title: 10x_8193


title: 10x_8194

status: Public on May 01 2020

type: SRA

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

library_source: transcriptomic

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted. For the subset of cells processed with 10X, we used CellRanger with the default parameters.
We examined as quality control the number of genes detected in each cell and conservatively excluded cells with fewer than 2,000 detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited files containing log2(TPM/10+1) values (TPM=transcript-per-million reads) of 9609 cells profiled by 10x droplet scRNA-seq (10x file) and of 1297 cell profiled by SmartSeq2 (SS2 file). All quantified 23,686 genes are included in the SS2 file and 11,548 genes detected in at least 10 cells are included in the 10x file. Header lines include Cell ID, patient ID, time point of sample acquisition, and the cells assignment into clusters and coordinates in a tSNE analysis (as shown in an associated manuscript).

molecule: polyA RNA

organism: Homo sapiens

source_name: Malignant ascites  single cell

extract_protocol:
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina). For a subset of samples, single cells were processed through the 10X Chromium 3 Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

treatment_protocol: Ascites fluid was drained by an interventional radiologist and transferred for further processing in closed vacuum bottles. De-identified patient information, including their ovarian cancer histology, stage, treatment history, and BRCA mutation status were collected. Immediately following drainage, malignant ascites was transported on ice, aliquoted into 50 mL conical tubes (BD Falcon) and spun for 5 min at 580 × g at 4°C. The supernatant was aspirated and the remaining pellet was resuspended with 5 mL of hypotonic lysis buffer ACK (Life technologies) and incubated on ice for 5 min. 20 ml of PBS was used to quench the lysis buffer. Cell suspensions were pooled and pipetted into a new 50 mL conical tube through a 100 µm mesh and spun for 5 min at 580 × g at 4°C. Hypotonic lysis was repeated until no visible red blood cell component was present, usually for a total of 2-3 times (for the plate-based approach). Following red blood cell lysis, the cell pellet was resuspended in PBS with 2% (v/v) FBS. These cells were then used for both plate-based and droplet-based scRNA-seq. For plate-based scRNA-seq, cells were labeled with the following fluorophore-conjugated flow-cytometry antibodies: live/dead stain with Calcein-AM (LifeTechnologies), 7-AAD (7-Aminoactinomycin D) (LifeTechnologies), CD45-FITC (LifeTechnologies), EpCAM-PE (Miltenyi Biotec) and CD24-PE/Cy7 (BioLegend). Cells were incubated for 30 min on ice in the dark. Cells were washed twice by resuspending with PBS with 2% (v/v) FBS and spun 5 min at 580 × g at 4°C. Flow-cytometry and sorting was performed on a BD Biosciences cell sorter (IIu or UV). Following doublet exclusion, Calceinhigh7AAD-CD45-EPCAM+CD24+ single cells were sorted into 96-well microtiter plates (on a plate chiller) that were prepared with 10uL cell lysis buffer (TCL + 1% β-mercaptoethanol). Following completion of cell sorting, plates were covered with aluminum lids, vortexed for 10 seconds, centrifuged for 2 min at 580 × g at 4°C and immediately placed on dry ice prior to storage at -80°C.

tag: cell type

value: Malignant ascites  single cell

tag: patient id

tag: time point


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title: RNA from Normal Liver D4_4

city: Barcelona

first: Benjamin

last: Lang

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
1) Raw reads were inspected for quality using FastQC (v0.11.5).
2) Reads were then trimmed with skewer (version 0.2.2) for removing the adapters and low quality reads.
3) Processed reads were aligned to the reference genome (human, GENCODE release 27, GRCh38.p10) using STAR aligner (version 2.5.3a).
4) bedtools "genomecov" was then run on the aligned reads with the "-split" option for calculating the coverage.
5) The coverage was then multiplied for a scaling factor (using the parameter "-scale") that is obtained by dividing 1 billion / (number of mapped reads * read size).
6) The BED graph was converted to bigWig using bedGraphToBigWig.
7) An annotation BED file describing the miRNAs and +/-120 bp regions of interest was generated from the miRNA symbol list in "pri-miRNA IDs.txt". This resulted in "microRNAs_120ext.bed".
8) bigWigAverageOverBed was run on the ±120 bp regions (pri-miRNAs). Command: bigWigAverageOverBed [bigwig file] microRNAs_120ext.bed [output file]
9) Read count averages from the output file were parsed using a custom script.
10) Processing ratios (pre_mean / pri_mean) were calculated using a custom script.
11) The final output matrix ("In vivo processing.xlsx") was produced using a custom script.
Genome_build: GRCh38.p10 (GENCODE release 27)
Supplementary_files_format_and_content: bigWig files containing scaled coverage values, as described in the processing steps.
Supplementary_files_format_and_content: In vivo processing.xlsx: A matrix table containing pri-miRNA processing efficiencies to pre-miRNAs for all samples (horizontal) and miRNAs of interest (vertical) (Excel format).
Supplementary_files_format_and_content: pri-miRNA IDs.txt: The list of miRNAs of interest which were analyzed here.
Supplementary_files_format_and_content: microRNAs_120ext.bed: An annotation BED file used to calculate pri-miRNA processing efficiencies for the miRNAs of interest.

molecule: total RNA

source_name: Normal Liver

extract_protocol:
RNA was isolated from Normal Liver with TRIzol and depleted for rRNA. Library construction was done for an Illumina HiSeq2500. Targets were enriched with the custom enrichment probe library.
RNA was isolated from HCC or NL with TRIzol and depleted for rRNA.
Library construction was done for an Illumina HiSeq2500 (2x50 bp).
Targets were enriched with a custom enrichment probe library.

tag: tissue

value: Normal Liver

tag: disease state

value: healthy


title: RNA from Normal Liver D4_10


title: RNA from Normal Liver D4_5


title: RNA from Normal Liver D4_6


title: RNA from Normal Liver D4_7


title: RNA from Normal Liver D4_3


title: 10x_348


title: 10x_346


title: 10x_347


title: RNA from Normal Liver D4_2


title: RNA from Normal Liver D4_1


title: shRNA FGFR1 rep 3

type: RNA

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

country: USA

institute: The Ohio State University

description: Gene expression Parental

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 12.1 software.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 24 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering and Volcano filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.Further data analysis was performed using Agilent GeneSpring GX 12.1 software. To identify differentially expressed genes, we performed a Fold Change filtering between two samples and a Volcano Plot filtering between two groups. The default threshold is Fold Change>=2.0, P-value<=0.05.

