title: genotype: CNAG_01626, librarydate: 2012-02-13, sample: 1374

description: Library name: sample_1374


title: A549_rep1

status: Public on May 27 2025

type: SRA

city: Beijing

first: Shaodong

last: Huang

address: Peking University Health Science Center, Beijing, China

department: Department of Biomedical Informatics

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
RNA-Seq raw reads were mapped to the human genome version hg19. CircRNAs were identified by call module of CIRI-long with default parameters. Isoforms were determined by isoform collapsing modules of CIRI-long.
Assembly: hg19
Supplementary files format and content: A text file contains the summarized epxression level of circRNAs in all samples.

molecule: total RNA

organism: Homo sapiens

source_name: Lung adenocarcinoma

extract_protocol:
RNA was harvested using Takara RNAiso Plus. 2 ug of total RNA was used for librarires construction.
CircRNA libraries for RNA-seq were prepared following CIRI-long protocols. KAPA RNA HyperPrep Kit with RiboErase (HMR) was used for rRNA depletion. SMARTer PCR cDNA Synthesis Kit(Takara) was used for rolling circular reverse transcription.

tag: tissue

value: Lung adenocarcinoma

tag: cell line

tag: cell type

value: Lung


title: genotype: CNAG_01626, librarydate: 2012-02-13, sample: 1372

city: St Louis

first: Chase

last: Mateusiak

state: MO

address: 4515 McKinley Ave

department: Genetics

country: USA

institute: Washington University, St Louis

description: Library name: sample_1372

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: gzipped tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation.

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

value: yeast

tag: strain

tag: genotype

value: deletion CNAG_01626

tag: treatment

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

tag: time

value: 90 min


title: genotype: CNAG_01551, librarydate: 2012-03-26, sample: 2420

description: Library name: sample_2420

value: deletion CNAG_01551


title: genotype: CNAG_01551, librarydate: 2012-03-26, sample: 2419

description: Library name: sample_2419


title: IMR-90_rep2

source_name: Fetal lung

value: Fetal lung


title: IMR-90_rep1


title: genotype: CNAG_01454, librarydate: 2017-10-03, sample: 1473

description: Library name: sample_1473

value: deletion CNAG_01454


title: genotype: CNAG_01454, librarydate: 2017-10-03, sample: 1452

description: Library name: sample_1452


title: genotype: CNAG_01454, librarydate: 2017-08-09, sample: 767

description: Library name: sample_767


title: STCO_5-3_S41

city: VILLEJUIF

first: AZIZA

last: CAIDI

address: 114 RUE EDUARD VAILLANT

country: France

institute: GUSTAVE ROUSSY

description:
Library name: Sample12
Illumina

data_processing:
Quality control was performed on raw FastQ files with FastQC (v0.11.8). Quality reports were obtained with MultiQC (v1.10.1). Abundance was estimated with Salmon (v0.9.0)
Differential analysis was performed using DESEQ2  (v1.26.0).
Assembly: GENCODE (GRCm38, vm20)
Supplementary files format and content: Salmon output files

organism: Mus musculus

source_name: B16 melanoma cell line

extract_protocol:
Total RNA was extracted from sorted CD103+, CD49a+ and CD103negCD49aneg CD8 TIL populations with a single-cell RNA purification kit (Norgen Biotek) used in accordance with the manufacturer’s instructions. RNA integrity (RNA Integrity Score≥7.0) was checked on an Agilent 2100 Bioanalyzer, and the amount of RNA was determined with Qubit (Invitrogen).
The SureSelect Automated Strand-Specific RNA Library Preparation Kit was used, and the fragmented mRNA samples were used for cDNA synthesis. The cDNAs were converted into double-stranded (ds)DNA, and the final dsDNA libraries were subjected to paired-end sequencing on a HiSeq-2000 sequencer (Illumina),

value: B16 melanoma cell line

tag: batch


title: genotype: CNAG_01438, librarydate: 2016-10-04, sample: 2479

description: Library name: sample_2479

value: deletion CNAG_01438


title: STCO_5-1_S39

description:
Library name: Sample10
Illumina


title: genotype: CNAG_01438, librarydate: 2016-10-04, sample: 2478

description: Library name: sample_2478


title: STCO_4-3_S38

description:
Library name: Sample9
Illumina


title: STCO_4-2_S37

description:
Library name: Sample8
Illumina


title: genotype: CNAG_01438, librarydate: 2016-10-04, sample: 2477

description: Library name: sample_2477


title: STCO_4-1_S36

description:
Library name: Sample7
Illumina


title: FOXS1.ref_451

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs). Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Cy3 signal was scanned to assess double-stranding efficiency and Alexa488 signal was scanned at multiple photomultiplier tube gain settings on a Molecular Devices GenePix 4400A microarray scanner.

