title: U2OS_KRAB_H3K9me3

extract_protocol: Cells were collected and crosslinked by 1% formaldehyde. Cells were suspended in cell lysis buffer B (50 mM Tris-HCl PH 8.0, 20 mM EDTA, 0.3% SDS, freshly added protease inhibitor) for 10 min on ice before sonication. 4mg beads (Invitrogen) were washed wiPBS+5 mg/mL BSA for three times and incubated with 5µg antibody at 4°Cfor 6-8 hours before adding chromatin. Sonicated chromatin was diluted in dilution buffer (16.7mM Tris-HCl PH 8.0, 1.1% Triton X-100, 1.2 mM EDTA, 167mM NaCl, freshly added protease inhibitor), and was incubate with pre-treated beads and antibodies by rotation at 4°C overnight. Then beads were washed with washing buffer (50mM Hepes PH8.0, 1% NP-40, 0.7% DOC, 0.5 M LiCl, freshly added protease inhibitor) for 5 times followed by wash with TE once. 100µL elution buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) was added and beads were incubated in Thermo mixer at 65°C for 30 min with max speed. Supernatant was collected and treated with protease K at 55°C for 2 hours, then purified with DNA purification kit (Tiangen). RNA was removed by treatment of RNase at 37°C for 1 hour. DNA was then purified by AMPure Beads (Beckman) and subjected to DNA library preparation. Purified DNA or cDNA was subjected to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The DNA was resuspended in 25 μL ddH2O, followed by end-repair/A-tailing with 3.5 μL End Prep buffer and 1.5 μL enzyme mix according to manufactory instruction. The ligation reaction was then performed by adding diluted 1.25 μL adaptors (NEB), 15 μL Ligation master mix, 0.5 μL Ligation enhancer, at 4°C for overnight. The ligation reaction was treated with 1.5μL USERTM enzyme according to the instruction and was purified by AMPure beads. The 1st round PCR was performed by adding 25 μL 2 × KAPA HiFi HotStart Ready Mix (KAPA biosystems) with primers of NEB Oligos kit, with the program of 98°C for 45 s, (98°C for 15 s and 60°C for 10 s) with 8-9 cycles and 72°C for 1 min. DNA was purified using 1xAMPure beads and a 2nd round PCR was performed with 25 μL 2xKAPA HiFi HotStart Ready Mix with Illumina universal primers, and same PCR program for 8 cycles. The final libraries were purified by 1xAMPure beads and subjected to next-generation sequencing.ng.


title: U2OS_dCas9_H3K9me3

status: Public on Nov 04 2020

type: SRA

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C sapples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the hg19 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For RNA-seq samples: RNA-seq reads were aligned to the hg19 genome assembly using tophat2 version 2.0.11and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
For ChIP-seq samples: The paired-end ChIP reads were aligned using Bowtie2. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the ChIP signals in the UCSC genome browser, we generated the RPKM values on a 100bp-window base.
Genome_build: hg19
Supplementary_files_format_and_content: The bedgraph files contains the values  counted by the number of reads falling into 200bp bin in the genome. The gene rpkm txt file contains FPKM value for all samples. with number for each bin. While the validpair txt file indicates the paired interaction reads for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: U2OS cell line

growth_protocol: The U2OS (human bone osteosarcoma epithelial, female) cell were cultured in DMEM (Life Technologies) with high glucose in 10% FBS (fetal bovine serum, Life Technologies). All cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol: Cells were collected and crosslinked by 1% formaldehyde. Cells were suspended in cell lysis buffer B (50 mM Tris-HCl PH 8.0, 20 mM EDTA, 0.3% SDS, freshly added protease inhibitor) for 10 min on ice before sonication. 3mg beads (Invitrogen) were washed wiPBS+5 mg/mL BSA for three times and incubated with 5µg antibody at 4°Cfor 6-8 hours before adding chromatin. Sonicated chromatin was diluted in dilution buffer (16.7mM Tris-HCl PH 8.0, 1.1% Triton X-100, 1.2 mM EDTA, 167mM NaCl, freshly added protease inhibitor), and was incubate with pre-treated beads and antibodies by rotation at 4°C overnight. Then beads were washed with washing buffer (50mM Hepes PH8.0, 1% NP-40, 0.7% DOC, 0.5 M LiCl, freshly added protease inhibitor) for 5 times followed by wash with TE once. 100µL elution buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) was added and beads were incubated in Thermo mixer at 65°C for 30 min with max speed. Supernatant was collected and treated with protease K at 55°C for 2 hours, then purified with DNA purification kit (Tiangen). RNA was removed by treatment of RNase at 37°C for 1 hour. DNA was then purified by AMPure Beads (Beckman) and subjected to DNA library preparation. Purified DNA or cDNA was subjected to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The DNA was resuspended in 25 μL ddH2O, followed by end-repair/A-tailing with 3.5 μL End Prep buffer and 1.5 μL enzyme mix according to manufactory instruction. The ligation reaction was then performed by adding diluted 1.25 μL adaptors (NEB), 15 μL Ligation master mix, 0.5 μL Ligation enhancer, at 4°C for overnight. The ligation reaction was treated with 1.5μL USERTM enzyme according to the instruction and was purified by AMPure beads. The 1st round PCR was performed by adding 25 μL 2 × KAPA HiFi HotStart Ready Mix (KAPA biosystems) with primers of NEB Oligos kit, with the program of 98°C for 45 s, (98°C for 15 s and 60°C for 10 s) with 8-9 cycles and 72°C for 1 min. DNA was purified using 1xAMPure beads and a 2nd round PCR was performed with 25 μL 2xKAPA HiFi HotStart Ready Mix with Illumina universal primers, and same PCR program for 8 cycles. The final libraries were purified by 1xAMPure beads and subjected to next-generation sequencing.ng.

tag: tissue

value: human bone osteosarcoma epithelial cell line (female)

tag: antibody

tag: genotype/variation

value: transduced with PCP-GFP, sgRNA targeting to C19Q, dCas9


title: Patient_ASSESS_350

type: RNA

city: Strasbourg

first: Jacques-Eric

last: Gottenberg

address: 15 Renee Descartes Street

country: France

institute: Institut de Biologie Moleculaire et Cellulaire

hyb_protocol: After purification according to Affymetrix’s protocol, 5.5 µg of Sens Target DNA were fragmented and biotin-labelled. After control of fragmentation using Bioanalyzer 2100, cDNA was then hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips were washed on the GeneChip Fluidics Station 450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (.cel files) and Quality Control metrics

data_processing: Data were loaded  and normalised using the oligo R package. Briefly Cel files were loaded using the read.celfiles function and normalised with the rma function with default parameter. Absence of possible outliers was checked using hist function. Correspondance between probes and genes was obtained through the clariomshumanhttranscriptcluster.db package.

label: biotin

molecule: total RNA

source_name: Whole blood

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 75 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit (Affymetrix) without globin mRNA reduction. Briefly, the resulting double-stranded cDNA was used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix)

extract_protocol: whole bood

value: Whole blood

tag: Sex

value: female

tag: antissa status

value: Positive

tag: antissb status

value: Negative

tag: disease state

value: Sjögren’s syndrome


title: Patient_ASSESS_351


title: Patient_ASSESS_346


title: Patient_ASSESS_348


title: U2OS_HP1a_H3K9me3

extract_protocol: Cells were collected and crosslinked by 1% formaldehyde. Cells were suspended in cell lysis buffer B (50 mM Tris-HCl PH 8.0, 20 mM EDTA, 0.3% SDS, freshly added protease inhibitor) for 10 min on ice before sonication. 2mg beads (Invitrogen) were washed wiPBS+5 mg/mL BSA for three times and incubated with 5µg antibody at 4°Cfor 6-8 hours before adding chromatin. Sonicated chromatin was diluted in dilution buffer (16.7mM Tris-HCl PH 8.0, 1.1% Triton X-100, 1.2 mM EDTA, 167mM NaCl, freshly added protease inhibitor), and was incubate with pre-treated beads and antibodies by rotation at 4°C overnight. Then beads were washed with washing buffer (50mM Hepes PH8.0, 1% NP-40, 0.7% DOC, 0.5 M LiCl, freshly added protease inhibitor) for 5 times followed by wash with TE once. 100µL elution buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) was added and beads were incubated in Thermo mixer at 65°C for 30 min with max speed. Supernatant was collected and treated with protease K at 55°C for 2 hours, then purified with DNA purification kit (Tiangen). RNA was removed by treatment of RNase at 37°C for 1 hour. DNA was then purified by AMPure Beads (Beckman) and subjected to DNA library preparation. Purified DNA or cDNA was subjected to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The DNA was resuspended in 25 μL ddH2O, followed by end-repair/A-tailing with 3.5 μL End Prep buffer and 1.5 μL enzyme mix according to manufactory instruction. The ligation reaction was then performed by adding diluted 1.25 μL adaptors (NEB), 15 μL Ligation master mix, 0.5 μL Ligation enhancer, at 4°C for overnight. The ligation reaction was treated with 1.5μL USERTM enzyme according to the instruction and was purified by AMPure beads. The 1st round PCR was performed by adding 25 μL 2 × KAPA HiFi HotStart Ready Mix (KAPA biosystems) with primers of NEB Oligos kit, with the program of 98°C for 45 s, (98°C for 15 s and 60°C for 10 s) with 8-9 cycles and 72°C for 1 min. DNA was purified using 1xAMPure beads and a 2nd round PCR was performed with 25 μL 2xKAPA HiFi HotStart Ready Mix with Illumina universal primers, and same PCR program for 8 cycles. The final libraries were purified by 1xAMPure beads and subjected to next-generation sequencing.ng.