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: Total RNA was isolated using Qiagen kits, following which Integrity and concentration of RNA was assessed after RNA extraction and prior to sample labeling.

treatment_protocol: The stable Cell lines  with FGFR1 Knockdown were cultured and maintained at 2ug/ml Puromycin and gene expression profiled.

tag: genotype/variation

value: FGFR1 Knockdown

tag: cell line

value: Mantle cell lymphoma

tag: drug (ibrutinib) sensitivity

value: Resistant


title: shRNA FGFR1 rep 2

description: Gene expression Parental


title: Vector control rep 2

description: Gene expression Parental

value: control


title: Vector control rep 3

description: Gene expression Parental


title: RNA from HCC C3_16

source_name: Liver HCC (hepatocellular carcinoma)

extract_protocol:
RNA was isolated from HCC with TRIzol and depleted for rRNA. Library construction was done for an Illumina HiSeq2500. Targets were enriched with the custom enrichment probe library.
RNA was isolated from HCC or NL with TRIzol and depleted for rRNA.
Library construction was done for an Illumina HiSeq2500 (2x50 bp).
Targets were enriched with a custom enrichment probe library.

value: Liver HCC (hepatocellular carcinoma)

value: cancer


title: shRNA FGFR1 rep 1

description: Gene expression Parental


title: 10x_345


title: RNA from Normal Liver D4_8


title: Vector control rep 1

description: Gene expression Parental


title: RNA from HCC C3_15


title: 10x_342


title: 10x_344


title: RNA from HCC C3_14


title: RNA from HCC C3_13


title: RNA from HCC C3_12


title: 10x_341


title: RNA from HCC C3_11


title: 10x_339


title: 10x_343


title: RNA from HCC C3_8


title: RNA from HCC C3_10


title: 10x_337


title: 10x_338


title: RNA from HCC C3_7


title: RNA from HCC C3_6


title: RNA from HCC C3_5


title: 10x_335


title: 10x_334


title: RNA from HCC C3_1


title: 10x_336


title: 10x_333


title: 10x_331


title: RNA from HCC B2_25


title: RNA from HCC B2_23


title: RNA from HCC B2_27


title: RNA from HCC B2_22


title: 10x_330


title: 10x_328


title: RNA from HCC B2_19


title: RNA from HCC B2_20


title: 10x_326


title: RNA from HCC B2_18


title: 10x_325


title: 10x_340


title: 10x_324


title: RNA from HCC B2_16


title: 10x_323


title: 10x_322


title: RNA from HCC B2_11


title: RNA from HCC B2_4


title: 10x_321


title: 10x_332


title: RNA from HCC B2_3


title: RNA from HCC B2_2


title: RNA from HCC B2_21


title: 10x_320


title: 10x_319


title: RNA from HCC A1_14


title: 10x_317


title: RNA from HCC A1_12


title: RNA from HCC A1_11


title: 10x_318


title: 10x_329


title: 10x_316


title: 10x_327


title: 10x_315


title: RNA from HCC A1_10


title: RNA from HCC B2_15


title: 10x_313


title: 10x_312


title: RNA from HCC A1_7


title: RNA from HCC A1_6


title: RNA from HCC A1_8


title: 10x_311


title: RNA from HCC A1_13


title: 10x_309


title: RNA from HCC A1_5


title: 10x_308


title: RNA from HCC A1_2


title: RNA from HCC A1_3


title: RNA from HCC A1_4


title: 10x_310


title: 10x_305


title: RNA from HCC A1_1


title: 10x_304


title: 10x_307


title: 10x_306


title: 10x_303


title: S134A-GR Veh 3

city: Minneapolis

first: Carol

last: Lange

state: Minnesota

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop. A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.
Quality of raw RNA-seq sequences for each sample was assessed with FastQC. Trimmommatic(v0.33) was used to remove low quality bases and trim adapters. FastQC(v0.11.7) was used again on each filtered FASTQ files to generate a sequence quality plot.
Abundance of transcript was estimated with the featureCounts program in the SubRead package. DESeq2 (Version 1.22.2) was used to evaluate differential expression across groups and generate Principal Component Analysis (PCA) plots
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 expressing either wt-GR or S134A-GR were serum starved in IMEM containing 1% DCC for 18 hrs.

treatment_protocol: Cells were treated with vehicle treatment or either 10 ng/mL of TGFβ for 6 hrs.

tag: gr status (genotype)

tag: treatment

value: Veh


title: S134A-GR TGF-beta 3

extract_protocol:
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop.
A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.

value: TGF-beta


title: S134A-GR TGF-beta 1


title: 10x_302


title: 10x_314


title: 10x_301


title: S134A-GR Veh 2


title: S134A-GR TGF-beta 2


title: RNA from HCC A1_9


title: 10x_300


title: 10x_299


title: 10x_297


title: 10x_298


title: S134A-GR Veh 1


title: WT-GR TGF-beta 3

value: WT


title: WT-GR TGF-beta 1


title: WT-GR Veh 3


title: 10x_296


title: WT-GR Veh 2


title: 10x_293


title: 10x_294


title: 10x_295


title: 10x_292


title: LPS_human_Mir146KO_3

city: Cincinnati

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Sample name: s914
sgMir146a-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv

data_processing:
Paired-end fastq files were aligned to hg38 (human) or mm10 (mouse) genomes using HISAT2 (CD34Mir146aKO-LPS, Tet2-LSK datasets)  and Tophat (VavTRAF6-LPS dataset)
Raw counts were calculated using featureCounts.
Genome_build: hg38 (human) or mm10 (mouse)
Supplementary_files_format_and_content: raw counts

source_name: human CD34+ BM

growth_protocol: Cells were cultured in StemSpan containing SCF and TPO

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the Illumina protocol (Nextera 817 XT DNA Sample Preparation Kit).

treatment_protocol: Cells were treated with PBS or LPS (1µg/mL) for 90 minutes

value: CD34+ BM

tag: tumor stage

value: Normal

tag: genotype

value: LPS


title: 10x_291


title: WT-GR Veh 1


title: LPS_human_Mir146KO_2

description:
Sample name: s913
sgMir146a-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: LPS_human_Mir146KO_1

description:
Sample name: s912
sgMir146a-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 10x_290


title: 10x_289


title: PBS_human_Mir146KO_1

description:
Sample name: s903
sgMir146a-Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv

value: PBS


title: PBS_human_Mir146KO_3

description:
Sample name: s905
sgMir146a-Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 10x_287


title: 10x_288


title: LPS_human_WT_3

description:
Sample name: s902
sgCTL-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: LPS_human_WT_2

description:
Sample name: s901
sgCTL-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 10x_286


title: LPS_human_WT_1

description:
Sample name: s900
sgCTL-LPS
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: WT-GR TGF-beta 2


title: 10x_284


title: 10x_283


title: 10x_285


title: PBS_human_WT_3

description:
Sample name: s893
Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: PBS_human_WT_2

description:
Sample name: s892
Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 10x_282


title: PBS_human_WT_1

description:
Sample name: s891
Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 10x_281


title: 163_SPTB

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Preprocessing was done in Qiagen GeneGlobe Data Analysis Center; read alignment, quantification and annotation to the known miRNA / piRNA sequences. miRBase v21 is used for miRNA and piRNABank is used for piRNA.
Read alignment was done using Bowtie.
Supplementary_files_format_and_content: File is excel file containing the genewise UMIs and read counts for each sample containing these small RNA sections: miRNA_piRNA, tRNA, otherRNA, notCharacterized_mappable. They are not normalized values.

