title: vector rep3

city: Bethesda

first: Jennifer

middle: Patterson

last: West

state: Md

address: 8 Center Drive

department: Laboratory of Cell and Molecular Biology

institute: NIDDK

data_processing:
Read data in fastq format was demultiplexed and aligned to E. coli B str. DE3 (NC_012971.2) reference genome using STAR v2.5.2
Default alignment behavior was altered with the following arguments: --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --clip3pAdapterSeq AGATCGGAAGAGCGTCGTGTA --alignIntronMax 1.
RNA gene counts in both reference genomes were then quantified using the same NCBI gene definitions utilized in mapping index construction using the subread featureCounts v1.4.6-p3 package
Count data was normalized using Deseq2, which utilizes a normalization of means method for sample normalization and comparison.
Differential expression between conditions was represented as a fold change, and genes with both a fold change ≥2 and adjusted p value ≤ 0.05 were considered significant.
Genome_build: NC_012971.2
Supplementary_files_format_and_content: DE3.counts.edit.txt
Results_man2_M0_W0_Eco.csv:  Comma seperated value text files include: 1) the fold change of each gene in two different samples determined using subread featureCounts v1.4.6-p3 package; 2) Benjamini-Hochberg p-value.

organism: Escherichia coli BL21(DE3)

source_name: Bacteria

growth_protocol: BL21(DE3) E. coli containing either pNW129 or pNW129-MotB were grown to early log phase (OD600 ~ 0.3)  then induced with 0.2% arabinose for 20 minutes.

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
The cDNA library was prepared using a modified RNATagSeq workflow as previously described (Shishkin, A.A. et al. 2015 Nat Methods). Optimum fragmentation of the total RNA samples in this library was determined to be 3 min at 94C in FastAP buffer (Thermo Fischer Scientific).  The cDNA Library was run on a Bioanalyzer using the Agilent High Sensitivity DNA Kit to evaluate the quality of the library.  The concentration of the cDNA library was determined by qPCR using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA).

tag: plasmid


title: STG139M_284 rep3

status: Public on Jun 11 2020

type: SRA

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

library_source: genomic

data_processing:
Fastq files were trimmed from adapters using cutadapt (options: -q 20 -O 3 http://dx.doi.org/10.14806/ej.17.1.200, ver: 1.16) and aligned32 to a combined genome consisting of hg19 (H. Sapiens), dm6 (D. melanogaster) and mm10 (M.musculus) with bwa-mem (ver. 0.7.17-r1188). Bam files were generated from the alignment with samtools view (options: -Sb -F2308 -q 10, ver: 1.9) and subsequently split by organisms to obtain 3 bam files for each sample.
Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).
For all organisms, the total sequencing coverage (total recovery) was quantified as the total number of unique reads aligning to the respective genome
Standard peak calling was performed for each sample using MACS2 (ver. 2.1.2) with default options on hg19 and dm6 bam files respectively.
For each human PDTX model, peak regions were considered positive if confirmed in 2 out of 4 technical replicates (multi2) with bedtools v2.27.1 multiinter. All human confirmed G4-ChIP-seq peak files (multi2) of the 22 models were merged (bedtools merge) and regions more than 99 bp long retained to generate a single G4 DNA consensus of 26,103 G4 regions. Finally, the coverage of the samples was quantified over the consensus human set (bedtools coverage).
Reference normalization factor estimation and human ChIP signal normalization. For each PDTX biopsy, four technical qG4-ChIP experiments were performed and sequenced alongside one input chromatin (control). In each experiment, a similar amount of reference (D. melanogaster) chromatin from the same batch was added. To estimate PDTX normalization factors, reference coverage was determined at a pre-defined consensus consisting of 1,367 intervals (see Supplementary Data 2). The reference consensus set was defined from, and covers, G4-enriched regions observed in more than 110 pull-down experiments. The normalization factor of each ChIP sample has been defined as the ratio between the maximum observed coverage (across all ChIP samples) and the individual sample coverage. Note that only ChIP experiments were used for this step (i.e. inputs are excluded and forced to 1). . The normalization factors were then exported and used as input for a customized R script performing the normalization of the human signal. For each G4-ChIP-seq experiment, human signal (i.e. read coverage within human G4 consensus) was quantified by performing input subtraction and normalization with their respective reference reads and human library sizes. To assess if the normalization step has globally improved the experimental reproducibility, a quantitative parameter, the Improvement Factor IF, was devised that measures both the increase (i.e. improvement) in data similarity  between experiments corresponding to the same technical and biological samples and the increase dissimilarity between different samples. Specifically, the improvement factor of each biological sample has been estimated as: IF = sum_N(D_ratio_inter) - sum_N(D_ratio_intra).  Where: o  D_ratio: euclidean_distance_after_normalization/euclidean_distance_before_normalization;  o  N: total N. ChIP samples  o  euclidean_distance_after_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted, drosophila normalized data and rescaled to its  maximum value;  o  euclidean_distance_before_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted data and rescaled to its maximum value;   o  D_ratio_inter: similarity values among samples belonging to the same technical or  biological group;   o  D_ratio_intra: similarity values among samples not belonging to the same  technical or biological group;   135 individual samples (ChIP + Input) were processed from 22 different PDTX models. Some   PDTX models have more than one biological sample.
Genome_build: hg19, dm6, mm10
Supplementary_files_format_and_content: bigwig files  *nodup.w10.rpm.bw were generated from the duplicates removed bam files binning the regions in 10bp windows and normalizing the coverage in those regions by the total number of unique reads. The bigwig files *nodup.dm6.sorted.bw were generated starting from **nodup.w10.rpm.bw and following those steps: 1. bw converted to begraph; 2.using bedtools unionbedg  perform input subtraction (pull-down minus input RPM) and multiply by drosophila normlization factors.

molecule: genomic DNA

organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

source_name: fixed human breast cancer PDTX tissue

extract_protocol:
PDTX chromatin prep and G4-ChIP-seq: Briefly, D. melanogaster S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Scientific, cat no. R69007) containing 10% fetal bovine serum (FBS) Medium (Thermo Fisher Scientific, cat no. 10500064). To prepare spike-in Drosophila chromatin, 100 million cells were i) harvested by centrifugation, ii) fixed for 10 min in a solution of media containing 10 % FBS, 1% Formaldehyde (Thermo Fisher Scientific, cat no. 28908) and iii) quenched for 5 min by addition of 125 mM glycine (Fisher Scientific, cat no. 11545005). The cell pellet was washed with 10 mL PBS, pelleted by centrifugation and subsequently stored on ice for the lysis procedure. The 2-step chromatin lysis procedure was performed according to the Chromatrap procedure ("Spin column ChIP kit for qPCR v6.4"). 500 µL intact chromatin was sonicated into 100-500 bp fragments using a Bioruptor Plus (Diagenode cat. no. B02010003 with cooling) at 4C. Sonicated chromatin was diluted with 1.5 mL lysis buffer (Chromatrap cat no. 100005) before snap-freezing as 25 µL aliquots. PDTX chromatin was prepared essentially as described in Schmidt et al. (Methods 2009)30. Briefly, a snap-frozen PDTX biopsy, ~1 cm3, was transferred into a 50 mL falcon tube, on dry-ice, and crushed into smaller chunks on dry-ice using a scalpel followed by fixation for 20 min in 30 ml solution A, containing 1% formaldehyde, and then quenched for 5 min by adding 125 mM glycine. The supernatant of the pelleted tissue was discarded, and the pellet washed twice with 10 mL ice-cold PBS before resuspending in 1 mL PBS and transferred to a 1 mL glass Douncer (Fisher scientific, cat no. 11591295). 10 strokes were employed for each douncing step with a loose and then tight pestle, and the remaining tissue slurry was transferred to a 15 mL tube, centrifuged for 5 min at 2500xg and subjected to lysis according to Schmidt et al30. Briefly, after the 10 mL LB2 treatment and nuclei pelleting step, the pellet was resuspended in 500 µL LB3 and LB3-chromatin solution split into two Bioruptor TBX (Diagenode, cat no. C30010010-300) sonication tubes. The samples were sonicated until the desired fragment length (100-500 bp) was achieved. Finally, 50 µL of a 10% Triton X-100 LB3 solution was mixed with the sonicated solution and aliquoted into 50 µL aliquots before snap-freezing in liquid nitrogen. 5 μL of PDTX chromatin was quantified by Qubit using the "broad range kit" (Thermo Fisher Scientific, cat. no. Q32853). In each qG4-ChIP-seq reaction, 225ng of PDTX chromatin, 102ng of spike-in drosophila chromatin and 2% RNaseA (Invitrogen, cat. no. AM2271) in blocking buffer (25mM HEPES, pH 7.5, 10.5mM NaCl, 110mM KCl, 1mM MgCl2 and 1% BSA (Merck, cat. no. A7030) in Milli-Q water were mixed and incubated at 37C for 30min at 800rpm. All PDTX chromatin batches containing a different concentration than 30 ng/μL were balanced to the same level, either by dilution with LB3 containing 1% Triton X-100 or by up-scaling the ChIP reaction. For PDTX chromatin with a concentration of 30 ng/μL, 7.5 μL of the PDTX chromatin was added to a solution containing 270 μL blocking buffer including 2% RNase A and 7.5 μL spike-in drosophila chromatin. After RNaseA treatment, 15 μL of 2M BG4, prepared as described previously31, was added to each qG4-ChIP-seq reaction and the reaction mixture shaken at 1,400 rpm at 16C for 1 hour. Meanwhile, 65 μL of anti-FLAG magnetic beads (Sigma-Aldrich, cat. no. M8823) were washed three times with 650 μL of blocking buffer and resuspended in 1,300 μL blocking buffer. The pre-washed beads were incubated at 16C at 1,400rpm and 300 μL of pre-washed beads added to the reaction mixture after BG4 incubation. The reaction mixture with beads was incubated at 16C for 1 hour at 1,400rpm. Then, the beads were washed four times in 400 μL cold wash buffer (100mM KCl, 0.1% Tween 20 and 10mM Tris, pH 7.4 in Milli-Q water) in the cold room and twice at 37C for 15min at 1,400rpm, followed by one cold wash on magnetic stand. The enriched chromatin on beads was resuspended in 75 μL TE buffer and 1 μL Proteinase K (Invitrogen, cat. no. AM2546) added. 6 μL Proteinase K was added to input sample which refers to a qG4-ChIP-seq reaction mixture without BG4 and beads. The reaction mixture was incubated at 65C for 3 hours at 1,400 rpm and purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206).
Purified DNAs were subjected to Nextera DNA library preparation.For 40 μL library preparation reaction, 3-5ng of the ChIP or input DNA (Qubit high sensitivity kit, Thermo Fisher Scientific, cat. no. Q32854), 20 μL 2X tagmentation buffer (Illumina, cat. no. 15027866), 1.25 μL Tn5 enzyme (Illumina, cat no. 18027865) and nuclease-free water was incubated at 37°C for 20min at 800rpm. The reaction mixture was purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206) according to the manufacturer’s instruction and eluted in 20 μL EB buffer. To amplify the library, 20 μL of the DNA was then mixed with 25 μL NEB Next High Fidelity 2X PCR Master Mix (New England Biolabs, cat. no. N0541S), 2.5 μL Nextera index kit i5 primer (Illumina, cat. no. 15055290) and 2.5 μL Nextera index kit i7 primer (Illumina, cat. no. 15055290). The PCR program was as follows: 72°C for 5 minutes, 98°C for 30 seconds, followed by 8 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Libraries were quantified using a Bioanalyzer (Agilent) to estimate the average library size and concentration determined via Qubit HS. The library concentration was corrected for the library size using the following relationship:1 ng/µL = 3nM = 500 bp. Samples were subjected to single-end sequencing with a read length of 75bp on an Illumina NextSeq instrument.”

