title: HP-High-R2

city: Birmingham

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Paired end sequencing reads were trimmed using Trim Galore (Krueger F, 2021) with the parameters --nextera --length 70 –paired.
The reads were then aligned to the mm10 genome using bowtie2 using parameters --very-sensitive --fr --no-discordant -X 600 --no-mixed.
Aligned reads were filtered for only those which were properly paired and with a mapq score of over 40 using Samtools and output as a bedpe file.
This was further converted to a bed file of enhancer fragments by taking the first co-ordinate of read 1 and the final co-ordinate of read 2 for each pair. Duplicate fragments were removed using the uniq function and fragments were further filtered using the intersect function on Bedtools for any which had 100% overlap with an off target background fragment list which was created by producing a library from un-transfected cells.
The fragments were then filtered using Bedtools intersect for those which were found in open chromatin, defined by DNaseI-Seq, in Goode et al (2016) and further by a corresponding ATAC peak in the correct differentiation stage in HM-1 cells.
Finally, the enhancer fragments were annotated using the annotatePeaks function of Homer for those within 1.5 kb of a TSS (promoter fragments) and distal fragments representing genuine enhancers.
Assembly: mm10
Supplementary files format and content: Bed files of filtered enhancer fragment co-ordinates

source_name: Hematopeitic Porgenitor (HP)

growth_protocol: A genome-wide enhancer reporter assay was designed based on an enhancer reporter system designed by Wilkinson et al. (2013). Briefly the enhancer reporter functions by inserting a fragment of interest upstream of a HSP68 minimal promoter and Venus-YFP reporter by Gateway® cloning. The reporter construct is then transfected into the HM-1 ES cell line which has a non-functional HPRT locus. Using HPRT homology arms the report cassette becomes integrated into the HPRT locus by homologous recombination, also repairing the locus, enabling selection of clones with successful recombination. This enhancer reporter system was modified and optimised for genome-wide screening. To obtain genome-wide enhancer fragments for cloning into the reporter we isolated tn5 tagmented open-chromatin fragments based on the ATAC-Seq protocol 33 from cells of the five differentiation stages. Cells were obtained (2.5x105) from each differentiation stage (ES, HB, HE1, HE2, HP) as detailed in the serum IVD method. Cells were pelleted in 5 aliquots of 50x103 cells and following the ATAC-Seq protocol each cell pellet had a transposition mix added (2x TD Buffer 25µl, TN5 Transposase 2.5 µl, PBS 16.5 µl, 1% Digitonin 0.5 µl, 10 % Tween-20 0.5 µl, H2O 5 µl) and cells were gently resuspended by pipetting. The transposition reaction was then incubated in a shaker at 700 RPM, 37°C for 30 minutes. The 5 reactions were then combined and DNA purified using the Qiagen MinElute® Reaction Clean-up kit and eluted in 26.5 µl H2O. One fifth of the purified reaction from each stage was used to produce ATAC-Seq libraries for direct sequencing and the remainder had linkers added incorporating AttB Gateway® cloning sites to enable insertion into a Gateway® donor vector (pDONR 221). The linkers were designed based on the tn5 transposase sequence and added by PCR in 2 steps. Initially 5 cycles of PCR were performed (Transposed DNA 20 µl, H2O 20 µl, 25 µM AttB tn5 Fwd primer 5 µl, 25 µM AttB tn5 Rev primer 5 µl, NEBNext Master Mix 50 µl) with the following conditions, 72°C for 5 minutes, 98°C for 30 seconds, 5 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute and a final hold at 4°C.   To optimize the required cycle number, the material from the initial PCR reaction was split and a 5 µl was used for a separate qPCR reaction (0.125 µM AttB tn5 Fwd Primer, 0.125 µM AttB tn5 Rev Primer, 1 x SYBR Green I, NEBNext Master Mix) with the following conditions: 72°C for 5 minutes, 98°C for 30 seconds, 35 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute using a StepOnePlus™ Real-Time PCR System (Thermo Fisher). Using the raw data from the cyan channel the number of cycles for 25% amplification was calculated. The number of cycles obtained from the qPCR side reaction was then used to amplify the remainder of the material as follows, 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. The resulting material was size selected, to optimise for material originating from enhancers, for fragments between 350 and 650 bp by electrophoresis on a 1.2% agarose gel with ethidium bromide and gel extraction was performed using the Qiagen MinElute® Gel Extraction Kit following manufactures protocol.  To generate attL-flanked entry clones compatible with cloning into the reporter vector the size selected material was cloned into the pDONR™221 (Thermo Fisher) by BP Gateway® reaction (100 fmol pDONR221, 100 fmol PCR material, 2 µl BP Clonase II, made up to 20µl with TE buffer (pH 8.0) the reaction was incubated for 18 hours at 25°C and ended by treatment with 0.2µg proteinase K and incubation at 37°C for 10 minutes. NEB 10-beta Electrocompetent cells were transformed with the plasmid by electroporation with a Bio-Rad GenePulser using program EC1 (2.0 kV, 200 Ohm, 25 µF), after addition of outgrowth media and incubation at 37°C, 250 rpm for 1 hour the bacteria were spread onto 150 mm agar plates containing 50 µg/ml kanamycin. Following overnight incubation at 37°C, 10 ml of LB was added to each plate and the bacterial lawn scraped off using a cell scraper. Plasmid DNA was extracted from the collected bacteria by Maxi-prep using the NucleoBond Xtra Midi EF kit following manufacturer’s instructions. The resulting product was eluted in 500 µl H2O.   The chromatin fragments were then transferred into the enhancer reporter cassette in the pSKB-GW-Hsp68-Venus vector 1 by Gateway® LR reaction (150ng Entry clone (pDONR), 150 ng pSKB, 2 µl LR Clonase II, made up to 10µl with TE buffer (pH 8.0) ) the reaction was incubated for 1 hour at 25°C and ended by treatment with 0.2 µg proteinase K and incubation at 37°C for 10 minutes. As with the BP reaction product, NEB 10-beta Electrocompetent cells were transformed with the material and after overnight incubation on agar plates containing 200 µg/ml ampicillin the bacteria were collected and the plasmid library extracted by Maxi-Prep. To obtain the highest possible diversity of fragments the cloning was carried out 10 times for material from each differentiation stage with the pDONR 221 library material  being combined before moving to the LR clonase reaction.   The HM-1 ES cell line was cultured on gelatinised culture plates in ES-Media (DMEM, 15% FCS, 1 mM Sodium pyruvate, 1x Pen/Strep, 1x L-glutamine, 0.15 mM MTG, 25 mM Hepes buffer and 1u/ml ESGRO LIF (Sigma-Aldrich)) at 37 °C, 10% CO2 and split every 48 hours to maintain healthy cells. Prior to transfection the cells were treated for 1 week with 1 x 6-TG to remove any cells with a functional HPRT locus. The plasmid libraries were mixed and digested with PmeI (NEB) to linearise the plasmids prior to transfection. To obtain optimum homologous recombination efficiency CRISPR guides were designed flanking the region and cloned into the PX458 Cas9 and sgRNA expression vector.  For each experiment, 500x106 cells were transfected using a Nucleofector®-4D (Lonza) with the P3 Primary Cell X kit with 5x106 per cuvette 10 ug pSKB enhancer reporter plasmid and 10 ug of PX458-HPRT CRISPR plasmid using program CG-104. Following electroporation, the cells were plated on gelatinised plates in ES-media with the addition of 50 µM SCR7 pyrazine (Sigma) to inhibit Non-homologous end joining, promoting homologous recombination following cutting by Cas9. After 12 hours the media was changed and 1 x HAT (Hypoxanthine-Aminopterin-Thymidine (Sigma)) was added to select for clones with successful recombination. The cells were then maintained in media containing HAT for one week and HT (hypoxanthine and thymidine (Sigma)) for a further 2 passages to prevent the cells from dying after the withdrawal of HAT, whereby all cells were kept and replated after splitting.  The selected cells were then put into IVD cultures and differentiated into HB, HE1, HE2 and HP (as described in Obier et al (2016)) and sorted by FACS. In addition to the previously mentioned gating for obtaining the cell populations the cells were also sorted into negative, low, medium and high Venus-YFP populations representing the activity of the enhancer fragment driven minimal promoter. The YFP-Venus negative population was gated based on a cell line containing a reporter construct with only the minimal promoter and reporter with no enhancer fragment.

extract_protocol:
Genomic DNA was extracted from the sorted cell populations using the Qiagen DNA Micro kit following manufacturer’s instructions.
To amplify the fragments contained in the reporter cassettes and add sequencing adaptors a PCR using indexed primers compatible with Illumina sequencing and targeted against the tn5 transposase sequence ((0.5 µM Nextera PCR Primer i5, 0.5 µM Nextera PCR Primer i7, 25 µl NEBNext Master Mix). Dependant on the amount of DNA obtained from the sorted cells between 25 and 30 PCR cycles were performed with the following conditions 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. Libraries were quantified using a Bioanalyzer 2100 (Agilent) with a High Sensitivity DNA Chip and pooled at equal concentration for sequencing. The final pool concentration and size was then confirmed by Kappa Library Quantification Kit (Roche) and Bioanalyzer. The pooled libraries were sequenced on a Next-Seq 550 as a paired end run with a 150 cycle High Output kit by the Genomics Birmingham Sequencing Facility.
Enhancer Reporter Sequencing

value: HM-1 ES dervied Hematopetic progenitor cells

tag: mouse strain


title: hippocampus, surgery, day 3, rep1

status: Public on Dec 09 2022

type: SRA

city: Beijing

first: Yi

last: Sun

address: No.8 Gongti Nanlu, Chao-Yang District

country: China

institute: Beijing Chao-Yang hospital

library_source: transcriptomic

data_processing:
Data was aligned using the HISAT2 program (Johns Hopkins University, Baltimore, MD, USA) with default parameters
The Python package HTseq (version 5.4.2) was used for quantification
R (version 5.2.0) was used for bioinformatics analysis
ClusterProfile (version 3.10) was used for Gene Ontology (GO) and network analysis.
Gene set enrichment analysis (GSEA) was performed using MSigDB (version 7.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
the mice were anesthesized and hippocampus were taken. Total RNA was extracted from the mouse hippocampus using Trizol (Tiangen, Beijing, China).
Complementary DNA was synthesized with DNA polymerase I and RNaseH. Products were purified by polymerase chain reaction to generate the sequencing  library and then quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: hippocampus

tag: genotype

value: WT

tag: treatment

value: surgery

tag: age

value: 12 months

tag: time

value: postoperative day3


title: WTi2

type: RNA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ S (mouse) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

label: biotin

molecule: polyA RNA

source_name: alveolar macrophages

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: Female C57BL/6 wildtype mice (Envigo CRS GmbH - Rossdorf, Germany) and CD47-/- mice (JAX stock #003173; Jackson Laboratory - Bar Habor-Maine, USA) were anesthetized by ketamine (100 mg/kg body weight)/ xylazine (5 mg/kg body weight) and intranasally infected with 75 PFUs influenza virus A/PR/8/34 (25 µl). 3dpi isolation of murine alveolar macrophages was achieved by repeated BAL (5x 1ml PBS) and a subsequent sorting of the cells based on their autofluorescence via the BD FACSAria II to obtain an untouched aMФ population.