value: co-transfected pHAGE-TO-Cas9,pLH-sgRNA1-HP1 and pDONOR-HP1a-HaloTag to knock-in HaloTag into HP1a locus


title: Patient_ASSESS_347


title: Patient_ASSESS_342


title: Patient_ASSESS_343


title: Patient_ASSESS_337


title: Patient_ASSESS_339


title: Patient_ASSESS_344


title: Patient_ASSESS_338


title: Patient_ASSESS_345


title: Patient_ASSESS_340


title: Patient_ASSESS_349

value: male


title: Patient_ASSESS_335


title: Patient_ASSESS_334


title: Patient_ASSESS_336


title: Patient_ASSESS_333


title: Patient_ASSESS_332


title: Patient_ASSESS_341


title: Patient_ASSESS_329


title: Patient_ASSESS_327


title: Patient_ASSESS_330


title: Patient_ASSESS_328


title: PN19-26-Treated_rep3

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

library_source: transcriptomic

data_processing:
Libraries were sequenced as single reads (75 bp read length) on a NextSeq500 (Illumina) with a depth of >20 million reads.
Data quality of raw RNA-seq reads in FASTQ files was assessed using ReadQC (ngs-bits version 2018_04)
Reads were preprocessed with Skewer (version 0.2.2) and aligned using STAR (version 2.5.4a) allowing spliced read alignment to the mouse reference genome (Ensembl Mus musculus GRCm38). Alignment quality was analyzed using MappingQC (ngs-bits version 2018_04) and visually inspected with Broad Integrative Genome Viewer (version 2.4.0).
Based on the genome annotation ITAG (Ensembl 75), normalized read counts for all genes were obtained using subread (version 1.6.0) and edgeR (version 3.22.3).
Normalized read counts were obtained using edgeR. Differentialy expressed genes (only proteins coding sequences) between control and TSA treated samples were obtained after applying permutation FDR based 2 tailed t-test with 250 randomization (FDR < 0.05).
Genome_build: Ensembl Mus musculus GRCm38.94

organism: Mus musculus

source_name: TNXL-positive cones sorted from TSA-treated rd1TN-XL retinal explants cultured at PN19 and harvested at P26

growth_protocol: Organotypic retinal cultures from rd1TN-XL animals including the retinal pigment epithelium (RPE) were prepared under sterile conditions. . The explant was cut into clover-leaf shape and transferred to a culture membrane insert . The membrane inserts were placed into six well culture plates with Neurobasal-A medium supplemented with 2% B27, 1% N2  and L-glutamine (0.8 mM), and incubated at 37°C in a humidified 5% CO2 incubator. The culture medium was changed every 2 days during the 7 culturing days.

extract_protocol:
2000 to 5000 frozen sorted-cells were lysed in approximatively 10µl of lysis buffer
cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit. First-strand cDNA synthesis was performed using 20 to 50% of the input and was followed by full-length double-strand cDNA amplification using 17 PCR cycles.

treatment_protocol: Retinal explants were treated with 10 nM TSA diluted in Neurobasal-A culture medium. For controls, the same amount of DMSO was diluted in culture medium.

value: Purified cone photoreceptors

tag: time point

value: Explants cultured at PN19 and harvested at PN31

tag: treatment

value: 10 nM TSA


title: Patient_ASSESS_321


title: Patient_ASSESS_331


title: Patient_ASSESS_322


title: PN19-26-Treated_rep2

value: Explants cultured at PN19 and harvested at PN30


title: PN19-26-Treated_rep1

value: Explants cultured at PN19 and harvested at PN29


title: Patient_ASSESS_325


title: Patient_ASSESS_326


title: Patient_ASSESS_318


title: PN19-26-Control_rep3

source_name: TNXL-positive cones sorted from untreated rd1TN-XL retinal explants cultured at PN19 and harvested at P26

value: Explants cultured at PN19 and harvested at PN28

value: DMSO


title: Patient_ASSESS_319


title: Patient_ASSESS_324


title: Patient_ASSESS_317


title: PN19-26-Control_rep2

value: Explants cultured at PN19 and harvested at PN27


title: Patient_ASSESS_320


title: Patient_ASSESS_315


title: Patient_ASSESS_316


title: Patient_ASSESS_323


title: PN19-26-Control_rep1

value: Explants cultured at PN19 and harvested at PN26


title: Patient_ASSESS_314


title: Napin:SCL15-3

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Trimmomatic34 was used to discard low-quality reads, trim adaptor sequences, trim low quality nucleotides at the beginning or end of the read (PHRED33 quality score of less than 3), and discard short reads (under 55 nt)
The retained paired high-quality reads were imported into the CLC genomics workbench 20.0.4 (https://digitalinsights.qiagen.com) and run through the RNASeq analysis pipeline.  The reference genome was Arabidopsis thaliana TAIR10, and reads had to be 80% identical over 80% of their length to map to the genome.  Count data and TPM (Transcripts per million) were calculated.
The CLC tool "Differential expression for two groups" was used to perform three pairwise statistical comparisons:  Napin:SCL15 vs wild type, scl15 vs wild type, and scl15 vs Napin:SCL15.  Expression changes were said to be significant if the false discovery rate (FDR) was ≤ 0.05 and the absolute value of the fold change was >2.
Genome_build: TAIR10
Supplementary_files_format_and_content: SCL15_TPM_VALUES.txt contains a row for each gene in the TAIR10 genome, and a column for each sample.  The TPM (Transcripts per million) value is reported for each gene in each sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 12 DPA siliques from Arabidopsis overexpressing SCL15

growth_protocol: Plants were grown in the greenhouse, with a photoperiod of 04:00 – 20:00 and a temperature setpoint range of 16 – 22 degrees Celsius.

extract_protocol:
Total RNA was extracted from 12 days past anthesis siliques using the RNeasy Plant Mini Kit (Qiagen Inc.).
cDNA libraries were prepared using the TruSeq Stranded mRNA and Total RNA Library Prep kits with TruSeq LT adaptors (Illumina Inc.).

treatment_protocol: Plant Genotype was the experimental variable tested.  Plants lacking a functional scl15 gene were compared to plants where SCL15 was overexpressed in seeds and to the background wild type plants.

tag: genotype

value: SCL15 overexpression in seeds

value: 12 DPA (days past anthesis) siliques

tag: biological replicate


title: Patient_ASSESS_313

value: Whole blood

value: female


title: Napin:SCL15-2


title: Patient_ASSESS_312

value: Positive


title: Patient_ASSESS_310

value: Negative

value: Sjögren’s syndrome


title: Napin:SCL15-1


title: Patient_ASSESS_308


title: Patient_ASSESS_309


title: Patient_ASSESS_311

value: male


title: Patient_ASSESS_307


title: scl15-2

source_name: 12 DPA siliques from Arabidopsis scl15 knockout

value: scl15 knockout


title: scl15-1


title: Patient_ASSESS_305


title: scl15-3


title: WT-3

source_name: 12 DPA siliques from Arabidopsis columbia

value: wild type


title: PHY_3_21_18h_S

city: Ghent

first: Thomas

last: Jacobs

address: Technologiepark-Zwijnaarde, 71

country: Belgium

institute: VIB Center for Plant Systems Biology

data_processing:
Quality control with FastQC
Read alignment with Tophat2
Read counting with HT-seq
Differential expression with EdgeR
Genome_build: TAIR10 genome
Supplementary_files_format_and_content: Read count files were generated with HT-seq

growth_protocol: Plants were grown in long day conditions (16/8h) in walk in growth chambers (Conviron, Winnipeg, Manitoba, Canada) at 21°C or 27°C, 50uM light intensity, 60% humidity. During nighttime, temperature was decreased to 15°C  and 21°C respectively

extract_protocol:
Total RNA was extracted from roots or shoot of plants 6 days after germination using RNA easy kit (Qiagen, Hilden, Germany). RNA was treated with DNAse using the Turbo DNA-free kit (Invitrogen, Carlsbad, CA, USA) and further purified on columns from the RNA easy kit.
Next generation sequencing (NGS) library was generated using the TruSeq Stranded mRNA library prep kits (Illumina, San Diego, CA, USA). Libraries were sequenced on HiSeq2500 (Illumina, San Diego, CA, USA) as single read 50bases.

treatment_protocol: For temperature shift experiments, plants were germinated and grown until 3 days after germination at 21°C to synchronize their development. On the third day, plants were shifted at ZT1-3 at 27°C and grown for 3 additional days at 21°C or 27°C.

value: Shoot

value: phyAB

tag: developmental stage

value: Seedling 6DAG

tag: temperature (oc)