source_name: placenta

extract_protocol:
MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel)
QIAseq miRNA Library Kit, QIAGEN (HB-2573-001)

tag: clinical information

value: spontaneous preterm birth


title: 150_SPTB


title: 10x_278

value: Malignant ascites  single cell


title: 10x_280


title: 10x_277


title: 72_SPTB


title: 10x_279


title: 45_SPTB


title: 141_STB

value: spontaneous term birth


title: PBS_human_Mir146KO_2

description:
Sample name: s904
sgMir146a-Vehicle
CD34Mir146aKO-LPS__rawCounts_for_GEO.csv
CD34Mir146aKO-LPS__metadata_for_GEO.csv


title: 1_SPTB


title: 39_STB


title: 10x_274


title: 10x_273


title: 89_SPTB


title: 37_STB


title: 10x_272


title: 10x_271


title: 25_STB


title: 154_ETB

value: elective term birth (caesarean section)


title: 10x_275


title: 24_STB


title: 47_ETB


title: 10x_269


title: 10x_270


title: 38_ETB


title: 84_STB


title: 134_ETB


title: 10x_267


title: 10x_268


title: 10x_266


title: 23_ETB


title: 10x_265


title: 10x_276


title: 30_ETB


title: 10x_264


title: 10x_263


title: 10x_262


title: WEHI-539 B

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Single-end FASTQ reads were aligned to human genome build GRCh38 using hisat2 with defaut parameters
SAM files were processed and sorted to BAM format using sambamba v 0.63
Transcript counts were generated with htseq-count (v0.5.4p3)
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data are raw counts of transcripts as determined by htseq-count

source_name: Pancreatic cells

growth_protocol: H9 cells were differentiated towards pancreatic lineage

extract_protocol:
RNA was extracted using USB affymetrix #78877 RNA extraction kit
Libraries were prepared using the TruSEQ Stranded Total RNA Prep with  Ribo-Zero Human Cat. No. RS-122-2201 as per manufacturer's protocol. Libraries sequenced using 150bp paired-end on HiSeq 2500 Platform.

treatment_protocol: D7 pancreatic lineage cells were treated with WEHI-539, a BCL-XL inhibitor

value: H9 differentiated

tag: passages

tag: Sex

value: Female


title: WEHI-539 A


title: WEHI-539 C


title: 10x_261


title: DMSO C


title: 10x_259


title: 10x_258


title: 10x_257


title: DMSO A


title: HUVEC R-VEC 4

city: New York

first: Brisa

last: Palikuqi

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
RNA-seq reads were aligned using STAR version 2.6.0c.  The STAR index was made with the GENCODE GRCh38.p12 or GENCODE GRCm38.p6 primary assembly and corresponding GENCODE annotation file --sjdbGTFfile gencode.v28.annotation.gtf or  --sjdbGTFfile gencode.vM17.annotation.gtf, respectively.
Fragments mapping uniquely to genes in the GENCODE v28 (for human samples) or GENCODE vM17 (for mouse samples) main GTF were counted using featureCounts version v1.6.2.
Genome_build: GRCh38.p12 (human), GRCm38.p6 (mouse)
Supplementary_files_format_and_content: featureCount output files

source_name: HUVEC

extract_protocol: RNA libraries were prepared for sequencing using Illumina's TruSeq RNA Library Preparation Kit v2

tag: growth protocol

value: R-VEC 2D

tag: treatment protocol

value: Complete EC media

tag: extraction protocol

value: qiagen


title: HUVEC R-VEC 3


title: 10x_255

tag: cell type

tag: patient id


title: HUVEC R-VEC 2


title: HUVEC R-VEC 1


title: 10x_253

tag: time point


title: 10x_252


title: HUVEC EC-4

value: CTRL-EC  2D


title: 10x_254


title: 10x_251


title: HUVEC EC-3

value: CTRL-EC 2D


title: 10x_250


title: HUVEC EC-1


title: 10x_248


title: 10x_249


title: 10x_247


title: 10x_260


title: 10x_246


title: DMSO B


title: CXCR4 BiFC Sort Replicate 2 [X4VC_BiFC2]

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: Deep mutational scan of CXCR4-VC for surface expression and BiFC signal in Expi293F cells over-expressing wildtype CXCR4-VN

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: CCR5 fragment A read 1: python Paired_read_fuser.py --path directory_fragA_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq GCCGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGAC --read1_overlap_start 46 --read1_overlap_end 244 --mode R1
Fuser script: CCR5 fragment A read 2: python Paired_read_fuser.py --path directory_fragA_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq GTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTAATGGTC --read2_overlap_start 19 --read2_overlap_end 229 --mode R2
Fuser script: CCR5 fragment B read 1: python Paired_read_fuser.py --path directory_fragB_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq ATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAA --read1_overlap_start 22 --read1_overlap_end 238 --mode R1
Fuser script: CCR5 fragment B read 2: python Paired_read_fuser.py --path directory_fragB_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq ATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGG --read2_overlap_start 6 --read2_overlap_end 231 --mode R2
Fuser script: CCR5 fragment C read 1: python Paired_read_fuser.py --path directory_fragC_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq TTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTA --read1_overlap_start 19 --read1_overlap_end 238 --mode R1
Fuser script: CCR5 fragment C read 2: python Paired_read_fuser.py --path directory_fragC_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq GTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGG --read2_overlap_start 13 --read2_overlap_end 205 --mode R2
Fuser script: CXCR4 fragment A read 1: python Paired_read_fuser.py --path directory_fragA_R1/ --read1 CXCR4_R1.fastq.bz2 --read2 CXCR4_R1.fastq.bz2 --wtseq GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGT --read1_overlap_start 51 --read1_overlap_end 240 --mode R1
Fuser script: CXCR4 fragment A read 2: python Paired_read_fuser.py --path directory_fragA_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_R2.fastq.bz2 --wtseq AAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATT --read2_overlap_start 24 --read2_overlap_end 228 --mode R2
Fuser script: CXCR4 fragment B read 1: python Paired_read_fuser.py --path directory_fragB_R1/ --read1 CXCR4_R1.fastq.bz2 --read2 CXCR4_R1.fastq.bz2 --wtseq GGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTAC --read1_overlap_start 20 --read1_overlap_end 236 --mode R1
Fuser script: CXCR4 fragment B read 2: python Paired_read_fuser.py --path directory_fragB_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_R2.fastq.bz2 --wtseq ATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAG --read2_overlap_start 25 --read2_overlap_end 229 --mode R2
Fuser script: CXCR4 fragment C read 1: python Paired_read_fuser.py --path directory_fragC_R1/ --read1 CXCR4_R1.fastq.bz2 --read2CXCR4_R1.fastq.bz2 --wtseq GACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATC --read1_overlap_start 21 --read1_overlap_end 237 --mode R1
Fuser script: CXCR4 fragment C read 2: python Paired_read_fuser.py --path directory_fragC_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_library_R2.fastq.bz2 --wtseq TGGATTTCCATCACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCT --read2_overlap_start 19 --read2_overlap_end 205 --mode R2
Aligner script: CCR5 fragment A read 1: python Fused_read_aligner.py --path directory_fragA_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA GCCGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGAC --referenceAA ADYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKRLKSMTD --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment A read 2: python Fused_read_aligner.py --path directory_fragA_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA GTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTAATGGTC --referenceAA VTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CCR5 fragment B read 1: python Fused_read_aligner.py --path directroy_fragB_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA ATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAA --referenceAA IYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALK --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment B read 2: python Fused_read_aligner.py --path directroy_fragB_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA ATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGG --referenceAA ICYSGILKTLLRCRNEKKRHRAVRLIFTIMIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CCR5 fragment C read 1: python Fused_read_aligner.py --path directroy_fragC_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA TTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTA --referenceAA LKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment C read 2: python Fused_read_aligner.py --path directory_fragC_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA GTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGG --referenceAA VTETLGMTHCCINPIIYAFVGEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment A read 1: python Fused_read_aligner.py --path directroy_fragA_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGT --referenceAA EGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment A read 2: python Fused_read_aligner.py --path directroy_fragA_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA AAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATT --referenceAA KVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCI --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment B read 1: python Fused_read_aligner.py --path directroy_fragB_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTAC --referenceAA GYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLDRY --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment B read 2: python Fused_read_aligner.py --path directroy_fragB_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA ATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAG --referenceAA IIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment C read 1: python Fused_read_aligner.py --path directroy_fragC_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATC --referenceAA DRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHI --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment C read 2: python Fused_read_aligner.py --path directory_fragC_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA TGGATTTCCATCACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCT --referenceAA WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTES --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: Example: python mapCounts.py --path directory_fragA_R1/ --infile CCR5_R1.fast_R1_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: Example: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: Example: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size ##
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Data was then assembled from the different fragments/reads to span the full sequence in Excel.  Where there was overlap, real enrichment ratios were averaged and converted back to log(base2). Maximum depletion was set to log(base2) enrichment ratio = -5.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the number of reads for each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