tag: cell type

value: alveolar macrophages

tag: Sex

value: female

value: infected with influenza A


title: KOn1

value: naive


title: WTi1


title: hippocampus, naïve, rep2


title: WTn1


title: CVX18_C2D10

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Fingerstick

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: patientid

tag: timepoint

value: Not treated

value: BOOST

value: Peripheral blood


title: CVX18_C2D09


title: CVX19_C2D07


title: CVX18_C2D08


title: hippocampus, naïve, rep1


title: CVX18_C2D07


title: WTn2


title: HE2-High-R2

first: Peter

library_source: genomic

molecule: genomic DNA

source_name: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: HP-Low-R2


title: CVX18_C2D03


title: CVX18_C2D05


title: GSYSD-contro_12h_1

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA after G3YSDcontrol stimulation at 12 hours

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: MEF cells

growth_protocol: MEF cells were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% fetal bovine serum (FBS) (Gibco), supplemented with 1% penicillin-streptomycin (Invitrogen) at 37°C and 5% CO2.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: Transfection experiments were conducted in mosue MEF cells.  Total RNA was prepared 2, 4, 6, 8, 10  and 12 hours after transfection, respectilvely. The RNA with polyA tails were isolated, ligated to the adapters, amplified, and sequenced following the standard RNAseq preparation protocol (Illumina, USA) with no modifications. The transfection experiments were conducted in duplicates.

tag: cell line

value: Mouse Embryonic Fibroblast cell line

tag: transfection

tag: time point

value: 12 hours


title: CVX18_C2D06


title: CVX18_C2D01


title: GSYSD-contro_10h_2

description: expressed RNA after G3YSDcontrol stimulation at 10 hours

value: 10 hours


title: HP-Medium-R2

value: HM-1 ES dervied Hematopetic progenitor cells


title: CVX17_C2D14


title: HE2-Low-R2


title: GSYSD-contro_10h_1


title: HE2-Medium-R2


title: CVX17_C2D10


title: GSYSD-contro_12h_2


title: HP-Negative-R2


title: GSYSD-contro_8h_2

description: expressed RNA after G3YSDcontrol stimulation at 8 hours

value: 8 hours


title: CVX17_C2D09


title: GSYSD-contro_8h_1


title: CVX18_C2D04


title: HE2-Negative-R2


title: CVX17_C2D06


title: GSYSD-contro_6h_2

description: expressed RNA after G3YSDcontrol stimulation at 6 hours

value: 6 hours


title: CVX17_C2D05


title: GSYSD-contro_6h_1


title: HE1-Medium-R2

source_name: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: HE1-High-R2


title: CVX17_C2D01


title: CVX17_C2D04


title: CVX18_C2D02


title: CVX17_C2D03


title: CVX17_C2D02


title: CVX16_C2D14


title: HE1-Low-R2


title: CVX16_C2D10


title: GSYSD-contro_4h_2

description: expressed RNA after G3YSDcontrol stimulation at 4 hours

value: 4 hours


title: CVX16_C2D08


title: CVX17_C2D07


title: CVX16_C2D06


title: CVX16_C2D09


title: CVX17_C2D08


title: HB-Low-R2

source_name: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: HB-Medium-R2


title: CVX16_C2D07


title: GSYSD_12h_2

description: expressed RNA after G3YSD stimulation at 12 hours


title: GSYSD-control_2h_1

description: expressed RNA after G3YSDcontrol stimulation at 2 hours

value: 2 hours


title: CVX16_C2D03


title: GSYSD-contro_4h_1


title: CVX16_C2D05


title: HE1-Negative-R2


title: GSYSD_12h_1


title: HB-Negative-R2


title: CVX16_C2D02


title: CVX15_C2D14


title: GSYSD-contro_2h_2


title: HB-High-R2


title: GSYSD_10h_2

description: expressed RNA after G3YSD stimulation at 10 hours


title: ES-High-R2

source_name: Embryonic Stem Cell

value: HM-1 ES cell


title: ES-Medium-R2


title: ES-Low-R2


title: CVX15_C2D10


title: CVX15_C2D07


title: CVX15_C2D08


title: GSYSD_10h_1


title: CVX15_C2D06


title: CVX16_C2D04


title: CVX15_C2D04


title: GSYSD_8h_2

description: expressed RNA after G3YSD stimulation at 8 hours


title: CVX16_C2D01


title: CVX15_C2D01


title: ES-Negative-R2


title: CVX14_C2D09


title: HP-Low-R1


title: CVX15_C2D05


title: HP-Negative-R1


title: HE2-High-R1


title: CVX14_C2D05


title: CVX14_C2D02


title: HP-High-R1


title: CVX14_C2D01


title: GSYSD_6h_2

description: expressed RNA after G3YSD stimulation at 6 hours


title: CVX15_C2D02


title: CVX14_C2D14


title: HP-Medium-R1


title: CVX13_C2D09


title: Fo5, anti-HER2/CD3-TDB, liver, #5 (scRNAseq)

city: South San Francisco

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

country: USA

institute: Genentech Inc.

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24400714

data_processing:
Reads were tallied and demultiplexed based on their association with cell-specific barcodes. Only barcodes with  >10K associated reads were considered for further processing.
Sequencing reads were aligned to the mouse genome (NCBI Build 38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E1 --pairmax-rna=200000 --clip-overlap’).
Only cells with a mitochondrial UMI fraction <0.25 were considered for analysis.
Per-gene UMI counts were normalized by the total number of transcripts per cell and scaled by the median number of transcripts across all cells.
Assembly: GRCm38
Supplementary files format and content: csv (count matrix and metadata )

source_name: Liver cells

growth_protocol: A 1-cm incision was made in the skin just rostral to the third mammary fat pad on female FVB WT mice obtained from Jackson Laboratory (FVB/NJ JAX stock number: 001800). A pocket for the tumor was made into the no. 2/3 mammary fat pad and a 2 × 2 mm MMTV-HER2-transgenic Founder #5 (Fo5) tumor section was placed into the pocket (Lewis Phillips et al., 2008). The skin was closed using wound clips. Wound clips were removed at 7–10 days post-surgery and mice were monitored for appearance of palpable tumors. When tumor volumes grew to an average of approximately 350 - 500 mm3, they were placed into treatment cohorts with an equivalent tumor volume average size. Only animals that appeared to be healthy and free of obvious abnormalities were used in the study.

extract_protocol:
Livers were perfused through the inferior vena cava (IVC) with 20 ml cold EGTA solution using a 22-gauge needle. The big liver lobe was dissociated using the Liver Dissociation Kit (ref: 130-105-807, Miltenyi Biotec) following manufacturer’s instructions. Samples were filtered through a 100‑μm cell strainer, washed with 10 ml DMEM and spun down at 300 x g for 10 minutes at 4°C. Red blood cells were lysed using ACK lysis buffer. Samples were washed with 10 ml DMEM, filtered through a 20‑μm cell strainer. For further downstream processing 3 ml of filtered cell suspension was used and spun down at 300 x g for 10 minutes at 4°C. Red blood cells were lysed for a second time using ACK lysis buffer. Samples were washed with 10 ml DMEM and spun down at 300 x g for 10 minutes at 4°C. Subsequently, samples were resuspended in 3 ml 10% FBS in PBS, centrifuged again (300 x g, 10 minutes at 4°C) before resuspending for final cell count in 3 ml 10% FBS.
cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (ref: 5067-4626, Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer’s sequencing specification (10X Genomics).
scRNAseq

treatment_protocol: For acute response studies, anti-HER2(4D5-2C11)/CD3 antibody diluted in vehicle solution (20mM Histidine acetate, 240mM sucrose, 0.02%Tween-20, pH 5.5 buffer) was administered once to mice intravenously (IV) by tail vein injection at 5 mg/kg (if not stated otherwise). The vehicle buffer was used as the control, and was given at the same volume as the treatment antibodies. Organs were harvested 24 h post treatment.

tag: strain

value: FVB/NJ

value: liver

value: anti-HER2/CD3 TDB


title: GSYSD_4h_2

description: expressed RNA after G3YSD stimulation at 4 hours


title: CVX14_C2D07

value: Not treated

value: BOOST


title: CVX13_C2D06

value: Peripheral blood


title: GSYSD_4h_1

value: Mouse Embryonic Fibroblast cell line


title: CVX14_C2D06


title: HE1-High-R1


title: CVX13_C2D05


title: CVX14_C2D08


title: GSYSD_8h_1


title: HE2-Medium-R1

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: Fo5, anti-HER2/CD3-TDB, liver, #1 (scRNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24386029


title: GSYSD_2h_2

description: expressed RNA after G3YSD stimulation at 2 hours


title: CVX13_C2D04


title: Fo5, Vehicle, liver, #5 (scRNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24400710

value: vehicle control


title: CVX13_C2D14


title: GSYSD_2h_1


title: CVX15_C2D03


title: HE1-Low-R1


title: CVX13_C2D02


title: KOn2

value: alveolar macrophages

value: female

value: naive


title: HE2-Low-R1


title: Fo5, Vehicle, liver, #4 (scRNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24400709


title: CVX13_C2D10


title: CVX13_C2D08


title: HE1-Negative-R1

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: HE2-Negative-R1


title: Fo5, anti-HER2/CD3-TDB, liver, #4 (scRNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24400713


title: GSYSD_6h_1

value: 6 hours


title: CVX13_C2D07


title: CVX13_C2D03


title: CVX12_C2D09


title: HE1-Medium-R1


title: Fo5, Vehicle, liver, #1 (scRNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3316_counts.csv.gz
NGS3316_meta.csv
SAM24386027


title: CVX12_C2D14


title: CVX12_C2D10


title: HB-High-R1

value: HM-1 ES dervied Hemangioblast cells


title: Fo5, anti-HER2/CD3-TDB, tumor, #3 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403487

data_processing:
Sequencing reads were aligned to the mouse genome (NCBI Build 38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E1 --pairmax-rna=200000 --clip-overlap’).
Gene expression levels were quantified by calculating the number of reads mapped to the exons of each RefSeq gene using the HTSeqGenie R package.
Read counts were scaled by library size, quantile normalized and precision weights calculated using the “voom” R package. Differential expression analysis on the normalized count data was performed using the “limma” R package by contrasting treated samples with control samples, respectively.
Gene expression was considered significantly different across groups if we observed an |log2-fold change| ≥ 1 (estimated from the model coefficients) associated with an FDR adjusted P-value ≤ 0.05.
Assembly: GRCm38
Supplementary files format and content: csv (count and fpkm matrix)

source_name: Tumor cell

extract_protocol:
Total RNA was extracted from tissues using the RNAeasy Mini Kit (Cat. #74104, Qiagen) following the provider’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols. The libraries were sequenced on Illumina HiSeq 4000.