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.

molecule: protein

source_name: in vitro trancription and translation

label_protocol: Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency; GST-tagged proteins were detected with Alexa488-labelled anti-GST antibody.

extract_protocol: GST fusion proteins were expressed by in vitro transcription and translation.

treatment_protocol: Reference alleles of human forkhead gene DNA-binding domains and flanks were obtained by commercial gene synthesis. Variants were generated by site-directed mutagenesis and Gateway cloned into pDEST15.

value: GST-tagged protein


title: STCO_3-2_S34

description:
Library name: Sample5
Illumina


title: genotype: CNAG_01438, librarydate: 2016-10-04, sample: 2457

description: Library name: sample_2457


title: STCO_3-3_S35

description:
Library name: Sample6
Illumina


title: FOXS1.ref_454


title: genotype: CNAG_01454, librarydate: 2018-05-25, sample: 1335

description: Library name: sample_1335


title: FOXS1.ref_444


title: FOXS1.ref_445


title: STCO_1-3_S32

description:
Library name: Sample3
Illumina


title: STCO_1-2_S31

description:
Library name: Sample2
Illumina


title: FOXS1.R81C_444


title: FOXS1.R81C_445


title: genotype: CNAG_01438, librarydate: 2015-05-19, sample: 2361

description: Library name: sample_2361


title: STCO_5-2_S40

description:
Library name: Sample11
Illumina


title: STCO_1-1_S30

description:
Library name: Sample1
Illumina


title: FOXS1.R38W_444


title: FOXS1.R38W_445


title: liver tissue, Gsdmd∆Hep mice 05, 10 weeks

city: Guangzhou

first: Aoran

last: Dong

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
GLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

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

value: liver

value: Gsdmd{delta}Hep

value: IR


title: FOXS1.N3wingH1face_445


title: FOXS1.N3wingH1face_444


title: genotype: CNAG_01438, librarydate: 2013-04-17, sample: 1037

description: Library name: sample_1037


title: liver tissue, Gsdmd∆Hep mice 04, 10 weeks


title: liver tissue, Gsdmd∆Hep mice 03, 10 weeks


title: STCO_3-1_S33

description:
Library name: Sample4
Illumina


title: genotype: CNAG_01438, librarydate: 2016-10-04, sample: 2456

description: Library name: sample_2456


title: genotype: CNAG_01438, librarydate: 2013-04-17, sample: 1036

description: Library name: sample_1036


title: genotype: CNAG_01438, librarydate: 2013-04-17, sample: 1035

description: Library name: sample_1035


title: liver tissue, Gsdmd∆Hep mice 02, 10 weeks


title: liver tissue, GsdmdFL/FL mice 05, 10 weeks

value: GsdmdFL/FL


title: liver tissue, GsdmdFL/FL mice 04, 10 weeks


title: FOXS1.N3wing_445


title: liver tissue, GsdmdFL/FL mice 03, 10 weeks


title: FOXS1.N3wing_444


title: genotype: CNAG_01069, librarydate: 2020-10-30, sample: 2314

description: Library name: sample_2314

value: deletion CNAG_01069


title: genotype: CNAG_01069, librarydate: 2020-09-10, sample: 2080

description: Library name: sample_2080


title: liver tissue, GsdmdFL/FL mice 01, 10 weeks


title: replicate3 pAKT mAb83-7 bin4

city: Edinburgh

first: Vahid

last: Aslanzadeh

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: The University of Edinburgh

library_source: genomic

data_processing:
PacBio sequencing data were aligned to INSR amplicon by minimp2 and variants were called by alignparse.
Barcode sequencing data were first trimmed by trimmomatic to get the only 30nts barcode sequences and then used Enrich2 to count frequency of each barcode in each bin.
Assembly: INSR reference gene was used for read alignment
Supplementary files format and content: CSV files contain processed CCS HiFi reads from PacBio data, listing mutations and barcode sequences
Supplementary files format and content: tsv files for barcode sequencings contain barcode counts in each bin

molecule: genomic DNA

source_name: Mouse Embryo Fibroblasts

growth_protocol: MEFs were cultured in DMEM  supplemented with 10% fetal bovine serum and Penicillin-Streptomycin (50 I.U./ml). Cells were passaged by trypsinization using 0.25% trypsin-EDTA and tested negative for Mycoplasma before use.

extract_protocol:
Used conventional phenol-chlorophorm methode to isolate gDNA
Plasmid library for PacBio sequencing was constructed using saturation mutagenesis, and library for sequencing barcodes from gDNA constructed using PCR primers tagged with p5 and p7 illumina sequencing primers
Amplicon sequencing by PacBio and illumina sequencing of PCR products from gDNA