growth_protocol: CXCR4-knockout Expi293F cells were cultured in Expi293 Expression Medium (Life Technologies). Stable lines were generated over-expressing FLAG-CXCR4-VN or FLAG-CCR5-VN (cloned into pcDNA3.1(+), Invitrogen).

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics) primed with a gene-specific primer (EBV_reverse).
In the first round of PCR (18 cycles), the CCR5 and CXCR4 coding sequences were amplified as three overlapping fragments of ~800 bp each.
Primer pair: CCR5 fragment A: MiSeq_CCR5_myctag_F (TCTTTCCCTACACGACGCTCTTCCGATCTCGAGCAAAAGCTGATCTCAG) and MiSeq_CCR5_652_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTAGGATTCCCGAGTAGCAG)
Primer pair: CCR5 fragment B: MiSeq_CCR5_176_F (TCTTTCCCTACACGACGCTCTTCCGATCTAAGGCTGAAGAGCATGACTG) and MiSeq_CCR5_875_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGATGCAGCAGTGCGTCAT)
Primer pair: CCR5 fragment C: MiSeq_CCR5_388_F (TCTTTCCCTACACGACGCTCTTCCGATCTCGTCCATGCTGTGTTTGCT) and MiSeq_Venus_468_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGATGCCGTTCTTCTGCTTG)
Primer pair: CXCR4 fragment A: MiSeq_CXCR4_myctag_F (TCTTTCCCTACACGACGCTCTTCCGATCTGCCGAGCAGAAATTGATCAG) and MiSeq_CXCR4_682_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTGTGACAGCTTGGAGATG)
Primer pair: CXCR4 fragment B: MiSeq_CXCR4_169_F (TCTTTCCCTACACGACGCTCTTCCGATCTGATTGGTCATCCTGGTCATG) and MiSeq_CXCR4_882_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACAGTGGAAGAAAGCTAGGG)
Primer pair: CXCR4 fragment C: MiSeq_CXCR4_375_F (TCTTTCCCTACACGACGCTCTTCCGATCTATCCTGGCCTTCATCAGTCT) and MiSeq_Venus_468_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGATGCCGTTCTTCTGCTTG)
In a second round of PCR (15 cycles), Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a HiSeq 2500 using a 2x250 nt paired end protocol, though data is analyzed as single reads.

treatment_protocol: Cells expressing DNA libraries of myc-CXCR4-VC or myc-CCR5-VC mutants (cloned into pCEP4, Invitrogen) were FACS sorted for receptor surface expression and Venus fluosrecence.

tag: mutagenized protein

tag: expi293f line

value: CXCR4-KO / FLAG-CXCR4-VN

tag: sort gate 1

value: Cells positive for surface expressed CXCR4-VC (anti-myc-Alexa 647 staining); square gate in FCS-vs-Alexa 647 plot

tag: sort gate 2

value: Top 10% for Venus fluorescence; sloped gate in YFP-vs-Alexa 647 plot

tag: # collected cells


title: 10x_245


title: CXCR4-VC Surface Expression Sort Replicate 1 [X4VC_expression1]

description: Deep mutational scan of CXCR4-VC for surface expression in Expi293F cells over-expressing wildtype CXCR4-VN


title: CXCR4 BiFC Sort Replicate 1 [X4VC_BiFC1]


title: CXCR4-VC SSM Library [X4VC_library]

description: CXCR4 SSM library

library_source: genomic

molecule: genomic DNA

tag: molecule subtype

value: plasmid DNA


title: 10x_243


title: 10x_256


title: CCR5 BiFC Sort Replicate 2 [R5VC_BiFC2]

description: Deep mutational scan of CCR5-VC for surface expression and BiFC signal in Expi293F cells over-expressing wildtype CCR5-VN

value: CXCR4-KO / FLAG-CCR5-VN

value: Cells positive for surface expressed CCR5-VC (anti-myc-Alexa 647 staining); square gate in FCS-vs-Alexa 647 plot


title: CCR5 BiFC Sort Replicate 1 [R5VC_BiFC1]


title: 10x_242


title: CCR5-VC Surface Expression Sort Replicate 2 [R5VC_expression2]

description: Deep mutational scan of CCR5-VC for surface expression in Expi293F cells over-expressing wildtype CCR5-VN


title: 10x_239


title: 10x_240


title: 10x_241


title: HUVEC EC-2


title: 10x_238


title: CXCR4-VC Surface Expression Sort Replicate 2 [X4VC_expression2]


title: Sample 4_K562r

city: London

first: Jamshid

middle: Sorouri

last: Khorashad

address: centre for haematology, Commonwealth building, Hammersmith Hospital

country: United Kingdom

institute: Imperial College London

description: 170508_K00345_0010_AHJG2JBBXX_K562R_S4_L004

data_processing:
FastQC software was used for base calling, to assess GC content, to look at sequence quality at each base and to assess adaptor content
Alignment and quantification was performed using Salmon 0.8.2 to human genome 38 cDNA. Psudeogenes and haplotypes were removed from the genome prior to running Salmon.
Tximport was used to create gene-level counts based on the transcript level counts produced from Salmon.
DESeq2 was used to identifiy the differentially expressed genes between the two cell lines.
Gene Set Enrichment Analysis (GSEA) was performed to identify overrepresented genes in different pathways.
Genome_build: Human genome 38 cDNA
Supplementary_files_format_and_content: csv file with ensembl ids in the first column and the normalised gene count for each sample for the particular gene