value: tumor


title: HB-Negative-R1


title: CVX12_C2D08


title: CVX13_C2D01


title: Fo5, anti-HER2/CD3-TDB, tumor, #1 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403485


title: HB-Medium-R1


title: CVX12_C2D07


title: CVX11_C2D09


title: Fo5, anti-HER2/CD3-TDB, tumor, #2 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403486


title: CVX12_C2D03


title: CVX12_C2D02


title: CVX12_C2D01


title: Fo5, Vehicle, tumor, #2 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403480


title: HB-Low-R1


title: CVX11_C2D10


title: Fo5, Vehicle, tumor, #3 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403481


title: Fo5, Vehicle, tumor, #1 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403479


title: CVX11_C2D14


title: CVX11_C2D05


title: CVX11_C2D07


title: ES-High-R1

source_name: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: ES-Negative-R1


title: CVX10_C2D09


title: ES-Low-R1


title: CVX11_C2D01


title: CVX11_C2D04


title: ES-Medium-R1


title: Fo5, anti-HER2/CD3-TDB, liver, #3 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403496

value: FVB/NJ


title: Fo5, anti-HER2/CD3-TDB, liver, #2 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403495

value: liver


title: CVX10_C2D14


title: CVX10_C2D08


title: Liver_EX10970_100 [1060_0084]

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Samples with RNA integrity number values of >7 were used for subsequent analysis.
Sequencing reads from the RNA-seq experiment were processed with a pipeline built upon the implementation of the ENCODE long RNA-seq pipeline: filtered reads were mapped against the Mus musculus (mouse) genome mm10/GRCm38 (primary assembly, excluding alternate contigs) using the STAR aligner software45 (STAR version 2.5.2b) allowing for soft clipping of adapter sequences.
For the quantification of transcript levels, the annotation files from Ensembl version 86 were used, corresponding to GENCODE 25.
Samples were quantified using RSEM46 (RSEM version 1.3.0) and featureCount47 (featureCount version 1.5.1).
Quality controls were implemented using FastQC48 (FastQC version 0.11.5), picardmetrics (picardmetrics version 0.2.4), and dupRadar49 (dupRadar version 1.0.0) at the respective steps.
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text files include raw values for each Sample (1060_uReads.txt: unique Reads per sample per gene; 1060_uTPM.txt: unique TPM per sample per gene)

source_name: Liver

extract_protocol:
Total RNAs were extracted using the Ambion Magmax™-96 total RNA isolation kit (Applied Biosystems, Waltham, MA, USA) according to the manufacturer’s instructions. As previously described43, 5 mg of tissue was placed in the lysis solution and homogenised in Tissuelyzer™ (Qiagen, Hilden, Germany) for 30 s. Nucleic acids were captured on magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. The RNA quality and concentration were measured using an RNA Pico chip on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The cDNA libraries for RNA-Seq  were prepared using 1.2 ng total RNA input with the SMART-Seq v4 Ultra Low Input RNA Kit for RNA-Seq (Clontech Laboratories, Mountain View, CA, USA). RNA-Seq was performed as 100 bp single reads on a High Seq 2500 (Illumina, Inc., San Diego, CA, USA) as previously described.  For all RNA-Seq analyses, approximately 10–30 million reads per sample were obtained.

value: Liver

value: Male

tag: treatment group

tag: treatment molecule

value: Semaglutide (GLP-1R agonist)


title: Fo5, anti-HER2/CD3-TDB, liver, #1 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403494

value: anti-HER2/CD3 TDB


title: Liver_EX10970_100 [1060_0083]


title: CVX10_C2D05

value: Not treated

value: BOOST

value: Peripheral blood


title: Fo5, Vehicle, liver, #3 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403490

value: vehicle control


title: CVX10_C2D10


title: CVX10_C2D04


title: CVX10_C2D03


title: CVX10_C2D01


title: Liver_EX10970_100 [1060_0082]


title: CVX9_C2D14


title: CVX9_C2D10


title: Fo5, Vehicle, liver, #2 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403489


title: Liver_EX10970_100 [1060_0080]


title: Liver_EX10970_100 [1060_0081]


title: CVX9_C2D08


title: Fo5, Vehicle, liver, #1 (bulk RNAseq)

description:
tumor-bearing mice treated i.v., takedown 24 h post treatment
NGS3884_counts.csv
NGS3884_fpkms.csv
SAM24403488


title: Liver_EX10970_100 [1060_0079]


title: eif4a3-eCLIP-IP, rep2

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Adapters were trimmed (cutadapt v1.18), and reads less than 18 bp were discarded using parameters -m 18 -a NNNNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g ACGCTCTTCCGATCT -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT for round 1 and parameters -m 18 -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT for round 2.
Mapping reads were then performed against mouse elements in RepBase with STAR (v2.6.1b). Repeat mapping reads were segregated, and all others were then mapped against the mouse mm9 genome with STAR (v2.6.1b).
PCR duplicates were removed from uniquely mapping reads to get usable reads. Multiple in-line barcodes were merged for usable reads, followed by peak identification with the clipper software (v0.2.0, https://pypi.org/project/clipper/) using parameters -s mm9 --bonferroni --superlocal --threshold-method binomial --save-pickle on read 2 only. In addition, only peaks with fold change > 2 were kept.
Genome_build: mm9
Supplementary_files_format_and_content: bed file - tab-delimited file containing peaks for RNA-binding proteins.

source_name: mESC J1

growth_protocol: Feeder-free murine ESCs were grown on 0.1% gelatin-coated tissue culture plates in ESC medium containing high-glucose DMEM, 15% fetal bovine serum (FBS), 100 μM nonessential amino acids, 1% nucleoside mix, 2 mM L-Glutamine, 50 U/mL Penicillin/Streptomycin, 0.1 mM 2-mercaptoethanol, and homemade recombinant leukemia inhibitory factor (LIF) tested for efficient self-renewal maintenance, at 37℃.

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al., 2016) by using an anti-eIF4a3 antibody (ProteinTech, 17504-1-AP).
Two biological replicates were performed for Input and eIF4a3 eCLIPed RNA. Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufactory protocol, and paired-end 50 bp-length reads were produced.

treatment_protocol: Feeder-free murine ESCs were UV crosslinked at 400 mJ/cm2 with 254 nm radiation before the cell collection.

value: Embryonic stem cells (ESCs)

value: mESC J1

tag: rip antibody


title: CVX9_C2D07


title: CVX9_C2D09


title: eif4a3-eCLIP-IP, rep1

value: anti-eIF4a3 antibody (ProteinTech, 17504-1-AP)


title: CVX9_C2D05


title: CVX9_C2D06


title: CVX9_C2D04


title: Liver_EX10970_20 [1060_0077]


title: Liver_EX10970_20 [1060_0078]


title: eif4a3-eCLIP-input, rep2


title: CVX8_C2D10


title: eif4a3-rnaseq-KD, rep2

data_processing:
RNAseq reads were aligned to the mouse mm9 genome using Bowtie2 (v2.3.4.3)
Aligned bam files were sorted by samtools (v1.9) using the parameter -n
HTSeq software (v0.11.2) was used to count reads for each gene using parameters -r name -f bam
Read counts were normalized with the trimmed mean of M-values (TMM) method for differential expression analysis using edgeR (v3.26.8)
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

source_name: mESC CCE

extract_protocol:
RNA was extracted with the Rneasy Plus kit (Qiagen, #74136) according to the manufacturer's instructions.
For ESCs, 1 µg total RNA from each sample was taken for the preparation of PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq platform. Single-end 100 bp-length reads or paired-end 150 bp-length reads were produced.

treatment_protocol: The transfection of the feeder-free murine ESCs was performed using Lipofectamine 3000 according to the manufacturer's manual. After drug selection, the transfected ESCs were infected with the lentiviruses. The infected ESCs were selected with 1 μg/mL puromycin for 2.5 days. The cells were collected at Day 4.5 after infection.

value: mESC CCE

value: eIF4A3 KD


title: eif4a3-eCLIP-input, rep1


title: CVX9_C2D02


title: Liver_EX10970_20 [1060_0074]


title: Liver_EX10970_20 [1060_0076]


title: CVX9_C2D01


title: CVX8_C2D14


title: Liver_EX10970_20 [1060_0075]


title: CVX8_C2D09


title: LCH patient_4

city: Stockholm

first: Egle

last: Kvedaraite

address: Tomtebodavägen 18A, floor 8

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw reads were aligned to the human reference genome GRCh38 using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the human GENCODE annotation version 25.
Genome_build: GRCh38 version 25 release, Gencode
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: lesion

extract_protocol:
Samples were collected during routine diagnostic procedures, either as fine needle aspirations or as surgical specimens. After prompt transportation to the laboratory, single cell suspensions were obtained from the samples by filtering them through 70 μm cell strainer, no digestion was used. Cell suspensions were then preserved in freezing medium containing 10 % DMSO in FCS (Sigma Aldrich, St. Louis, MO, USA). Cell suspensions were washed and incubated in 5% heat-inactivated FCS (Sigma Aldrich, St. Louis, MO, USA) for 15 min at 4°C. For extracellular staining, cells were resuspended in PBS containing 2% FCS and 2 mM EDTA and a mixture of antibodies, and incubated for 30 min at 4°C. For sorting, cells were washed twice, kept on ice until the sort, and resuspended in DAPI (Thermo Fisher Scientific, Waltham, MA, USA) right before the sorting procedure. For phosphoflow staining, extracellular antibody mix was supplemented with Live/Dead Fixable Blue (Thermo Fisher Scientific, Waltham, MA, USA), and extracellular staining was performed as described above, followed by fixation in 100 µl BD Cytofix Fixation Buffer (BD Biosciences, Cat. 554655) for 15 min at 4°C. Next, cells were permeabilized in 200 µl ice-cold BD Phosflow Perm Buffer III (BD Biosciences, Cat. 558050) for 30 min at 4°C, and intracellular staining was performed for 30 min at room temperature. Lesional cell suspensions from pediatric LCH patients were indexed-sorted on FACSARIAIII (BD Biosciences) into 96 well plates containing 3 µl Lysis buffer (see specified below) using a 100 µm nozzle.
The indexed (FACS) data was subjected to unsupervised clustering using tSNE and Phenograph algorithms, and cells that qualified for scRNA-seq (Smart-seq2) were further subjected to manual gating verifying cellular identities, using Seqgeq software (BD Biosciences). Single-cell cDNA libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2014) with the following modifications: (1) 1 mg/mL BSA Lysis buffer (Ambion® Thermo Fisher Scientific, Waltham, MA, USA); and (2) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA), with all 293 samples/lane.

value: Myeloid/LCH


title: eif4a3-rnaseq-KD, rep1


title: CVX8_C2D07


title: CVX8_C2D08


title: CVX8_C2D04


title: CVX8_C2D06


title: CVX8_C2D03


title: Liver_BI456906_30 [1060_0071]

value: BI 456906 (dual GLP-1R/GCGR agonist)


title: LCH patient_2


title: LCH patient_1


title: CVX8_C2D05


title: LCH patient_3


title: Liver_EX10970_20 [1060_0073]


title: Liver_BI456906_30 [1060_0072]


title: CVX9_C2D03


title: CVX8_C2D01


title: Liver_BI456906_30 [1060_0070]


title: CVX7_C2D09


title: CVX7_C2D08


title: CVX8_C2D02


title: Liver_BI456906_30 [1060_0069]


title: neutrophil-D3

first: Yutian

last: Kang

state: Shanghai

address: 197 ruijin'er road, shanghai

department: Burn Institute

institute: Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: neutrophil

growth_protocol: HL-60 and neutrophils were routinely cultured by RPIM 1640 with 10%FBS.