title: WT-1


title: PHY_3_27_18h_S


title: Patient_ASSESS_306


title: PHY_2_27_18h_S


title: PHY_2_21_18h_S


title: Patient_ASSESS_298


title: Patient_ASSESS_303


title: Patient_ASSESS_302


title: Patient_ASSESS_299


title: Patient_ASSESS_297


title: WT-2


title: HY5_3_27_18h_S


title: PHY_1_27_18h_S


title: Patient_ASSESS_300


title: HY5_3_21_18h_S


title: Patient_ASSESS_304


title: Patient_ASSESS_294


title: Patient_ASSESS_293


title: Patient_ASSESS_301


title: Patient_ASSESS_296


title: Patient_ASSESS_295


title: HY5_1_27_18h_S


title: HY5_2_21_18h_S


title: Patient_ASSESS_291


title: Patient_ASSESS_292


title: Patient_ASSESS_290


title: HY5_1_21_18h_S


title: PHY_1_21_18h_S


title: COL_3_27_18h_S


title: COL_3_21_18h_S


title: Patient_ASSESS_287


title: COL_2_27_18h_S


title: HY5_2_27_18h_S


title: Patient_ASSESS_288


title: COL_2_21_18h_S


title: COL_1_27_18h_S


title: Patient_ASSESS_285


title: PHY_3_27_18h_R

value: Root


title: PHY_3_21_18h_R


title: PHY_2_27_18h_R


title: PHY_2_21_18h_R


title: PHY_1_27_18h_R


title: PHY_1_21_18h_R


title: Patient_ASSESS_284


title: HY5_3_27_18h_R


title: COL_1_21_18h_S


title: HY5_3_21_18h_R


title: HY5_2_27_18h_R


title: HY5_2_21_18h_R


title: Patient_ASSESS_280


title: Patient_ASSESS_279


title: Patient_ASSESS_277


title: Patient_ASSESS_282


title: Patient_ASSESS_286


title: Patient_ASSESS_278


title: Patient_ASSESS_283


title: Patient_ASSESS_275


title: HY5_1_27_18h_R


title: HY5_1_21_18h_R


title: COL_3_27_18h_R


title: COL_3_21_18h_R


title: COL_2_27_18h_R


title: Patient_ASSESS_270


title: Patient_ASSESS_289


title: Patient_ASSESS_272


title: Patient_ASSESS_268


title: Patient_ASSESS_276


title: Patient_ASSESS_281


title: Patient_ASSESS_273


title: COL_2_21_18h_R


title: Patient_ASSESS_274


title: Patient_ASSESS_267


title: Patient_ASSESS_271


title: COL_1_27_18h_R


title: Patient_ASSESS_266


title: COL_1_21_18h_R


title: phy_27_S_3


title: phy_27_S_2


title: phy_21_S_3


title: phy_27_S_1


title: phy_21_S_2


title: phy_21_S_1


title: Patient_ASSESS_263


title: Patient_ASSESS_265


title: hy5_27_S_3


title: Patient_ASSESS_269


title: Patient_ASSESS_261


title: Patient_ASSESS_260


title: Patient_ASSESS_262


title: Patient_ASSESS_258


title: Patient_ASSESS_264


title: Patient_ASSESS_259


title: Patient_ASSESS_257


title: hy5_21_S_3


title: hy5_27_S_2


title: hy5_21_S_2


title: hy5_21_S_1


title: hy5_27_S_1


title: Col_21_S_3


title: Col_27_S_2


title: Col_27_S_3


title: Col_21_S_2


title: Patient_ASSESS_256


title: Col_27_S_1


title: Patient_ASSESS_248


title: Patient_ASSESS_252


title: Patient_ASSESS_253


title: Patient_ASSESS_247


title: Patient_ASSESS_251


title: Patient_ASSESS_254


title: phy_21_R_1


title: Patient_ASSESS_249


title: Patient_ASSESS_250


title: phy_27_R_1


title: phy_21_R_3


title: hy5_27_R_3


title: Patient_ASSESS_255


title: Col_21_S_1


title: phy_27_R_2


title: Patient_ASSESS_245


title: phy_21_R_2


title: hy5_21_R_3


title: hy5_27_R_2


title: Patient_ASSESS_243


title: hy5_21_R_2


title: Patient_ASSESS_242


title: hy5_27_R_1


title: Col_27_R_3


title: hy5_21_R_1


title: Col_21_R_3


title: Col_27_R_2


title: Col_21_R_2


title: Patient_ASSESS_244


title: Col_21_R_1


title: Patient_ASSESS_240


title: Patient_ASSESS_241


title: Patient_ASSESS_232


title: Patient_ASSESS_233


title: Patient_ASSESS_229


title: Patient_ASSESS_234


title: Patient_ASSESS_239


title: Patient_ASSESS_227


title: Patient_ASSESS_237


title: Patient_ASSESS_226


title: Patient_ASSESS_246


title: Patient_ASSESS_230


title: Patient_ASSESS_235


title: Patient_ASSESS_231


title: Patient_ASSESS_238


title: Patient_ASSESS_236


title: Patient_ASSESS_228


title: Col_27_R_1


title: ChIP-Seq of total Flag-BirA-tagged histone H2A.Z, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description:
H2A.Z-flag_peaks_IDR0.05.bed
Merge.avi.flag_IDR0.05_sigAvi.bed
Merge.avi.flag_IDR0.05_sigFlag.bed

data_processing:
Illumina adapter sequences and low-quality bases were removed from 3'-ends of 85-nt reads.
Reads were mapped to the human hg19 genome using Bowtie. Duplicate reads were removed with samtools.
Peaks were called using MACS2 using H3 as a control. Normalized peaks from duplicate experiments were then averaged and matched H3 samples were subtracted to yield fragments per million reads (FPM). The irreproducible discovery rate (IDR) procedure employed by ENCODE was then used to generate a set of high-confidence peaks for both streptavidin and Flag precipitations.
Both sets of peaks were merged, reads in each Avi and Flag sample overlapping each peak were counted, and the R package edgeR was used in classic (non-GLM) mode to derive peaks with enrichment or depletion of Avi over Flag, analogously to differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: H2A.Z-avi_peaks_IDR0.05.bed and H2A.Z-flag_peaks_IDR0.05.bed contain streptavidin and Flag peaks, respectively, over H3 control at an IDR of 0.05. The files are in BED format with the IDR in the score column. The files Merge.avi.flag_IDR0.05_sigAvi.bed and Merge.avi.flag_IDR0.05_sigFlag.bed contain merged peaks with at least 25% enrichment or depletion, respectively, of streptavidin over Flag and at an edgeR FDR < 0.05. These files are in BED format with the FDR in the name column and the log2FC (streptavidin/Flag) in the score column. All files map to the hg19 genome release.

source_name: Human embryonic kidney cells

growth_protocol: HEK293T cells were grown in 15 cm plates in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (DMEM; Wisent).

extract_protocol:
Cells were trypsinized, counted, and washed in 1X PBS, 48 hrs following transfection. Cellular pellets were resuspended in buffer A (20mM HEPES, pH 7.5, 10mM KCl, 1.5mM MgCl2, 0.34M sucrose, 10% glycerol, 1mM dithiothreitol, 5mM sodium butyrate, 10mM NEM, and protease inhibitors), pelleted and then resuspended in buffer A containing 0.2% Triton X-100 and incubated on ice for 5 min. The nuclear suspension was centrifuged at 600 x g; nuclei were then washed once in buffer A, then resuspended in cutting buffer (15 mM NaCl, 60 mM KCl, 10 mM Tris pH 7.5, 5mM sodium butyrate, 10mM NEM, and protease inhibitors) plus 2mM CaCl2. Microccocal nuclease (MNase; Worthington) was added at a concentration of 10 units/1.0 x 10^7 cells then incubated at 37°C for 30 min. The reaction was stopped by the addition of 20mM EGTA (one twenty-fifth of the reaction volume) and immediate gentle mixing by inversion. The MNase-digested nuclei were centrifuged at 1300 x g. The resulting supernatant (S1) was saved and kept on ice. The digested nuclear pellet was subjected to hypotonic lysis by resuspension in TE buffer (10mM Tris-HCL, pH 8.0, 1mM EDTA). Samples were incubated on ice for 1 hr, with occasional mixing by pipette. The suspension was then centrifuged at 16 000 x g and the supernatant (S2) was transferred to a new tube. Salt was adjusted in S1 to 150mM NaCl by adding 2X buffer D (30 mM Tris pH 7.5, 225 mM NaCl, 3 mM MgCl2, 20% glycerol, 0.4% Triton-X 100, 5mM sodium butyrate, 10mM NEM, and protease inhibitors) drop-wise, with constant mixing on a vortex set to low speed. S2 was also titrated to 150mM NaCl by the drop-wise addition of 3X buffer E (60 mM HEPES pH 7.5, 450 mM NaCl, 4.5 mM MgCl2, 0.6 mM EGTA, 0.6 % Triton-X 100, 30% glycerol, 5mM sodium butyrate, 10mM NEM, and protease inhibitors). Insoluble material was pelleted via centrifugation. The clarified supernatants were combined and then used for affinity purification. Streptavidin-agarose, Flag M2-agarose, or H3 antibody were added and incubated overnight at 4°C on an end- over-end rotator. Beads were washed 4 times in 1X Buffer D, followed by 3 washes in 1X Buffer D containing 0.5% Triton X-100 and elution in buffer D containing 1% SDS by end-over-end rotation at room temperature for 2 X 10 min. DNA was treated with RNase A and proteinase K, purified by phenol-chloroform extraction, and then re-precipitated with ethanol and resuspended in water.
DNA was converted to libraries according to standard Illumina TruSeq ChIP-Seq protocols.

treatment_protocol: All transfections were carried out using polyethylenimine (PEI; Polysciences). All expression constructs used were based on the pcDNA 3.1 (+) (Invitrogen) backbone with the Flag-BirA cloned in-frame to the C-terminus of H2A.Z-1 (hereafter termed H2A.Z-FB). In addition, the AviTag was cloned in-frame to the N-terminus of ubiquitin. In co-transfection experiments, the ratio of H2A.Z-Flag-BirA to AviTag-Ub plasmids was 3:1.

tag: cell line

tag: chip antibody

value: Anti-Flag M2 affinity agarose gel (Sigma A2220)


title: ChIP-Seq of total Flag-BirA-tagged histone H2A.Z, replicate 1


title: Patient_ASSESS_225


title: ChIP-Seq of histone H3, replicate 1

description:
H2A.Z-avi_peaks_IDR0.05.bed
H2A.Z-flag_peaks_IDR0.05.bed

value: Anti-histone H3 antibody (Abcam ab1791)


title: ChIP-Seq of histone H3, replicate 2


title: Patient_ASSESS_224


title: ChIP-Seq of Avi-ubiquitylated, Flag-BirA-tagged histone H2A.Z, replicate 2

description:
H2A.Z-avi_peaks_IDR0.05.bed
Merge.avi.flag_IDR0.05_sigAvi.bed
Merge.avi.flag_IDR0.05_sigFlag.bed

value: Streptavidin-agarose (Signma S1638)


title: ChIP-Seq of Avi-ubiquitylated, Flag-BirA-tagged histone H2A.Z, replicate 1


title: BRD4: OCI-AML3 cells Combination Rep1 ChIP-seq

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

country: USA

institute: SBP medical discovery institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Bowtie2 version 2.1.0 with parameters --phred33 -p 16 -x hg19 --solexa-quals -p 8
Peaks of genomic occupancy were determined using SICER version 1.1 with the parameters hg19 1 200 150 0.75 200 .01
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including peak genomic locations and intensities

source_name: OCI-AML3 cells

growth_protocol: OCI-AML3 cells were obtained from DSMZ and were cultured at 37°C in a humidifed incubator with 5% CO2.

extract_protocol:
Crosslinking was quenched wih 2.5M Glycine, then chromatin lysates were produced using lysis buffer plus protease inhibitors. Samples were then sonicated on ice for 12 cycles of 30 seconds on, 1 minute off, and debris pelleted.  Input controls were removed from each sample.
Sonicated lysates were precleared with magnetic beads, then incubated overnight with antibody-bound beads. ChIP samples were then eluted in 50mM Tris-HCl, pH 8; 10mM EDTA; 1% SDS, and crosslinks were reversed by heating at 65°C for 6-18 hours. TE was added to each ChIP or Input sample. Solutions were incubated with RNaseA for 37 °C for 30 minutes, then with proteinase K at 55 °C for 1-2 hours. DNA samples were then purified using a  Qiagen MinElute PCR purification kit.
Libraries were constructed using the NEBNext Ultra DNA Lib Prep kit with NEBNext Multiplex Oligos.

treatment_protocol: Cells were treated with drugs at the stated concentrations for 6 hrs before proteins were crosslinked to DNA with paraformaldehyde.

