT Score 20, FEV1 88

tag: tissue

value: Whole blood


title: PN-C

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina Bcl2fastq2 (2.18)  software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded
Reads were then aligned against the Mus musculus genome from Ensembl version 88 using STAR (version 2.5.2b)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, Mus musculus GTF genome annotation version 88 from Ensembl was used
All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq2 1.8.1
Statistical treatments and differential analyses were also performed using DESeq2 1.8.1
Genome_build: Ensembl version 88
Supplementary_files_format_and_content: tsv files containing raw counts

source_name: Cerebral cortex

extract_protocol:
From each female, one embryo or pup was decapitated and the cerebral cortex was collected for RNA sequencing. A biological sample is a cortex isolated form one embryo (or pup). Three biological samples from 3 different litters were collected per age. The cortices of embryos or pups were immediately lysed for RNA extraction using the Nucleospin® RNA Kit (Macherey-Nagel) according to the manufacturer’s protocol.
Messenger (polyA+) RNAs were purified from 1 µg of total RNA using oligo(dT)
Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
Libraries were multiplexed by 12 on a flowcell. A 75 bp single read sequencing was performed on a NextSeq 500 device (Illumina).

value: Cerebral cortex

value: Post-natal day 1

tag: strain


title: DVE-1_input (hda-1) rep1


title: H10-a

value: Primary ileal organoids


title: Patient X6 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X6W6
FEV1 92

value: asthma

tag: age

value: Responder


title: Patient X6 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X6W0
ACT Score 17, FEV1 89, Serum IgE 38


title: Patient X5 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X5W6
FEV1 73, Former smoker

value: Female


title: Vehicle-a


title: PN-B


title: adult mouse cardiac ventricles_TBX5

value: anti-TBX5 (HPA008786, Sigma)


title: Patient X5 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X5W14
ACT Score 24, Former smoker


title: Patient X5 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X5W0
ACT Score 20, FEV1 70, Serum IgE 173, Former smoker


title: DVE-1_ChIP (L4440) rep1

description: DG-L-CHIP

value: Day1 of adulthood

value: GFP agarose (ChromoTek, gta-20)

value: L4440 RNAi


title: Patient X2 14 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X2W14

value: Male

value: Non-responder


title: Patient X2 26 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_3.txt
X2W26
ACT Score 17, FEV1 80


title: DVE-1_ChIP (L4440) rep2


title: E17-C

value: Embryonic day 17


title: E17-B


title: Patient X2 6 weeks after starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X2W6
FEV1 80


title: DVE-1_input  (L4440+atp-2) rep1

description: DG-LA-input


title: DVE-1_input  (L4440+atp-2) rep2


title: E17-A


title: Patient X2 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X2W0
ACT Score 12, FEV1 79, Serum IgE 281


title: Patient X2 1 Week before Omalizumab Treatment

description:
raw data file:
Non-normalized_data_1.txt
X2W-1


title: DVE-1_input (L4440) rep1

description: DG-L-input


title: Patient X7 Week Starting Omalizumab Treatment

description:
raw data file:
Non-normalized_data_2.txt
X7W0
ACT Score 7, FEV1 67, Serum IgE 138, former smoker


title: HDA-1_CHIP (L4440+atp-2) rep2


title: E13-C

value: Embryonic day 13


title: HDA-1_CHIP (L4440+atp-2) rep1

description: HG-LA-CHIP


title: Septic shock-3

city: Guangzhou

first: jiyou

last: yao

address: 1  Panfu Road

department: Department of HBP SURGERY I

institute: Guangzhou First People's Hospital, School of Medicine, South China University of Technology

description: Plasma derived from septic shock patient

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.       a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first             denatured for 2 min at 95°C, incubated on ice for 2 min      b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization             System - Nimblegen Systems, Inc., Madison, WI, USA)        c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Septic shock patient-3

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:      a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture             was incubated for 30 min at 37°C.         b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of             fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling             reaction was incubated for 1 h at 16°C      c, Terminated by incubation for 15 min at 65°C.

growth_protocol: Plasma was stored at -80 ℃ Refrigerator or liquid nitrogen tank

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: No special treatment required

tag: plasma

value: Septic shock

value: 33 years


title: E11-C

value: Embryonic day 11


title: PN-A

value: Cerebral cortex


title: HDA-1_ChIP (L4440) rep2


title: E13-B


title: Septic shock-1

source_name: Septic shock patient-1

value: 35 years


title: E11-A


title: Septic shock-2

source_name: Septic shock patient-2

value: 52 years


title: E13-A


title: Sepsis-3

description: Plasma derived from sepsis patient

source_name: Sepsis patient-3

value: Sepsis

value: 46 years


title: Normal-3

description: Plasma derived from normal healthy volunteer

source_name: normal control-3

value: normal

value: Female


title: HDA-1_input  (L4440+atp-2) rep2

source_name: the whole organism

value: Day1 of adulthood

value: L4440 and atp-2 RNAi


title: HDA-1_ChIP (L4440) rep1

description: HG-L-CHIP

value: GFP agarose (ChromoTek, gta-20)