extract_protocol:
Trizol (Invitrogen) was used to extract whole RNA of stimulated neutrophils
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neutrophils were stimulated with 0.05ug/mL AGEs，30mmol/L D-glucose, AGEs+D-glucose and 0.05ug/mL BSA (control) for 24-hours

value: 30mmol/L D-glucose for 24 hours


title: CVX7_C2D10


title: Liver_BI456906_30 [1060_0068]


title: CVX7_C2D06


title: neutrophil-D1


title: CVX7_C2D02


title: neutrophil-C3

value: 0.05ug/mL AGEs+30mmol/L D-glucose for 24 hours


title: CVX7_C2D03


title: Liver_BI456906_30 [1060_0067]

value: Liver


title: Liver_BI456906_20 [1060_0066]

value: Male


title: neutrophil-C2


title: CVX6_C2D14


title: Liver_BI456906_20 [1060_0065]


title: CVX6_C2D09


title: neutrophil-B3

value: 0.05ug/mL BSA for 24 hours


title: CVX6_C2D07


title: neutrophil-C1


title: CVX7_C2D14


title: Liver_BI456906_20 [1060_0064]


title: neutrophil-D2


title: CVX6_C2D06


title: CVX6_C2D08


title: Liver_BI456906_20 [1060_0063]


title: CVX6_C2D04


title: neutrophil-B2


title: Liver_BI456906_20 [1060_0062]


title: CVX7_C2D07


title: CVX6_C2D02


title: neutrophil-B1


title: CVX6_C2D01


title: Liver_BI456906_20 [1060_0061]


title: Liver_BI456906_10 [1060_0060]


title: CVX5_C2D09


title: CVX7_C2D01


title: CVX5_C2D10


title: neutrophil-A3

value: 0.05ug/mL AGEs for 24 hours


title: CVX6_C2D10

value: Not treated


title: CVX5_C2D07

value: BOOST


title: neutrophil-A2


title: CVX5_C2D06

value: Peripheral blood


title: CVX5_C2D03


title: neutrophil-A1


title: CVX5_C2D05


title: Liver_BI456906_10 [1060_0058]


title: CVX6_C2D03


title: Lewis-BN-3

city: shanghai

first: jing

last: lu

state: State...

address: Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China

institute: shanghai jiaotong university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver


title: Liver_BI456906_10 [1060_0057]


title: CVX5_C2D01


title: CVX4_C2D14


title: Liver_BI456906_10 [1060_0056]


title: CVX5_C2D14


title: Lewis-BN-1


title: Lewis-BN-2


title: CVX5_C2D02


title: CVX4_C2D10


title: Lewis-Lewis-3


title: Liver_BI456906_3 [1060_0054]


title: Lewis-Lewis-2


title: Liver_BI456906_3 [1060_0053]


title: CVX4_C2D06


title: CVX4_C2D07


title: CVX4_C2D08


title: CVX5_C2D08


title: Liver_BI456906_10 [1060_0059]


title: CVX4_C2D05


title: Lewis-Lewis-1


title: Liver_BI456906_3 [1060_0052]


title: CVX4_C2D01


title: CVX4_C2D02


title: S epidermidis SECOM030A

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description:
Strategy 1_RPKM higher than 1
Strategy 2_RPKM higher than 10000
Strategy 3_RPKM higher than 1
Strategy 3_RPKM higher than 10
Strategy 3_RPKM higher than 100
Strategy 3_RPKM higher than 1000
Strategy 3_RPKM higher than 5000

data_processing:
Base-calling was performed using Illumina CASAVA version 1.8.2.
CLC genomics version 5.5.1 was used for alignment and normalization to reads per kilobase per million mapped reads (RPKM).
Kal’s statistical test, with false discovery rate, was applied to identify statistically significant alterations in clinical vs. commensal isolates (when fold-change values were used).
Genes with RPKM values below 1, in all strains tested, were discarded.
Venn diagrams were used to identify the genes of interest among the conditions tested.
Genome_build: CP000029.1
Supplementary_files_format_and_content: Tab-delimited text files with gene locus tag and respective RPKM. The list of genes presented results from different in silico analysis strategies. First, genes expressed only in one of the groups of isolates were selected (Strategy 1_RPKM higher than 1). Secondly, genes highly expressed in both groups, but whose relative expression could differentiate clinical from commensal isolates were identified (Strategy 2_RPKM higher than 10 000). Finally, a third strategy was performed to search for genes differentially expressed between both groups but using different expression levels thresholds (Strategy 3_RPKM higher than 1, 10, 100, 1000, 5000).

organism: Staphylococcus epidermidis

source_name: Biofilm-released cells

growth_protocol: Biofilm-released cells (BRC) were grown as described in Franca et al., 2016, AMB Express 6(1): 23. In brief, biofilms were grown in 24-well plates by inoculating 1.5 µL of overnight culture into 1 mL of Tryptic Soy Broth supplemented with 0.4 % (v/v) glucose (TSB0.4%G), and by incubating at 37 oC with agitation at 120 rpm. After 24h of growth, biofilms were washed twice with a saline solution, fresh TSB0.4%G was added, and biofilms were grown for additional 24 hours under the same temperature and shaking conditions. The cells in the biofilm-bulk fluid, i.e, BRC, were collected and harvested by centrifugation.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) as described in França et al., 2012, PLoS One 7 (5): e37480. In brief, cells were suspended in 500 µL of the lysis buffer provided by the kit plus 500 µL of phenol. This suspension was transferred into BeadBug tubes (1.0 mm Zirconium beads, triple-pure, high impact, Sigma) and using an MPBio 24 (MPBio) cells disruptor, the cells were lysed (3× 6.5m/s for 35 seconds, with 5 minutes intervals on ice between cycles). Finally, the tubes were centrifuged, and the suspension transferred into a new tube. An equal volume of 70% of ethanol was added, the suspension transferred into the RNeasy mini kit columns and the manufacturer's instructions were strictly followed. RNA quality was determined using Experion™ Automated Electrophoresis System and RNA quality indicators were above 9 for all samples. Thereafter, total RNA obtained from three independent experiments were mixed and treated with TURBO DNase (Ambion) and acid-phenol:chloroform: isoamyl alcohol (125:24:1) (Ambion, MA, USA) to degrade and isolate, respectively, genomic DNA. Additionally, total RNA was treated with MICROBEnrichTM (Ambion) to remove contaminating eukaryotic RNA. Finally, before the library construction, a Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) was used to remove bacterial ribosomal RNA.
Libraries were constructed using ScriptSeq RNAseq Library preparation kit (low input) (Epicentre) and strictly following the manufacturer's indications. The quality of the libraries constructed was assessed by quantitative PCR and Hi-Sensitivity D1K TapeStation (Agilent 2200 TapeStation). Finally, all libraries were multiplexed, and sequencing data were generated in a MiSeq® sequencer (Illumina) from paired-end reads (2 × 150 bp).

treatment_protocol: BRC concentration was adjusted to 1E9 CFU/mL with saline solution and 100 µL of this suspension was incubated with 900 µL of whole human blood (in a 2 mL tube) for 2 h at 37 oC and 80 rpm (in a 10 mm orbit shaker). BRC were then collected by centrifugation (16000 g, 5 minutes) and immediately suspended in 1 mL of RNA protect bacteria reagent (Qiagen), diluted 2:1 in RNase-free water, as indicated by the manufacturer. After 5 minutes of incubation at room temperature, BRC were harvested by centrifugation (5000 g, 10 minutes) and RNA isolation was performed. This assay was performed three independent times.

value: Commensal isolate

value: Skin


title: CVX3_C2D14


title: Liver_BI456906_10 [1060_0055]


title: S epidermidis SECOM020A.1


title: S epidermidis SECOM005A


title: Liver_BI456906_3 [1060_0050]


title: CVX3_C2D09


title: Liver_BI456906_3 [1060_0049]


title: S epidermidis 1457

value: Clinical isolate

value: Infected central venous catheter


title: CVX3_C2D05


title: CVX4_C2D09


title: CVX3_C2D08


title: Liver_Vehicle [1060_0048]

value: Vehicle


title: S epidermidis PT12003

value: Blood culture upon stomach surgery


title: CVX3_C2D04


title: CVX3_C2D03


title: CVX3_C2D02


title: S epidermidis IE214

value: Blood culture of an infective endocarditis case


title: CVX2_C2D14


title: CVX3_C2D01


title: Liver_Vehicle [1060_0046]


title: CVX4_C2D04


title: CVX2_C2D10


title: CVX4_C2D03


title: CB6_Input

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-5 for MLL2 and 10^-15 for H3K4me1 and H3K4me3.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: tonsil

extract_protocol:
ChIP was performed on two independent pools of GC cells, each comprising 3-5 donors. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 4ug of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads, obtaining on average 25x10^6 reads/sample

value: tonsil

value: not applicable

value: GC B cells, centroblast

value: nd

tag: antibody


title: CVX2_C2D09

source_name: Fingerstick

tag: tissue


title: Liver_Vehicle [1060_0045]

value: Liver

value: Male

tag: genotype


title: Liver_Vehicle [1060_0044]


title: CVX2_C2D07

value: Not treated


title: CVX2_C2D08

value: BOOST


title: CVX2_C2D03

value: Peripheral blood


title: CVX2_C2D04


title: CVX2_C2D05


title: CVX2_C2D02


title: Liver_Vehicle [1060_0043]


title: eWAT_EX10970_100 [1060_0042]

source_name: Epididymal White Adipose Tissue

value: Epididymal White Adipose Tissue

value: Semaglutide (GLP-1R agonist)


title: CVX2_C2D01


title: eWAT_EX10970_100 [1060_0041]


title: CVX2_C2D06


title: Liver_Vehicle [1060_0047]


title: CVX1_C2D10


title: CVX1_C2D14


title: eWAT_EX10970_100 [1060_0040]


title: eWAT_EX10970_100 [1060_0039]


title: CVX1_C2D07


title: CVX1_C2D05


title: eWAT_EX10970_100 [1060_0038]


title: CVX1_C2D03


title: CVX1_C2D04


title: eWAT_EX10970_100 [1060_0037]


title: CVX1_C2D02


title: CB6_MLL2

tag: treatment

value: ChIP using anti-MLL2 (Sigma, HPA035977, Lot. A69497)


title: eWAT_EX10970_20 [1060_0036]


title: CVX26_C1D14

value: PRIME


title: CVX1_C2D01


title: CVX26_C1D10


title: eWAT_EX10970_20 [1060_0035]


title: CVX1_C2D08


title: CVX26_C1D06


title: eWAT_EX10970_20 [1060_0033]


title: CVX26_C1D07


title: eWAT_EX10970_20 [1060_0034]


title: CVX26_C1D08


title: adriamycin-resistant cell line A2780-ADR_rep3

city: Bethesda

first: Wei

last: Zheng

state: MD

address: 9800 Medical Center Drive

institute: National Center for Advancing Translational Sciences

data_processing:
Input sequences were 50bp paired-end reads. STAR Aligner was used to align the reads against GRCh38 Ensembl Human Genome.
HTSeq to associate reads to genes and to produce per-gene read counts. The DESeq package in R for was used for normalization and statistical analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: A matrix file containing normalized read counts.

growth_protocol: Cells were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS) and 100 U/mL penicillin-streptomycin at 37 °C with 5% CO2.