value: OCI-AML3 cells

tag: drug treatment


title: BRD4: OCI-AML3 cells Nutlin-3a Rep1 ChIP-seq

value: Nutlin-3a (2.5uM)


title: BRD4: OCI-AML3 cells CPI-203 Rep2 ChIP-seq


title: BRD4: OCI-AML3 cells Nutlin-3a Rep2 ChIP-seq


title: BRD4: OCI-AML3 cells DMSO Rep1 ChIP-seq

value: DMSO


title: p53: OCI-AML3 cells Combination Rep4 ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Bowtie2 version 2.1.0 with parameters --phred33 -p 16 -x hg19 --solexa-quals -p 8
Peaks of genomic occupancy were determined using MACS version 1.4.2 with the parameters --format BAM --gsize hs --pvalue 1e-5 --bdg --single-profile –call-subpeaks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including peak genomic locations and intensities


title: BRD4: OCI-AML3 cells DMSO Rep2 ChIP-seq


title: p53: OCI-AML3 cells Combination Rep3 ChIP-seq


title: Patient_ASSESS_221

value: Whole blood

value: female


title: p53: OCI-AML3 cells Combination Rep2 ChIP-seq


title: p53: OCI-AML3 cells Combination Rep1 ChIP-seq


title: Patient_ASSESS_222

value: Positive


title: BRD4: OCI-AML3 cells CPI-203 Rep1 ChIP-seq


title: Patient_ASSESS_223

value: Negative

value: Sjögren’s syndrome


title: Patient_ASSESS_217


title: p53: OCI-AML3 cells Nutlin-3a Rep3 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep2 ChIP-seq


title: Patient_ASSESS_212


title: Patient_ASSESS_216


title: Patient_ASSESS_218


title: p53: OCI-AML3 cells CPI-203 Rep4 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep4 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep1 ChIP-seq


title: Patient_ASSESS_220


title: Patient_ASSESS_208

value: male


title: Patient_ASSESS_215


title: Patient_ASSESS_211


title: Patient_ASSESS_213


title: p53: OCI-AML3 cells CPI-203 Rep2 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep1 ChIP-seq


title: Patient_ASSESS_214


title: p53: OCI-AML3 cells DMSO Rep4 ChIP-seq


title: p53: OCI-AML3 cells DMSO Rep3 ChIP-seq


title: Patient_ASSESS_219


title: p53: OCI-AML3 cells DMSO Rep2 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep3 ChIP-seq


title: Patient_ASSESS_209


title: Patient_ASSESS_207


title: Patient_ASSESS_210


title: Patient_ASSESS_204


title: p53: OCI-AML3 cells DMSO Rep1 ChIP-seq


title: Patient_ASSESS_206


title: Patient_ASSESS_205


title: Patient_ASSESS_203


title: OCI-AML3 cells shp53 Combination Rep3 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

growth_protocol:
OCI-AML3 cells were obtained from DSMZ and were cultured at 37°C in a humidifed incubator with 5% CO2.
Virus expressing either empty vector or sh-p53 was produced from HEK293T packaging lines, then used to infect OCI-AML3 cells for 3-6 hrs, before cells were grown overnight. A second round of infection was then performed.

extract_protocol:
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
RNA libraries were prepared using an Illumina TruSeq Stranded Lib Prep kit

treatment_protocol: Cells with and without p53 were treated with drugs at the stated concentrations for 24 hrs prior to RNA extraction.

tag: gene knockdown

value: shRNA knockdown of p53


title: Patient_ASSESS_202

tag: tissue


title: Patient_ASSESS_201


title: OCI-AML3 cells shp53 Combination Rep2 RNA-seq


title: OCI-AML3 cells shp53 Combination Rep1 RNA-seq


title: Patient_ASSESS_197


title: Patient_ASSESS_198


title: Patient_ASSESS_199


title: OCI-AML3 cells shp53 Nutlin-3a Rep3 RNA-seq


title: Patient_ASSESS_196


title: OCI-AML3 cells shp53 Nutlin-3a Rep1 RNA-seq


title: OCI-AML3 cells shp53 Nutlin-3a Rep2 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep2 RNA-seq


title: Patient_ASSESS_200


title: Patient_ASSESS_195


title: Patient_ASSESS_194


title: OCI-AML3 cells shp53 DMSO Rep3 RNA-seq


title: OCI-AML3 cells EV Combination Rep2 RNA-seq

value: Empty vector control


title: OCI-AML3 cells shp53 DMSO Rep2 RNA-seq


title: OCI-AML3 cells EV Combination Rep3 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep1 RNA-seq


title: OCI-AML3 cells EV Combination Rep1 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep3 RNA-seq


title: Patient_ASSESS_192


title: OCI-AML3 cells shp53 DMSO Rep1 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep2 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep1 RNA-seq


title: OCI-AML3 cells EV CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells EV CPI-203 Rep2 RNA-seq


title: OCI-AML3 cells EV CPI-203 Rep1 RNA-seq


title: Patient_ASSESS_187


title: Patient_ASSESS_189


title: OCI-AML3 cells EV DMSO Rep2 RNA-seq


title: Patient_ASSESS_188


title: Patient_ASSESS_184


title: Patient_ASSESS_185


title: Patient_ASSESS_190


title: Patient_ASSESS_191


title: Patient_ASSESS_181


title: Patient_ASSESS_193


title: Patient_ASSESS_179


title: Patient_ASSESS_182


title: OCI-AML3 cells EV DMSO Rep1 RNA-seq


title: Patient_ASSESS_186


title: Patient_ASSESS_183


title: Patient_ASSESS_178


title: Patient_ASSESS_175


title: Patient_ASSESS_180


title: OCI-AML3 cells EV DMSO Rep3 RNA-seq


title: Patient_ASSESS_176


title: Patient_ASSESS_174


title: Patient_ASSESS_177


title: BRD4: OCI-AML3 cells Combination Rep2 ChIP-seq


title: Patient_ASSESS_173


title: Patient_ASSESS_171


title: phy_27_R_3

value: phyAB


title: Patient_ASSESS_172


title: wt-3 [RNA-Seq]

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

description:
Homo sapiens
Awt_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl 38.85
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: L02 cells

growth_protocol: L02 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual.   medium consists of basal medium, foetal bovine serum (FBS),  L02 cells growth supplement, and penicillin/streptomycin solution.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries.By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform

value: L02 cells

value: wildtype


title: mut-2 [RNA-Seq]

description:
Homo sapiens
Cmut_2
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.

value: mutant


title: mut-1 [RNA-Seq]

description:
Homo sapiens
Cmut_1
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.


title: mut-3 [RNA-Seq]

description:
Homo sapiens
Cmut_3
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.


title: wt-2 [RNA-Seq]

description:
Homo sapiens
Awt_2


title: Patient_ASSESS_170


title: wt-1 [RNA-Seq]

description:
Homo sapiens
Awt-1


title: mut-2 [miRNA-Seq]

description:
C12_2_2
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl 38.85
Supplementary_files_format_and_content: RPKM.xlsx


title: mut-1 [miRNA-Seq]

description:
C12_2_1
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.


title: mut-3 [miRNA-Seq]

description:
C12_2_3
mutant lo2 cells which wild-type CT genotype of rs13282783 in L02 cells was successfully altered to mutant TT based on CRISPR-Cas9 without double-stranded DNA cleavage.


title: Patient_ASSESS_168


title: wt-3 [miRNA-Seq]


title: wt-2 [miRNA-Seq]


title: LO2mR3AgO2 [RIP-Seq]

growth_protocol: L02 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual.   medium consists of basal medium, foetal bovine serum (FBS),  L02 cells growth supplement, and penicillin/streptomycin solution.L02 cells were lysed and then incubated with anti-Ago2 antibody (Abnova Corporation, Taiwan, China) after transfected with miR-320a mimics or miR-con for 24 h. After incubating at 4 °C overnight, protein A/G magnetic beads (Thermo Scientific, Shanghai, China) were added into the solution and incubated for another 2 h at 4 °C. Then, the beads were washed five times with PBST and the remaining products were extracted with TRIzol agent.

tag: antibody


title: wt-1 [miRNA-Seq]


title: LO2mR2AgO2 [RIP-Seq]


title: Patient_ASSESS_167


title: Patient_ASSESS_166


title: Patient_ASSESS_165


title: Patient_ASSESS_164


title: Patient_ASSESS_169


title: LO2mR1AgO2 [RIP-Seq]


title: LO2m3AgO2 [RIP-Seq]


title: Patient_ASSESS_162


title: LO2m1AgO2 [RIP-Seq]


title: 222-2

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

data_processing:
Sample libraries were sequenced by DNBSEQ-G400 with 100nt paired end reads
Raw outputs were automatically converted to fastq file by the sequencer built-in software. Then raw fastq files were de-multiplexed into relative fastq file for each samples with truncated index sequence through software splitBarcode version 0.1.6.
Fastq files were mapped to hg19 whole genome using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: raw data (read counts) and normalized read counts processed by DESeq2

source_name: Tumor-infiltrating CD8 T cells

growth_protocol: Cells were isolated from fresh tisuse with MACS tumor dissociation kit.

extract_protocol:
RNA was extracted from cells with TRIzol RNA isolation reagents.
Ovation® RNA-Seq System V2 kit (NuGen 7102-32).

treatment_protocol: Untreated

value: ovary

tag: cell type

value: CD137- PD-1high CD39+ CD8 T cells

value: Untreated

value: Metastatic ovarian cancer


title: 222-3


title: 222-1

value: PD-1+ CD39- CD8 T cells


title: Patient_ASSESS_158

value: Whole blood

tag: Sex


title: 220-3

value: CD137+ PD-1high CD39+ CD8 T cells


title: 220-2


title: Patient_ASSESS_159

value: female

tag: antissa status

value: Positive


title: LO2m2AgO2 [RIP-Seq]


title: 220-1


title: 133-3


title: Patient_ASSESS_154

value: Negative

tag: antissb status

value: Sjögren’s syndrome


title: Patient_ASSESS_156

value: male

tag: disease state


title: Patient_ASSESS_163


title: Patient_ASSESS_161


title: 133-2


title: Patient_ASSESS_151


title: Patient_ASSESS_149


title: Patient_ASSESS_153


title: Patient_ASSESS_148


title: 133-1


title: Patient_ASSESS_145


title: Patient_ASSESS_150


title: Patient_ASSESS_160


title: Patient_ASSESS_155


title: Patient_ASSESS_147


title: Patient_ASSESS_152


title: Patient_ASSESS_146


title: Patient_ASSESS_143


title: Mouse 3 mCRAMP

city: Edinburgh

first: Emily

last: Gwyer Findlay

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: NanoString protocol

scan_protocol: NanoString protocol

data_processing: NanoString data were normalized using internal reference (housekeeping) genes.

source_name: Splenic CD4+ T cells

growth_protocol: Whole single cell splenic suspensions were cultured under Th17-driving conditions (i.e. with 5 ug/ml plate-bound aCD3, 20 ng/ml IL-6, 20 ng/ml IL-23 and 3 ng/ml TGFb) for 24 hours.

extract_protocol: live singlet CD4+ T cells were isolated by FACS on day 1. Total RNA was isolated the same day using a Qiagen RNeasy Mini Kit, according to the manufacturer's protocol. RNA was quantified by using a NanoDrop spectrophotometer.

treatment_protocol: Untreated cells were compared to mCRAMP-treated (2.5 uM) cells from the same splenic suspension

tag: gender

tag: age

value: 10 weeks

value: Splenic CD4+ T cells

value: mCRAMP


title: Mouse 3 untreated

tag: treatment

value: untreated


title: Mouse 2 mCRAMP

value: 11 weeks


title: Mouse 1 mCRAMP

value: 9 weeks


title: M17_leaf

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FDR < =0.05 and FC >2
Genome_build: Maize(B73)
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

organism: Zea mays

source_name: ear leaf

growth_protocol: Maize inbred line Mo17 was grown in the field in the summer of 2013 in Chengdu, China. Ears were self-pollinated on the same day.