value: Mouse Embryo Fibroblasts

value: Igf1r knockout with doxycycline-inducible INSR knockdown


title: replicate3 pAKT mAb83-7 bin3


title: genotype: CNAG_01069, librarydate: 2017-10-03, sample: 1472

description: Library name: sample_1472

value: yeast


title: replicate3 pAKT mAb83-7 bin2


title: FOXS1.K88R_454


title: replicate3 pAKT mAb83-7 bin1


title: replicate3 pAKT mAb83-14 bin4


title: liver tissue, Gsdmd∆Hep mice 01, 10 weeks


title: genotype: CNAG_01069, librarydate: 2017-09-07, sample: 177

description: Library name: sample_177


title: liver tissue, GsdmdFL/FL mice 02, 10 weeks


title: FOXS1.D82G_445


title: FOXS1.D82G_444


title: replicate3 pAKT mAb83-14 bin3


title: FOXS1.A28P_454


title: replicate3 pAKT mAb83-14 bin1


title: FOXS1.K88R_451


title: replicate5 pAKT insulin bin3


title: replicate5 pAKT insulin bin2


title: genotype: CNAG_01014, librarydate: 2017-06-12, sample: 1639

description: Library name: sample_1639

value: deletion CNAG_01014


title: FOXS1.A28P_451


title: replicate3 pAKT mAb83-14 bin2


title: genotype: CNAG_01014, librarydate: 2017-06-12, sample: 1638

description: Library name: sample_1638

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_01069, librarydate: 2017-10-03, sample: 1451

description: Library name: sample_1451

value: 90 min


title: replicate4 pAKT insulin bin4


title: genotype: CNAG_01014, librarydate: 2018-08-14, sample: 387

description: Library name: sample_387


title: replicate4 pAKT insulin bin2


title: replicate4 pAKT insulin bin1


title: genotype: CNAG_00896, librarydate: 2021-03-10, sample: 2670

description: Library name: sample_2670

value: deletion CNAG_00896


title: replicate3 pAKT insulin bin4


title: FOXS1.H1face_445


title: replicate5 pAKT insulin bin4


title: genotype: CNAG_01014, librarydate: 2017-06-12, sample: 1640

description: Library name: sample_1640


title: FOXO3.ref_442


title: FOXS1.H1face_444


title: replicate3 pAKT insulin bin3


title: replicate3 pAKT insulin bin2


title: genotype: CNAG_00896, librarydate: 2021-03-10, sample: 2669

description: Library name: sample_2669


title: replicate3 pAKT insulin bin1


title: FOXO3.ref_443


title: replicate2 pAKT insulin bin4


title: replicate5 pAKT insulin bin1


title: FOXO3.N3wingH1face_443


title: genotype: CNAG_00896, librarydate: 2021-01-13, sample: 1780

description: Library name: sample_1780


title: replicate4 pAKT insulin bin3


title: replicate2 pAKT insulin bin3


title: genotype: CNAG_00896, librarydate: 2021-01-13, sample: 1779

description: Library name: sample_1779


title: FOXO3.N3wing_443


title: replicate2 pAKT insulin bin1


title: FOXO3.N3wingH1face_442


title: PBMC, Fluent v4, sample F5B

city: Seattle

first: Anna

last: Elz

state: WA

address: 1201 Eastlake Ave E

institute: Fred Hutchinson Cancer Center

description: Library name: fluent_v4_F5B

library_source: transcriptomic single cell

data_processing:
Sequencing Depth and Downsampling: Sample sequencing was conducted to achieve a depth exceeding 25,000 reads per cell for WT libraries except for FLEX which targeted 10,000 reads per cell.  TCR libraries all targeted for 5000 reads per cell. When sequencing surpassed the targets, FASTQs were downsampled to 25,000 reads per cell for the WT libraries and 5000 reads per cells for TCR libraries using seqtk version 1.3 with random seed 100 (Li, 2012).
Generating count matrices: The software provided by each kit vendor was utilized to generate UMI count matrices from the downsampled FASTQs. Pipelines were run with default parameters unless otherwise specified. For the 10x kits, CellRanger version 8.0.0 with the multi subcommand was employed with the reference version refdata-gex-GRCh38-2024-A. Parse data was processed with splitpipe v1.2.1 using parse’s hg38_V1.1.3 reference. Fluent data was processed with PIPseeker version 3.3.0 with reference gex-reference-GRCh38-2022.04. For each sample, PIPseeker generates 5 outputs of varying sensitivity for calling cells from background. We selected the sensitivity levels on a per-sample basis informed by the knee plots and vendor guidelines. Scale data was processed through scaleRNA version 1.5 with default parameters, library structure version 1.1 and the prebuilt GRCH38 reference genome provided by Scale. FASTQs were generated at the library level by passing raw BCL folders into the first scaleRNA run. We then ran Scale’s bc_parser (distributed with the nextflow pipeline) with the `--demux` flag and options to output 2 read files and 2 index files for each sample. These were downsampled and ran with default parameters to produce the filtered expression matrix.
Assembly: GRCh38
Supplementary files format and content: The first set of processed files are pipeline outputs from downsampled data. For WT/GEX libraries, processed files include files needed to construct the counts matrix. Either h5 files, or matrix + barcode + feature files. For VDJ/TCR libraries, the processed data files have the final clone assemblies.
Supplementary files format and content: The second set of processed files are the Seurat RDS files for each kit, with all samples for that kit merged. The datasets were processed to remove low quality cells and low-abundance genes. Data was clustered at the kit level and annotated manually using reference mapping and key gene expression. See the manuscript for full details.