tag: cell type

value: breast cancer tissue

tag: strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

tag: chip antibody

value: BG4 single-chain antibody

tag: spike-in reference organsms

value: Drosophila melanogaster

tag: spike-in cell line

value: Drosophila S2 cells


title: Replicate 1 Blood_Fed_day 10

city: Slingerlands

first: Dilip

middle: K

last: Nag

state: NY

address: 5668 State Farm Road

department: Division of Infectious Diseases

country: USA

institute: Griffin Laboratory, Wadsworth Center, New York State Department of Health

description: RNA was isolated using mrVana miRNA kisolation kit

library_source: transcriptomic

data_processing:
The raw sequences were subjected to quality check by FastQC
Bioinformatics analysis was carried out using CLC Genomics workbench v.20 software.
Gene expression tracks after mapping are shown
Genome_build: Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa.gz

molecule: total RNA

organism: Aedes aegypti

source_name: Ovary

growth_protocol: 4-7 days old A. aegypti (from Poza Rica, Mexico) were fed with warmed sheep blood. No additional blood meals were given for the entire study period. Control mosquitoes were given sugar meal.

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Invitrogen) following the manufacturer’s suggestions.
RNA libraries were prepared following the Illumina Stranded total RNA library prep kit with Ribo-Zero Gold protocol.
Following library concentration and quality control, final libraries were pooled to 10 nM. After dilution and denaturing, the pooled library was loaded onto a NovaSeq6000 S1 flow cell (PE200) for sequencing.

treatment_protocol: All mosquitoes, both sugar fed and blood fed, were maintained with 10% sucrose and reared identically. Ovary samples were collected on day 3, 10, and 20 post blood meal (PBM) and stored immediately at -80oC.

tag: age

value: 4-7 day old mosquito

tag: diet

value: Fed with blood meal

tag: timepoint

value: Ovary collected on day 10 PBM


title: STG139M_181 rep4


title: Wild-type strain

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

country: China

institute: Second Military Medical University

description: Sample 1-H99 strain

data_processing:
Adapter was removed by Flexbar. Data quality was checked by FastQC.
Reads were mapped to genome of CNA3 by tophat.  Transcriptome was assembled by cufflinks. Differential expression genes were calculated by cuffdiff.
Genome_build: CNA3
Supplementary_files_format_and_content: FKPM obtained by cuffdiff.

organism: Cryptococcus neoformans H99

source_name: clinical strain

extract_protocol:
C. neoformans were cultured in liquid YPD media till mid-log phase, pelleted, washed twice, frozen at -80°C, and lyophilized overnight. The cell pellets were broken with glass beads (2mm diameter), and then total RNA was isolated using Qiagen RNeasy Plant Minikit (Qiagen, Valencia, CA) following manufacturer provided protocol.
Library preparation and RNA sequencing were performed by Genergy Biotech (Shanghai) Co., Ltd. Total RNA samples were purified and prepared as previously described.

tag: genotype

value: wild-type


title: STG139M_284 input


title: Ubi1∆ mutant strain

description: Sample 2-ubi1∆ mutant strain

source_name: mutant with Ubi1 deletion

value: ubi1{delta} mutant


title: vector rep2


title: vector rep1


title: Replicate 1 Blood_Fed_day 3

value: Ovary collected on day 3 PBM


title: H4CAPE1 (miRNA-seq)

city: Chengdu

first: Ya

last: Luo

address: 17, 3rd Section, Renmin South Road

institute: Sichuan University

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software v2.20
miRNA sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using miRDeep2 v0.0.8 with parameters -e -j -h -l 18 -m
Processed data of miRNA was quantified using miRDeep2 v0.0.8 with parameters -t hsa
For mRNA data, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to GRCh38 and quantified using kallisto v0.46.1 with parameters -i transcripts.idx -b 100
Genome_build: GRCh38
Supplementary_files_format_and_content: CAPE_miRNA_raw_counts.csv:  Matrix table with raw miRNA counts for every miRNA and every sample
CAPE_mRNA_raw_gene_counts.csv:  Matrix table with raw gene counts for every gene and every sample
CAPE_mRNA_TPM.csv:  Comma-delimited text file includes TPM values for each Sample

organism: Homo sapiens

source_name: small-cell lung cancer H446 cells

growth_protocol: H446 cells were cultured and maintained in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, USA) supplemented with 10% fetal bovine serum (FBS; Gibco), penicillin (100 U/ml; Beyotime, SH, China), and streptomycin (100 mg/ml; Beyotime). The cells were cultured in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. Transcriptome sequencing was performed on an Illumina platform by Shanghai Personal Biotechnology Co. Ltd. Finally, 150-bp paired-end raw reads were obtained.

treatment_protocol: H446 cells were harvested for RNA extraction after 8 h of CAPE treatment at a concentration of 40 µM. The cells incubated with the same volume of DMSO as the CAPE (40 μM)-treated group were used as the control.

tag: cell line

tag: treatment

value: CAPE (40 μM in DMSO)


title: H4Ctrl2 (miRNA-seq)

value: control (DMSO)


title: H4Ctrl3 (miRNA-seq)


title: Replicate 1 Sugar_Fed_day 20

value: Fed with sugar meal

value: Ovary collected on day 20 PSM


title: STG139M_181 rep3


title: T4motB rep3


title: Replicate 1 Sugar_Fed_day 10

value: Ovary collected on day 10 PSM


title: T4motB rep2


title: STG139M_181 rep2


title: H4Ctrl1 (miRNA-seq)


title: STG139M_181 input


title: H4CAPE3 (miRNA-seq)


title: STG139M_181 rep1


title: T4motB rep1


title: STG139M_284 rep1


title: Replicate 1 Blood_Fed_day 20

value: Ovary collected on day 20 PBM


title: myl7:nucDsRed+ CMs ATAC-Seq rep1

status: Public on Jun 10 2020

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.6.1d with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignIntronMax 1 --outFilterMultimapNmax 1" (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.18.16 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
The Macs2 peak caller version 2.1.1 was employed for each sample with parameters “-q 0.0001” (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
In order to be able to compare peaks in different samples to assess reproducibility, the resulting lists of significant peaks were overlapped and unified to represent identical regions. Reads were recounted after normalization for sequencing depth with bamCoverage 2.5.7 using bigWigAverageOverBed (UCSC Toolkit) (Fidel Ramírez  et al., deepTools: a flexible platform for exploring deep-sequencing data).
DESeq2 1.18.1 was used to normalize the resulting matrix of union peaks to compensate for differences in sequencing depth, library composition, and pull-down effectivity (Anders et al., Differential expression analysis for sequence count data).
Genome_build: DanRer11
Supplementary_files_format_and_content: Deseq normalized and background corrected counts in peaks

organism: Danio rerio

source_name: adult zebrafish cardiomyocytes

growth_protocol: Zebrafish were grown under standard conditions (zfin.org) and in accordance with institutional (MPG) and national ethical and animal welfare guidelines.

extract_protocol:
Adult ventricles were dissected in 1x HBSS (Gibco) and minced into 1-2 mm pieces using microdissecting spring scissors.  Minced ventricle pieces from 6 adult hearts were washed twice in 1x HBSS, HBSS was removed and ventricle pieces were dissociated by enzymatic digestion in 90 μL Cardiomyocyte Isolation Enzyme #1 (Thermo Fisher Scientific) and 4.5 μL Cardiomyocyte Isolation Enzyme #2 (Thermo Fisher Scientific).  Enzymatic digestion was performed at 37°C for 30 minutes, followed by two washes in HBSS and resuspension in tissue culture medium (DMEM/F-12 1:1, 10% FBS, 1x Penicillin-Streptomycin).  Uninjured Tg(myl7:nucDsRed)+ or Tg(gata4:EGFP)+ cardiomyocytes at 4 dpci were isolated by FACS sorting using a FACS Aria III.  CM:A-Fos (+) and CM:A-Fos (-) cardiomyocytes at 4 dpci and uninjured CM:junbaOE and CM:junbbOE at 7 days post induction of overexpression were isolated by density gradient centrifugation according to (Golden et al., 2012).
Cardiomyocytes were harvested by centrifugation at 500 g for 5 minutes at 4°C.  Cells were washed once with 50 μL of cold PBS and spun down at 500 g for 5 minutes at 4°C.  Cell pellets were resuspended in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spun down immediately at 500 g for 10 minutes at 4°C.  For 50000 cells, nuclei were gently resuspended in 25 μL 2x TD Buffer (Illumina #FC-121-1030), 2.5 μL Tn5 Transposase (Illumina #FC-121-1030) and 22.5 μL nuclease-free H2O and incubated at 37°C for 30 minutes.  Immediately following transposition, transposed DNA was purified using a PCR purification MinElute kit (Qiagen) and eluted in 10 μL nuclease-free H2O.  For 5000 cells, nuclei were resuspended 5 μL 2x TD Buffer, 0.35 μL Tn5 Transposase, and 4.65 μL nuclease-free H2O.  Transposition reactions were incubated at 37°C for 30 minutes, followed by the addition of 1.2 μL 500 mM EDTA and incubation at 50°C for 30 minutes.  1.2 μL of 500 mM MgCl2 was added to each reaction and no purification was performed prior to PCR amplification.  Transposed DNA fragments were amplified using NEBNext High-Fidelity 2x PCR Master Mix (NEB #M0541) and 1.25 μM Nextera bar-coded primers with the following cycling conditions: 1x: 72°C, 5 mins/1x: 98°C, 30 seconds/5x: 98°C, 10 seconds, 63°C, 10 seconds, 72°C, 1 minute.  qPCR was performed to determine the optimal number of additional cycles according to (Buenrostro et al., 2015) and additional cycles were performed as above.  Amplified library DNA was purified using a PCR purification MinElute kit (Qiagen) according to manufacturer’s instructions and an additional clean-up step was performed to remove excess primers with 1:1 (vol/vol) AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions.