value: L4440 RNAi


title: DVE-1_input (L4440) rep2


title: GFP-DNMT1-dCAT

description: GFP tagged DNMT1 without the catalytic domain

data_processing:
Raw paired-end seqeuncing read were trimmed using 'Trim_galore' with '--paired' to remove adapters sequences and low quality bases.
Then, trimmed reads were mapped on mouse reference genome (mm9) using 'bwa' with dafault parameters.
For quantification, genomic enrichments of GFP/GFP-Dnmt1-Full/GFP-Dnmt1-dCAT were calculated using ' HOMER' in the default option, and GFP-Dnmt1 intensities were normalized by a GFP control.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
For ChIP sequencing, 293T cells were plated on a 6-well dish and, when they reached at 70~80% confluency, 2 µg of pEGFP-Dnmt1s, pEGFP-Dnmt1sc-, or pEGFP-c2 (Clontech) plasmid was transfected into the cells using Lipofectamine LTX (Thermo) according to manufacturer’s protocol. Cells were harvested 72 hrs after transfection and 1 x 106 cells were used in chromatin immunoprecipitation (ChIP) as described previously. Briefly, for cross-linking of chromatin and proteins, cells were incubated in 1% formaldehyde solution for 10 min at RT, neutralized by glycine treatment, and lysed to extract chromatin. The resulting chromatin was sheared to the size ranging from 200 - 500 bp, reacted with 2 µg a-GFP antibodies (Santa Cruz) or IgG control (Cell Signaling), and captured by Protein A magnetic beads (Bio-Rad). After reverse cross-linking and purification, the eluted DNA fragments were proceeded for Illumina sequencing library generation.
ChIP-seq libraries were prepared using NEBNext DNA Library Prep modules (NEB) and NEBNext Multiplex Oligos (NEB) according to manufacturer’s protocol, and paired-end sequencing data were generated by NEXTseq 550 (Illumina).

tag: genotype


title: HDA-1_input  (L4440+atp-2) rep1

description: HG-LA-inpu


title: Normal-1

source_name: normal control-1

value: 26 years

value: Male


title: HDA-1_input (L4440) rep2


title: GFP-DNMT1-Full

description: GFP tagged full length DNMT1

value: GFP tagged full length DNMT1


title: HDA-1_input (L4440) rep1

description: HG-L-input


title: Normal-2

source_name: normal control-2

value: 24 years


title: GFP-only

description: GFP only

value: GFP only


title: E11-B

value: Embryonic day 11


title: Sepsis-2

description: Plasma derived from sepsis patient

source_name: Sepsis patient-2


title: Sepsis-1

description: Plasma derived from sepsis patient

source_name: Sepsis patient-1

value: 32 years


title: 42_S42_R1_001_sw620-vector+DMSO

status: Public on Jul 18 2020

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Colorectal Adenocarcinoma cell sw620

growth_protocol: Cancer cell lines were obtained from ATCC. Cell lines were cultured in High Glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS, Excell), 1% nonessential amino acids (NEAA, Thermo Fisher), and 1% GlutaMAX (Thermo Fisher). Cells were maintained at 37 °C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Cells were cultured with 4ng/ml TGFβ1, 1 um repsox  and dmso for 24h. The cells were then used for further analysis.
Lentivirus was packaged by co-transfection of vectors encoding Tet2CD or  empty vector with the packaging plasmids pMD2.G and psPAX2 into HEK293T cells. Viruses were collected and used to infect cell lines. 5  ug/ml puromycin was used to select cell lines with genomic incorporation and stable expression of the target genes.

tag: cell line

tag: cell type

value: human colon cancer cells

value: vector

value: DMSO


title: 41_S41_R1_001_sw620-tet2+REPSOX

tag: treatment

value: REPSOX


title: 43_S43_R1_001_sw620-vector+TGFB1


title: 44_S44_R1_001_sw620-vector+REPSOX


title: 38_S38_R1_001_sw480-vector+REPSOX

source_name: Colorectal Adenocarcinoma cell sw480


title: 37_S37_R1_001_sw480-vector+TGFB1


title: 34_S34_R1_001_sw480-tet2+TGFB1


title: 39_S39_R1_001_sw620-tet2+DMSO


title: 36_S36_R1_001_sw480-vector+DMSO


title: 40_S40_R1_001_sw620-tet2+TGFB1


title: 33_S33_R1_001_sw480-tet2+DMSO


title: 32_S32_R1_001_sw620-vector+REPSOX


title: 31_S31_R1_001_sw620-vector+TGFB1


title: 35_S35_R1_001_sw480-tet2+REPSOX


title: 30_S30_R1_001_sw620-vector+DMSO


title: LSK_AGE_DRUG

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

data_processing:
Sample demultiplexing was completed by the Wellcome Trust Centre for Human Genetics, University of Oxford
FASTQ files were aligned to the mm10 reference genome using CellRanger (v2.0.1; 10X Genomics)
Samples were aggregated using the CellRanger::Aggregate function.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered gene-barcode matrix was generated from the h5 file using CellRanger::mat2csv function.  The barcode-1 columns correspond to sample LSK_AGE_VEHICLE and the barcode-2 columns to sample LSK_AGE_DRUG.