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Benchmark I:  3’ Whole transcriptome comparison Multiple donor leukopak frozen aliquots were purchased from Bloodworks Northwest.  PBMCs from two healthy donors F1 and F5, stored in liquid nitrogen were thawed at 37 degrees C., transferred into 10ml prewarmed thawing media (Gibco RPMI 1640 + 10% FBS) and centrifuged at 500 x g for 5 minutes at 4 degrees. Cells were washed in 10ml cold 1XPBS -MgCl and -CaCl (Gibco), followed by subsequent centrifugation at 500 x g for 5 minutes and the pellet resuspended in 10ml 1X PBS.  The CellacaMX (Revvity) live-dead assay was used to count AOPI stained cells. Viability was 83% and 88% respectively.  Each cell suspension was aliquoted for use in the 10X Genomics GEM-X and NextGEM assays in which the cell suspensions were loaded in replicate, with a targeted recovery of 20,000 and 10,000 cells, respectively.  The remaining cell suspensions were aliquoted out in technical replicates of 1 million cells and fixed using Parse’s Cell Fixation v3 User Manual (UM0027 v1.1), Fluent’s Demonstrated Protocol DSP-Methanol Fixation for Cells (FB0004708), and 10x Demonstrated Protocol Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling (FLEX) (CG000478 Rev C). Separate aliquots of F1 and F5 donors were processed as above except with PBS 1% BSA for the final resuspension.  One set was fixed in technical replicates of 1 million cells following the Scale’s standard fixation kit protocol Rev. B.  The second set of aliquots was processed as above with PBS + 0.04% BSA and Promega RNase Inhibitor resuspension and no fixation for Fluent’s PIPseq V.  Benchmark II:  5’ WT, TCR single cell comparison Frozen PBMCs from four healthy donors (F1, F2, F4, and F5) of mixed sex (3 males, 1 female) and ethnicity (3 persons of Caucasian descent and 1 person of Asian descent) supplied by Bloodworks Northwest were processed in two batches one week apart (F1, F2 followed by F4, F5). Cells were thawed in a 37°C water bath before transfer to thawing media (Gibco RPMI 1640 + 10% FBS). Samples were then centrifuged at 400 x g for 10 minutes at 4°C. The supernatant was decanted, and the pellet resuspended in 10 mL of sorting media (cold Gibco 1X PBS + 1% BSA), followed by an additional centrifugation at 400 x g for 10 minutes. Each sample was next resuspended in 200 µL of stain media. Cells were stained to enrich for T-cells and to remove as many B-cells as possible. We stained the samples with human CD3, CD45, and CD19 (citation for antibodies). 7AAD was used to assess the in-flight viability of the cells during the sort. We sorted T cells using the Becton-Dickenson Symphony S6 cytometer. The final population was CD3+, CD45+, and CD19-. An aliquot of the sorted T-cells was stained with AOPI and assessed for viability and cell counts using the Nexcelom CellacaMX (Revvity).  Viabilities ranged from 88-90 % (F1 and F2) and 83-87% (F4 and F5).  An aliquot of the of each donor T-cells was utilized for 10x Genomics GEM-X 5′ v3 (CG000733 RevA) and NextGEM 5′ v2 (CG000331 RevE) assays, in which 20,000 and 10,000 cells were targeted for recovery, respectively. The remaining cell suspension, ~1.5 million cells, was fixed following Parse Evercode Cell Fixation v2 (UM0039 v2.3). Cells were frozen and later processed as directed by Evercode TCR Human WT + TCR v1 (UM0018).
Benchmark I:  3’ Whole transcriptome comparison 10x Genomics FLEX Fixed RNA profiling Per the 10x Genomics CG000527 Rev E protocol, fixed cells were incubated overnight with mRNA transcript probes targeting ~18K genes, with the left handle containing a sample specific barcode. Following probe hybridization, samples were counted and pooled equally before a series of washes to remove unbound probes.  After counting the pool, a volume targeting a recovery of 40,000 cells was combined with a master mix that contains enzymes that ligate and extend the probes during GEM incubation. This mixture was then loaded into the NEXT GEM Chip Q with gel beads and partitioning oil. Following microfluidic GEM generation on the ChromiumX, the GEMs were recovered and amplified to generate product to put into library preparation.  A portion of the amplified material was re-amplified with library specific P5 and P7 indices. 