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). RNA integrity was further verified by 1.5% agrose gel electrophoresis.
For each sample, 5 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen). Purified mRNAs were fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified with RNA-Seq Library Preparation Kit (Gnomegen). And PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ until before sequencing.

treatment_protocol: Samples (seed, endosperm and leaf) were collected by manual dissection at midday and frozen immediately in liquid nitrogen, and stored at -80℃ before processing.

tag: time period

value: 13 days after pollination

tag: line

value: ear leaf


title: M17_25

source_name: endosperm

value: 25 days after pollination

value: endosperm


title: Mouse 2 untreated


title: Mouse 1 untreated


title: M17_20

value: 20 days after pollination


title: M17_13


title: M17_15

value: 15 days after pollination


title: M17_9

value: 9 days after pollination


title: M17_7

value: 7 days after pollination


title: M17_leaf [BS-seq]

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt and removed reads which over 30% base quality lower than 20
Reads were mapped using bismark --bowtie2 -p 30 -N 1.
bismark_methylation_extractor were used to analysis methylation with parameters :-s --comprehensive --multicore 30 --buffer_size 20G --bedGraph --counts
Genome_build: Maize(B73)

extract_protocol:
Genomic DNA was sheared by DNA Shearing Instrument (30W%,3sON,9sOFF，20min) . The sheared DNAs size were between 400-500 bp and verified by 1.5% agrose gel electrophoresis. The quantity of the sheared DNAs was measured by Qubit 2.0(Invitrogen).
For each sample, 4μg of genomic DNA was used for bisulfite-seq library preparation. Sheared DNAs were denaturated at 98℃ followed by bisulfite conversion. Then DNA was synthesized with DNA synthesis primer harboring tagging sequence. The DNA was purified and amplified and PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 ℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Hiseq 2000 system for 101 nt pair-end sequencing by Majorbio. Inc (Shanghai, China).


title: Patient_ASSESS_140

value: Whole blood

value: female

value: Negative


title: Patient_ASSESS_141

value: Positive

value: Sjögren’s syndrome


title: Patient_ASSESS_142


title: M17_11

value: 11 days after pollination


title: M17_5

source_name: seed

value: 5 days after pollination

value: whole seed


title: Patient_ASSESS_138


title: Patient_ASSESS_137


title: Patient_ASSESS_139


title: Patient_ASSESS_136


title: Patient_ASSESS_144


title: M17_25 [BS-seq]


title: Patient_ASSESS_135


title: M17_10

value: 10 days after pollination


title: M17_15 [BS-seq]


title: M17_13 [BS-seq]

value: 13 days after pollination


title: M17_11 [BS-seq]


title: M17_20 [BS-seq]


title: M17_9 [BS-seq]


title: Patient_ASSESS_134


title: Patient_ASSESS_133


title: M17_10 [BS-seq]


title: M17_7 [BS-seq]


title: M17_5 [BS-seq]


title: Patient_ASSESS_132


title: 2D_CM_CHIR_3

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
20200506_CHIRvsDMSO_CPM
20200506_CHIRvsDMSO_Myo
20200506_CHIRvsDMSO_Count_matrix

data_processing:
FASTQ files were quality trimmed with Trimmomatic
Reads were mapped to hg38 or mm10 using RNA STAR
Count matrix was calculated using Htseq tools
EdgeR was used for all comparisons
Genome_build: GRCh38/hg38 or GRCm38/mm10

source_name: human cardiac 2D cultures

growth_protocol: Briefly, HES3 and H9 hESCs (WiCell) or hiPSC (Sendai-virus reprogrammed CD34+ cells, ATCC) were maintained as TypLE (ThermoFisher Scientific) passaged cultures using mTeSR-1 (Stem Cell Technologies)/Matrigel (Millipore). hPSCs were seeded at 2´104 cells/cm2 in Matrigel-coated flasks and cultured for 4 days using mTeSR-1. They were then differentiated into cardiac mesoderm using RPMI B27- medium (RPMI1640 GlutaMAX+ 2% B27 supplement without insulin, 200 μM L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate (Sigma) and 1% Penicillin/Streptomycin (all ThermoFisher Scientific) containing 5 ng/ml BMP-4 (RnD Systems), 9 ng/ml Activin A (RnD Systems), 5 ng/ml FGF-2 (RnD Systems) and 1 μM CHIR99021 (Stem Cell Technologies) with daily medium exchange for 3 days. Subsequently, they were specified into a cardiomyocyte/stromal cell mixture using RPMI B27- containing 5 μM IWP-4 (Stem Cell Technologies) followed by another 7 days of RPMI B27+ (RPMI1640 GlutaMAX + 2% B27 supplement with insulin, 200 μM L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin) with medium exchange every 2-3 days. The differentiated cells were then cultured in RPMI B27+ until digestion at 15 days using 0.2% collagenase type I (Sigma) in 20% fetal bovine serum (FBS) in PBS (with Ca2+ and Mg2+) for 60 min at 37°C, followed by 0.25% trypsin-EDTA for 10 min. The cells were filtered using a 100 mm mesh cell strainer (BD Biosciences), centrifuged at 300 x g for 3 min, and resuspended at the required density in CTRL medium: α-MEM GlutaMAX, 10% FBS, 200 μM L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted using trizol and precipitated using glycogen according to manufacturers instructions. Clean-up and DNAse protocols was performed using Rneasy MinElute Cleanup Kit (QIAGEN)
libraries were constructed with Nugen Ovation RNA-Seq system V2 (for SPIA amplifications and cDNA generation) coupled with the Ovation Ultralow System (NuGEN). Libraries were read with 50bp SR Rapid Mode on a HiSeq1500. Barcode information : SampleULN_i7index _LaneNumber_ReadNumber.fastq

treatment_protocol: human 2D cardiac cultures were treated with either 0.05% DMSO or 5 µM CHIR99021 (Stem Cell Technologies) for 24 hours

value: FACS isolated CD90- (cardiomyocyte) cell populations


title: Patient_ASSESS_131


title: 2D_CM_DMSO_3


title: 2D_CD90+_DMSO_3

description:
20200506_CHIRvsDMSO_CPM
20200506_CHIRvsDMSO_CD90+
20200506_CHIRvsDMSO_Count_matrix

value: FACS isolated CD90+ cell populations


title: 2D_CD90+_CHIR_3


title: 2D_CD90+_CHIR_2


title: 2D_CM_DMSO_2


title: Patient_ASSESS_129


title: Patient_ASSESS_130


title: Patient_ASSESS_157


title: 2D_CM_CHIR_1


title: 2D_CD90+_CHIR_1


title: 2D_CD90+_DMSO_2


title: Patient_ASSESS_128


title: Patient_ASSESS_126


title: Sporangia Control 2

city: Amherst

first: Gregory

middle: Alan

last: DeIulio

state: MA

address: 240 Thatcher Road

department: Biochemistry and Molecular Biology

institute: Umass Amherst

data_processing:
Data was denovo assembeled using Trinity denovo assembler version 2.4.0, using default parameters
Data was mapped back to the assembly using bowtie version 1.0.0 and expression was called using RSEM version 1.2.29, using all default parameters
Supplementary_files_format_and_content: Data consists of gene ID and FPKM as called by RSEM including transcripts per million, expected count, length, effective length

organism: Peronospora belbahrii

source_name: Sporangia

extract_protocol:
Four disks per true leaf were sampled from both genotypes at 12, 24 and 72 hpi and immediately flash frozen in liquid nitrogen. The water control leaves were harvested at 12 hpi only. Total RNA was extracted from freshly ground tissue using the Spectrum™ Plant Total RNA Kit (Sigma Aldrich).
RNA samples were used to generate sequence libraries using a library prep kit from the New England Biolabs (NEB #E7530).

treatment_protocol: A 1 mL subsample from the filtered inoculum was pipetted into an eppendorf tube and frozen at -80C to serve as pathogen control. The remaining inoculum was centrifuged at 1,000g for 1 min and diH20 decanted. The resulting sporangia pellet was resuspended in diH2O and inoculum adjusted to 1 x 105 sporangia/mL. Plants were inoculated at the 6-leaf (3 true leaf set) growth stage with approximately ~1 mL/leaf and plants were incubated at 100% relative humidity. MRI and SB22 were sprayed with sterile diH2O in triplicate to serve as the mock inoculated control.