extract_protocol: Total RNA, including miRNA, will be isolated from fresh frozen tissue or cell pellet using the Qiagen miRNeasy Mini Kit.  The cell samples are homogenized in QIAzol Lysis Reagent and after addition of chloroform, the homogenates are separated into aqueous and organic phases by centrifugation. RNA partitions to the upper, aqueous phase, while DNA partitions to the interphase and proteins to the lower, organic phase or the interphase.  The upper, aqueous phase is extracted, and ethanol is added to provide appropriate binding conditions for all RNA molecules greater than 18 nucleotides. The sample mixture is applied to an RNeasy Mini spin column, where the total RNA binds to the membrane and phenol and other contaminants are efficiently washed away.  High quality RNA (including miRNA) is eluted with nuclease-free water. The purified RNA is stored at -80°C.

tag: phenotype

value: adriamycin-resistant

value: untreated


title: CVX1_C2D09


title: CVX26_C1D04


title: eWAT_EX10970_20 [1060_0032]


title: CVX26_C1D01


title: CVX26_C1D02


title: adriamycin-resistant cell line A2780-ADR_rep2


title: CVX26_C1D03


title: eWAT_EX10970_20 [1060_0031]


title: CVX25_C1D14


title: CVX25_C1D10


title: adriamycin-resistant cell line A2780-ADR_rep1


title: eWAT_BI456906_30 [1060_0030]

value: BI 456906 (dual GLP-1R/GCGR agonist)


title: CVX25_C1D08


title: eWAT_BI456906_30 [1060_0029]


title: CVX25_C1D09


title: CVX25_C1D06


title: doxorubicin-sensitive human ovarian cancer cell line A2780_rep3

value: doxorubicin-sensitive


title: eWAT_BI456906_30 [1060_0028]


title: CVX25_C1D07


title: CVX25_C1D05


title: CVX26_C1D09


title: Liver_BI456906_3 [1060_0051]


title: doxorubicin-sensitive human ovarian cancer cell line A2780_rep1


title: CVX25_C1D04


title: eWAT_BI456906_30 [1060_0026]


title: CVX25_C1D01


title: VEGF-HP

data_processing:
Single-end reads from ATAC-seq experiments were processed with Trimmomatic (version 0.39.
Processed reads were aligned to the mm10 mouse genome using Bowtie2 v2.4.4 using the options -very-sensitive-local
BedGraph files were produced using BedTools v9.3.0
Assembly: mm10
Supplementary files format and content: bedGraph of ATACseq sequence pileups

source_name: Hematopeitic Porgenitor (HP)

growth_protocol: Standard ES cell differentiation used serum and the purification of differentiating cells was conducted essentially as described in Obier et al. (2016) Serum Free I.V.D Culture Embryoid bodies (EBs) were generated from HM-1 mouse embryonic stem cells by plating at 5.0x105 cells/ml in serum free (SF) media into petri-grade dishes. BMP4 was added to a concentration of 5ng/ml. Cultures were left to incubate at 37°C and 5% CO2 for 60 hours before bFGF and Activin A were added at a concentration of 5ng/ml each. The cells were incubated for 16 hours at 37°C 5% CO2 and then sorted for FLK1+ cells as described in Obier et al. (2016). FLK1+ cells were plated in serum free media on 0.1% gelatine coated plates or for larger cultures flasks at 2.25x104 cells per cm. BMP4, Activin-A and bFGF were added to a concentration of 5ng/ml for 16 hours. Media was then removed, the blast culture was washed with PBS and fresh SF media was added containing BMP4 (5ng/ml), VEGF (5ng/ml), TPO (5ng/ml), SCF (100ng/ml), IL6 (10ng/ml) and IL3 (1ng/ml). For cytokine withdrawal experiments, one of BMP4, VEGF, IL6 or IL3 was not added at this stage. Blast cultures were left to incubate at 37°C and 5% CO2 for 72 hours before cells were harvested for cell sorting and FACS analysis. Inhibition of trypsin was achieved using Trypsin Inhibitor (Thermofisher) following the manufacturer’s instructions.

extract_protocol:
Extraction was performed as part of the ATAC-Seq library preparation protocol
ATAC-Seq was performed as described in Buenrostro et al (2015), briefly 5000-50,000 HB, HE1, HE2 and HP cells were sorted by FACS and transposed in 1x tagment DNA buffer Tn5 transposase and 0.01% Digitonin for 30 minutes incubated at 37°C with agitation. DNA was purified using a MinElute Reaction Cleanup Kit and DNA was amplified by PCR using Nextera primers.

value: HM-1 ES derived Hematopetic progenitor cells

tag: mouse strain

tag: cytokine treatment

value: VEGF withdrawn


title: CVX21_C1D10


title: eWAT_BI456906_30 [1060_0025]

tag: Sex


title: eWAT_BI456906_20 [1060_0024]


title: CVX21_C1D14

tag: patientid


title: CVX21_C1D09

tag: timepoint


title: CVX21_C1D08


title: CVX21_C1D07


title: VEGF-HE2

source_name: Hemogenic Endothelium 2 (HE2)

tag: cell type

value: HM-1 ES derived Hemogenic Endothelium 2 cells


title: CVX21_C1D06


title: eWAT_BI456906_20 [1060_0023]


title: eWAT_BI456906_20 [1060_0022]


title: VEGF-HB

source_name: Hemangioblast Cell (HB)

value: HM-1 ES derived Hemangioblast cells


title: IL6-HP

value: IL6 withdrawn


title: doxorubicin-sensitive human ovarian cancer cell line A2780_rep2

tag: cell line


title: eWAT_BI456906_20 [1060_0021]

value: Male


title: CVX25_C1D03

value: Not treated


title: CVX25_C1D02


title: CVX21_C1D03


title: eWAT_BI456906_30 [1060_0027]


title: CVX21_C1D02


title: CVX21_C1D04


title: IL6-HE2


title: eWAT_BI456906_20 [1060_0020]


title: CVX21_C1D01


title: VEGF-HE1

source_name: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES derived Hemogenic Endothelium 1 cells


title: CVX20_C1D14

value: Turbo Treated

value: Peripheral blood


title: CVX20_C1D09


title: eWAT_BI456906_20 [1060_0019]

value: Epididymal White Adipose Tissue


title: CVX20_C1D10


title: IL6-HB


title: CVX20_C1D08


title: IL3-HP

value: IL3 withdrawn


title: CVX20_C1D05

value: PRIME


title: CVX20_C1D07


title: IL3-HE2


title: eWAT_BI456906_10 [1060_0016]


title: CVX21_C1D05


title: eWAT_BI456906_10 [1060_0017]


title: CVX20_C1D03


title: eWAT_BI456906_10 [1060_0018]


title: IL3-HE1


title: eWAT_BI456906_10 [1060_0015]


title: IL3-HB


title: eWAT_BI456906_10 [1060_0014]


title: CVX18_C1D14


title: CVX20_C1D02


title: CVX19_C1D08


title: BMP4-HE2

value: BMP4 withdrawn


title: CVX20_C1D01


title: CVX19_C1D05


title: IL6-HE1


title: CVX20_C1D06


title: BMP4-HE1


title: CVX18_C1D09


title: BMP4-HB


title: CVX18_C1D06


title: CVX18_C1D05


title: CVX18_C1D07


title: All-HP

value: All cytokines present


title: eWAT_BI456906_3 [1060_0011]

value: BI 456906 (dual GLP-1R/GCGR agonist)


title: CVX18_C1D04


title: CVX18_C1D02


title: eWAT_BI456906_3 [1060_0012]


title: eWAT_BI456906_3 [1060_0009]


title: CVX18_C1D03


title: eWAT_BI456906_3 [1060_0010]


title: All-HE2


title: CVX18_C1D01


title: eWAT_BI456906_10 [1060_0013]


title: CVX17_C1D14


title: eWAT_BI456906_3 [1060_0008]


title: CVX18_C1D10


title: All-HE1


title: eWAT_BI456906_3 [1060_0007]


title: CVX17_C1D07


title: All-HB


title: CVX17_C1D10


title: CVX17_C1D06


title: HP-Serum-R2

data_processing:
Single-end reads from ATAC-seq experiments were processed with Trimmomatic (version 0.39) and aligned to the mm10 mouse genome using Bowtie2 2.4.4 using the options -very-sensitive-local.
Open chromatin regions (peaks) were identified using MACS2 2.2.7.1 using the options -B -trackline -nomodel.
The peak sets were then filtered against the mm10 blacklist.
Assembly: mm10
Supplementary files format and content: Bed files of ATAC-Seq peak co-ordinates

extract_protocol:
Extraction was performed as part of the ATAC-Seq library preparation protcol
ATAC-Seq was performed as described in Buenrostro et al (2015), briefly 5000-50,000 HB, HE1, HE2 and HP cells were sorted by FACS and transposed in 1x tagment DNA buffer Tn5 transposase and 0.01% Digitonin for 30 minutes incubated at 37°C with agitation. DNA was purified using a MinElute Reaction Cleanup Kit and DNA was amplified by PCR using Nextera primers.

value: HM-1 ES dervied Hematopetic progenitor cells


title: CVX18_C1D08


title: CVX17_C1D02


title: HE2-Serum-R2

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: eWAT_Vehicle [1060_0005]

value: Vehicle


title: CVX17_C1D01


title: eWAT_Vehicle [1060_0006]


title: HE1-Serum-R2

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: CVX16_C1D07


title: CVX16_C1D05


title: HB-Serum-R2

value: HM-1 ES dervied Hemangioblast cells


title: CVX16_C1D04


title: eWAT_Vehicle [1060_0004]


title: eWAT_Vehicle [1060_0003]


title: CVX16_C1D03


title: CVX16_C1D14


title: ES-Serum_R2

value: HM-1 ES cells


title: CVX16_C1D01


title: eWAT_Vehicle [1060_0002]

value: Male


title: CVX15_C1D09


title: CVX15_C1D10


title: CVX15_C1D08


title: CVX15_C1D07


title: HE2-Serum-R1


title: HP-Serum-R1


title: eWAT_Vehicle [1060_0001]


title: eif4a3-totalRNA-KD, rep1

description: eif4a3 KD rep1 for total RNA

data_processing:
Ribo-seq data reads were firstly adapter trimmed using FASTX-Tookit (v0.0.14; http://hannonlab.cshl.edu/fastx_toolkit) with the parameter -a AGATCGGAAGAGCACACGTCT.
Ribosomal RNA and transfer RNA reads were removed using Bowtie (v1.2.3).
The remained reads are aligned to the mouse mm9 genome using TopHat (v2.1.1). The matched total RNA-seq data were also processed with the same processing procedure.
These aligned bam files were sorted by name with the parameter –n, and counted by HTSeq (v0.11.2).
All read counts are normalized using the TMM method using edgeR (v3.26.8).
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

extract_protocol:
Ribosome profiling was performed according to the manufacturer's instructions. Total RNA and RPF libraries were prepared using the TruSeq Ribo Profile (Mammalian) Kit (Illumina, RPHMR12126) according to the manufacturer’s reference guide (document #15066016 v01) with Ribo-Zero Gold Kit (H/M/R) (Illumina, MRZG126).
Two biological replicates were performed for total RNA and RPF RNA of eIF4a3 shRNA-infected ESCs. Massively parallel sequencing was performed with the Illumina HiSeq2500 according to the manufactory protocol, and single-end 50 bp-length reads were produced. For RPF samples, each sample was sequenced four times  to get enough reads.