treatment_protocol: Cryoinjury was performed using adult male and female zebrafish between the ages of 4 and 12 months according to (Chablais et al., 2011; González-Rosa et al., 2011; Schnabel et al., 2011).  Induction of transgene expression was performed by intraperitoneal injection of 4-hydroxytamoxifen (0.5 mg/mL) or ethanol vehicle as a control.

tag: developmental stage

value: adult

value: Uninjured

tag: number of cells

value: cardiomyocytes

tag: cardiomyocyte isolation protocol

value: FACS


title: myl7:nucDsRed+ CMs ATAC-Seq rep2


title: junba OE CMs ATAC-Seq rep2

description: junba

value: Uninjured, 7 days post induction of overexpression

value: density gradient centrifugation

value: junba OE


title: gata4:EGFP+ CMs ATAC-Seq rep2

value: 4 days post cryoinjury


title: junba OE CMs ATAC-Seq rep1

description: junba


title: gata4:EGFP+ CMs ATAC-Seq rep1


title: junbb OE CMs ATAC-Seq rep2

description: junbb

value: junbb OE


title: A-Fos (-) CMs ATAC-Seq rep3

value: A-Fos (-)


title: A-Fos (-) CMs ATAC-Seq rep2


title: A-Fos (+) CMs ATAC-Seq rep2

value: A-Fos (+)


title: A-Fos (-) CMs ATAC-Seq rep1


title: A-Fos (+) CMs ATAC-Seq rep3


title: Replicate 1 Sugar_Fed_day 3

value: 4-7 day old mosquito

value: Ovary collected on day 3 PSM


title: junbb OE CMs ATAC-Seq rep1

description: junbb


title: A-Fos (+) CMs ATAC-Seq rep1


title: Zhu_066_glioma cell line (early biopsy)

type: RNA

city: WASHINGTON

first: Yuan

last: Zhu

state: DC

address: 111 Michigan Ave NW

institute: Childrens National Medical Center

hyb_protocol: Hybridization was performed following a published protocol (Miller D et al, Curr. Protoc. Hum. Genet. 2012. PMID: 18633976)

scan_protocol: GeneChips were scanned according to manufacturer recommendation

data_processing: The CEL files were preprocessed and normalized by the aroma package using a custom CDF file from AffyProbeMiner (GPL9523)

label: biotin

organism: Mus musculus

label_protocol: Complementary RNA synthesis and labeling/hybridization/scanning of Mouse Genome 430 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual (see below fields).

growth_protocol: Cell cultures were prepared based on a previously published protocol (Wang et al., Cell 150, 816-830, 2012), and chromosome metaphase assays were performed according to an established protocol.

extract_protocol: Total RNAs were extracted from wild-type control brain tissues, high-grade gliomas and early passage of glioma derived cell lines by using AllPrep DNA/RNA Mini Kit (Qiagen). cDNA synthesis was performed using QuantiTect Reverse Transcription Kit (Qiagen) and RT-PCR was performed using SYBR Select Master Mix (Applied Biosystems).

treatment_protocol: Mice carry various genotypic configurations as indicated for each case.

tag: phenotype

value: malignant glioma


title: Zhu_060_glioma


title: Zhu_064_glioma


title: Zhu_061_glioma cell line


title: Zhu_067_glioma


title: Zhu_054_glioma


title: Zhu_062_glioma


title: Zhu_059_glioma cell line


title: Zhu_065_glioma cell line


title: Zhu_068_glioma cell line


title: Zhu_057_glioma cell line


title: Zhu_058_glioma


title: Zhu_069_glioma cell line (early biopsy)


title: Zhu_055_glioma cell line


title: Zhu_056_glioma


title: Zhu_053_glioma cell line


title: Zhu_052_glioma


title: Zhu_063_glioma cell line


title: Zhu_045_glioma


title: Zhu_046_glioma


title: Zhu_044_glioma


title: Zhu_042_glioma


title: Zhu_047_glioma cell line


title: Zhu_041_glioma


title: Zhu_043_glioma


title: Zhu_049_glioma cell line


title: Zhu_050_glioma


title: Zhu_051_glioma cell line


title: Zhu_040_glioma


title: H3K9me3 ChIP-Seq of 1.2Bind proliferating postinduction

city: Barcelona

first: Oriol

last: Llorà-Batlle

address: Carrer Rosselló 153, 1st floor

country: Spain

institute: ISGlobal

description:
The reference genome PlasmoDB-39_Pfalciparum3D7 was edited according to modified genome of the strains.
12B_me_Ind_In_Revised_sort_noDup_depth_RPM_normIN.bdg
PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_In_Revised.fas

data_processing:
Repetitive kmers removed from the reads using BBDuK (v36.99) with parameters ktrim=r k=22 mink=6.
Reads aligned using Bowtie (v1.2) with parameters --very-sensitive --local -5 4 -3 4 -I 50 -X 200.
Duplicate reads removed using PicardTools MarkDuplicates (v2.9.4).
Per base coverage calculated using BEDtools (v.2.27.1) with parameters -ibam -pc -d. Coverage values where then divided by the number of milion reads (RPM) and then divided by input (ChIP_rpm/input_rpm) with a pseudocount of 0.1.
Genome_build: PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_NI_Revised.fas (preinduction samples), PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_In_Revised.fas (postinduction samples)
Supplementary_files_format_and_content: Bed files are in standard BED format. Last column corresponds to normalized coverage (by number of reads and input).  Reference genomes according to the genotype of the strains used are provided in fasta format.

organism: Plasmodium falciparum

source_name: Cell culture

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based media containing Albumax II without human serum, in a 5% CO2, 3% O2, balance N2 atmosphere. For E5ind and 1.2Bind WR99210 selection was always maintained.

extract_protocol:
Chromatin was obtained from saponin-extracted parasites at the late trophozoite or schizont stage, crosslinked with formaldehyde and lysed following the MAGnifyTM Chromatin Immunoprecipitation System (Life Technologies). Samples were sonicated using an M220 sonicator (Covaris) at 10% duty factor, 200 cycles per burst, 140 W of peak incident power for 10 min. Immunoprecipitations were performed overnight at 4ºC with 4 µg of chromatin and 8 µg of antibodies against H3K9me3 (Diagenode pAb-193–050) coupled to protein A/G magnetic beads provided in the kit. Washing, de-crosslinking and elution were performed following the MAGnifyTM Chromatin Immunoprecipitation System recommendations, but avoiding high temperatures that may result in denaturation of extremely AT-rich intergenic regions: de-crosslinking, proteinase K treatment and elution were performed at 45ºC (for 2 h, over-night, and 1.5 h, respectively).
Libraries for Illumina sequencing were prepared from 5 ng of immunoprecipitated DNA using a protocol adapted to a genome with an extremely high AT-richness (Kensche et al., 2016. PMID: 26578577). In brief, after end-repair and addition of 3′ A-overhangs, NEBNext Multiplex Oligos for Illumina (NEB, E7335, E7500) were ligated. Purification steps were performed with Agencourt AMPure XP beads (Beckman Coulter, A63880). Libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KK2103) in KAPA HiFi Fidelity Buffer (5X) with the following conditions: 95°C for 3 min; 9 cycles at 98°C for 20 s and 62°C for 2 min 30 s; and 62 °C for 5 min. Amplified libraries were purified using 0.9X AMPure XP beads to remove adapter dimers. The library size was analyzed in a 4200 TapeStation System (Agilent Technologies).

treatment_protocol: No treatment done in preinduction samples. Postinduction samples (E5ind+Rapa_prol and 1.2Bind+Rapa_prol cultures) were obtained from the parasites that kept replicating after the induction with rapamycin.

tag: original strain

value: 3D7-B subclone 1.2B

value: Excised 5'cam-hdhfr cassette upstream pfap2-g and DiCre integration into lisp1

value: H3K9me3 (Diagenode pAb-193-050)


title: Input of E5ind preinduction

description:
The reference genome PlasmoDB-39_Pfalciparum3D7 was edited according to modified genome of the strains.
E5_me_sort_noDup_depth_RPM_normIN.bed
PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_NI_Revised.fas

value: 3D7-B subclone E5

value: E5ind non-induced

value: Floxed 5'cam-hdhfr cassette upstream pfap2-g and DiCre integration into lisp1


title: H3K9me3 ChIP-Seq of E5ind proliferating postinduction

description:
The reference genome PlasmoDB-39_Pfalciparum3D7 was edited according to modified genome of the strains.
E5_me_Ind_In_Revised_sort_noDup_depth_RPM_normIN.bdg
PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_In_Revised.fas


title: Input of E5ind proliferating postinduction


title: H3K9me3 ChIP-Seq E5ind preinduction


title: H3K9me3 ChIP-Seq 1.2Bind preinduction

description:
The reference genome PlasmoDB-39_Pfalciparum3D7 was edited according to modified genome of the strains.
12B_me_sort_noDup_depth_RPM_normIN.bed
PlasmoDB-39_Pfalciparum3D7_Genome_Ind_System_NI_Revised.fas

value: 3D7-A subclone 1.2B

value: 1.2Bind non-induced


title: Input of 1.2Bind before preinduction


title: Zhu_048_glioma


title: Input of 1.2Bind proliferating postinduction


title: Zhu_038_glioma


title: Zhu_037_glioma


title: Zhu_039_glioma


title: Zhu_032_normal cortex

value: normal


title: Zhu_031_normal cortex


title: Zhu_034_normal cortex


title: Zhu_036_glioma


title: 0h-Rep1

city: New York

first: Chandrika

last: Rao

address: 619 West 54th Street, 3rd Floor

institute: New York Stem Cell Foundation Institute

data_processing:
Libraries were sequenced on the Illumina HiSeq 4000 platform. This platform features an integrated Real-Time Analysis software, which performs base calling and assigns a quality score to each base for each cycle.
Reads were trimmed using Cutadapt (version cutadapt-1.9.dev2). Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the kit: TruSeq stranded mRNA kit (AGATCGGAAGAGC). Reads were aligned to the reference genome using STAR2 (version 2.5.2b) specifying paired-end reads and the option --outSAMtype BAM Unsorted.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using the rpkm() function of edgeR (version 3.16.5) and normalized effective library sizes. Gene lengths for the FPKM calculation were the number of bases in the exons of each gene.
Differential analysis was carried out with edgeR (version 3.16.5). Fold changes were estimated as per the default behaviour of edgeR, to avoid artefacts which occur with empirical calculation.
Genome_build: GRCm38
Supplementary_files_format_and_content: A comma-separated value (csv) file of raw gene-wise Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for every sample
Supplementary_files_format_and_content: A comma-separated value (csv) file of gene-wise differential expression log fold changes and false discovery rates (FDR), including individual expression values

source_name: doxycycline-inducible cell line used to drive overexpression of a forced homodimer construct of E2A

growth_protocol: Embryonic stem cells were maintained in LIF/serum medium

extract_protocol:
Total RNA was extracted using the Absolutely RNA Miniprep Kit (Agilent).
Library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: 24h and 48h samples were treated with doxycycline.