extract_protocol:
15x106 cells were collected, washed and pelleted for both cell lines. 1ml of RLT buffer (Qiagen, UK) supplemented with β-mercaptoethanol (Sigma-Aldrich) in a 100:1 ratio, was added to each centrifuge tube and the pellet was resuspended. Total RNA was extracted using the RNeasy mini kit (Qiagen) as per manufacturer’s instructions.
RNA libraries were prepped using the TruSeq RNA sample Preparation Kit from Illumina

tag: cell line

value: human chronic myeloid lukeaemia cell line

tag: phenotype

value: resistant to the standard treatment imatinib


title: Sample 6_K562r

description: 170508_K00345_0010_AHJG2JBBXX_K562R_S6_L004


title: Sample 5_K562r

description: 170508_K00345_0010_AHJG2JBBXX_K562R_S5_L004


title: Sample 2_K562s

description: 170508_K00345_0010_AHJG2JBBXX_K562S_S2_L004

value: sensitive to the standard treatment imatinib


title: 10x_235

value: Malignant ascites  single cell


title: CCR5-VC SSM Library [R5VC_library]

description: CCR5-VC SSM library


title: 10x_234


title: Sample 1_K562s

description: 170508_K00345_0010_AHJG2JBBXX_K562S_S1_L004


title: Sample 3_K562s

description: 170508_K00345_0010_AHJG2JBBXX_K562S_S3_L004


title: HCT116 mut9 doxorubicin treated rep3

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

data_processing:
Reads were mapped to the 2019 release of the Homo sapiens genome (GRCh38.p12) using the STAR aligner (STAR version 2.6.1a)
Transcripts per Million mapped reads (TPM) were calculated using the SALMON software (version 0.9.1).
Read counts were analyzed using the R environment (R 3.5.1) and the DESeq2 package (version 1.22.0) according to the suggestions in DEseq2’s vignette.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: Human HCT116 cell line mutant

growth_protocol: HCT116 and Tp53 mutant cell lines were cultured in RPMI, 10% heat inactivated Fetal Bovine Serum, 100U/ml Penicillin and 100ug/ml Streptomycin, cultured at 37oC with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol (LifeTech 15596018)
RNA libraries were prepared for sequencing using standard protocols following the Illumina TruSeq_RNA_SamplePrep_Guide. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000  at Beijing Genomics Institute.

treatment_protocol: HCT116 and Tp53 mutant cell lines were either untreated or treated with 1μM doxorubicin for 24 hours.

tag: subclone

tag: treatment

value: 1uM doxorubicin for 24 hours


title: 10x_233


title: 10x_244


title: HCT116 mut9 doxorubicin treated rep2


title: 10x_232


title: HCT116 mut9 doxorubicin treated rep1


title: 10x_230


title: 10x_229


title: CCR5-VC Surface Expression Sort Replicate 1 [R5VC_expression1]


title: HCT116 mut5 doxorubicin treated rep3


title: HCT116 mut5 doxorubicin treated rep1


title: HCT116 mut5 doxorubicin treated rep2


title: 10x_227


title: HCT116 mut4 doxorubicin treated rep3


title: 10x_237


title: HCT116 mut4 doxorubicin treated rep2


title: 10x_236


title: HCT116 mut4 doxorubicin treated rep1


title: 10x_225


title: 10x_226


title: HCT116 doxorubicin treated rep3

source_name: Human HCT116 cell line WT


title: 10x_224


title: HCT116 doxorubicin treated rep2


title: HCT116 doxorubicin treated rep1


title: 10x_222


title: 10x_223


title: 10x_220


title: HCT116 mut9 rep3


title: 10x_221


title: 10x_231


title: 10x_219


title: 10x_218


title: HCT116 mut9 rep1


title: HCT116 mut5 rep3


title: 10x_217


title: HCT116 mut5 rep2


title: 10x_228


title: HCT116 mut5 rep1


title: 10x_216


title: 10x_215


title: HCT116 mut4 rep2


title: 10x_214


title: HCT116 mut4 rep1


title: HCT116 mut9 rep2


title: 10x_213


title: HCT116 rep3


title: HCT116 rep2


title: 10x_211


title: HCT116 mut4 rep3


title: 10x_209


title: HCT116 rep1


title: 10x_210


title: R2shp53-WNT1_SA_replicate1

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

country: France

institute: IRCM

hyb_protocol: 12 mg of cRNA fragmented were hybridized for 16 h at 45 C, washed and stained in the Affymetrix Fluidics Station 450 with Hybridization Wash & Stain kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Robust Multi-array Average (RMA) method (R package affy)

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Express

growth_protocol: MEBM medium supplemented with antibiotics (Gibco/Thermo-Fisher), 1M HEPES, lhydrocortisone, insulin, EGF, BPE and Gentamycine (MEGM single Quots, Lonza, Levallois-Perret, France)

extract_protocol: RNA were isolated using the Rneasy Mini Kit (Qiagen).

treatment_protocol: Primary HMEC cultures were transduced with amphotropic retroviral supernatants produced by 293T cells transfected with one of the   following retroviral constructs: pSUPER.retro.hygro-shp53, pBABE.neo-CCNE1, pLNC-WNT1, pBABE.puro-HRASV12.   Transduction was followed by a 3 weeks period of antibiotic selection.

tag: gender

value: female

value: primary human mammary epithelial cells (HMECs)