tag: infection time

value: Control

tag: basil cultivar

value: Isolated from Rutgers Agricultural Research and Extension Center Inn Bridgeton NJ in 2012

value: Sporangia

tag: developmental stage

value: Sporulating


title: Patient_ASSESS_125


title: M17_3 [BS-seq]

value: 3 days after pollination


title: SB22 72hpi 3

organism:
Ocimum basilicum
Peronospora belbahrii

source_name: Infected Leaf

value: 72 hpi

value: SB22, Rutgers University

value: Leaf Disc

value: 6 leaves


title: Patient_ASSESS_123

source_name: Whole blood

value: Whole blood

value: female

value: Negative

value: Sjögren’s syndrome


title: 2D_CM_CHIR_2


title: SB22 72hpi 2


title: SB22 12hpi 3

value: 12 hpi


title: SB22 24hpi 3

value: 24 hpi


title: SB22 48hpi 3

value: 48 hpi


title: SB22 48hpi 2


title: Patient_ASSESS_124

value: Positive


title: Patient_ASSESS_121


title: Patient_ASSESS_122


title: Patient_ASSESS_127


title: 2D_CM_DMSO_1

value: FACS isolated CD90- (cardiomyocyte) cell populations


title: SB22 24hpi 2


title: 2D_CD90+_DMSO_1

value: FACS isolated CD90+ cell populations


title: Sporangia Control 3

value: Control

value: Isolated from Rutgers Agricultural Research and Extension Center Inn Bridgeton NJ in 2012

value: Sporangia


title: Patient_ASSESS_120


title: Sporangia Control 1

value: Sporulating


title: SB22 12hpi 2

value: SB22, Rutgers University


title: Patient_ASSESS_118


title: SB22 48hpi 1

value: Leaf Disc


title: SB22 24hpi 1

value: 6 leaves


title: MRI 72hpi 3

value: 72 hpi

value: Mirihani


title: Patient_ASSESS_119

value: Whole blood

value: female


title: MRI 48hpi 3


title: Patient_ASSESS_116

value: Sjögren’s syndrome


title: MRI 12hpi 3

value: 12 hpi


title: Patient_ASSESS_117


title: MRI 48hpi 2

value: 48 hpi


title: dm-ter-merged-bc-gDNA-post-3: Barcoded H1 teratoma 3 gDNA post-inject reads

first: Yan

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description: Post-teratoma injection gDNA data from barcoded H1 teratoma 3 used for cell type discovery in Figure 1 and clonal analysis in Figure 2

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger count with default parameters
Convert genotype barcode fastq files to unaligned bam, tag each read with cell and molecule barcodes, and assign one of more genotypes to each cell
Merge cellranger runs from replicate teratomas using cellranger aggr
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Files ending in ".counts.tar.gz" are counts matrices output by 10X CellRanger in sparse matrix format
Supplementary_files_format_and_content: Files ending in "_doublets.txt" specify which cells are doublets as determined by DoubletDetection
Supplementary_files_format_and_content: Files ending in ".matrices.tar.gz" are directories with multiple counts matrices output by 10X CellRanger
Supplementary_files_format_and_content: Files ending in "pheno_dict.csv" are genotype to cell dictionaries. Each line begins with the name of the genotype, followed by the cell barcodes mapped to that genotype separated by commas

source_name: Human teratoma

growth_protocol: hiPSC or hESC cells were maintained under feeder-free conditions in mTesR1 medium, in growth-factor reduced Matrigel coated tissue coated plates. Cellls were dissociated and passaged using Versene. 1 million cells were combined with an equivalent volume of matrigel and injected into mice for teratoma formation. Teratomas were grown for approximately 10 weeks in mice before extraction and processing

extract_protocol:
Teratomas were excised and dissociated using the GentleMACS tuomor dissociation protocol, resuspended in PBS-BSA and loaded onto the 10X Genomics Chromium system as per manufacturer's instructions
Single cell libraries were constructed with the Single Cell 3' Reagent Kit from 10X genomics

tag: cell line

tag: genetic/chemical perturbation

value: Lentiviral barcode

tag: molecule subtype

value: Genomic DNA


title: Patient_ASSESS_114

data_processing: Data were loaded  and normalised using the oligo R package. Briefly Cel files were loaded using the read.celfiles function and normalised with the rma function with default parameter. Absence of possible outliers was checked using hist function. Correspondance between probes and genes was obtained through the clariomshumanhttranscriptcluster.db package.

tag: tissue

value: male

value: Positive


title: MRI 12hpi 2


title: dm-ter-merged-bc-gDNA-pre-3: Barcoded H1 teratoma 3 gDNA pre-inject reads

description: Pre-teratoma injection gDNA data from barcoded H1 teratoma 3 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: dm-ter-merged-bc-gDNA-post-1: Barcoded H1 teratoma 1 gDNA post-inject reads

description: Post-teratoma injection gDNA data from barcoded H1 teratoma 1 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: MRI 72hpi 1


title: SB22 72hpi 1


title: dm-ter-merged-bc-gDNA-pre-2: Barcoded H1 teratoma 2 gDNA pre-inject reads

description: Pre-teratoma injection gDNA data from barcoded H1 teratoma 2 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: Patient_ASSESS_115

value: Negative


title: SB22 12hpi 1


title: Patient_ASSESS_112


title: MRI 48hpi 1


title: Patient_ASSESS_113


title: dm-ter-merged-bc-gDNA-pre-1: Barcoded H1 teratoma 1 gDNA pre-inject reads

description: Pre-teratoma injection gDNA data from barcoded H1 teratoma 1 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: MRI 12hpi 1


title: OCI-AML3 cells Combination Rep3 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2 version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

treatment_protocol: Cells were treated with drugs at the stated concentrations for 24 hrs prior to RNA extraction.

value: OCI-AML3 cells

tag: drug treatment


title: MRI 24hpi 2

value: 24 hpi


title: dm-ter-merged-bc-gDNA-post-2: Barcoded H1 teratoma 2 gDNA post-inject reads

description: Post-teratoma injection gDNA data from barcoded H1 teratoma 2 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: MRI 24hpi 3


title: Patient_ASSESS_111

tag: Sex


title: OCI-AML3 cells Combination Rep2 RNA-seq


title: MRI 72hpi 2


title: OCI-AML3 cells Combination Rep1 RNA-seq


title: OCI-AML3 cells Nutlin-3a Rep2 RNA-seq

value: Nutlin-3a (2.5uM)


title: OCI-AML3 cells Nutlin-3a Rep3 RNA-seq


title: MRI 24hpi 1

value: Leaf Disc


title: OCI-AML3 cells CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells Nutlin-3a Rep1 RNA-seq


title: Patient_ASSESS_108

tag: antissa status


title: OCI-AML3 cells CPI-203 Rep2 RNA-seq


title: OCI-AML3 cells DMSO Rep3 RNA-seq

value: DMSO


title: OCI-AML3 cells DMSO Rep2 RNA-seq


title: OCI-AML3 cells DMSO Rep1 RNA-seq


title: OCI-AML3 cells CPI-203 Rep1 RNA-seq


title: Patient_ASSESS_109

tag: antissb status


title: Patient_ASSESS_107

tag: disease state


title: Patient_ASSESS_105


title: Patient_ASSESS_104


title: Patient_ASSESS_102


title: Patient_ASSESS_101


title: Patient_ASSESS_103


title: Patient_ASSESS_100


title: Patient_ASSESS_110


title: V630: Non-treated_iron overload

city: Prague 2

first: Hana

last: Votavova

address: U Nemocnice 1

department: Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

hyb_protocol: Standard Illumina hybridization protocol. Biotinylated cRNA (750 ng) was hybridized on HumanHT-12 v4 Expression Bead Chips.

scan_protocol: Standard Illumina scanning protocol on BeadStation 500.

data_processing: Raw data were extracted using BeadStudio Software and R software lumi package was used for further data processing. Quantile normalization was applied .

source_name: transfusion dependent

label_protocol: Biotinylated cRNA was prepared with  Illumina TotalPrep RNA Amplification kit.

extract_protocol: Total RNA was extracted using the acid guanidine-thiocyanate-phenol-chloroform method. Samples were incubated with DNase I (Qiagen) and RNA quality was evaluated on Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The myelodysplastic syndrome patients with iron overload were treated with iron chelator deferasirox (Exjade, Novartis-Pharma GmbH) according to guidelines in MDS. The patients did not receive any other therapy during follow-up.

value: bone marrow CD34+ cells

tag: diagnosis

value: MDS MLD

tag: gender

value: M

tag: serum ferritin level (ng/ml)

tag: deferasirox treatment

value: NO


title: Patient_ASSESS_106

extract_protocol: whole bood

value: Whole blood

value: female

value: Sjögren’s syndrome


title: V558: Treated with deferasirox

source_name: after iron chelation therapy

tag: age

value: YES


title: 43204760_RNA

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

description: patient 74 tumor tissue RNA_seq

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 whole genome using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

source_name: colorectal tumor tissue

extract_protocol:
Total RNA was isolated from the colorectal tumor tissues using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

tag: patient number

value: patient 74

value: colorectal tumor


title: V883: Non-treated_iron overload

value: MDS RS


title: V539: Treated with deferasirox


title: 43199642_RNA

description: patient 75 tumor tissue RNA_seq

value: patient 75


title: V869: Treated with deferasirox


title: 43294989_RNA

description: patient 73 tumor tissue RNA_seq

value: patient 73


title: Patient_ASSESS_99

value: Negative


title: V1045: Non-treated_normal ferritin level

source_name: transfusion independent

value: MDS EB


title: V1048: Treated with deferasirox

value: MDS del(5q)

value: F


title: V1096: Treated with deferasirox

value: bone marrow CD34+ cells


title: Patient_ASSESS_96

value: Positive


title: V1343: Non-treated_iron overload

value: M


title: V1002: Non-treated_normal ferritin level

value: NO


title: V1488: Treated with deferasirox

value: MDS MLD


title: Patient_ASSESS_98

value: Whole blood

value: female


title: Patient_ASSESS_97

value: Sjögren’s syndrome


title: 43285853_RNA

description: patient 72 tumor tissue RNA_seq

value: patient 72


title: 43291517_RNA

description: patient 71 tumor tissue RNA_seq

value: patient 71

value: colorectal tumor


title: V1618: Non-treated_iron overload


title: V1271: Treated with deferasirox

value: YES


title: M17_3

tag: time period

value: 3 days after pollination

tag: line

value: whole seed


title: V1658: Non-treated_iron overload


title: V384: Non-treated_normal ferritin level


title: 43149399_RNA

description: patient 70 tumor tissue RNA_seq

value: patient 70


title: 43200326_RNA

description: patient 69 tumor tissue RNA_seq

value: patient 69


title: Patient 6 F

city: Shanghai

first: Yangyang

last: Zhang

state: Shanghai

address: 150 Jimo Road

department: Department of Cardiovascular Surgery

institute: Shanghai East Hospital, Tongji University School of Medicine

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 11 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”)were retained for further analyses.

source_name: Control

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs weredigested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

extract_protocol: Blood samples were collected from the coronary arteries of six participants (three with ST-elevation myocardial infarction (STEMI) and three without AMI) undergoing percutaneous coronary intervention (PCI) due to undiagnosed chest pain, and then prepared according to the arraystar’s standard protocols.