value: embryonic stem cell line

value: Untreated


title: 24h-Rep2

value: Treated with 1 ug/mL doxycycline for 24h


title: 18h-Rep3

value: Treated with 1 ug/mL doxycycline for 18h


title: 0h-Rep2


title: 18h-Rep1


title: 0h-Rep3


title: 24h-Rep3


title: 18h-Rep2


title: 24h-Rep1


title: E14.5 NICD GOF Plet1+ rep1

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14GOF_703517

data_processing:
Illumina RTA software used for basecalling and then FASTQ files were generated with bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (version 0.32, default parameters).
Trimmed reads were then mapped to GRCm38.p5 whole genome using STAR  (version 2.5.1a) with default parameters for paired end reads.
featureCounts (version 1.5.1) was used to quantify the gene counts with default options for paired-end reads.
Genome_build: GRCm38.p5 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file were generated with featureCounts.

source_name: Thymus

growth_protocol: In vivo

extract_protocol:
Dissociated TECs were directly FACS-sorted into Smartseq-2 buffer.
Libraries were prepared according to Smartseq-2 protocol (Picelli et al, 2013). Libraries were sequenced on Illumina HiSeq4000 using 75bp paired end sequencing.

tag: tissue

value: thymus

tag: batch

value: embryo


title: Zhu_030_normal cortex


title: E14.5 NICD GOF Plet1+ rep4

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14GOF_707517

tag: strain


title: E14.5 RBPJ LOF Plet1- rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_709506

value: Foxn1Cre RbpjFL/FL


title: E14.5 NICD GOF Plet1+ rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14GOF_706517


title: E14.5 NICD GOF Plet1+ rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14GOF_705517


title: Zhu_033_normal cortex


title: E14.5 RBPJ LOF Plet1+ rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_705505


title: E14.5 RBPJ LOF Plet1+ rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_703505


title: E14.5 RBPJ LOF Plet1+ rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_701505


title: E14.5 NICD GOF Plet1+ rep5

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14GOF_708517


title: E14.5 RBPJ LOF Plet1- rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_707506


title: E14.5 RBPJ WT Plet1- rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_712506

value: wild type


title: E14.5 RBPJ LOF Plet1- rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_711506


title: E14.5 RBPJ WT Plet1- rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_710506


title: Zhu_035_glioma

value: malignant glioma


title: E14.5 RBPJ WT Plet1- rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_708506


title: E14.5 RBPJ WT Plet1+ rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_704505


title: E14.5 RBPJ WT Plet1+ rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_706505


title: E12.5 RBPJ LOF Plet1+ rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_704506


title: E12.5 RBPJ LOF Plet1+ rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_702506


title: E14.5 RBPJ WT Plet1+ rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: e14LOF_702505


title: E12.5 RBPJ WT Plet1+ rep2

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_703506


title: E12.5 RBPJ LOF Plet1+ rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_706506


title: E12.5 RBPJ WT Plet1+ rep1

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_701506


title: WT_220

first: Shuai

last: Zhang

state: Shanghai

address: 320 YueYang Road

institute: SIBCB

data_processing:
After quality assessment of the corresponding FASTQ files with FastQC, adapter sequences were trimmed from the reads.
Raw reads were mapped to mm10 using Tophat with default parameters.
Differential gene expression was analyzed with Cuffdiff using the University of California Santa Cruz (UCSC) mm10 assembly as the reference sequence. In addition, genes with an expression fold change of >|2| were selected for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample. The columns are gene symbols, fold_change and FPKM.

source_name: Primary NSC prepared from the hippocampus of 2-month-old mouse

growth_protocol: TAM (200 mg/kg) was administered once daily by oral gavage for 5 consecutive days in adult (2 months) Med23 CKO mice. Littermate control mice received the same treatment. TM-treated mice were allowed to recover 3-4 weeks and then used in most experiments.

extract_protocol:
Total RNAs was extracted using Trizol reagent, and 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain hippocampus

tag: cell type

value: primary NSCs


title: E12.5 RBPJ WT Plet1+ rep3

description:
RBPJ_mutants-RawCounts.txt
processed data header: WTCHG_273884_705506


title: TDP43_iCLIP_seq1

city: Beijing

first: Wei

last: Liu

address: 5 Dongdan Santiao Road

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

description: RAW264.7 cells without VSV infection.

data_processing:
Library strategy: iCLIP-Seq
Primary sequencing data that produced by Illumina HiSeq 2500, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing, mapping and CITS analysis with raw data followed CLIP Tool Kit pubulished in the article named CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in DMEM (Corning) supplemented with 10% fetal bovine serum (FBS) (Gibco).

extract_protocol:
iCLIP was performed using anti-TDP43 antibody, and the isolated RNA was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were treated with PBS for 8 hours and then were crosslinked with UV at 254 nm for 300 mJ/cm2.

value: macrophage cell line

tag: passages

tag: strain/background

tag: infection

tag: ip antibody

value: TDP43 (Cell Signaling technology, G400, 3448)


title: KO_117

value: Med23 CKO

tag: age


title: KO_218

tag: genotype


title: KO_214


title: WT_116


title: TDP43_iCLIP_seq2

description: RAW264.7 cells with VSV infection for 8 hours.

treatment_protocol: RAW264.7 cells were infected with VSV for 8 hours and then were crosslinked with UV at 254 nm for 300 mJ/cm2.

tag: cell line

value: Vesicular stomatitis virus (VSV) for 8h


title: WT_213


title: KO ERRa/g-1 heart-2

city: Philadelphia

first: Tomoya

last: Sakamoto

state: PA

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Reads from 6 samples were mapped to mouse genome, mm10, using tophat 2.0.
Mapped reads were filtered based on the mapping quality. The overall mapping rates were about 90%. mRNA quantification and normalization was done using Partek Genomics Suite 6.6, annotation database using RefSeq Transcript.
R package DeSeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html) was used to analyze the differential expression of mRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Nkx2.5-Cre positive ERRa/g floxed E17.5 ventricles

growth_protocol: ERR a and g floxed mice, kindly provided by Dr. Anastasia Kralli (Johns Hopkins), were bred with mice expressing a Cre recombinase under control of the Nkx2-5 promoter (obtained from Jackson Laboratory, Stock No:024637) to generate cardiac-specific ERRa and ERRγ-deficient mice. Timed breedings were performed with the date of the vaginal plug defined as embryonic day (E) 0.5.

extract_protocol:
Bi-ventricles were harvested from the E17.5 embryos and RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.

value: ERRalpha/gamma KO

value: Embryonic age 17.5

value: bi-ventricles


title: K562 EU-seq PladB 4 hours DG4G

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

description: K562 EU-seq PladB 4 hours DG4G

data_processing:
Library strategy: EU-seq
Reads were mapped with STAR v2.7.0f_0328 with default parameters.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: All wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

source_name: K562 cell line

extract_protocol:
EU-RNA was enriched using Click-iT Nascent RNA Capture Kit (Invitrogen), with 5 µg of EU-RNA for biotinylation by click reaction and 1 µg of biotinylated RNA for binding to Streptavidin T1 magnetic beads.
cDNA was generated using iScript Select cDNA Synthesis Kit (Bio-Rad) and cleaned up before 2nd-strand synthesis. cDNA was ligated to Illumina barcoded adapters for sequencing. Library quality was checked on an Agilent BioAnalyzer and sequencing was performed on Illumina HiSeq or NovaSeq instruments.

treatment_protocol: PladB treated and control K562 cells were harvested 2 and 4 hours after PladB treatment. At each time point, genomic DNA was isolated from 5x10E6 cells and extracted.


title: K562 EU-seq Control DG4H

description: K562 EU-seq Control DG4H


title: K562 EU-seq PladB 2 hours DG4E

description: K562 EU-seq PladB 2 hours DG4E


title: K562 EU-seq DMSO 4 hours DG4F

description: K562 EU-seq DMSO 4 hours DG4F


title: K562 EU-seq PladB 4 hours DG4C

description: K562 EU-seq PladB 4 hours DG4C


title: K562 EU-seq DMSO 2 hours DG4D

description: K562 EU-seq DMSO 2 hours DG4D


title: WT E17.5 heart-3

source_name: Nkx2.5-Cre negative ERRa/g floxed E17.5 ventricles


title: KO ERRa/g-1 heart-3


title: WT_215


title: K562 EU-seq Control DG4A

description: K562 EU-seq Control DG4A


title: WT E17.5 heart-2


title: WT E17.5 heart-1


title: K562 sDRIP-seq Control DG3D

description: K562 sDRIP-seq Control DG3D

data_processing:
Library strategy: sDRIP-seq
Reads were mapped with STAR v2.7.0f_0328 with default parameters.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: All wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

extract_protocol:
Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA was amplified as per standard Illumina TruSeq Single end protocol.


title: K562 sDRIP-seq PladB 4 hours DG3C

description: K562 sDRIP-seq PladB 4 hours DG3C


title: K562 sDRIP-seq DMSO 4 hours DG3E

description: K562 sDRIP-seq DMSO 4 hours DG3E


title: K562 sDRIP-seq DMSO 4 hours DG3B

description: K562 sDRIP-seq DMSO 4 hours DG3B


title: KO ERRa/g-1 heart-1


title: K562 RNA-seq PladB 4 hours DG2H

description: K562 RNA-seq PladB 4 hours DG2H

data_processing:
Reads were mapped with STAR v2.7.0f_0328 with default parameters.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: All wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.
Standard paired-end TruSeq protocol.


title: K562 sDRIP-seq Control DG3A

description: K562 sDRIP-seq Control DG3A


title: K562 RNA-seq PladB 2 hours DG2G

description: K562 RNA-seq PladB 2 hours DG2G


title: K562 RNA-seq DMSO 4 hours DG2F

description: K562 RNA-seq DMSO 4 hours DG2F


title: WHIM12_ZNF446_ChIP_rep2

city: Dallas

first: Angelique

last: Whitehurst

state: TX

address: 6001 Forest Park Rd

institute: University of Texas Southwestern Medical Center

description: Cells were made to stably express ZNF446-V5 via lentiviral transduction followed by selection with blasticidin.