tag: transduced with


title: 10x_208


title: R2shp53-WNT1_Late_replicate1


title: R2shp53-RASV12_Late_replicate1


title: R2shp53-WNT1_SA_replicate2


title: R2shp53-CCNE1_SA_replicate2


title: R2shp53-RASV12_SA_replicate2


title: 10x_212


title: 10x_207


title: R2shp53-CCNE1_SA_replicate1


title: R2shp53-CCNE1_Late_replicate2


title: R2shp53-WNT1_Late_replicate2


title: R2shP53_Late_replicate2


title: R2shP53_Early_replicate2


title: R2shP53_Late_replicate1


title: R2shp53-RASV12_SA_replicate1


title: 10x_206


title: 10x_205


title: R2_replicate2


title: R2shP53_Early_replicate1


title: R2_replicate1


title: R2shp53-RASV12_Late_replicate2


title: R2shp53-CCNE1_Late_replicate1


title: 10x_204


title: 10x_203


title: 10x_202


title: 10x_200


title: 10x_199


title: 10x_201


title: Normal Colonic Mucosa (control) Replicate 5

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

description: Biopsy of Normal Colon (control) from subject N5

hyb_protocol: 825ng of sample and 825ng of Cy5 labelled reference RNA were added to a nuclease free microcentrifuge tube. Subsequently, 11 µl of 10x blocking agent and 2.2 µl of fragmentation buffer (Agilent, catalogue number 5188-5281) were added. Nuclease free water was added to each sample to bring the total volume to 55 µl. Each sample was then incubated to 60 degrees centigrade for 30 minutes in the dark.    55µl of 2xGExhybridisation buffer (HI-RPM, Agilent, catalogue number 5188-5281) was then added to each sample and gently mixed using the pipette.     Hybridization Chamber Gaskett slides (Agilent, catalogue number G2534-60011) were loaded into the Agilent SureHyb chamber base (Agilent, catalogue number G2534A) with the label facing up and sitting flush. Each sample was then loaded onto the gasket slides, ensuring not to introduce air bubbles. The whole Human Genome microarray slides (4x44k, Agilent, catalogue number G4112F) were then placed flush on top of the gasket slides with the samples ‘sandwiched’ in between. The SureHyb chamber cover was added and the clamp ‘hand-tightened’. Care was taken to ensure any air-bubbles were moving freely with rotation, as bubbles that were stuck would have created artefacts. SureHyb chambers were then placed into a rotisserie inside a hybridisation oven rotator (Agilent, catalogue number G2530-60029), and incubated at 65 degrees centigrade for 17 hours, rotating at 10rpm.    The microarray slides were then washed in pre-warmed gene expression wash buffer solutions I, II and III (Agilent, catalogue number 5188-5327). The solutions were pre-warmed and used if there was no precipitate. Slides were removed from the oven, and carefully separated from the gasket slide submerged in buffer I. Each slide was then placed into a universal tube filled with buffer I using servile forceps, and rotated on a spiramix (Spiramix 5, Denley, Serial Number: 2672) for 1 minute in the dark. Each slide was then carefully placed into a tube with buffer II, and rotated as before for 1 minute. Each slide was then carefully submerged in buffer III for 3 seconds, and slowly removed. Each slide was then inserted into a Hybridization Chamber (Agilent, catalogue number G2534A), placed into the Agilent Microarray Scanner (Agilent, catalogue number G2565BA), and scanned immediately.    Feature extraction was then undertaken. Feature extraction was a process by which information from the probe features was extracted from the microarray scan data. The raw images were evaluated using Agilent Feature Extraction software (version X). The Feature Extraction files were then imported into GeneSpring X and normalised.

scan_protocol: Each slide was inserted into a Hybridization Chamber (Agilent, catalogue number G2534A), placed into the Agilent Microarray Scanner (Agilent, catalogue number G2565BA).

data_processing: Agilent Feature Extraction v9.1.3.1 standard Common reference image analysis protocol was used. Following feature extraction Data was imported into GeneSpring 10 (Agilent Technologies) using the standard two colour experiment protocol. Note that as the universal Human Reference was labelled with Cy5 all arrays were dye swapped such that the ratio of interest (Cy3/Cy5) could be obtained

source_name: Biopsy of Normal Colon (control)

label_protocol: 500 ng of RNA was added to a sterile microcentrifuge tube and the volume was increased to 8.3 µl using nuclease free water. Spike-mix A (Agilent, catalogue number 5188-5279) was then diluted with dilution buffer 3 times; 1:20, then 1:40 then 1:16 dilutions. Two microlitres of diluted Spike-mix A and 1.2 µl of T7 promoter primer (Agilent, catalogue number 5190-2306) were added, to total the volume at 11.5 µl.    T7 promoter primer was denatured in a water bath at 65 degrees centigrade for 10 minutes and then placed on ice. 5x First Strand buffer (Agilent, catalogue number 5190-2306) was heated in a water bath at 800C for 4 minutes. The cDNA master mix was then produced.    The cDNA master mix was mixed in a separate sterile microcentrifuge tube. The following volumes were added per sample being labelled. The cDNA master mix per sample included; 4 µl 5x First Strand buffer, 2 µl 0.1 M DTT (Agilent, catalogue number 5190-2306), 1 µl 10mM dNTP mix (Agilent, catalogue number 5190-2306), 1 µl MMLV-RT (Agilent, catalogue number 5190-2306)) and 0.5 µl RNaseOut (Agilent, catalogue number 5190-2306). The total volume, per sample being labelled, was 8.5µl. Subsequently, 8.5µl of the cDNA master mix solution was then added to each sample. Samples were then incubated in a water bath for 2 hours at 40 degrees centigrade.    Each sample was then incubated at 650C for 15 minutes, in a water bath, briefly spun in the variable speed microcentrifuge for a few seconds and then placed on ice.     50% polyethylene glycol (PEG, Agilent, catalogue number 5190-2306) solution was then warmed to 40 degrees centigrade for 1 minute and the transcription master mix was then constructed in a separate nuclease free microcentrifuge tube. Transcription master mix consisted of 15.3 µl nuclease free water, 20 µl 4x transcription buffer, 6µl 0.1 M DTT, 8µl NTP mix (Agilent, catalogue number 5190-2306), 6.4µl 50% PEG, 0.5µl RNaseOut, 0.6µl inorganic pyrophosphatase (Agilent, catalogue number 5190-2306), 0.8µl T7 RNA polymerase (Agilent, catalogue number 5190-2306) and 2.4µl of Cyanine 3-CTP (Cy3, Agilent, catalogue number 5190-2306). The total volume per sample being labelled was 60µl.    Sixty microlitre of the transcription master mix was then added to each sample and mixed using gentle pipetting. Samples were then incubated in a water bath at 40 degrees centigrade for 4 hours. Samples were then stored at -80 degrees centigrade in the dark.

growth_protocol: Following liver resection, the specimen was removed from the abdominal cavity under sterile conditions. Sterile techniques were employed to minimise exposure of the tissue samples to ribonucleases. Also, samples were taken from the liver within 10 minutes of removing of the liver from the abdominal cavity. Three tissue samples of approximately 30-50 mg were taken from the liver specimen of each patient; the metastasis, the ‘halo’ and the liver parenchyma respectively, using a size 22 sterile blade scalpel, sterile forceps and 3 sterile tru-cut biopsy needles.

extract_protocol: 15 to 30 mg of stored tissue was placed into RNase-free microcentrifuge eppendorfs (Eppendorf, catalogue 5417R), each containing a 5 mm stainless steel bead.  600 µl of prepared Buffer RPE was then added. Each column was then placed into a rotor-stator homogeniser (manufactured by Retsch) which simultaneously disrupted and homogenise the tissue for 2 minutes. The plate containing the columns was then rotated by 1800C and the process was repeated for a further 2 minutes. The columns were inspected and the process repeated as necessary until the samples were uniformly homogeneous.     The lysate was transferred into a QIAshredder spin column (Qiagen, Inc., catalogue number 74134) placed in a 2 ml collection tube.    Seventy percent ethanol was then added to the flow-through solution at a ratio of 1:1, and mixed well by pipetting. 700 µl of the sample was then added to an RNeasy spin column and placed in a 2 ml collection tube. This was then spun in the variable speed microcentrifuge for 30s at 10,000 rpm at 210C. The remainder of the solution for each sample was then pipetted into the appropriate RNeasy spin column and this process was repeated until all the sample volume, including any precipitant, was used.    700 µl of Buffer RW1 (Qiagen, Inc., catalogue number 74134) was added to the RNeasy spin column and spun in the variable speed microcentrifuge for 30s at 10,000 rpm at 210C. The flow-through was discarded and the RNeasy spin column was retained.    500 µl of Buffer RPE was then added to the RNeasy spin column and spun in the variable speed microcentrifuge for 30 s at 10,000 rpm at 210C. The flow-through was discarded and the RNeasy spin column was retained. The wash with 500 µl of Buffer RPE was repeated and spun in the variable speed microcentrifuge for 2 minutes at 10,000 rpm at 210C and the flow-through was discarded. The RNeasy spin column was then spun in the variable speed microcentrifuge for a further 1 minute at 10,000 rpm at 210C to eliminate any possible carryover of Buffer RPE or residual flow-through.    The RNA was then eluted into RNase-free water (Qiagen, Inc., catalogue number 74134). The RNeasy spin column was transferred to a new 1.5ml microcentrifuge tube. 50 µl of RNase-free water was added directly to the spin column membrane, allowed to stand for 1 minute, and then spun in the variable speed microcentrifuge for 1 minute at 10,000 rpm at 210C, to elute the RNA. The test tubes containing the RNA were placed into a bucket of ice, using sterile conditions, and stored at -80 degrees centigrade.