10x Genomics GEM-X 3’v4 and NextGEM v3.1 Following the 10X Genomics GEM-X 3’v4 (CG000731) and NextGEM v3.1 (CG000315) protocols, PBMCs from donor F1 and donor F5 were combined with a reverse transcript mastermix and loaded on to a microfluidic chip (Chromium GEM-X 3’ chip and NextGEM Chip G) along with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads using the ChromiumX instrument and subsequently underwent reverse transcription. The cDNA was recovered, cleaned, and amplified to create enough material for library preparation. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final amplification. Fluent Biosciences PIPseq v.4 Fixed cells were partitioned, and libraries generated using the PIPseq T20 3’ Single Cell RNA Kit v4.0PLUS User Guide (FB0002130 Rev 8.3). To target a recovery of 20,000 cells per sample, 8uls of a cell suspension at a concentration of approximately 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices.  Fluent Biosciences PIPseq V Sample replicates of live cells (40,000 each) were loaded into PIPs for capture and barcoding as described in PIPseq V T20 3’ Single Cell RNA kit User Guide (FB0005261). To target a recovery of 20,000 cells per sample, 8ul of 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices. Parse Evercode v3 Following the Parse protocol UMWT3300, fixed and permeabilized PBMCs were thawed, and counted using trypan blue and a hemocytometer, diluted and added to 12 wells per replicate of Plate 1 as directed by the sample loading table (48 wells total across all replicates). Following reverse transcription, cells were pooled and split an additional two times, the last of which added a barcode containing R2 and Biotin for magnetic bead enrichment Cells were pooled again, counted, and distributed into eight sublibraries each targeting under 12,500 cells where they were lysed and the biotin labelled cDNA recovered with binder beads. cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned. A portion of this cleaned product was fragmented, adapter ligated and had p5 and p7 indices added in a final PCR. Scale Biosciences Following the Scale 1020796 Rev A protocol, fixed cells at a concentration of approximately 2000 cells/ul were added to 96 wells of barcode plate 1 and well IDs documented to map back cells to their sample of origin. The cells underwent reverse transcription and were then pooled by centrifugation into a funnel. Cells were washed and then split across a 384 well ligation plate where cells were barcoded. Cells were again pooled by centrifugation, washed, and counted to assess for recovery. The cell stock was diluted to approximately 460 cells/ul and 4uls loaded into each well of the final distribution plate, with the remainder saved at -80 degrees. In the final distribution plate, the cell membrane is broken down, cDNA is tagmented with a transposase, and the library specific P5 and P7 indexes added.  Benchmark II:  5’ WT, TCR single cell comparison 10X Genomics GEM-X 5’v3 and Next GEM 5’v2 Following the 10X Genomics GEM-X 5’v3 (CG000733) and NextGEM 5’v2 (CG000331) protocols, sorted T cells were added to a reverse transcription mastermix and loaded on to a microfluidic chip (Chromium GEM-X 5’ chip and NextGEM Chip K respectively) with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads (GEMS) and subsequently underwent reverse transcription.  The cDNA was recovered and cleaned before being amplified to create enough material for library preparation for gene expression and TCR. To generate TCR libraries, a small amount of cDNA underwent 2 rounds of PCR with a set of TCR specific primers. A portion of the PCR product was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR.  Parse Evercode TCR Fixed and permeabilized T cells were thawed, counted using trpyan blue and a hemocytometer, following Parse protocol UMIT2300.  Each sample was diluted according to the sample loading table and recounted before dispensing into 12 wells per sample of Plate 1 (48 wells total). Following reverse transcription, cells were pooled and split an additional two times to add barcodes, the last pool and split also adding the R2 and biotin. Cells were pooled, counted, and distributed into eight sublibraries each targeting 12,500 cells. Cells were lysed and biotin labelled cDNA recovered with binder beads.  cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned to be usable in TCR and whole transcriptome library preparation. Whole transcription libraries undergo library preparation as described in Evercode TCR Human WT + TCR v1 (UM0018), which utilized the Parse v2 WT chemistry. The TCR library is generated from a subset of the WT cDNA in a PCR reaction targeting the V(D)J segments of the CDR3 region of the T cell.