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using Bowtie2 (ver 2.3.2) with "sensitive" parameter enabled; mapped reads were sorted and indexed with SAMtools (ver 1.4.1).
The HOMER (ver 4.9) findPeaks module was used to call peaks, with size and minimum distance parameters set to 150 bp and 370 bp, respectively. Otherwise, default parameters were used.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using DeepTools (ver 2.3.5); counts represent the number of reads per 10-bp bin.

source_name: Human triple-negative breast cancer cells

growth_protocol: Cells were grown to ~90% confluency on 150mm plates prior to harvesting. WHIM12 cells were cultured in MEM supplemented with 10% FBS. SUM159 cells were cultured in Ham's F-12 supplemented with 5% FBS, 1 μg/mL hydrocortisone, and 5 μg/mL insulin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 15 min at 37°C. Crosslinking was quenched with 0.125 M glycine for 5 min at 4°C, followed by multiple washes with cold PBS. Nuclei were harvested via hypotonic lysis and subjected to sonication in a lysis buffer containing 1% SDS. Sheared chromatin lysates were then pre-cleared with Protein A/G agarose beads for 1 hour, followed by immunoprecipitation with appropriate antibody overnight at 4°C. Protein A/G agarose beads blocked with BSA were added to lysates for 2 hours the next day, followed by extensive washes. Protein/DNA complexes were eluted from the beads with 100 mM NaHCO3 and 1% SDS, and de-crosslinking was carried out overnight at 65°C. RNA and protein were digested with RNase A and Proteinase K, respectively. DNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated overnight at -20°C.
Libraries of ChIP DNA were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to manufacturer's instructions, and samples were multiplexed with Illumina adapters (NEB).

value: triple-negative breast cancer

tag: chip antibody

value: V5 (Abcam, ab9116)


title: SUM159_ZNF165_ChIP_rep1

description: Cells were made to stably express ZNF165-V5 via lentiviral transduction followed by selection with puromycin.


title: WHIM12_ZNF446_input_rep2

value: input


title: K562 EU-seq PladB 2 hours DG4B

description: K562 EU-seq PladB 2 hours DG4B


title: WHIM12_ZNF446_ChIP_rep1


title: SUM159_ZNF446_ChIP_rep2


title: K562 RNA-seq PladB 4 hours DG2C

description: K562 RNA-seq PladB 4 hours DG2C


title: K562 RNA-seq Control DG2D

description: K562 RNA-seq Control DG2D


title: SUM159_ZNF446_ChIP_rep1


title: SUM159_ZNF446_input_rep2


title: K562 RNA-seq PladB 2 hours DG2B

description: K562 RNA-seq PladB 2 hours DG2B


title: SUM159_ZNF446_input_rep1


title: SUM159_ZNF165_ChIP_rep2


title: K562 DRIP-seq PladB 4 hours DG1H

description: K562 DRIP-seq PladB 4 hours DG1H

data_processing:
Library strategy: DRIP-seq
Reads were mapped with STAR v2.7.0f_0328 with default parameters.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: All wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).


title: K562 RNA-seq Control DG2A

description: K562 RNA-seq Control DG2A


title: K562 DRIP-seq PladB 2 hours DG1G

description: K562 DRIP-seq PladB 2 hours DG1G


title: WHIM12_SMAD3_ChIP_rep2

value: SMAD3 (Abcam, ab28379)


title: SUM159_ZNF165_input_rep1


title: K562 DRIP-seq DMSO 4 hours DG1F

description: K562 DRIP-seq DMSO 4 hours DG1F


title: WHIM12_SMAD3_input_rep2


title: WHIM12_ZNF446_input_rep1


title: K562 DRIP-seq Control DG1D

description: K562 DRIP-seq Control DG1D


title: K562 RNA-seq DMSO 2 hours DG2E

description: K562 RNA-seq DMSO 2 hours DG2E


title: WHIM12_SMAD3_input_rep1


title: SUM159_SMAD3_ChIP_rep2


title: WHIM12_SMAD3_ChIP_rep1


title: K562 DRIP-seq PladB 2 hours DG1B

description: K562 DRIP-seq PladB 2 hours DG1B


title: K562 DRIP-seq PladB 4 hours DG1C

description: K562 DRIP-seq PladB 4 hours DG1C


title: SUM159_SMAD3_ChIP_rep1


title: K562 DRIP-seq DMSO 2 hours DG1E

description: K562 DRIP-seq DMSO 2 hours DG1E


title: SUM159_SMAD3_input_rep1


title: K562 DRIP-seq Control DG1A

description: K562 DRIP-seq Control DG1A


title: Healthy_NKcells_800_73-

city: Solna

first: Andreas

last: Lundqvist

address: Solnavägen 30, J6:20

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalls were performed using CASAVA version 1.8 and sequencing data was uploaded to Illumina's BaseSpace for demultiplexing run (bcl) files to fastq files.
For each sample, lane technical reads were concatenated and paired-end reads were uploaded for 10 samples to Partek Flow (20 fastq files). Paired-end reads were quality trimmed to Phred 20 and aligned to the human genome (GENCODE hg38 version 28) with rRNA sequences removed (command grep -wv 'rRNA\|tRNA\|Mt_rRNA\|Mt_tRNA' gencode.v28.gtf > gencode.v28.annotation.norRNA.gtf ) using STAR v2.5.3a with default parameters.
Gene level counts were normalized using counts per million (CPM) (+1.0E-4) and quantified using a mixed-model ANOVA for differential gene expression analysis using donor ID as a random effect and CD73+/- expression status as a fixed factor in Partek Flow.
Genome_build: hg38 (GENCODE version 28)
Supplementary_files_format_and_content: GTF file includes hg38 annotations with rRNA sequences removed; tab-delimited text files include raw gene counts (Gene_counts.txt) and normalized counts (Normalized_counts.txt)

source_name: Healthy donor PBMC

growth_protocol: 48 hours prior to tumor co-culture, NK cells were activated with 1000IU/mL of IL-2 in XVIVO-20 media (Lonza).

extract_protocol:
Total RNA was isolated from FAC-sorted NK cell populations with Qiagen RNAeasy Microkit based on the manufacturer's protocol.
Total RNA was normalized to 28 picograms of input for full-length cDNA generation using Takara’s SMART-Seq v4 Ultra Low Input RNA Kit (Cat # 634888) following the manufacturer’s recommendations. Amplified cDNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (Cat # Q32854) and validated using the Agilent 2100 High Sensitivity DNA Kit (Cat # 5067-5584 and 5067-5585). cDNA was normalized to 1 nanogram of input for sequencing library generation using Illumina’s Nextera XT DNA Library Preparation Kit (Cat # FC-131-1024) following the manufacturer’s protocol. Final cDNA libraries were assessed on the Agilent TapeStation 4200 using the High Sensitivity D1000 ScreenTape assay. cDNA libraries were quantified by qPCR using Kapa Biosystems’ Library Quantification Kit (Cat # KK4854) on the Roche LightCycler 480 Instrument II following the manufacturer’s protocol. cDNA libraries were normalized to 1.5-2 nM, pooled and denatured following Illumina’s NextSeq System Denature and Dilute Libraries Guide. Final pooled libraries (n=5 samples) were spiked with 1% PhiX as an internal control and loaded at a final concentration of 1.6 pM onto the Illumina NextSeq 500 platform. cDNA libraries were sequenced on a 2x75 bp paired-end run using the NextSeq 500 High Output v2 Kit (150 cycles) for n=2 sequencing runs.

treatment_protocol: IL-2 pre-activated NK cells were co-cultured with 786O cell line for 4 hours in the absence of IL-2 before FACS based on acquired CD73 surface expression.

tag: donor id

tag: disease state

value: healthy

value: Natural Killer cells

tag: passage

value: Primary

tag: surface expression


title: SUM159_SMAD3_input_rep2


title: Healthy_NKcells_800_73+


title: Healthy_NKcells_152_73+


title: Healthy_NKcells_152_73-


title: Healthy_NKcells_151_73-


title: Healthy_NKcells_36_73-


title: Healthy_NKcells_36_73+


title: Human NKT cell unstimulated sample 3

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

description: Unstimulated NKT cells from PBMCs.

data_processing:
Sequencing read demultiplexing, aligning to the hg19 human reference genome, barcode processing, and UMI counting were performed using the 10X Genomics Cell Ranger (v2.0.1) pipeline.
Estimated number of cells captured per sample were between 1,681-3,117 with 53,649-75,267 mean reads per cell, 583-776 median genes per cell, and 1,452-2,357 median UMI counts per cell.
A filtered gene-barcode matrix for each sample containing only detected cellular barcodes was generated and subsequently analyzed using the R Seurat package.
Samples have 3 fastq files associated with them with a tag in the filename, namely I1, R1, and R2. The I1 contains the sample index. The R1 contains the 10x barcode (16 base pairs) followed by UMI (10 bp). The R2 contains the transcript reads.
Genome_build: hg19
Supplementary_files_format_and_content: Cell Ranger filtered gene-barcode matrix outputs of cell barcode, gene name, and UMI count matrix files.

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood within 2 hours of collection using ficoll-Paque density gradient centrifugation. Single cell suspensions were stained with PE-hCD1d PBS-57 (NIH Tetramer Core Facility), followed by anti-PE microbeads (Miltenyi Biotec), and cell separation by autoMACS (Miltenyi Biotec). Separated NKT-enriched PBMCs were then stained with anti-hCD3 and hCD1d PBS-57 antibodies and NKT cells (CD3+CD1d PBS57+) were then sorted on BD FACSAriaII.  For stimulated NKT cells, freshly isolated PBMCs were first stimulated with PMA/Ionomycin for 2 hours, followed by NKT cell enrichment and sorting as aforementioned.
Single cell sequencing libraries were generated using the 10X Genomics Chromium Single Cell 3’ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller. Reverse transcription of the GEM (GEM-RT) was performed in a Thermocycler (Veriti™ 96-Well Fast Thermal Cycler, Applied Biosynthesis; 53 °C 45 min, 85 °C 5 min, 4 °C hold). cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) with the same Thermocycler (98 °C 3 min; 98 °C 15 sec, 67 °C 20 sec, 72 °C 1 min, repeat 12 cycles; 72 °C 1 min, 4 °C hold). Amplified cDNA is cleaned up with SPRIselect Reagent Kit (Beckman Coulter) and followed by library construction procedure, including fragmentation, end repaired, adaptor ligation, and library amplification. A Bioanalyzer (Agilent) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using paired-end flow cell: Read 1, 26 cycles, i7 index 8 cycles; Read 2: 110 cycles.

value: Blood

value: NKT cells

tag: treatment

value: unstimulated


title: Human NKT cell unstimulated sample 2

description: Unstimulated NKT cells from PBMCs.

tag: tissue


title: Human NKT cell unstimulated sample 1

description: Unstimulated NKT cells from PBMCs.


title: Human NKT cell stimulated sample 2

description: PMA/ionomycin-stimulated NKT cells from human PBMCs.