molecule: polyA RNA

extract_protocol:
LSK cells were isolated from mouse bone marrow by FACS and processed using the 10X Genomics droplet based sampler.
Library preparation was performed following the Chromium Single Cell 3’ Reagents Kit v2 users guide (CG00052, Rev C).

treatment_protocol: For SB 525334 treatment aged mice were treated for 13 consecutive days, once daily, with either 30mg/kg SB525334 dissolved in corn oli or vehicle (corn oil alone) via oral gavage.

value: Bone marrow

value: hematopoietic stem and progenitor cells (LSK population)

tag: phenotype

value: aged

value: Tgfb1 inhibitor (SB)


title: 29_S29_R1_001_sw620-tet2+REPSOX


title: VEC_CBM_YOUNG_3

data_processing:
RNAseq: Raw reads were trimmed using TrimmGalore! software and inspected using FastQC
RNAseq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using STAR software.
RNAseq: The featureCounts software was used to count reads on the basis of the RefSeq gene model
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Raw count matrix generated by featureCounts software

extract_protocol:
Stromal cells were isolated from mouse bone marrow by FACS and cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

value: stromal cells

value: YOUNG


title: LSK_AGE_VEHICLE

value: control


title: K562_K27me3nf_(20190927_SH_Hs_K27m3_NX_0918)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag for H3K27me3 in crosslinked nuclei from 120000 K562 cells

data_processing:
Library strategy:  CUT&TAG
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19.bed.gz).

extract_protocol:
CnT_Protocols_io_v2.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: Guinea pig anti-rabbit Antibodies-Online ABIN101961

value: K562 human immortalised myelogenous leukemia cell line


title: VEC_CBM_YOUNG_1


title: 28_S28_R1_001_sw620-tet2+TGFB1


title: 25_S25_R1_001_sw480-vector+TGFB1


title: VEC_CBM_YOUNG_2


title: 24_S24_R1_001_sw480-vector+DMSO


title: VEC_CBM_OLD_3

value: OLD


title: 23_S23_R1_001_sw480-tet2+REPSOX


title: 27_S27_R1_001_sw620-tet2+DMSO


title: VEC_CBM_OLD_1


title: 21_S21_R1_001_sw480-tet2+DMSO


title: 22_S22_R1_001_sw480-tet2+TGFB1


title: VEC_CBM_OLD_2


title: VEC_BLC_YOUNG_1


title: IgG_PRECFUE_2

extract_protocol:
Bone marrow cells from treated mice were isolated by FACS and cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

treatment_protocol: Aged mice were injected 3 times via i.p. with 100 ug of mouse IL-6 neutralizing antibody or Rat IgG2a isotype control dissolved in 1 mL of sterile saline solution at 1 week intervals

value: erythorid progenitors

value: AGED

value: IgG


title: VEC_BLC_OLD_2


title: HCC-1 T/N ratio

city: Taoyuan

first: Yang-Hsiang

last: Lin

address: Wenhua 1st Rd., Guishan Dist.

department: Department of Biochemistry

country: Taiwan

institute: Chang Gung University

description: HCC-1 (paired)

hyb_protocol: Cy5 and Cy3 channel input cRNA amount for hybridization(micro gram)

scan_protocol: microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA)

data_processing: Mean signal intensity of g(r) channel - mean background light intensity of g(r) channel. Normalized Expression Ratio is performed by the statistic method 'rank consistant lowess.

source_name: HCC

label_protocol: Cy5 and Cy3 channel input RNA amount for labeling(micro gram)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: HCC liver

source_name: adjacent normal tissue

value: adjacent normal liver


title: IgG_PRECFUE_1


title: VEC_BLC_OLD_1


title: Anti_IL6_PRECFUE_2


title: VEC_BLC_OLD_3


title: 26_S26_R1_001_sw480-vector+REPSOX

value: human colon cancer cells

value: vector


title: Anti_IL6_PRECFUE_3

value: Bone marrow


title: Anti_IL6_PRECFUE_1


title: YOUNG_PRECFUE_3

data_processing:
RNAseq: Raw reads were trimmed using TrimmGalore! software and inspected using FastQC
RNAseq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using STAR software.
RNAseq: The featureCounts software was used to count reads on the basis of the RefSeq gene model
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Raw count matrices were generated by featureCounts software

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated by FACS and cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.


title: PDGFRA_MSC_BLC_YOUNG_1


title: PDGFRA_MSC_BLC_YOUNG_2


title: VEC_BLC_YOUNG_3


title: IgG_PRECFUE_3


title: PDGFRA_MSC_BLC_YOUNG_3


title: VEC_BLC_YOUNG_2


title: PDGFRA_MSC_BLC_OLD_3


title: OLD_PRECFUE_3


title: OLD_PRECFUE_2


title: PDGFRA_MSC_BLC_OLD_1


title: PDGFRA_MSC_BLC_OLD_2


title: OLD_PRECFUE_1


title: YOUNG_PRECFUE_1


title: YOUNG_PRECFUE_2


title: LEPR+_PDGFRA+_CBM_OLD_2


title: LEPR+_PDGFRA+_CBM_YOUNG_2