value: PBMC

value: Fluent Biosciences PIP Seq T20 3′ v4


title: replicate2 pAKT insulin bin2


title: replicate2 pAKT mAb83-14 bin3


title: replicate2 pAKT mAb83-14 bin4


title: FOXO3.N3wing_442


title: genotype: CNAG_00883, librarydate: 2012-02-13, sample: 1386

description: Library name: sample_1386

value: deletion CNAG_00883


title: replicate2 pAKT mAb83-14 bin1


title: FOXO3.H1face_443


title: genotype: CNAG_00883, librarydate: 2012-02-13, sample: 1385

description: Library name: sample_1385


title: replicate2 pAKT mAb83-14 bin2


title: replicate2 pAKT mAb83-7 bin4


title: FOXO3.H1face_442


title: genotype: CNAG_00883, librarydate: 2012-02-13, sample: 1384

description: Library name: sample_1384


title: replicate2 pAKT mAb83-7 bin2


title: genotype: CNAG_00871, librarydate: 2012-03-19, sample: 2415

description: Library name: sample_2415

value: deletion CNAG_00871


title: replicate2 mAb83-14 bind bin3


title: replicate2 pAKT mAb83-7 bin1


title: replicate2 mAb83-14 bind bin4


title: FOXN4.ref_374

value: GST-tagged protein


title: genotype: CNAG_00871, librarydate: 2012-03-19, sample: 229

description: Library name: sample_229


title: genotype: CNAG_00896, librarydate: 2020-09-10, sample: 2067

description: Library name: sample_2067


title: genotype: CNAG_00871, librarydate: 2012-03-19, sample: 228

description: Library name: sample_228


title: replicate2 mAb83-14 bind bin1


title: replicate2 mAb83-7 bind bin4


title: genotype: CNAG_00841, librarydate: 2016-10-04, sample: 2488

description: Library name: sample_2488

value: deletion CNAG_00841


title: replicate2 mAb83-7 bind bin3


title: replicate2 mAb83-7 bind bin2


title: FOXN4.G265V_374


title: FOXN4.ref_371


title: replicate2 pAKT mAb83-7 bin3


title: replicate2 mAb83-7 bind bin1


title: replicate2 Insulin bind bin2


title: genotype: CNAG_00841, librarydate: 2016-10-04, sample: 2487

description: Library name: sample_2487


title: replicate2 Insulin bind bin4


title: genotype: CNAG_00841, librarydate: 2017-06-12, sample: 1637

description: Library name: sample_1637


title: replicate1 pAKT mAb83-14 bin4


title: FOXN3.T156S_376


title: replicate1 pAKT mAb83-14 bin3


title: FOXN4.ref_373


title: replicate2 Insulin bind bin1


title: genotype: CNAG_00841, librarydate: 2017-06-12, sample: 1636

description: Library name: sample_1636


title: replicate2 Insulin bind bin3


title: replicate2 mAb83-14 bind bin2


title: FOXN4.G265V_371


title: FOXN4.G265V_373


title: FOXN3.T156S_471


title: replicate1 pAKT mAb83-14 bin1


title: replicate1 pAKT mAb83-14 bin2


title: replicate1 pAKT mAb83-7 bin4


title: FOXN3.T156S_375


title: genotype: CNAG_00841, librarydate: 2016-10-04, sample: 2486

description: Library name: sample_2486


title: replicate1 pAKT mAb83-7 bin1


title: FOXN3.T156I_471


title: genotype: CNAG_00830, librarydate: 2021-05-06, sample: 2820

description: Library name: sample_2820

value: deletion CNAG_00830


title: FOXN3.T156I_371


title: replicate1 pAKT mAb83-7 bin3


title: replicate1 pAKT insulin bin4


title: replicate1 pAKT insulin bin3


title: FOXN3.T156I_369


title: genotype: CNAG_00830, librarydate: 2021-04-28, sample: 2804

description: Library name: sample_2804


title: genotype: CNAG_00841, librarydate: 2017-06-12, sample: 1635

description: Library name: sample_1635


title: replicate1 pAKT insulin bin2


title: genotype: CNAG_00830, librarydate: 2017-06-12, sample: 1634

description: Library name: sample_1634


title: replicate1 pAKT insulin bin1


title: replicate1 mAb83-14 bind bin2


title: replicate1 mAb83-14 bind bin4


title: genotype: CNAG_00841, librarydate: 2018-08-14, sample: 378

description: Library name: sample_378


title: FOXN3.T156D_471


title: genotype: CNAG_00830, librarydate: 2021-04-28, sample: 2803

description: Library name: sample_2803


title: replicate1 pAKT mAb83-7 bin2


title: FOXN3.T156D_376


title: replicate1 mAb83-14 bind bin1


title: genotype: CNAG_00830, librarydate: 2017-06-12, sample: 1633

description: Library name: sample_1633


title: replicate1 mAb83-14 bind bin3


title: replicate1 mAb83-7 bind bin4


title: FOXN3.T156D_375


title: genotype: CNAG_00830, librarydate: 2017-06-12, sample: 1632

description: Library name: sample_1632


title: replicate1 mAb83-7 bind bin2


title: FOXN3.T156A_471


title: FOXN3.T156A_376


title: replicate1 Insulin bind bin4


title: replicate1 mAb83-7 bind bin1


title: replicate1 Insulin bind bin3


title: genotype: CNAG_00828, librarydate: 2017-06-12, sample: 1631

description: Library name: sample_1631

value: deletion CNAG_00828


title: FOXN3.T156A_375


title: genotype: CNAG_00828, librarydate: 2017-06-12, sample: 1630

description: Library name: sample_1630


title: replicate1 Insulin bind bin2


title: replicate1 Insulin bind bin1


title: FOXN3.ref_470


title: genotype: CNAG_00828, librarydate: 2020-10-07, sample: 1081

description: Library name: sample_1081


title: replicate1 mAb83-7 bind bin3


title: genotype: CNAG_00791, librarydate: 2017-06-12, sample: 1627

description: Library name: sample_1627

value: deletion CNAG_00791


title: FOXN3.ref_471


title: genotype: CNAG_00791, librarydate: 2017-06-12, sample: 1628

description: Library name: sample_1628


title: genotype: CNAG_00791, librarydate: 2021-01-13, sample: 1792

description: Library name: sample_1792


title: FOXN3.ref_469


title: DNA from FFPE Meningioma Sample PT32-R1

type: genomic

city: St. Louis

first: Sangami

last: Pugazenthi

address: 4949 W Pine Blvd

institute: Washington University School of Medicine

hyb_protocol: The standard Illumina Infinium HD Restore protocol was used to repair the degraded FFPE samples

scan_protocol: Methylation chips were processed using a Tecan instrument and read using the iScan instrumentation.