value: PMA/ionomycin-stimulated


title: Human NKT cell stimulated sample 3


title: Healthy_NKcells_489_73+


title: Human NKT cell stimulated sample 1


title: T98G_control

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner
Aligned reads were quantified the expression against the ENSEMBL (hg38_ensembl_release79_v2) database by the Partek Expectation-Maximization algorithm using the counts per million normalization and added 0.0001
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: hg88
Supplementary_files_format_and_content: counts per million

source_name: Cell line

extract_protocol:
RNA was isolated using Trizol (#15596-018, Thermo Scientific)
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

tag: sipool

value: non-target


title: LNT229_HOTAIRM1_KD


title: U251_HOTAIRM1_KD


title: CD4_NA_NA_CD154Pos_Dup2_Batch2

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
Single-cell RNA-seq with 10x Genomics 3' v2
allergen_Teff_umi.txt.gz
allergen_Th2_umi.txt.gz

data_processing:
mkfastq (Cell Ranger 2.0.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 2.0.0) was used to generate the filtered UMI matrix from multiple runs with default parameters
Seurat (3.0) was used to filter, normalize and scale the UMI matrix
Genome_build: hg19
Supplementary_files_format_and_content: allergen_Teff_annotation.txt.gz annotation table for T effector cells
Supplementary_files_format_and_content: allergen_Teff_umi.txt.gz UMI matrix for T effector cells
Supplementary_files_format_and_content: allergen_Th2_annotation.txt.gz annotation table for Th2 cells
Supplementary_files_format_and_content: allergen_Th2_umi.txt.gz UMI matrix for Th2 cells
Supplementary_files_format_and_content: allergen_Treg_annotation.txt.gz annotaion for T regulatroy cells
Supplementary_files_format_and_content: allergen_Treg_umi.txt.gz UMI matrix for T regulatory cells
Supplementary_files_format_and_content: allergen_Tneg_annotation.txt.gz annotation table for unstimulated T cells
Supplementary_files_format_and_content: allergen_Tneg_umi.txt.gz UMI matrix for unstimulated T cells

growth_protocol: Not applicable

extract_protocol:
For single cell RNA-seq assays (10x Genomics), 1000 to 2000 HDM-reactive T cells per subject were collected by sorting in low retention and sterile ice-cold 1.5 mL collection tubes containing 500 µL of PBS:FBS (1:1 vol:vol) with RNAse inhibitor (1:100). HDM-reactive T cells from 6 subjects in each of the 4 groups (asthma with HDM-allergy, asthma without HDM allergy, HDM-allergy without asthma and healthy without HDM-allergy) were collected in the same tube. Collection tubes with ~9,000 to 12,000 sorted cells/study group were inverted a few times, ice-cold PBS was added to reach a volume of 1400 µl, and centrifugated for 5 minutes at a speed of 600 g at 4 ˚C. Supernatant was cautiously removed leaving 5 to 10 µl of volume. Pellets were then resuspended with 25 µl of 10x Genomics resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin (0.04 %, Sigma-Aldrich). 33 µl of cell suspension were transferred to an 8 PCR-tube strip for downstream steps as per manufacturer’s instructions (10x Genomics, San Francisco).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol
100 x 100 bp paired-end reads, 3'TAG, Hg19 human reference genome.

treatment_protocol: For each donor, PBMC cryovials were thawed, washed and, plated overnight in 6-well culture plates at a concentration of 10 x 106 cells/ml in 2 ml of serum-free TexMACS medium (Miltenyi Biotec) (5 % CO2, 37 ˚C). In presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec), cells were then stimulated by addition of HDM peptide pool (1 µg/ml; Hintz et al, 2015) for 6 h (Bacher et al.,2016). Subsequently, cells were stained with fluorescence-labeled antibodies and a biotinylated CD154 antibody (clone 5C8; Miltenyi Biotec). Anti-biotin microbeads (Miltenyi Biotec) were added to allow MACS-based enrichment of CD154+ cells using MS columns (Miltenyi Biotec). 5 % of cells were kept as control sample (‘input’) and used for FACS sorting of HDM– T cells and analysis of cell frequencies before enrichment. Positively selected cells (CD154+) were eluted from the column and used for FACS sorting of CD154+ memory CD4+ T cells. The flow-through from the MACS column was collected, stained with a biotinylated CD137 antibody (clone REA765; Miltenyi Biotec) and anti-biotin MicroBeads and applied to a second MS column. Positively selected cells (CD137+) were used for FACS sorting of CD137+ cells.

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+

tag: disease group

value: Non Asthmatic & Non Allergic to HDM


title: LNT229_control


title: U251_control


title: CD4_NA_AL_CD154Pos_Dup2_Batch2

tag: cell type

value: Non Asthmatic & Allergic to HDM


title: MB3

first: Ping

last: Xue

address: Rd Wanyuan

institute: Children's Hospital of Fudan University

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads
the trimmed reads were aligned to merged pre-miRNA databases,using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression
The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Genome_build: miRBase v21
Supplementary_files_format_and_content: text files include TPM values for each Sample

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps：1) 3'-adaptor ligation;2) 5'-adaptor ligation3) cDNA synthesis;4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

value: peripheral blood

value: medulloblastoma


title: CK3

value: healthy control


title: MB2


title: T98G_HOTAIRM1_KD


title: CD4_AS_AL_CD154Neg_CD137Neg_Batch2

description:
Single-cell RNA-seq with 10x Genomics 3' v2
allergen_Tneg_umi.txt.gz
allergen_Tneg_umi.txt.gz

value: Memory CD4 T cells:CD3+ CD4+ CD45RA- CD154- CD137-

value: Asthmatic & Allergic to HDM


title: MB4


title: CD4_AS_AL_CD154Pos_Dup2_Batch2


title: Healthy_NKcells_151_73+


title: MB1


title: Healthy_NKcells_489_73-


title: CK1


title: CK2


title: CD4_AS_NA_CD154Pos_Dup2_Batch2

value: Asthmatic & Non Allergic to HDM


title: CD4_NA_AL_CD137Pos_CD154Neg_Batch2

description:
Single-cell RNA-seq with 10x Genomics 3' v2
allergen_Treg_umi.txt.gz
allergen_Treg_umi.txt.gz

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi


title: CD4_NA_AL_CD154Pos_Batch1


title: CD4_AS_AL_CD154Pos_Dup2_Batch1


title: CK4


title: CD4_NA_NA_CD137Pos_CD154Neg_Batch2


title: Six2 Cre Tsc1 fl/fl + Rapamycin treated proximal tubule cells repeat 1

city: Jerusalem

first: Morris

last: Nechama

state: Israel

address: Hadassah Medical Center, Ein Karem

department: Pediatric

country: Israel

institute: Hadassah Hebrew University Medical Center

data_processing:
Raw reads were quality trimmed at both ends with a threshold of 32. Adapter sequences were removed with cutadapt, version 1.18, using parameters -O 1, --match-read-wildcards and -m 15. Remaining reads were filtered with fastq_quality_filter (FASTX package, version 0.0.14), using parameters -q 20 and -p 90.
Processed reads were aligned to the mouse genome with TopHat, version 2.1.1, using parameters -G genes.gtf, -N 6, --read-gap-length 5, --read-edit-dist 11, --segment-length 20, --read-realign-edit-dist 3, --no-coverage-search and --library-type fr-firststrand.
Raw counts were obtained with htseq-count, version 0.6.0, using parameter -s reverse and masking short non-coding RNAs, e.g. miRNA.
Genes with less than 10 reads were discarded, then normalized counts and differential expression were calculated with DESeq2, version 1.22.1. Default parameters were used, except setting independentFiltering=F.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with a header row, followed by data for each gene. Columns include general gene details (A-K), raw counts in each sample (L-T), normalized counts (U-AC), average expression in the system as a whole (AD), results of comparing Tsc1 knockout to wild-type (AE-AI), results of comparing Tsc1 knockout + rapamycin to wild-type (AJ-AN), results of comparing Tsc1 knockout + rapamycin to Tsc1 knockout (AO-AS), and columns with binary indication of significance (AT-AV). A '?' denotes missing value.

source_name: Six2 Cre Tsc1 fl/fl + Rrapamycin

growth_protocol: Tsc1 fl/fl mice were mated with Six2 Cre Tsc1fl/+ to generate embryos with the Six2Cre Tsc1 fl/fl genotype. All mice were maintained in the Hebrew University Specific-Pathogen-Free (SPF) Animal Facility Unit

extract_protocol:
kidneys of the matching genotype were  excised in ice-cold HBSS buffer. The kidneys were sliced and chopped into ~0.5-1 mm pieces on ice using a surgical scalpel. The chopped kidneys were transferred into HBSS solution containing 1 μg/μl collagenase/Dispase and incubated for 25 minutes at 370 C. The cells were filtered through a 40 μm nylon cell strainer and washed twice with cold HBSS. For proximal tubular cell isolation, the cells were stained with PE-conjugated anti-CD133/prominin-1 antibody and PE+ cells were isolated by cell flow cytometry-based cell sorting. RNA was extracted using Trizol
Libraries were prepared from RNA samples using a KAPA Stranded mRNA-Seq Kit (KK8401, Roche). The libraries were barcoded and pooled for multiplex sequencing (1.5 pM total, including 1.5% PhiX control library). The pooled cDNA was loaded on NextSeq 500 High Output v2 kit (75 cycles) cartridge (Illumina) and sequenced on Illumina NextSeq 500 System

treatment_protocol: pregnant mice as indicated were IP injected with Rapamycin (0.2 mg/kg) or vehicle every other day between embryonic date E12.5-E16.5

value: Proximal Tubule cells

tag: strain

value: Rapamycin treatment

value: Six2 Cre Tsc1 fl/fl

tag: disease

value: Tuberous sclerosis


title: Six2 Cre Tsc1 fl/fl + Rapamycin treated proximal tubule cells repeat 3


title: Six2 Cre Tsc1 fl/fl + Rapamycin treated proximal tubule cells repeat 2


title: CD4_AS_AL_CD137Pos_CD154Neg_Batch2

value: Blood


title: Six2 Cre Tsc1 fl/fl proximal tubule cells repeat 3

source_name: Six2 Cre Tsc1 fl/fl

value: DMSO


title: CD4_AS_NA_CD137Pos_CD154Neg_Batch2


title: Six2 Cre Tsc1 fl/fl proximal tubule cells repeat 1


title: CD4_AS_AL_CD154Pos_Dup1_Batch1


title: CD4_NA_AL_CD154Pos_Dup1_Batch2


title: CD4_NA_NA_CD154Pos_Dup1_Batch2


title: Wild type proximal tubule cells repeat2

source_name: WT

value: Tsc1 fl/fl

value: No disease


title: Wild type proximal tubule cells repeat1


title: S7_S6

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

data_processing:
Base calling software: RTA v2
Reads were quasi-mapped to the mouse genome (modified to include the cOVA transgene) and quantified at the transcript level using Salmon v0.11.2 ( settings: -p 20 --seqBias --validateMappings --gcBias --biasSpeedSamp 5 -i GRCm38_index -l A -1) followed by summary to the gene level using tximport v1.10.1.
Differential gene expression was performed with DESeq2 v1.22.2. Gene set enrichment analysis was performed with the MSigDB canonical pathways gene sets using FGSEA v1.8.0 run with 100,000 permutations.
Genome_build: mm10
Supplementary_files_format_and_content: The processed csv file contained raw (not normalized) gene level counts for all samples.