treatment_protocol: Having been taken from the resected liver, the biopsy samples were immediately stored in RNAlater RNA stabilisation reagent in a sterile microcentrifuge tube at room temperature for 1-2 hours and subsequently stored at -20 degrees centigrade until processed and analysed.

tag: tissue

value: Colon

tag: tumour stage

source_name: Stratagene Universal Human Reference

tag: universal human reference

value: total RNA from 10 human cell lines


title: 10x_198

tag: cell type

tag: patient id


title: Liver metasis Replicate 33

description: Liver biopsy of metasis from subject 33

source_name: Liver Biopsy of metasis

value: Liver

value: Metasis


title: Normal Colonic Mucosa (control) Replicate 4

description: Biopsy of Normal Colon (control) from subject N4


title: 10x_197

tag: time point


title: Normal Colonic Mucosa (control) Replicate 3

description: Biopsy of Normal Colon (control) from subject N3


title: Liver parenchyma (control) Replicate 33

description: Liver biopsy of parenchyma (control) from subject 33

source_name: Liver Biopsy of parenchyma (control)


title: Normal Colonic Mucosa (control) Replicate 2

description: Biopsy of Normal Colon (control) from subject N2


title: Liver metasis Replicate 32

description: Liver biopsy of metasis from subject 32


title: Liver parenchyma (control) Replicate 32

description: Liver biopsy of parenchyma (control) from subject 32


title: Normal Colonic Mucosa (control) Replicate 1

description: Biopsy of Normal Colon (control) from subject N1


title: Liver parenchyma (control) Replicate 31

description: Liver biopsy of parenchyma (control) from subject 31


title: Normal Colonic Mucosa (control) Replicate 6

description: Biopsy of Normal Colon (control) from subject N6


title: 10x_196


title: Liver Halo of metasis Replicate 33

description: Liver biopsy of Halo of metasis from subject 33

source_name: Liver Biopsy of Halo of metasis

value: Halo of Metasis


title: Liver parenchyma (control) Replicate 30

description: Liver biopsy of parenchyma (control) from subject 30


title: Liver Halo of metasis Replicate 32

description: Liver biopsy of Halo of metasis from subject 32


title: 10x_195


title: Liver Halo of metasis Replicate 29

description: Liver biopsy of Halo of metasis from subject 29


title: Liver metasis Replicate 29

description: Liver biopsy of metasis from subject 29


title: Liver Halo of metasis Replicate 28

description: Liver biopsy of Halo of metasis from subject 28


title: Liver parenchyma (control) Replicate 28

description: Liver biopsy of parenchyma (control) from subject 28


title: Liver Halo of metasis Replicate 31

description: Liver biopsy of Halo of metasis from subject 31


title: Liver parenchyma (control) Replicate 29

description: Liver biopsy of parenchyma (control) from subject 29


title: Liver Halo of metasis Replicate 30

description: Liver biopsy of Halo of metasis from subject 30


title: Liver metasis Replicate 31

description: Liver biopsy of metasis from subject 31


title: Liver metasis Replicate 30

description: Liver biopsy of metasis from subject 30


title: 10x_194


title: 10x_193


title: 10x_192


title: 10x_191


title: 10x_189


title: 10x_190


title: 10x_188


title: 10x_186


title: 10x_187


title: Liver Halo of metasis Replicate 27

description: Liver biopsy of Halo of metasis from subject 27


title: R-VEC Pre-Plug 2

tag: growth protocol

value: R-VEC flat 2D

tag: treatment protocol

value: R-VEC right before injecting in mice, complete EC medium

tag: extraction protocol

value: picopure


title: Liver parenchyma (control) Replicate 27

description: Liver biopsy of parenchyma (control) from subject 27


title: Liver Halo of metasis Replicate 26

description: Liver biopsy of Halo of metasis from subject 26


title: Liver metasis Replicate 26

description: Liver biopsy of metasis from subject 26


title: Liver metasis Replicate 28

description: Liver biopsy of metasis from subject 28


title: 10x_185


title: Liver Halo of metasis Replicate 24

description: Liver biopsy of Halo of metasis from subject 24


title: Liver parenchyma (control) Replicate 24

description: Liver biopsy of parenchyma (control) from subject 24


title: Liver Halo of metasis Replicate 25

description: Liver biopsy of Halo of metasis from subject 25


title: Liver parenchyma (control) Replicate 25

description: Liver biopsy of parenchyma (control) from subject 25


title: Liver Halo of metasis Replicate 23

description: Liver biopsy of Halo of metasis from subject 23


title: R-VEC Pre-Plug 1


title: Liver metasis Replicate 23

description: Liver biopsy of metasis from subject 23


title: 10x_184


title: Liver parenchyma (control) Replicate 22

description: Liver biopsy of parenchyma (control) from subject 22


title: Liver metasis Replicate 25

description: Liver biopsy of metasis from subject 25


title: Liver parenchyma (control) Replicate 23

description: Liver biopsy of parenchyma (control) from subject 23


title: Liver metasis Replicate 27

description: Liver biopsy of metasis from subject 27


title: R-VEC Plug 3

value: R-VEC in plug in vivo

value: 1 month in vivo LEC, sorted as GFP+


title: Liver metasis Replicate 22

description: Liver biopsy of metasis from subject 22


title: Liver metasis Replicate 21

description: Liver biopsy of metasis from subject 21


title: Liver Halo of metasis Replicate 21

description: Liver biopsy of Halo of metasis from subject 21


title: Liver parenchyma (control) Replicate 21

description: Liver biopsy of parenchyma (control) from subject 21


title: Liver parenchyma (control) Replicate 20

description: Liver biopsy of parenchyma (control) from subject 20


title: Liver metasis Replicate 24

description: Liver biopsy of metasis from subject 24


title: Liver parenchyma (control) Replicate 26

description: Liver biopsy of parenchyma (control) from subject 26


title: Liver Halo of metasis Replicate 22

description: Liver biopsy of Halo of metasis from subject 22


title: 10x_183


title: 10x_182


title: R-VEC Plug 2


title: 10x_181


title: Pulmonary-EC

source_name: adult lung EC

value: Pulmonary CTRL-EC 2D

value: promocell, MV2 media

value: qiagen


title: Liver metasis Replicate 20

description: Liver biopsy of metasis from subject 20


title: Liver parenchyma (control) Replicate 19

description: Liver biopsy of parenchyma (control) from subject 19


title: Adipose-EC

source_name: adult adipose EC

value: Adipose CTRL-EC 2D


title: 10x_179

source_name: Malignant ascites  single cell