value: 55 years

value: male

tag: coronary disease

value: Normal

tag: culprit artery

value: negative

tag: group

value: Control

value: blood

tag: rna population

value: circular RNA


title: Patient 4 D

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 9 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

value: 49 years

tag: tissue


title: V917: Treated with deferasirox

value: bone marrow CD34+ cells

value: MDS MLD

value: M


title: 43088665_RNA

description: patient 68 tumor tissue RNA_seq

value: patient 68

value: colorectal tumor


title: Patient 5 E

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 10 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

value: 53 years


title: Patient_ASSESS_95

value: Whole blood

tag: Sex

value: Positive

value: Sjögren’s syndrome


title: Patient_ASSESS_94

value: female

tag: antissa status


title: Patient_ASSESS_92

value: Negative

tag: antissb status


title: 43111743_RNA

description: patient 67 tumor tissue RNA_seq

value: patient 67


title: Patient_ASSESS_91

tag: disease state


title: V448: Non-treated_normal ferritin level

tag: diagnosis

value: MDS del(5q)

value: F

value: NO


title: Patient 2 B

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 7 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: Acute myocardial infarction

value: 52 years

tag: gender

value: male

value: STEMI

value: LAD

value: Acute myocardial infarction

value: blood

value: circular RNA


title: Patient_ASSESS_93


title: Patient_ASSESS_90


title: Patient 1 A

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

value: 55 years


title: 26178804_RNA

description: patient 65 tumor tissue RNA_seq

value: patient 65

value: colorectal tumor


title: Patient_ASSESS_89

value: Whole blood

value: Positive

value: Sjögren’s syndrome


title: S9: stroke-3

city: Nanjing

first: Lei

last: Zuo

address: Dingjiaqiao 87th

institute: Southeast University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: S, stroke patients who is admitted into hospital in 72 hours after symptom onset

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the plama of each stroke patient or control using a miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. The RNA quantity and quality were measured by NanoDrop ND-1000 (NanoDrop products, Wilmington, DE, USA). The RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Whole blood was drawn into EDTA-containing tubes (BD Biosciences) prior to the administration of any therapies, then centrifuged at 1000 × g for 10 minutes at 4°C,  supernatant was gathered as plasma

value: Acute ischemia stroke

value: plasma

value: Female


title: S8: stroke-2

value: Male


title: Patient_ASSESS_88

first: Jacques-Eric

last: Gottenberg

address: 15 Renee Descartes Street

institute: Institut de Biologie Moleculaire et Cellulaire

value: female


title: 42852476_RNA

description: patient 64 tumor tissue RNA_seq

value: patient 64


title: V452: Treated with deferasirox

value: bone marrow CD34+ cells

value: MDS del(5q)

value: M

tag: serum ferritin level (ng/ml)

value: YES


title: S5: stroke-1


title: V480: Non-treated_normal ferritin level

value: F

tag: deferasirox treatment

value: NO


title: 24016481_RNA

description: patient 63 tumor tissue RNA_seq

value: patient 63


title: V440: Treated with deferasirox

value: MDS MLD

tag: age


title: V239: Non-treated_iron overload


title: 42872557_RNA

description: patient 66 tumor tissue RNA_seq

tag: patient number

value: patient 66

value: colorectal tumor


title: 42942951_RNA

description: patient 62 tumor tissue RNA_seq

value: patient 62


title: Patient_ASSESS_86

value: Whole blood

value: Positive

value: Sjögren’s syndrome


title: Patient_ASSESS_87


title: Patient_ASSESS_85

value: Negative


title: 42899583_RNA

description: patient 61 tumor tissue RNA_seq

value: patient 61


title: V224: Non-treated_iron overload


title: Patient 3 C

description: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 8 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

value: 47 years

value: male

value: STEMI

value: LAD

value: Acute myocardial infarction

value: blood

value: circular RNA


title: M-tumor-2

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

description: male tumor replicate 2

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v3.0.1 (10x Genomics) and bcl2fastq v2.20.0.422 (Illumina)
Cell Ranger v3.0.1 count was used to align the demultiplexed reads to the reference genome (mm10), perform filtering, barcode counting, UMI (unique molecule identifier) counting and estimate the number of cells.
Data analysis was performed in R using Seurat v3 package.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcodes list: barcode sequences correspond to column indices of feature-barcode matrices. Each barcode sequence includes a suffix with a dash separator followed by a number.
Supplementary_files_format_and_content: cell features (genes) list: features correspond to row indices of feature-barcode matrices. For each feature, its feature ID and name are stored in the first and second column of the (unzipped) features.tsv file, respectively. The third column identifies the type of feature, which in this case will be Gene Expression (the feature ID corresponds to gene_id in the annotation field of the reference GTF).
Supplementary_files_format_and_content: feature-barcode count matrix: each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. Contains only cellular barcodes detected by CellRanger.

source_name: brain CD11b+

extract_protocol:
Animals were perfused with PBS and brains taken out. Brain tissue was enzymatically dissociated to single cell suspension with Neural Tissue Dissociation Kit [Miltenyi Biotec] and gentleMACS Octo Dissociator [Miltenyi Biotec]. Myelin was removed by density gradient centrifugation and CD11b+ cells FACS sorted to 20% FBS in PBS. Cell suspension from FACS was loaded directly onto Chromium™ Single Cell A Chip [10x Genomics].
Preparation of Gel Beads in Emulsion and libraries were performed with Chromium Controller and Single Cell Gene Expression v2 Chemistry [10x Genomics, USA] according to the Chromium Single Cell 3’ Reagent Kits v2 User Guide provided by the manufacturer. Libraries quality and quantity was verified with High Sensitivity DNA Kit [Agilent Technologies, USA] on 2100 Bioanalyzer [Agilent Technologies, USA]. Next, sequencing was run in the rapid run flow cell and paired-end sequenced (read 1 – 26 bp, read 2 – 100 bp) on HiSeq 1500 [Illumina, USA]

tag: strain

value: 12 weeks

tag: tumor stage

value: 14 days post implantation

tag: implanted cell line

value: GL261 luc+ tdT+


title: N7: control-2

source_name: N, healthy controls underwent physical examniation who were matched with stroke patients in age and gender

value: healthy control

value: plasma

value: Male


title: N4: control-1

value: Female


title: Patient_ASSESS_84

value: Whole blood

value: female

value: Positive

value: Sjögren’s syndrome


title: Patient_ASSESS_83

value: Negative


title: 42895202_RNA

description: patient 60 tumor tissue RNA_seq

value: patient 60

value: colorectal tumor


title: M-tumor-1

description: male tumor replicate 1

value: male


title: V91: Treated with deferasirox

value: bone marrow CD34+ cells

value: MDS del(5q)

value: F

value: YES


title: N9: control-3


title: 42836948_RNA

description: patient 59 tumor tissue RNA_seq

value: patient 59


title: V221: Non-treated_iron overload

value: MDS EB

value: NO


title: V328: Treated with deferasirox

value: MDS MLD


title: Patient_ASSESS_82


title: M-ctrl-2

description: male control replicate 2

value: 12 weeks


title: V175: Treated with deferasirox

value: M


title: V220: Non-treated_normal ferritin level


title: 41890855_RNA

description: patient 57 tumor tissue RNA_seq

value: patient 57


title: 14934436_RNA

description: patient 58 tumor tissue RNA_seq

value: patient 58


title: Patient_ASSESS_81

value: Whole blood

value: female

value: Positive

value: Sjögren’s syndrome


title: 39248569_RNA

description: patient 56 tumor tissue RNA_seq

value: patient 56

value: colorectal tumor


title: Patient_ASSESS_80

value: Negative


title: F-tumor-2

description: female tumor replicate 2

value: 14 days post implantation

value: GL261 luc+ tdT+


title: V568: Treated with deferasirox

value: bone marrow CD34+ cells

value: MDS del(5q)

value: F

value: YES


title: Patient_ASSESS_79


title: V300: Non-treated_iron overload

value: NO


title: V1505: Treated with deferasirox


title: 39136433_RNA

description: patient 55 tumor tissue RNA_seq

value: patient 55


title: F-tumor-1

description: female tumor replicate 1

value: 12 weeks


title: M-ctrl-1

description: male control replicate 1

value: male


title: F-ctrl-2

description: female control replicate 2


title: 38519679_RNA

description: patient 54 tumor tissue RNA_seq

value: patient 54


title: Patient_ASSESS_78

value: Whole blood

value: female


title: V105: Non-treated_normal ferritin level


title: Patient_ASSESS_77

value: Positive

value: Sjögren’s syndrome


title: F-ctrl-1

description: female control replicate 1


title: 38519523_RNA

description: patient 53 tumor tissue RNA_seq

value: patient 53

value: colorectal tumor


title: 38465842_RNA

description: patient 52 tumor tissue RNA_seq

value: patient 52


title: V887: Non-treated_iron overload

value: MDS MLD

value: M


title: 201113-chromophobe rcc

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: chromophobe rcc

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

value: Chromophobe renal cell carcinoma


title: 200020-chromophobe rcc


title: 38430651_RNA

description: patient 51 tumor tissue RNA_seq

value: patient 51


title: 192618-chromophobe rcc


title: 38394142_RNA

description: patient 50 tumor tissue RNA_seq

value: patient 50


title: Patient_ASSESS_75

city: Strasbourg

value: Negative


title: 38365074_RNA

description: patient 49 tumor tissue RNA_seq

value: patient 49


title: timecourse-23C-120min

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Library strategy: Micro-C
1. Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
2. allValidPairs files were generated by HiC-Pro package (>2.10 version)
3. mcool files were converted from allValidPairs by Cooler package
4. hic file were converted from allValidPairs by Juicer tools
Genome_build: sacCer3
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Cells were grown to early-log phase (OD600 0.1-0.2) at the temperature indicated (23°C or 30°C) overnight and arrested in G1 using the pheromone alpha-factor at a concentration of 10-8M. Cells were released from G1 by washing with YPD containing auxin (if indicated) and 0.15 mg/mL pronase E three times, and once with YPD. After the last wash, cells were resuspended in YPD medium containing 15 µg/mL nocodazole and auxin if indicated. Cultures were then once again incubated at 23°C/30°C for 3h. For the time course, cells were released from alpha-factor into fresh media and collected every 15min with no other drugs.