data_processing: ChAMP R Package

source_name: DNA from FFPE Meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen Allprep DNA/RNA extraction protocol

value: DNA from FFPE Meningioma

tag: patient

value: AG

tag: primary/recurrence

value: MRM


title: genotype: CNAG_00559, librarydate: 2017-06-12, sample: 1625

description: Library name: sample_1625

value: yeast

value: deletion CNAG_00559


title: DNA from FFPE Meningioma Sample PT31-P

value: AF

value: Primary

value: NRM


title: DNA from FFPE Meningioma Sample PT32-P


title: DNA from FFPE Meningioma Sample PT30-P

value: AE


title: FOXN3.ref_376


title: FOXN3.ref_453


title: FOXN3.ref_448


title: genotype: CNAG_00559, librarydate: 2017-06-12, sample: 1624

description: Library name: sample_1624

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: DNA from FFPE Meningioma Sample PT29-P

value: AD


title: genotype: CNAG_00828, librarydate: 2017-06-12, sample: 1629

description: Library name: sample_1629


title: FOXN3.ref_371

value: GST-tagged protein


title: FOXN3.ref_375


title: FOXN3.ref_442


title: genotype: CNAG_00559, librarydate: 2017-06-12, sample: 1623

description: Library name: sample_1623


title: DNA from FFPE Meningioma Sample PT27-P

value: AB


title: FOXN3.ref_369


title: DNA from FFPE Meningioma Sample PT26-P

value: AA


title: FOXN3.P155A_471


title: DNA from FFPE Meningioma Sample PT24-P

value: Y


title: genotype: CNAG_00559, librarydate: 2018-08-14, sample: 386

description: Library name: sample_386


title: DNA from FFPE Meningioma Sample PT25-P

value: Z


title: FOXN3.ref_443


title: genotype: CNAG_00514, librarydate: 2021-06-08, sample: 2916

description: Library name: sample_2916

value: deletion CNAG_00514


title: DNA from FFPE Meningioma Sample PT23-P

value: DNA from FFPE Meningioma

value: X


title: DNA from FFPE Meningioma Sample PT28-P

value: AC


title: FOXN3.P155A_371


title: DNA from FFPE Meningioma Sample PT22-P

value: W


title: DNA from FFPE Meningioma Sample PT21-P

value: V


title: genotype: CNAG_00514, librarydate: 2017-06-12, sample: 1621

description: Library name: sample_1621

value: yeast


title: FOXN3.N1loop_470


title: FOXN3.P155A_369


title: MCF10CA1a Exo Replicate 1

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description: Library name: MCF10CA1a Exo1

data_processing:
Each library was indexed to four multiplex samples per sequencing run on the Illumina MiSeq platform using MiSeq 50 cycle Reagent Kits v2.
Assembly: Human miRbase, version 21
Supplementary files format and content: Tab-delimited text file of normalized microRNA readcounts for all samples

source_name: breast cancer cell line

extract_protocol:
Total RNA from sEVs isolated from the conditioned medium of MCF10 cell line series or cultured cells was prepared using TRIzol reagent (Thermo-Fisher), followed by column clean-up using the Monarch RNA Cleanup kit according to the manufacturer’s protocol for whole transcriptome isolation (New England Biolabs, T2030S). RNA quality was checked using an Agilent 2100 Bioanalyzer, and concentrations from ThermoFisher’s NanoDrop readings were used.
Small RNA libraries were constructed using the New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencing and the NEB standard protocol

value: breast cancer cell line

value: invasive ductal carcinoma


title: MCF10CA1a Exo Replicate 3

description: Library name: MCF10CA1a Exo3


title: genotype: CNAG_00514, librarydate: 2017-06-12, sample: 1620

description: Library name: sample_1620

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: MCF10CA1a Exo Replicate 2

description: Library name: MCF10CA1a Exo2


title: MCF10DCIS Exo Replicate 2

description: Library name: MCF10DCIS Exo2

value: ductal carcinoma in situ


title: MCF10DCIS Exo Replicate 3

description: Library name: MCF10DCIS Exo3


title: genotype: CNAG_00514, librarydate: 2020-10-05, sample: 710

description: Library name: sample_710

value: 90 min


title: MCF10DCIS Exo Replicate 1

description: Library name: MCF10DCIS Exo1


title: genotype: CNAG_00505, librarydate: 2017-10-03, sample: 1446

description: Library name: sample_1446

value: deletion CNAG_00505


title: MCF10AT1 Exo Replicate 2

description: Library name: MCF10AT1 Exo2

value: Benign proliferative


title: genotype: CNAG_00514, librarydate: 2017-06-12, sample: 1622

description: Library name: sample_1622


title: MCF10AT1 Exo Replicate 1

description: Library name: MCF10AT1 Exo1


title: genotype: CNAG_00505, librarydate: 2017-10-03, sample: 1445

description: Library name: sample_1445


title: MCF10A Exo Replicate 2

description: Library name: MCF10A Exo2

value: Normal


title: FOXN3.N1loop_469

value: GST-tagged protein


title: MCF10A Exo Replicate 3

description: Library name: MCF10A Exo3


title: NK cells CITE-seq

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

department: Microbial Infection and Immunity

institute: The Ohio State University

description: Library name: Sample 1

library_source: other

data_processing:
Normalized libraries were sequenced on a NovaSeq 6000 S4 flowcell to a depth of 50,000 reads per cell. Downstream analysis was done using Seurat (v. 4.0.3), excluding cells with a high mitochondrial read percentage (> 5%), or doublets (> 5000 genes per cell).
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix_Tonsil_V_Blood includes cell barcode (columns) x genes / ADT that are the proteins (rows). This is the integrated Blood and Tonsil data into one file.
Library strategy: CITE-seq