source_name: Sham_24hr_Intracranial B16F1cOVA

growth_protocol: Male C57BL/6 mice were purchased from Charles River and maintained on a 12/12 hour light/dark cycle. Mice used in the experiments weighed between 22 and 28 g and were given food and water ad libitum. All animal experiments were approved by the Animal Care and Use Committee at the University of Virginia and conformed to the National Institutes of Health regulations for the use of animals in research.

extract_protocol:
Immediately following euthanasia, the mouse brains were harvested and the B16F1cOVA tumors (FUS-treated region) were excised, placed in RNAlater (Qiagen), and stored at -80 °C. RNA extraction was performed using the RNeasy Mini Kit (Qiagen). mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, Massachusetts).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was performed using a NextSeq 500 (Illumina, San Diego, California) at a target depth of 25 million 2 x 75 bp paired end reads per sample.

treatment_protocol: FUS treatments were applied at day 3 after tumor cell implantation. Mice were anesthetized with a mixture of Ketamine (40 mg/kg; Zoetis, Kalamazoo, MI) and Dextomitor (0.2 mg/kg, Zoetis, Kalamazoo, MI) in 0.9% sterile saline and tail veins were cannulated to allow for intravenous injections. The MR-guided FUS system (RK-100, FUS Instruments) sat directly on the patient table of a clinical 3T MRI scanner (Siemens Avanto). Mice were placed supine on the MR-guided FUS system with the skull sonically coupled to a 1.1 MHz spherically focused ultrasound transducer (with a 550 kHz hydrophone mounted in the center for passive cavitation detection) immersed in a degassed water bath. For the general treatment procedure, MultiHance gadolinium contrast agent (Bracco Diagnostics) was administered intravenously and a pre-FUS T1-weighted contrast-enhanced MR image of the entire brain was acquired using a custom-built 3-cm loop receive RF coil and three-dimensional spoiled gradient echo pulse sequence. Pulse-sequence parameters for all T1-weighted images were as follows: TR/TE =  11/5.33 ms, flip angle = 15°, readout bandwidth = 250 Hz/Px, FOV = 46×67×45 mm, resolution = 0.35 mm isotropic, total time per image = 3:05. A single target spot was chosen from this pre-sonication MR image to cover the entire tumor and surrounding tissue. To open the BTB/BBB, albumin-shelled MBs (1 x 105/gram body weight; manufactured as previously described) were intravenously injected and FUS was applied to the targets using specified peak negative pressures (0.5 MPa measured in water). FUS was applied in 10 ms pulses with a 2 s pulsing interval (i.e. 0.5% duty cycle) for a total of 2 minutes. Animals were then re-injected with gadolinium contrast agent and post-sonication T1-weighted contrast-enhanced MR images were acquired to confirm BTB/BBB opening. Once the treatment was completed, mice were given Antisedan to reverse the anesthesia and allowed to recover on a heating pad.

tag: Sex

value: male

tag: harvest timepoint

value: Sham


title: Wild type proximal tubule cells repeat3


title: CD4_AS_NA_CD154Pos_Dup1_Batch2

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+


title: CD4_AS_AL_CD154Pos_Dup1_Batch2


title: S9_S7


title: CD4_AS_NA_CD154Pos_Batch1


title: S4_S4


title: S2_S2


title: Six2 Cre Tsc1 fl/fl proximal tubule cells repeat 2


title: CD4_NA_NA_CD154Pos_Batch1

value: Non Asthmatic & Non Allergic to HDM


title: S6_S5

source_name: FUS_24hr_Intracranial B16F1cOVA

value: FUS


title: S10_S8


title: S1_S1


title: S16_S14

source_name: Sham_6hr_Intracranial B16F1cOVA


title: S19_S16


title: S13_S11


title: S11_S9


title: 091_41BB_15_AR

description: 200 cells bulk, full-transcriptome (Smart-seq2, Rosales et al.,  2018)

data_processing:
RNA-seq data were mapped against the hg19 reference using TopHat (v1.2.1 (--library-type fr-unstranded --no-coverage-search) with FastQC (v0.11.2), Bowtie108 (v1.1.2), Samtools 0.1.18.0) and we employed Cutadapt (v1.3) was used to remove adapters. The RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s no -t exon -i gene_name,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: allergen_Tcells_raw_counts.txt.gz contains Transcript per Million normalized counts
Supplementary_files_format_and_content: allergen_Tcells_TPM.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count

extract_protocol:
Cells of interest were directly collected by sorting 200 cells into 0.2 ml PCR tubes (low-retention, Axygen) containing 8 μl of ice-cold lysis buffer (Triton X-100 [0.1 %, Sigma-Aldrich] containing RNase inhibitor (1:100, Takara). Once collected, tubes were vortexed for 10 seconds, spun for 1 minute at 3000 g and stored at -80 ˚C.
We followed the Samert-Seq2 protocol as described previously (Picelli et al.,2013; Rosales et al.,2018) with following modifications: (i) the pre-amplification PCR cycle for T cells was set at 22 cycles; (ii) to eliminate any traces of primer-dimers, the PCR pre-amplified cDNA product was purified using 0.8x Ampure-XP beads (Beckman Coulter) before using the DNA for sequencing library preparation. One ng of pre-amplified cDNA was used to generate barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) in 8 µl reaction volume. Samples failing any quality control step (DNA quality assessed by capillary electrophoresis (Fragment analyzer, Advance analytical) and quantity (Picogreen quantification assay, Thermofisher) were eliminated from further downstream steps. Libraries were then pooled at equal molar concentration and sequenced using the HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (HiSeq SBS Kit v4; Illumina).
50 bp single-end reads, full transcriptome, Hg10 human reference genome.

value: Non-Asthmatic & Allergic to HDM


title: 090_41BB_14_AR


title: 095_41BB_22_HC

value: Non-Asthmatic & Non-Allergic to HDM


title: 094_41BB_21_HC


title: 093_41BB_18_AR


title: 096_41BB_23_HC


title: S17_S15

source_name: FUS_6hr_Intracranial B16F1cOVA


title: 092_41BB_16_AR


title: 089_41BB_6_AS_AL

value: Asthmatic & Allergic to HDM


title: 088_41BB_5_AS_AL

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi


title: S15_S13


title: Genomic DNA from FC1749

type: genomic

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Atopic dermatitis sample from FC1749

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

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

data_processing: GenomeStudio methylation module v.1.9.0

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: age

value: Atopic dermatitis

tag: ige

value: PBMC


title: 087_41BB_4_AS_AL


title: S14_S12


title: Genomic DNA from FC1109

description: Atopic dermatitis sample from FC1109


title: Genomic DNA from FC1655

description: Atopic dermatitis sample from FC1655


title: Genomic DNA from FC1720

description: Atopic dermatitis sample from FC1720


title: 086_41BB_3_AS_AL


title: Genomic DNA from FC1711

description: Atopic dermatitis sample from FC1711


title: S12_S10


title: Genomic DNA from FC1100

description: Atopic dermatitis sample from FC1100


title: Genomic DNA from FC1761

description: Atopic dermatitis sample from FC1761


title: 085_41BB_2_AS_AL


title: Genomic DNA from FC1557

description: Atopic dermatitis sample from FC1557


title: wild-type heart 7 days post myocardial Infarction

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NextSeq 500 Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to human reference genome (refdata-cellranger-mm10-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: MI7D_metadata.txt.gz contains cell barcode and cell type

source_name: heart cell

extract_protocol:
1wk post MI hearts were harvested and digested by liberase as described later. After digestion, cells were incubated with 10µM Calcein AM (Abcam, ab141420) and flow sorted to identify live cells followed by library preparation.
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).

value: heart

tag: genotype

value: wildtype

value: 7 days post myocardial Infarction


title: Genomic DNA from FC1536

description: Atopic dermatitis sample from FC1536


title: 084_41BB_1_AS_AL

value: Blood


title: Genomic DNA from FC1624

description: Atopic dermatitis sample from FC1624


title: Genomic DNA from FC1694

description: Atopic dermatitis sample from FC1694


title: mRNA seq of control liver (ARID1B f/f; Alb-Cre-) [ARID1B-F7-WT]

city: DALLAS

first: Zixi

last: Wang

address: 5323 HARRY HINES BLVD

department: CRI

institute: UT SOUTHWESTERN MEDICAL CENTER

description:
ARID1B-F7-WT
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt

data_processing:
Reads with phred quality scores less than 20 and read length less than 35bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then mapped to the mouse reference genome GRCm38 (mm10) using the HISAT (version 2.1.0) aligner with default settings.
After mapping, rRNA reads were filtered from resulting .bam files according to their overlap with the coordinates of rRNA gene list obtained from UCSC genome browser site.
Mapped reads were counted using featureCounts (version 1.6.2) program to obtain raw read counts for each gene.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: *.normalized.bigwig: bigWig genome browser tracks.
Supplementary_files_format_and_content: *txt: Tab-delimited text files include the raw counts from featureCounts.

source_name: liver

growth_protocol: All mice were handled in accordance with the guidelines of the Institutional Animal Care and Use Committee at UTSW.

extract_protocol:
Liver total RNA was extracted from BKO, DKO and corresponding WT using TRIzol reagent followed by purification using RNeasy Mini kit (Qiagen).
RNA-seq libraries were prepared with the Ovation RNASeq Systems 1-16 (Nugen).

value: Liver

tag: genotype/variation

value: ARID1B f/f; Alb-Cre-


title: Genomic DNA from FC1628

description: Atopic dermatitis sample from FC1628


title: Genomic DNA from FC1450

description: Atopic dermatitis sample from FC1450


title: Genomic DNA from FC1672

description: Atopic dermatitis sample from FC1672


title: Genomic DNA from FC1680

description: Atopic dermatitis sample from FC1680


title: Genomic DNA from FC1671

description: Atopic dermatitis sample from FC1671


title: Genomic DNA from FC1523

description: Atopic dermatitis sample from FC1523


title: Genomic DNA from FC1575

description: Atopic dermatitis sample from FC1575


title: Genomic DNA from FC1544

description: Atopic dermatitis sample from FC1544


title: Genomic DNA from FC1739

description: Atopic dermatitis sample from FC1739


title: 081_41BB_8_AS_NA

value: Asthmatic & Non Allergic to HDM


title: mRNA seq of control liver (ARID1B f/f; Alb-Cre-) [ARID1B-F5-WT]

description:
ARID1B-F5-WT
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: 082_41BB_10_AS_NA


title: Genomic DNA from FC1613

description: Atopic dermatitis sample from FC1613


title: mRNA seq of ARID1B KO liver (ARID1B f/f; Alb-Cre+) [ARID1B-F6-KO]

description:
ARID1B-F6-KO
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt

value: ARID1B f/f; Alb-Cre+


title: mRNA seq of control liver (ARID1B f/f; Alb-Cre-) [ARID1B-F5-WT-2]

description:
ARID1B-F5-WT-2
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: 080_41BB_24_HC


title: Genomic DNA from FC1525

description: Atopic dermatitis sample from FC1525


title: 079_41BB_23_HC


title: Genomic DNA from FC481

description: Control sample from FC481

value: Control


title: Genomic DNA from FC479

description: Control sample from FC479


title: Genomic DNA from FC1534

description: Atopic dermatitis sample from FC1534


title: Genomic DNA from FC1521

description: Atopic dermatitis sample from FC1521


title: mRNA seq of ARID1B KO liver (ARID1B f/f; Alb-Cre+) [ARID1B-F3-KO]

description:
ARID1B-F3-KO
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: mRNA seq of ARID1B KO liver (ARID1B f/f; Alb-Cre+) [ARID1B-F4-KO]

description:
ARID1B-F4-KO
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: 078_41BB_22_HC


title: N21_4

city: Saint Louis

first: Bo

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to mm10 using STAR_2.5.4b with gencode vM15 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Quantified reads were corrected for batch effect using RUVr from the RUVSeq R package (v 1.16.1) according to the protocol described in the vignette using option k=3.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts .txt file

source_name: 21 DPA, proximal amputation

extract_protocol:
Frozen tissues were crushed with a pestle and the tissue lysates homogenized. Total RNA was isolated (RNeasy Mini Kit, QIAGEN) following the manufacturer’s protocol, depleted of ribosomal RNA via a hybridization method (Ribo-Zero Gold rRNA Removal Kit, Illumina), and purified with DNase treatment (Ambion DNA-free DNA Removal Kit, Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using 1 µg of total RNA per sample (average RNA integrity number of 8) and standard Illumina protocols.