extract_protocol:
Micro-C products were extracted as the following steps: 1) Digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP by DNA Polymerase I, Large (Klenow) Fragment ; 3) Proximal ligation by T4 DNA ligase and remove unligated ends by Exonuclease III; 4) Purify ligated dinucleosomal DNA by the standard Phenol:Chloroform:Isoamyl Alcohol (25:24:1) and ethanol precipitation procedure.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with the individual enzymes purchased from Lucigen or the NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme or NEB Q5 enzyme with the lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 on the Illumina HiSeq 4000 sequencer.

treatment_protocol:
If indicated, auxin was added to a final concentration of 500 µM to deplete AID-tagged proteins after a 2.5 hours arrest.
We used the Micro-C protocol reported in (Hsieht et al., 2016, Nature Methods) with some minor modifications. Yeast cultures in the indicated conditions were immediately crosslinked with 3% formaldehyde for 15 minutes at 30°C, then quenched with 125 mM glycine at room temperature for 5 minutes.  Washed yeast cells were then spheroplasted with 250 ug/mL Zymolyase in the Buffer Z at 30°C. Washed spheroplasts were resuspended in the 3mM DSG crosslinking solution and incubated at 30°C for 40 minutes. Crosslinking reaction was quenched with 125 mM glycine at room temperature for 5 minutes. Crosslinked cells can be stored at -80 ̊C for few months or proceed to chromatin fragmentation immediately.

tag: genetic background


title: timecourse-23C-105min


title: Patient_ASSESS_76


title: 37903411_RNA

description: patient 48 tumor tissue RNA_seq

value: patient 48


title: Patient_ASSESS_74


title: timecourse-23C-90min


title: timecourse-23C-75min


title: 37505800_RNA

description: patient 46 tumor tissue RNA_seq

value: patient 46


title: V359: Treated with deferasirox

value: bone marrow CD34+ cells

value: MDS del(5q)

value: YES


title: Patient_ASSESS_73

value: Whole blood

value: female

value: Positive


title: V104: Non-treated_normal ferritin level

value: F

value: NO


title: Patient_ASSESS_72

value: Sjögren’s syndrome


title: V720: Treated with deferasirox

value: MDS MLD

value: M


title: V602: Non-treated_normal ferritin level


title: V649: Non-treated_iron overload


title: timecourse-23C-60min


title: Patient_ASSESS_69


title: 37446141_RNA

description: patient 45 tumor tissue RNA_seq

value: patient 45

value: colorectal tumor


title: V1235: Treated with deferasirox


title: V234: Non-treated_iron overload


title: V1478: Treated with deferasirox


title: Patient_ASSESS_70


title: V770: Non-treated_iron overload


title: timecourse-23C-45min


title: 37759777_RNA

description: patient 47 tumor tissue RNA_seq

value: patient 47


title: 34343337_RNA

description: patient 44 tumor tissue RNA_seq

value: patient 44


title: Patient_ASSESS_71

value: Negative


title: 33588360_RNA

description: patient 43 tumor tissue RNA_seq

value: patient 43


title: V949: Treated with deferasirox

value: bone marrow CD34+ cells


title: timecourse-23C-15min


title: Patient_ASSESS_66


title: Patient_ASSESS_67


title: timecourse-30C_90min


title: V513: Non-treated_iron overload

value: MDS del(5q)


title: 29142006_RNA

description: patient 41 tumor tissue RNA_seq

value: patient 41


title: timecourse-23C-30min


title: timecourse-30C_75min


title: 28645379_RNA

description: patient 40 tumor tissue RNA_seq

value: patient 40


title: WCL-Tbk1-/--2

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

data_processing:
Library strategy: MeRIP-seq
Base calling was performed using  the software bcl2fastq (v2.17.1.14) to obtain pass filter data through preliminary quality analysis.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Gene expression was quantified as fragments per kilobase of coding sequence per million fragments (FPKM) algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: immortalized mouse embryonic fibroblasts

growth_protocol: Cells were cultured in DMEM containing 10% FBS, 1% glutamine and 1% streptomycin-penicillin in a 10 cm dish for further study

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen),or use magnetic beads to enrich mRNA, and finally enrich mRNA with m6a modification by m6a antibody
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells without any treatment

tag: cell line

tag: genotype


title: timecourse-30C_60min


title: 23274068_RNA

description: patient 38 tumor tissue RNA_seq

value: patient 38

tag: tissue


title: Patient_ASSESS_68

value: Whole blood

tag: Sex

value: female

value: Positive


title: timecourse-30C_45min


title: 30913835_RNA

description: patient 42 tumor tissue RNA_seq

value: patient 42


title: WCL-WT-2

value: immortalized mouse embryonic fibroblasts

value: WT


title: WCL-Tbk1-/--1


title: 21717057_RNA

description: patient 37 tumor tissue RNA_seq

value: patient 37


title: 27694392_RNA

description: patient 39 tumor tissue RNA_seq

value: patient 39

value: colorectal tumor


title: timecourse-30C_30min


title: Patient_ASSESS_65

tag: antissa status

value: Sjögren’s syndrome


title: Patient_ASSESS_64

value: Negative

tag: antissb status


title: V340: Treated with deferasirox

value: MDS MLD

value: F

value: YES


title: Patient_ASSESS_61

tag: disease state


title: Patient_ASSESS_62


title: V83: Non-treated_normal ferritin level

value: bone marrow CD34+ cells

tag: diagnosis

value: MDS RS

value: M

value: NO


title: V581: Treated with deferasirox

tag: gender


title: WCL-WT-1


title: Patient_ASSESS_63

value: Whole blood

value: female


title: timecourse-30C_15min


title: V1607: Treated with deferasirox

tag: serum ferritin level (ng/ml)


title: 11753506_RNA

description: patient 35 tumor tissue RNA_seq

value: patient 35


title: pds5-AID_rep1

description:
pds5-AID.hic
pds5-AID.mcool


title: m6a-Tbk1-/--1

value: immortalized mouse embryonic fibroblasts

tag: fraction

value: m6a modified mRNA


title: Patient_ASSESS_59

value: Positive


title: 12523481_RNA

description: patient 36 tumor tissue RNA_seq

value: patient 36


title: m6a-Tbk1-/--2


title: Patient_ASSESS_60


title: m6a-WT-2

value: WT


title: wpl1-AID_rep2

description:
wpl1-AID_merged.hic
wpl1-AID_merged.mcool


title: 11374415_RNA

description: patient 34 tumor tissue RNA_seq

value: patient 34

value: colorectal tumor


title: wpl1-AID_rep1


title: 36930991_RNA

description: patient 33 tumor tissue RNA_seq

value: patient 33


title: m6a-WT-1


title: parent_tumor

city: Boston

first: Sarah

middle: J.

last: Hill

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The single-cell RNA sequencing reads were aligned to human GRCh38 reference genome and quantified using Cell Ranger (v3.1.0) from 10X Genomics
Cell filtering and clustering were performed with the Seurat package (v3.0.0).
Genome_build: hg38
Supplementary_files_format_and_content: gene count matrix

source_name: Ovarian tumor

growth_protocol: The tumor was digested and a single cell suspension was frozen in FBS/10% DMSO

extract_protocol:
CD45+ and negative viable cells were sorted and then RNA was prepared using 10X Genomics single cell RNAsequencing kit
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

tag: cell type

value: Mixture of tumor cells from single cell suspension used for organoid co-culture below listed as "organoid"

tag: treatment

value: Untreated patient

tag: tumor type

value: High grade seorus ovarian cancer


title: mcd1-AID_brn1-AID_rep2

description:
mcd1-AID-brn1-AID_merged.hic
mcd1-AID_brn1-AID_merged.mcool

tag: strain

value: MCD1-AID and BRN1-AID


title: mcd1-AID_brn1-AID_rep1


title: 36618936_RNA

description: patient 31 tumor tissue RNA_seq

tag: patient number

value: patient 31


title: organoid

source_name: Organoid co-culture generated from ovarian tumor

growth_protocol: Organoid co-cultures were grown in DMEM/10% FBS/pen/strep with IL2.

extract_protocol:
For single cell RNA sequencing, CD45+ viable cells were sorted from the various treated co-cultures, cells were hashed for the four different treatments, and RNA was extracted using a 10X genomics kit.
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

treatment_protocol: Co-cultures were treated with the listed agent for 96 hours prior to harvest.

value: Organoid co-culture of above parent tumor

value: Isotype control, anti-PD-L1, anti-PD-1, or bispecific anti-PD-1/P-L1


title: brn1-AID_rep2

description:
brn1-AID_merged.hic
brn1-AID_merged.mcool

tag: genetic background


title: BISGZMBN_rep2

data_processing:
The RNA sequencing reads were aligned to the human GRCh38 reference genome using STAR (v2.6.1)
Genes were quantified using RSEM (v1.3.3)
Genome_build: hg38
Supplementary_files_format_and_content: gene expression matrix output from RSEM V1.3.3

extract_protocol:
For bulk RNA sequencing, NK or CD8 T cells were sorted from the treated co-cultures and RNA was extracted using a Qiagen RNEasy mini kit.
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

value: CD8 T cell

value: Bispecific anti-PD-1/PD-L1


title: Patient_ASSESS_55

value: Whole blood

value: female

value: Negative

value: Sjögren’s syndrome


title: Patient_ASSESS_56

value: male


title: 36599655_RNA

description: patient 30 tumor tissue RNA_seq

value: patient 30


title: Patient_ASSESS_57

value: Positive


title: brn1-AID_rep1


title: 19641599_RNA

description: patient 28 tumor tissue RNA_seq

value: patient 28

value: colorectal tumor


title: BISGZMBN_rep1


title: PEMGZMBN_rep2


title: 36613809_RNA

description: patient 29 tumor tissue RNA_seq

value: patient 29


title: mcd1-AID_rep2

description:
mcd1-AID_merged.hic
mcd1-AID_merged.mcool


title: mcd1-AID_rep1


title: PEMGZMBN_rep1

value: High grade seorus ovarian cancer


title: 36541911_RNA

description: patient 27 tumor tissue RNA_seq

value: patient 27


title: PDL1GZBN_rep2


title: 36501331_RNA

description: patient 26 tumor tissue RNA_seq

value: patient 26


title: A364_rep2

description:
A364_merged.hic
A364_merged.mcool


title: Patient_ASSESS_58


title: A364_rep1

description:
A364_merged.hic
A364_merged.mcool


title: PDL1GZBN_rep1


title: 23660537_RNA

description: patient 25 tumor tissue RNA_seq

value: patient 25


title: Patient_ASSESS_52


title: Patient_ASSESS_54