treatment_protocol: Ribosome profiling was performed using ESCs infected with eIF4a3 shRNAs. ESCs were infected with eIF4a3 shRNAs (sheIF4a3-2, sheIF4a3-3) (day 0). After 3 days of 1 μg/mL puromycin selection, on day 4.5, the ESCs were cultured in fresh serum/LIF ESC medium supplemented with 0.1 mg/mL cycloheximide for 1 min, followed with ice-cold PBS supplemented with 0.1 mg/mL cycloheximide wash before the cell lysis.

value: Embryonic stem cells (ESCs)

value: mESC J1

value: eIF4A3 KD

tag: fraction

value: total RNA


title: eif4a3-totalRNA-KD, rep2

description: eif4a3 KD rep2 for total RNA

tag: strain


title: CVX15_C1D01

value: Turbo Treated

value: Peripheral blood


title: HE1-Serum-R1


title: CVX14_C1D10

value: PRIME


title: CVX14_C1D14


title: HB-Serum-R1


title: CVX14_C1D09


title: CVX17_C1D03


title: CVX14_C1D05


title: ES-Serum_R1


title: V372-SubGingival2_S100

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter.
QIIME2.0 microbiome pipeline.
Centered log-ratio (CLR) transformation.
Assembly: hg38
Supplementary files format and content: *.genus.txt: Genus-level taxon datasets; CLR transformed values.
Library strategy: 16S RNA amplicon sequencing

organism: human oral metagenome

source_name: Oral microbiome

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010).
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Subgingival sites

tag: condition

value: not provided

tag: donor id


title: CVX14_C1D07

data_processing:
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)


title: CVX13_C1D14


title: CVX14_C1D01


title: eif4a3-RPF-KD, rep1

description: eif4a3 KD rep1 for ribosome protected fragments

data_processing:
Library strategy: Ribo-seq
Ribo-seq data reads were firstly adapter trimmed using FASTX-Tookit (v0.0.14; http://hannonlab.cshl.edu/fastx_toolkit) with the parameter -a AGATCGGAAGAGCACACGTCT.
Ribosomal RNA and transfer RNA reads were removed using Bowtie (v1.2.3).
The remained reads are aligned to the mouse mm9 genome using TopHat (v2.1.1). The matched total RNA-seq data were also processed with the same processing procedure.
These aligned bam files were sorted by name with the parameter –n, and counted by HTSeq (v0.11.2).
All read counts are normalized using the TMM method using edgeR (v3.26.8).
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

value: RPF


title: V367-SubGingival2_S84


title: CVX13_C1D09


title: 148-mut

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
COUNTING - htseq-count_0.9.1 -q -f bam -s no -r pos -i gene_name clt_${SAMPLE}_R1.bam ${STARREF}genes.gtf > ${SAMPLE}_counts.txt
DIFFERENTIAL EXPRESSION - DESeq2_1.10.1
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: The processed data files contains the combined counts for all samples for use within DeSeq2 as well as the results of differential expression across the 2 condition groups

source_name: cochlea

extract_protocol:
Tamoxifen was administered to P0/P1 pups as previously described.  Cochlear tissues from 6 Sox2CreER/+Jag1fl/fl and wildtype littermate controls were dissected under the dissecting microscope in ice-cold DEPC-treated PBS and stored in RNAlater (Invitrogen) at 4°C.
The RNAs were purified by RNeasy Micro Kit (QIAGEN).  The quality and quantity of RNAs were measured by a 2100 bioanalyzer (Agilent). All RNAs had an RNA Integrity Number (RIN) value of 9.7-10. Illumina compatible sequencing libraries were generated by the University of Rochester Genomics Research Center. Libraries were hybridized to the Illumina flow cell and single-end reads of 100nts were generated.

value: cochlea

tag: age

value: postnatal day 6

value: Sox2CreER;Jag1-/- mutant


title: CVX13_C1D07


title: 151-ctr

value: Sox2+/+ control


title: CVX14_C1D08


title: CVX13_C1D08


title: eif4a3-RPF-KD, rep2

description: eif4a3 KD rep2 for ribosome protected fragments


title: CVX14_C1D03


title: 145-ctr


title: V369-SubGingival2_S26


title: V358-SubGingival2_S60


title: CVX13_C1D03


title: CVX13_C1D05


title: 159-mut


title: V335-SubGingival2_S127


title: CVX13_C1D04


title: 152-ctr


title: V337-SubGingival2_S49


title: 146-mut


title: CVX13_C1D02


title: CVX13_C1D01


title: 154-mut


title: CVX12_C1D10


title: CVX13_C1D06


title: V331-SubGingival2_S90


title: 147-mut


title: V328-SubGingival2_S44


title: CVX12_C1D09


title: CVX12_C1D08


title: CVX12_C1D06


title: CVX12_C1D05


title: 156-ctr


title: 150-mut


title: V326-SubGingival2_S7


title: CVX12_C1D04


title: 163-ctr


title: V314-SubGingival2_S81


title: V306-SubGingival2_S1


title: CVX12_C1D03


title: CVX12_C1D02


title: CVX11_C1D14


title: V321-SubGingival2_S102


title: V302-SubGingival2_S68


title: 161-cr


title: CVX12_C1D01


title: CVX11_C1D10


title: 46_Cordelia_i

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: pooled RNA from leaves

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary files format and content: trimmed redundant list, each read with its number of repeats

organism: Malus domestica

source_name: leaf

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar

value: cultivar Cordelia

tag: place of origin

value: Ujfeherto

tag: year of sampling


title: Minimal Change Disease [Sample_99]

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease

data_processing:
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Assembly: GRCh 38.86
Supplementary files format and content: voom transformation of RNA-seq counts

source_name: Tubulointerstitium from human kidney biopsy

growth_protocol: Not applicable

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

treatment_protocol: Not applicable

tag: tissue

tag: disease

value: Minimal Change Disease


title: 45_Artemisz_i

description: pooled RNA from leaves

value: cultivar Artemisz


title: V289-SubGingival2_S13


title: CVX12_C1D07


title: CVX11_C1D08


title: CVX11_C1D07


title: 41_Rosmerta_i

description: pooled RNA from leaves

value: cultivar Rosmerta


title: Focal Segmental Glomerulosclerosis [Sample_96]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: CVX11_C1D06

value: Turbo Treated


title: 42_Hesztia_i

description: pooled RNA from leaves

value: cultivar Hesztia


title: CVX11_C1D05

value: PRIME

value: Peripheral blood


title: 48_Cordelia_of

description: pooled RNA from leaves

value: Soroksar


title: V266-SubGingival2_S76

value: Subgingival sites

value: not provided


title: 47_Artemisz_of

description: pooled RNA from leaves


title: Focal Segmental Glomerulosclerosis [Sample_93]


title: Focal Segmental Glomerulosclerosis [Sample_97]


title: V259-SubGingival2_S78


title: 44_Hesztia_of

description: pooled RNA from leaves


title: V257-SubGingival2_S21


title: CVX11_C1D02


title: V253-SubGingival2_S72


title: 43_Rosmerta_of

description: pooled RNA from leaves


title: Minimal Change Disease [Sample_95]


title: CVX11_C1D03


title: V234-SubGingival2_S3


title: Minimal Change Disease [Sample_92]


title: Focal Segmental Glomerulosclerosis [Sample_98]


title: Minimal Change Disease [Sample_91]


title: CVX10_C1D14


title: 29_Freedom

description: pooled RNA from leaves

value: cultivar Freedom


title: V278-SubGingival2_S79


title: V265-SubGingival2_S12


title: V225-SubGingival2_S82


title: Focal Segmental Glomerulosclerosis [Sample_94]


title: Focal Segmental Glomerulosclerosis [Sample_90]


title: V224-SubGingival2_S2


title: 38_JG

description: pooled RNA from leaves

value: cultivar Jonagold

value: Vamosmikola


title: CVX10_C1D09


title: CVX11_C1D01


title: 8_golden

description: pooled RNA from leaves

value: cultivar Golden D


title: CVX10_C1D08


title: Minimal Change Disease [Sample_9]


title: 7_idared

description: pooled RNA from leaves

value: cultivar Idared


title: Focal Segmental Glomerulosclerosis [Sample_89]


title: V219-SubGingival2_S98


title: Minimal Change Disease [Sample_88]

value: Minimal Change Disease


title: 111_Apple_biotest

description: pooled RNA from leaves

value: mixture of 10 culltivars

value: Erd


title: V216-SubGingival2_S110


title: CVX10_C1D06


title: Focal Segmental Glomerulosclerosis [Sample_87]

value: Tubulointerstitium from human kidney biopsy


title: 39_SS

description: pooled RNA from leaves

value: non identified cultivar


title: CVX10_C1D07

value: Turbo Treated


title: 35_SZH

description: pooled RNA from leaves

value: Tamasi


title: CVX10_C1D05

value: PRIME


title: V200-SubGingival2_S14


title: Minimal Change Disease [Sample_86]


title: CVX10_C1D04

value: Peripheral blood


title: 40_ZSz

description: pooled RNA from leaves

value: cultivar Fuji

value: Zalaszanto


title: CVX10_C1D10


title: Focal Segmental Glomerulosclerosis [Sample_85]

value: Focal Segmental Glomerulosclerosis


title: V199-SubGingival2_S105

value: Subgingival sites

value: not provided


title: Minimal Change Disease [Sample_84]


title: CVX10_C1D03


title: V217-SubGingival2_S6


title: V196-SubGingival2_S42


title: Focal Segmental Glomerulosclerosis [Sample_83]


title: CVX10_C1D02


title: CVX10_C1D01


title: CVX9_C1D14


title: V193-SubGingival2_S58


title: SETD1AKO_FKBP-SETD1A_DMSO_K4me3 ChIP-Seq

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector  were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 hours.

tag: vector

tag: chip antibody

value: H3K4me3 (#ab7766, Abcam)

tag: stimulation

value: DMSO

tag: time


title: V195-SubGingival2_S121


title: V212-SubGingival2_S54


title: SETD1AKO_FKBP-SETD1A_dTAG_K4me3 ChIP-Seq


title: V180-SubGingival2_S39


title: Minimal Change Disease [Sample_81]


title: Minimal Change Disease [Sample_80]


title: CVX9_C1D10

tag: patientid

tag: timepoint


title: MOLM13_WT_SETD1A ChIP-Seq

value: WT

value: SETD1A (#61702 Cell Signaling)


title: SETD1AKO_FKBP-SETD1A_DMSO_HA ChIP-Seq

value: HA (#3724 Cell Signaling)


title: V174-SubGingival2_S93


title: CVX9_C1D09


title: SETD1AKO_FKBP-SETD1A_dTAG_HA ChIP-Seq


title: Minimal Change Disease [Sample_8]

value: Minimal Change Disease


title: CVX9_C1D08


title: MOLM13_WT_HA ChIP-Seq


title: Kat7 deleted replicate 4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
GenewiseCounts.txt.gz
S8

data_processing:
FASTQ files were geneated using Illumina CASAVA pipeline version 1.8.2.
Reads were aligned to the mouse genome using Rsubread version 1.12.4.
Read counts were summarized using the Rsubread's featureCounts function and inbuilt RefSeq NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.
Supplementary files format and content: The supplementary file GewiseCounts.txt.gz contains the matrix of read counts for all samples.