value: Malignant ascites  single cell


title: Dermal-EC

source_name: adult dermal EC

value: Dermal CTRL-EC 2D


title: Aortic-EC

source_name: adult aortic EC

value: Aortic CTRL-EC 2D


title: Cardiac-EC

source_name: adult cardiac EC

value: Cardial CTRL-EC 2D


title: 10x_178


title: 10x_177


title: Liver Halo of metasis Replicate 20

description: Liver biopsy of Halo of metasis from subject 20

value: total RNA from 10 human cell lines


title: 10x_180


title: Adipose R-VEC

value: Adipose R-VEC 2D


title: 10x_175


title: 10x_176


title: Liver Halo of metasis Replicate 19

description: Liver biopsy of Halo of metasis from subject 19

value: Liver


title: Liver Halo of metasis Replicate 18

description: Liver biopsy of Halo of metasis from subject 18

value: Halo of Metasis


title: Liver Halo of metasis Replicate 17

description: Liver biopsy of Halo of metasis from subject 17


title: Liver metasis Replicate 19

description: Liver biopsy of metasis from subject 19

value: Metasis


title: Liver Halo of metasis Replicate 16

description: Liver biopsy of Halo of metasis from subject 16


title: Liver metasis Replicate 16

description: Liver biopsy of metasis from subject 16


title: Liver parenchyma (control) Replicate 15

description: Liver biopsy of parenchyma (control) from subject 15


title: Pulmonary R-VEC

value: Pulmonary R-VEC 2D


title: 10x_173


title: 10x_174


title: Liver metasis Replicate 18

description: Liver biopsy of metasis from subject 18


title: Liver metasis Replicate 17

description: Liver biopsy of metasis from subject 17


title: Aortic R-VEC

value: Aortic R-VEC 2D


title: Liver Halo of metasis Replicate 13

description: Liver biopsy of Halo of metasis from subject 13


title: 10x_172


title: Liver parenchyma (control) Replicate 18

description: Liver biopsy of parenchyma (control) from subject 18


title: Liver parenchyma (control) Replicate 13

description: Liver biopsy of parenchyma (control) from subject 13


title: Liver parenchyma (control) Replicate 17

description: Liver biopsy of parenchyma (control) from subject 17


title: Liver parenchyma (control) Replicate 16

description: Liver biopsy of parenchyma (control) from subject 16


title: Liver parenchyma (control) Replicate 12

description: Liver biopsy of parenchyma (control) from subject 12


title: Liver metasis Replicate 15

description: Liver biopsy of metasis from subject 15


title: Liver metasis Replicate 13

description: Liver biopsy of metasis from subject 13


title: Liver Halo of metasis Replicate 12

description: Liver biopsy of Halo of metasis from subject 12


title: Liver metasis Replicate 12

description: Liver biopsy of metasis from subject 12


title: Dermal R-VEC

value: Dermal R-VEC 2D


title: Cardiac R-VEC

value: Cardiac R-VEC 2D


title: Cultured HUVEC 3

value: matched cultured HUVECs

value: cultured complete EC media


title: 10x_171


title: Cultured HUVEC 4

value: qiagen


title: Liver Halo of metasis Replicate 15

description: Liver biopsy of Halo of metasis from subject 15


title: 10x_169


title: Cultured HUVEC 2


title: 10x_170


title: Liver parenchyma (control) Replicate 10

description: Liver biopsy of parenchyma (control) from subject 10


title: Liver metasis Replicate 10

description: Liver biopsy of metasis from subject 10


title: R-VEC Plug

value: R-VEC in plug in vivo

value: 1 month in vivo LEC, sorted as GFP+

value: picopure


title: Cultured HUVEC 1

value: cultured, complete EC media


title: Freshly Isolated HUVEC 4

value: Freshly sorted HUVECs

value: non-cultured, freshly isolated VEcad+ CD31


title: 10x_167

value: Malignant ascites  single cell


title: 10x_168


title: Liver Halo of metasis Replicate 10

description: Liver biopsy of Halo of metasis from subject 10

value: Liver

value: total RNA from 10 human cell lines


title: Freshly Isolated HUVEC 3


title: 10x_166


title: 10x_165


title: Freshly Isolated HUVEC 2


title: Freshly Isolated HUVEC 1


title: 10x_164


title: 10x_163


title: Liver Halo of metasis Replicate 9

description: Liver biopsy of Halo of metasis from subject 9

value: Halo of Metasis


title: R-VEC Tubes 4 weeks 3

value: R-VEC stabilization

value: 4 weeks tube formation, Stem Span tube media


title: Liver parenchyma (control) Replicate 9

description: Liver biopsy of parenchyma (control) from subject 9


title: 10x_162


title: Liver Halo of metasis Replicate 8

description: Liver biopsy of Halo of metasis from subject 8


title: R-VEC Tubes 1 week 3

value: R-VEC remodeling

value: d7 tube formation, tube media


title: Liver metasis Replicate 8

description: Liver biopsy of metasis from subject 8

value: Metasis


title: 10x_161


title: Liver Halo of metasis Replicate 7

description: Liver biopsy of Halo of metasis from subject 7


title: Liver parenchyma (control) Replicate 8

description: Liver biopsy of parenchyma (control) from subject 8


title: Liver metasis Replicate 9

description: Liver biopsy of metasis from subject 9


title: Liver metasis Replicate 7

description: Liver biopsy of metasis from subject 7


title: Liver Halo of metasis Replicate 6

description: Liver biopsy of Halo of metasis from subject 6


title: Liver parenchyma (control) Replicate 5

description: Liver biopsy of parenchyma (control) from subject 5


title: Liver parenchyma (control) Replicate 7

description: Liver biopsy of parenchyma (control) from subject 7


title: R-VEC Flat 3

value: R-VEC induction

value: d0 tube formation, Stem Span tube media


title: Liver parenchyma (control) Replicate 3

description: Liver biopsy of parenchyma (control) from subject 3


title: Liver metasis Replicate 6

description: Liver biopsy of metasis from subject 6


title: 10x_160


title: Liver metasis Replicate 5

description: Liver biopsy of metasis from subject 5


title: Liver parenchyma (control) Replicate 6

description: Liver biopsy of parenchyma (control) from subject 6


title: Liver Halo of metasis Replicate 3

description: Liver biopsy of Halo of metasis from subject 3


title: Liver parenchyma (control) Replicate 2

description: Liver biopsy of parenchyma (control) from subject 2


title: Liver parenchyma (control) Replicate 1

description: Liver biopsy of parenchyma (control) from subject 1


title: Liver Halo of metasis Replicate 5

description: Liver biopsy of Halo of metasis from subject 5


title: Liver Halo of metasis Replicate 2

description: Liver biopsy of Halo of metasis from subject 2


title: 10x_159


title: R-VEC Tubes 4 weeks 2