value: 10-12 weeks old

value: Hind limb digit tip (bone, cartilage, marrow, dermis, epidermis)

value: proximal amputation

tag: time

value: 21 DPA


title: mRNA seq of control liver (ARID1B f/f; Alb-Cre-) [ARID1B-F2-WT]

description:
ARID1B-F2-WT
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: Genomic DNA from FC497

description: Control sample from FC497


title: 077_41BB_21_HC

value: Non-Asthmatic & Non-Allergic to HDM


title: Genomic DNA from FC470

description: Control sample from FC470


title: N21_3


title: Genomic DNA from FC473

description: Control sample from FC473


title: 076_41BB_20_HC

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi


title: mRNA seq of control liver (ARID1A f/f; ARID1B f/f; Alb-Cre-) [WT-7139]

description:
WT-7139
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt

value: ARID1A f/f; ARID1B f/f; Alb-Cre-


title: 075_41BB_19_HC


title: N21_1


title: N21_2


title: mRNA seq of ARID1B KO liver (ARID1B f/f; Alb-Cre+) [ARID1B-F1-KO]

description:
ARID1B-F1-KO
mRNA-seq
processed data file: RawCount_feature_inVivo_KO_ARID1B.txt


title: Genomic DNA from FC459

description: Control sample from FC459

value: PBMC


title: Genomic DNA from FC940

description: Control sample from FC940


title: mRNA seq of control liver (ARID1A f/f; ARID1B f/f; Alb-Cre-) [WT-7069]

description:
WT-7069
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt


title: mRNA seq of control liver (ARID1A f/f; ARID1B f/f; Alb-Cre-) [WT-7114]

description:
WT-7114
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt


title: Genomic DNA from FC477

description: Control sample from FC477


title: 074_41BB_18_AR

value: Non-Asthmatic & Allergic to HDM


title: Genomic DNA from FC456

description: Control sample from FC456


title: Genomic DNA from FC939

description: Control sample from FC939


title: N14_3

source_name: 14 DPA, proximal amputation

value: 14 DPA


title: N14_2


title: 083_41BB_12_AS_NA


title: 072_41BB_16_AR


title: mRNA seq of ARID1A/1B double KO liver (ARID1A f/f; ARID1B f/f; Alb-Cre+) [DKO-7137]

description:
DKO-7137
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt

value: ARID1A f/f; ARID1B f/f; Alb-Cre+


title: Genomic DNA from FC466

description: Control sample from FC466


title: Genomic DNA from FC923

description: Control sample from FC923


title: 071_41BB_15_AR

value: Blood


title: mRNA seq of ARID1A/1B double KO liver (ARID1A f/f; ARID1B f/f; Alb-Cre+) [DKO-7112]

description:
DKO-7112
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt

value: Liver


title: RNA_Seq2

description:
8h
RAW264.7 cells with VSV infection for 8 hours.
processed data file: RAW264.7_VSV_0h_8h.txt

data_processing:
Primary sequencing data that produced by Illumina Xten, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by scripts.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into mm10 transcripts was processed by Stringtie.
Differential expression analysis between sample 1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RAW264.7_VSV_0h_8h.txt: Tab-delimited text

source_name: RAW264.7 cells

extract_protocol:
Cytoplasmic and nuclear RNAs in RAW264.7 cells treated with VSV for 8 hours were separated with 0.1% NP40-PBS buffer or 0.5% NP40-PBS buffer respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were infected with VSV for 8 hours and then washed with ice-cold PBS. Extracted RNAs were analyzed using Illumina Xten sequencing.

tag: cell line

value: macrophage cell line

tag: passages

tag: strain/background

tag: infection

value: Vesicular stomatitis virus (VSV) for 8h


title: N12_4

source_name: 12 DPA, proximal amputation

tag: tissue

tag: treatment

value: 12 DPA


title: mRNA seq of ARID1A/1B double KO liver (ARID1A f/f; ARID1B f/f; Alb-Cre+) [DKO-7070]

description:
DKO-7070
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt


title: Genomic DNA from FC472

description: Control sample from FC472

value: Control


title: RNA_Seq1

description:
0h
RAW264.7 cells without VSV infection.
processed data file: RAW264.7_VSV_0h_8h.txt

extract_protocol:
Cytoplasmic and nuclear RNAs in RAW264.7 cells treated with PBS for 8 hours were separated with 0.1% NP40-PBS buffer or 0.5% NP40-PBS buffer respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were treated with PBS for 8 hours and then washed with ice-cold PBS. Extracted RNAs were analyzed using Illumina Xten sequencing.


title: Genomic DNA from FC454

description: Control sample from FC454


title: 070_41BB_14_AR

description: 200 cells bulk, full-transcriptome (Smart-seq2, Rosales et al.,  2018)

tag: disease group


title: N14_1

value: 10-12 weeks old


title: mRNA seq of ARID1A/1B double KO liver (ARID1A f/f; ARID1B f/f; Alb-Cre+) [DKO-7068]

description:
DKO-7068
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt


title: N12_2

value: Hind limb digit tip (bone, cartilage, marrow, dermis, epidermis)


title: 069_41BB_13_AR

tag: cell type


title: 068_41BB_6_AS_AL

value: Asthmatic & Allergic to HDM


title: Splenic iNKT cell data

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

description:
Adipose_iNKT_and_splenic_iNKT_normalized_expression_matrix_processed.csv
N/A

data_processing:
Raw BCL files were demultiplexed using Cell Ranger v3.0.2 mkfastq to generate fastq files with default parameters.
Fastq files were aligned to the mm10 genome (v1.2.0) and feature reads were quantified simultaneously using Cell Ranger count for feature barcoding to generate filtered barcode.tsv, feature.tsv and matrix.mtx files
Filtered barcode.tsv, feature.tsv and matrix.mtx files were read using Seurat v.3.1.1. Dead, apoptotic and poor quality cells were removed for quality control and the raw gene expression data was normalized using sctransform v.0.2.0 with default parmeters
Genome_build: mm10 genome (v1.2.0)
Supplementary_files_format_and_content: SCT-Normalized gene expression data matrices for adipose iNKT cell-only analysis and adipose iNKT cell and splenic iNKT cell analysis. The first column contains gene names and all subsequent columns contain a cell barcode (header) with gene expression data for the respective barcoded cell. For the adipose iNKT and splenic iNKT analysis matrix the cell barcodes are are appended with a sample identifier (Adipose_) or (Spleen_).

source_name: Spleen

extract_protocol:
Spleens were manually disrupted and filtered through a 70uM filter and centrifged. Splenocytes were treated with ACK red blood cell lysis buffer (VWR) prior to further analysis.
FACS-Sort. Gated on TCRB+ CD1d-PBS57 Tetramer+ CD19- F4/80- CD45+ live single cells.
Single cell suspensions from the spleens of mice treated with saline or αGalCer were tagged by TotalSeq-A Mouse hashtag antibody #1 and #2 (Biolegend) respectively before the two samples were pooled for sequencing. In the HTO sample data hastag 1 labels unstimulated cells and hashtag 2 labels splenic iNKT cells stimulated in vivo with αGalCer for 4 hours
Cell suspensions were loaded onto a 10x Chromium controller to generate gel bead-in-emulsions (GEMs) according to the manufacturers instructions
Libraries were prepared according to standard protocols produced by 10X Genomics for sequencing using Chromium Single Cell 3' V3 chemistry. Briefly, cell suspensions loaded onto the 10x chromium controller were mixed with reagents from the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 according to the manufacturers instructions and libraries were sequenced using a NextSeq 500 sequencer (Illumina)

tag: strain

value: 8 weeks


title: Genomic DNA from FC922

description: Control sample from FC922

source_name: PBMC

tag: disease


title: Genomic DNA from FC921

description: Control sample from FC921

tag: Sex


title: Genomic DNA from FC926

description: Control sample from FC926


title: Genomic DNA from FC910

description: Control sample from FC910


title: N12_1

value: proximal amputation


title: 067_41BB_5_AS_AL

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi


title: R21_4

source_name: 21 DPA, distal amputation

value: distal amputation

value: 21 DPA


title: 066_41BB_4_AS_AL


title: Adipose iNKT cell data

description:
Adipose_iNKT_and_splenic_iNKT_normalized_expression_matrix_processed.csv
Adipose_iNKT_only_normalized_expression_matrix_processed.csv

source_name: Epididymal adipose tissue

extract_protocol:
Adipose tissue was carefully dissected and dissociated in 1mg/mL Type II collagenase (Worthington) for 25 minutes at 37 degrees celcius. Digested tissue was filtered through a 70uM filter and centrifuged at 15,000rpm for 7 minutes.
FACS-Sort. Gated on TCRB+ CD1d-PBS57 Tetramer+ CD19- F4/80- CD45+ live single cells
Cell suspensions were loaded onto a 10x Chromium controller to generate gel bead-in-emulsions (GEMs) according to the manufacturers instructions
Libraries were prepared according to standard protocols produced by 10X Genomics for sequencing using Chromium Single Cell 3' V3 chemistry. Briefly, cell suspensions loaded onto the 10x chromium controller were mixed with reagents from the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 according to the manufacturers instructions and libraries were sequenced using a NextSeq 500 sequencer (Illumina)


title: Genomic DNA from FC906

description: Control sample from FC906

value: PBMC


title: Genomic DNA from FC460

description: Control sample from FC460


title: Genomic DNA from FC919

description: Control sample from FC919