source_name: Proliferating NSPCs

growth_protocol: E14.5 neurospheres were cultured in neural stem cell proliferation medium.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy kit according to the manufacturer’s instructions.
Sequencing libraries were constructed using the Illumina TruSeq library construction kit according to the manufacturer’s instructions and sequenced on an Illumina HiSeq 200 sequencer to obtain 100bp single-end reads.

tag: genotype

value: Kat7 deleted

tag: mouse litter

tag: cell type

value: Proliferating NSPCs


title: V170-SubGingival2_S10

tag: condition


title: Focal Segmental Glomerulosclerosis [Sample_79]

value: Tubulointerstitium from human kidney biopsy


title: Focal Segmental Glomerulosclerosis [Sample_78]


title: Kat7 deleted replicate 3

description:
GenewiseCounts.txt.gz
S7

tag: strain


title: V167-SubGingival2_S133

tag: donor id


title: CVX9_C1D07

first: Darawan

last: Rinchai

institute: Sidra Medicine

value: Turbo Treated


title: Minimal Change Disease [Sample_82]


title: Kat7 deleted replicate 2

description:
GenewiseCounts.txt.gz
S6


title: V168-SubGingival2_S108


title: Kat7 deleted replicate 1

description:
GenewiseCounts.txt.gz
S5


title: Focal Segmental Glomerulosclerosis [Sample_76]


title: CVX9_C1D06

value: PRIME


title: CVX9_C1D05

value: Peripheral blood


title: CVX9_C1D03


title: Kat7 intact replicate 3

description:
GenewiseCounts.txt.gz
S3

value: Kat7 intact


title: V166-SubGingival2_S25


title: Focal Segmental Glomerulosclerosis [Sample_72]


title: Focal Segmental Glomerulosclerosis [Sample_73]


title: Minimal Change Disease [Sample_77]


title: Kat7 intact replicate 4

description:
GenewiseCounts.txt.gz
S4


title: CVX9_C1D01


title: CVX8_C1D14


title: V150-SubGingival2_S64


title: CVX8_C1D10


title: Focal Segmental Glomerulosclerosis [Sample_70]


title: Focal Segmental Glomerulosclerosis [Sample_71]


title: V164-SubGingival2_S120


title: CVX9_C1D04


title: Minimal Change Disease [Sample_75]


title: Focal Segmental Glomerulosclerosis [Sample_74]


title: Kat7 intact replicate 2

description:
GenewiseCounts.txt.gz
S2


title: V139-SubGingival2_S30


title: CVX9_C1D02


title: CVX8_C1D09


title: miR-497-195_2

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from BCP-ALL patient derived xenograft

hyb_protocol: Affymetrix GeneChip™ Human Gene 1.0 ST Arrays (Thermo Fisher Scientific, MA, US).

scan_protocol: Standard Affymetrix Protocol

data_processing: Background correction and normalization with RMA from Limma package in R

source_name: BCP-ALL cells from PDX-S2 transduced with miR-497~195

label_protocol: Standard Affymetrix Protocol

growth_protocol: BCP-ALL leukemia samples from pediatric patients were obtained at diagnosis. Blasts were transplanted into NOD/SCID mice (NOD.CB17-Prkdcscid, Charles River, Germany) as previously described (Meyer, Cancer Cell - 2011). Cells for further analyses were isolated from the spleen of the mice upon manifestation of clinical symptoms of leukemia.

extract_protocol: mOrange2-positive xenograft cells isolated from the spleen of the mice were sorted with BD FACS Aria III. RNA was extracted with Quick-RNA Microprep kit (Zymo Research, Irvine, CA, US). All the used samples had RIN>7

treatment_protocol: MiR-497~195 were cloned under control of a SFFV promoter in a lentiviral vector expressing mOrange2. Xenograft samples were transduced, mOrange2-positive cells were sorted and transplanted into NOD/SCID mice. Mice were sacrificed and cells were isolated from the spleen.

tag: transduction


title: Kat7 intact replicate 1

description:
GenewiseCounts.txt.gz
S1


title: miR-497-195_3


title: V151-SubGingival2_S114


title: V148-SubGingival2_S109


title: Minimal Change Disease [Sample_69]


title: V123-SubGingival2_S106


title: V162-SubGingival2_S38


title: V155-SubGingival2_S61


title: Minimal Change Disease [Sample_7]


title: miR-497-195_4


title: miR-497-195_1


title: V137-SubGingival2_S85


title: CVX8_C1D08

address: Al Gharrafa St


title: V114-SubGingival2_S46


title: V126-SubGingival2_S28


title: Focal Segmental Glomerulosclerosis [Sample_65]


title: CVX8_C1D07


title: ev_3

source_name: BCP-ALL cells from PDX-S2 transduced with empty vector

value: EV


title: CVX8_C1D03


title: Focal Segmental Glomerulosclerosis [Sample_68]

value: Focal Segmental Glomerulosclerosis


title: Focal Segmental Glomerulosclerosis [Sample_67]


title: CVX8_C1D02


title: ev_2


title: ev_5


title: ev_4


title: V120-SubGingival2_S40

value: Subgingival sites


title: Focal Segmental Glomerulosclerosis [Sample_66]


title: CVX8_C1D05


title: V104-SubGingival2_S117

value: not provided


title: CVX8_C1D04


title: V112-SubGingival2_S119


title: Focal Segmental Glomerulosclerosis [Sample_61]


title: V110-SubGingival2_S51


title: hCOs_scRNA_expt2_M20_4

first: Andrew

last: Ressler

description:
10X Genomics Single Cell Controller
Seurat_Robject.RData
orgDEGs.xlsx

data_processing:
For Bulk RNA Sequencing RTA (Illumina) was used for base calling and bcl12fastq2 (version 2.19) was used to convert BCL to fastq format, coupled with adaptor trimming. Pseudoalignment was performed to a kallisto index (Mouse: GRCm38) using kallisto (0.44.0).
For single-cell RNA-sequencing. 10X chromium pipeline defaults were used to generate barcoded matrices from BAM files. Then, Seurat v3.0 was used for downstream analyses, including DESeq2 for pseudobulk comparisons and MAST for analyses at single-cell resolution
Assembly: Grcm38 for Bulk RNA sequencing. Hg38 for human single-cell data
Supplementary files format and content: counts, Rdata, log2FoldChange
Supplementary files format and content: SampleDescriptions.csv includes all details on gender and batch of all samples included in this data repository.
Supplementary files format and content: hnrnpu_exp1and2_integrated_nfeatures2000_mtregress_dims11_respoint5_mt_umi.Rdata is processed Seurat object with all scRNA samples prior to naming of clusters to allow for any ad hoc analyses one might be interested in.

growth_protocol: Human samples (PGP1, D11 and M20) are all DIV42-45 human cortical organoids. Method from Xiang et al. 2017 (doi: 10.1016/j.stem.2017.07.007)

extract_protocol:
Single nuclei dissociated with Papain + DNAse for organoids. For bulk RNA-sequencing, cortices were dissociated embryonically or perinatally and either flash frozen or RNA extracted by Qiagen RNAeasy kit. If frozen, samples place in RNA later and then extracted at later date using Qiagen RNAeasy kit
10X Chromium Single Cell 3' Standard library construction from JP Sulzberger genomics core at Columbia University. For bulk RNA sequencing Poly-A pull-down was used to enrich mRNAs from total RNA samples and libraries were constructed using Illumina TruSeq chemistry. Libraries were then sequenced using Illumina NovaSeq 6000

treatment_protocol: No treatment

value: DIV45 human cortical organoids

tag: cell line

value: M20 CRISPR engineered iPSCs

value: HNRNPU+/-

tag: treatment

value: No treatment


title: Minimal Change Disease [Sample_63]

tag: tissue


title: hCOs_scRNA_expt2_M20_5


title: V103-SubGingival2_S65


title: ev_1


title: Focal Segmental Glomerulosclerosis [Sample_64]

tag: disease


title: CVX8_C1D01


title: Minimal Change Disease [Sample_6]


title: CVX7_C1D09


title: CVX7_C1D14


title: Focal Segmental Glomerulosclerosis [Sample_62]


title: V109-SubGingival2_S115


title: CVX7_C1D08


title: CVX8_C1D06


title: hCOs_scRNA_expt2_PGP1_4

value: PGP1 iPSCs

value: WT


title: hCOs_scRNA_expt2_D11_4

value: D11 CRISPR engineered iPSCs


title: Minimal Change Disease [Sample_59]

value: Minimal Change Disease


title: CVX7_C1D10


title: hCOs_scRNA_expt2_PGP1_5


title: V102-SubGingival2_S124


title: CVX7_C1D07


title: V100-SubGingival2_S83


title: Minimal Change Disease [Sample_58]

value: Tubulointerstitium from human kidney biopsy


title: V380-Saliva2_S45

value: Saliva


title: V372-Saliva2_S71


title: CVX7_C1D06

value: Turbo Treated

value: PRIME


title: V369-Saliva2_S88


title: hCOs_scRNA_expt1_M20_2


title: hCOs_scRNA_expt2_D11_5


title: hCOs_scRNA_expt1_M20_1

value: DIV42 human cortical organoids


title: CVX7_C1D05

value: Peripheral blood


title: Focal Segmental Glomerulosclerosis [Sample_57]

value: Focal Segmental Glomerulosclerosis


title: Minimal Change Disease [Sample_60]


title: Focal Segmental Glomerulosclerosis [Sample_56]


title: Minimal Change Disease [Sample_55]


title: hCOs_scRNA_expt1_D11_3


title: V367-Saliva2_S27


title: V358-Saliva2_S37


title: hCOs_scRNA_expt1_D11_2


title: Minimal Change Disease [Sample_54]


title: V337-Saliva2_S118


title: CVX7_C1D03


title: hCOs_scRNA_expt1_M20_3


title: CVX7_C1D02


title: hCOs_scRNA_expt1_D11_1


title: hCOs_scRNA_expt1_PGP1_3


title: CVX7_C1D01


title: Focal Segmental Glomerulosclerosis [Sample_53]


title: hCOs_scRNA_expt1_PGP1_2


title: V335-Saliva2_S113


title: V331-Saliva2_S33


title: V330-Saliva2_S92


title: Focal Segmental Glomerulosclerosis [Sample_50]


title: V328-Saliva2_S29


title: hCOs_scRNA_expt1_PGP1_1


title: Focal Segmental Glomerulosclerosis [Sample_51]


title: CVX6_C1D10


title: CVX7_C1D04


title: CVX6_C1D08


title: PXD60-3

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Reads near target crRNA regions were selected (+/- 1000bp) using BEDTools and then indexed and used for variant calling using SAMTools and Varscan v2.4.1.
Supplementary files format and content: Tab-delimited text files contain each indel position and percentage.

extract_protocol:
positive CAR-T cell genomic DNA was extracted
sample-specific barcode primer was used for PCR. The sequence of primer was listed in supplemary table.
PCR product library preparation

value: vector control


title: PXD60-2


title: Focal Segmental Glomerulosclerosis [Sample_5]


title: CVX6_C1D09

city: Doha


title: V326-Saliva2_S20

value: not provided


title: Minimal Change Disease [Sample_52]


title: CVX6_C1D07


title: PXD60-1


title: CVX6_C1D06


title: CVX6_C1D05


title: Focal Segmental Glomerulosclerosis [Sample_47]


title: V321-Saliva2_S107


title: MIP-2

value: 56crRNA pooled small library


title: MIP-3


title: V316-Saliva2_S125


title: Focal Segmental Glomerulosclerosis [Sample_46]


title: Focal Segmental Glomerulosclerosis [Sample_49]


title: MIP-1


title: CVX6_C1D03


title: V314-Saliva2_S53


title: CVX6_C1D04


title: V306-Saliva2_S97


title: CAR19_PRDM1_cr1_3

description: Nextera readout

data_processing:
For indel quantification, reads were mapped to expected amplicon sequences using  BWA-MEM with the -M option. 100bp reads from the SAM file that fully mapped within a +/-  75bp window of expected cut site within the amplicon were then identified.
Assembly: Reads were mapped to targeted gene amplicon
Supplementary files format and content: Tab-delimited text files contain each indel position and percentage.

extract_protocol:
positive CAR-T cell genomic DNA was extracted
Nextera XT DNA Library Preparation Kit, Illumina
PCR product library preparation


title: Focal Segmental Glomerulosclerosis [Sample_45]


title: CVX6_C1D02


title: CAR19_PRDM1_cr1_Con_3

description: Nextera readout


title: V302-Saliva2_S35


title: V325-Saliva2_S86


title: Minimal Change Disease [Sample_48]


title: Minimal Change Disease [Sample_42]


title: Minimal Change Disease [Sample_43]


title: V298-Saliva2_S57


title: CAR19_PRDM1_cr1_2

description: Nextera readout


title: CVX5_C1D14


title: CAR19_PRDM1_cr1_Con_2

description: Nextera readout


title: Focal Segmental Glomerulosclerosis [Sample_41]


title: V289-Saliva2_S96


title: CAR19_PRDM1_cr1_1

description: Nextera readout


title: Minimal Change Disease [Sample_40]


title: V293-Saliva2_S41


title: CVX5_C1D09


title: Focal Segmental Glomerulosclerosis [Sample_44]


title: V278-Saliva2_S17


title: CAR19_PRDM1_cr1_Con_1

description: Nextera readout


title: CVX5_C1D07


title: Focal Segmental Glomerulosclerosis [Sample_39]


title: CVX5_C1D08


title: V266-Saliva2_S87


title: Minimal Change Disease [Sample_4]


title: CAR22_PRDM1_cr1_3

description: Nextera readout


title: Minimal Change Disease [Sample_38]


title: CAR22_PRDM1_cr1_Con_3

description: Nextera readout


title: CAR22_PRDM1_cr1_2

description: Nextera readout


title: V276-Saliva2_S15


title: CVX5_C1D06


title: CVX5_C1D05


title: V259-Saliva2_S89


title: V265-Saliva2_S111


title: Minimal Change Disease [Sample_37]


title: CAR22_PRDM1_cr1_Con_2

description: Nextera readout


title: Minimal Change Disease [Sample_35]


title: CAR22_PRDM1_cr1_1

description: Nextera readout


title: CVX5_C1D04


title: V258-Saliva2_S55


title: CAR22_PRDM1_cr1_Con_1

description: Nextera readout


title: Focal Segmental Glomerulosclerosis [Sample_34]


title: CVX5_C1D03


title: CVX6_C1D01


title: V257-Saliva2_S129


title: Minimal Change Disease [Sample_33]


title: CAR22_PRDM1_cr2_con-2

description: Nextera readout


title: CVX4_C1D14


title: CVX5_C1D02


title: CAR22_PRDM1_cr2_con-3

description: Nextera readout


title: CAR22_PRDM1_cr2_con-1

description: Nextera readout


title: V253-Saliva2_S52


title: Minimal Change Disease [Sample_31]


title: CVX5_C1D01


title: V250-Saliva2_S4


title: CAR22_PRDM1_cr1_con-3

description: Nextera readout


title: V241-Saliva2_S16


title: CAR22_PRDM1_cr1_con-2

description: Nextera readout


title: V240-Saliva2_S130


title: V248-Saliva2_S56


title: Focal Segmental Glomerulosclerosis [Sample_3]


title: CAR22_PRDM1_cr1_con-1

description: Nextera readout


title: Minimal Change Disease [Sample_30]


title: V234-Saliva2_S19


title: CVX4_C1D10


title: CVX4_C1D07


title: CVX4_C1D09


title: CVX4_C1D05


title: Minimal Change Disease [Sample_36]


title: CVX4_C1D08


title: CVX4_C1D04


title: Focal Segmental Glomerulosclerosis [Sample_29]


title: Minimal Change Disease [Sample_26]


title: V224-Saliva2_S122


title: CVX4_C1D03


title: Minimal Change Disease [Sample_28]


title: CAR22_PRDM1_cr3_con-3

description: Nextera readout


title: V227-Saliva2_S104


title: CAR22_PRDM1_cr7/8_con-3

description: Nextera readout


title: Focal Segmental Glomerulosclerosis [Sample_25]


title: V225-Saliva2_S47


title: CAR22_PRDM1_cr6_con-3

description: Nextera readout


title: CVX4_C1D02


title: CAR22_PRDM1_cr7-3

description: Nextera readout


title: CAR22_PRDM1_cr8-3

description: Nextera readout


title: CAR22_PRDM1_cr6-3

description: Nextera readout


title: V222-Saliva2_S67


title: Focal Segmental Glomerulosclerosis [Sample_23]


title: CAR22_PRDM1_cr5-3

description: Nextera readout


title: CVX3_C1D10


title: CVX4_C1D01


title: Focal Segmental Glomerulosclerosis [Sample_24]


title: V219-Saliva2_S134


title: Focal Segmental Glomerulosclerosis [Sample_32]


title: CVX3_C1D14


title: Focal Segmental Glomerulosclerosis [Sample_220]


title: Focal Segmental Glomerulosclerosis [Sample_27]


title: CVX3_C1D08


title: CAR22_PRDM1_cr2-3

description: Nextera readout


title: V215-Saliva2_S9


title: CVX3_C1D09


title: V216-Saliva2_S132


title: V212-Saliva2_S75


title: V223-Saliva2_S62


title: Focal Segmental Glomerulosclerosis [Sample_219]


title: CVX3_C1D06


title: CAR22_PRDM1_cr4-3

description: Nextera readout


title: V217-Saliva2_S95


title: Focal Segmental Glomerulosclerosis [Sample_218]


title: CVX3_C1D07


title: CAR22_PRDM1_cr3-3

description: Nextera readout


title: V199-Saliva2_S131


title: CAR22_PRDM1_cr1-3

description: Nextera readout


title: Minimal Change Disease [Sample_217]


title: V196-Saliva2_S69


title: Focal Segmental Glomerulosclerosis [Sample_216]


title: CVX3_C1D04


title: Focal Segmental Glomerulosclerosis [Sample_215]


title: Focal Segmental Glomerulosclerosis [Sample_22]


title: CAR22_PRDM1_cr3_con-2

description: Nextera readout


title: CAR22_PRDM1_cr7/8_con-2

description: Nextera readout


title: CAR22_PRDM1_cr6_con-2

description: Nextera readout


title: CVX3_C1D03


title: Minimal Change Disease [Sample_214]


title: V195-Saliva2_S101


title: V200-Saliva2_S11


title: CAR22_PRDM1_cr8-2

description: Nextera readout


title: V193-Saliva2_S66


title: Minimal Change Disease [Sample_213]


title: CAR22_PRDM1_cr7-2

description: Nextera readout


title: CVX3_C1D02


title: Minimal Change Disease [Sample_212]


title: CVX5_C1D10


title: V192-Saliva2_S24


title: CVX3_C1D01


title: CAR22_PRDM1_cr6-2

description: Nextera readout


title: CVX2_C1D09


title: V180-Saliva2_S32


title: CAR22_PRDM1_cr5-2

description: Nextera readout


title: CVX3_C1D05


title: Focal Segmental Glomerulosclerosis [Sample_210]


title: CVX2_C1D08


title: V174-Saliva2_S80


title: CAR22_PRDM1_cr4-2

description: Nextera readout


title: Minimal Change Disease [Sample_21]


title: CVX2_C1D07


title: CAR22_PRDM1_cr3-2

description: Nextera readout


title: V172-Saliva2_S116


title: Minimal Change Disease [Sample_209]


title: CAR22_PRDM1_cr2-2

description: Nextera readout


title: V170-Saliva2_S18


title: Minimal Change Disease [Sample_208]


title: CAR22_PRDM1_cr1-2

description: Nextera readout


title: CVX2_C1D04


title: Minimal Change Disease [Sample_207]


title: CVX2_C1D03


title: V188-Saliva2_S73


title: Minimal Change Disease [Sample_211]


title: CAR22_PRDM1_cr7/8_con-1

description: Nextera readout


title: Minimal Change Disease [Sample_206]


title: V167-Saliva2_S34


title: CVX2_C1D02


title: CVX2_C1D01


title: Focal Segmental Glomerulosclerosis [Sample_205]


title: Minimal Change Disease [Sample_204]


title: CAR22_PRDM1_cr4/5_con-1

description: Nextera readout


title: CVX1_C1D08


title: CVX1_C1D09


title: CAR22_PRDM1_cr3_con-1

description: Nextera readout


title: V164-Saliva2_S48


title: V162-Saliva2_S8


title: CAR22_PRDM1_cr8-1

description: Nextera readout


title: V155-Saliva2_S70


title: CVX2_C1D06


title: CVX1_C1D07


title: V151-Saliva2_S77


title: CAR22_PRDM1_cr7-1

description: Nextera readout


title: V168-Saliva2_S94


title: CVX1_C1D06


title: Focal Segmental Glomerulosclerosis [Sample_202]


title: Minimal Change Disease [Sample_201]


title: CAR22_PRDM1_cr6-1

description: Nextera readout


title: V150-Saliva2_S43


title: Focal Segmental Glomerulosclerosis [Sample_200]


title: CAR22_PRDM1_cr6_con-1

description: Nextera readout


title: V166-Saliva2_S59


title: CVX1_C1D04


title: CVX1_C1D05


title: Minimal Change Disease [Sample_203]


title: V148-Saliva2_S99


title: CAR22_PRDM1_cr4-1

description: Nextera readout


title: Minimal Change Disease [Sample_20]


title: Focal Segmental Glomerulosclerosis [Sample_2]


title: CVX1_C1D03


title: CVX1_C1D02


title: Minimal Change Disease [Sample_199]


title: CAR22_PRDM1_cr2-1

description: Nextera readout


title: V126-Saliva2_S31


title: Focal Segmental Glomerulosclerosis [Sample_198]


title: V137-Saliva2_S91


title: CAR22_PRDM1_cr1-1

description: Nextera readout


title: Focal Segmental Glomerulosclerosis [Sample_197]


title: Focal Segmental Glomerulosclerosis [Sample_196]


title: V123-Saliva2_S112


title: CAR22_PRDM1_cr5-1

description: Nextera readout


title: V120-Saliva2_S128