source_name: Blood and Tonsil

extract_protocol:
Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ). Following the addition of the cocktail, density gradient centrifugation was performed using Ficoll-Paque to separate enriched NK cells from the remaining blood components. For tonsil NK isolation, Human innate lymphoid cells (ILCs) were enriched from fresh tonsil tissue. Single-cell suspensions from fresh human pediatric tonsils were generated by dissociation via a GentleMACS Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Cells were resuspended in FBS (Sigma-Aldrich) with leukocyte-depleted RBCs and a custom human NK cell enrichment RosetteSep reagent containing a mixture of bivalent antibodies against glycophorin A and CD3, CD4, CD19, CD20, CD36, CD66b, and CD123 (STEMCELL Technologies).
For CITE-seq, cells from different donors were first labeled with hash tag oligos (HTO) 20 minutes on ice, washed once, and then pooled together at equal numbers. Next, TotalSeq A (biolegend) antibodies containing antibody derived tags (ADT) were diluted in PBS-4% FBS, then used to label cells on ice for 20 minutes. Cells were then washed twice and processed for single cell expression analysis using the 10x Genomics kit.

value: Blood and Tonsil

value: NK cells


title: FOXN3.L199V_470


title: FOXN3.N153T_442


title: Ton_FRC_Control; R1

city: Houston

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Sample 7 RNA

data_processing:
To improve mapping rate and accuracy, RNA-seq reads were trimmed using Trimmomatic to remove adaptors, low-quality bases at the ends, and reads shorter than 36 bases after trimming, with quality control performed via FastQC both before and after trimming. The trimmed reads were aligned to the hg38 reference genome using STAR.
Read quantification was conducted with Salmon using the “salmon quant” command. Samples with fewer than 2 million transcript counts mapped to the reference genome were excluded from further analysis. DESeq2 was used for differential gene expression analysis
Assembly: hg38
Supplementary files format and content: tonsil_frc_salmon.cnts.csv

source_name: Tonsil

extract_protocol:
Tonsillar fibroblastic reticular cells (tFRCs) were isolated from fresh tonsils. The cells were passaged for six generations in Insulin-Transferrin-Selenium (Thermo Fisher) containing Dulbecco's Modified Eagle Medium (DMEM, Corning) supplemented with 10% fetal Bovine serum (FBS) and Penicillin (100 units/mL)-streptomycin (100 µg/mL). The tFRCs were stimulated with 10 ng/mL and 50 ng/mL TGFB (Peprotech). The cells were harvested after 48 hours post treatment and subjected to bulk RNA sequencing.
RNA was extracted using RNeasy micro kit (QIAGEN) according to the manufacturer’s protocol after washing the cells with PBS, followed by library preparation for RNAseq. Illumina NovaSeq 6000 platform, using the PE100 S4 flow cell for paired-end sequencing with a 200-cycle v1.5 kit

value: Tonsil

value: Tonsillar fibroblastic reticular cells

value: control


title: MCF10AT1 Exo Replicate 3

description: Library name: MCF10AT1 Exo3


title: FOXN3.L199V_369


title: genotype: CNAG_00505, librarydate: 2018-10-23, sample: 127

description: Library name: sample_127


title: genotype: CNAG_00505, librarydate: 2018-11-02, sample: 128

description: Library name: sample_128


title: Ton_FRC_Control; R2

description: Library name: Sample 8 RNA


title: FOXN3.N153T_443


title: FOXN3.L199V_371


title: FOXN3.J3wingH1face_443


title: Ton_FRC_50_ng_mL_48hr; R1

description: Library name: Sample 4 RNA

value: TGFB (50_ng_mL) for 48h


title: genotype: CNAG_00460, librarydate: 2017-10-03, sample: 1443

description: Library name: sample_1443

value: deletion CNAG_00460


title: genotype: CNAG_00505, librarydate: 2020-10-05, sample: 708

description: Library name: sample_708

value: yeast


title: MCF10A Exo Replicate 1

description: Library name: MCF10A Exo1

value: breast cancer cell line


title: FOXN3.J3wingH1face_442


title: Ton_FRC_10_ng_mL_48hr; R2

description: Library name: Sample 2 RNA

value: TGFB (10_ng_mL) for 48h


title: Ton_FRC_10_ng_mL_48hr; R3

description: Library name: Sample 3 RNA


title: Ton_FRC_50_ng_mL_48hr; R2

description: Library name: Sample 5 RNA


title: genotype: CNAG_00460, librarydate: 2017-10-03, sample: 1442

description: Library name: sample_1442

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: FOXN3.J3wing_443


title: FOXN3.J3wing_442


title: Ton_FRC_Control; R3

description: Library name: Sample 9 RNA


title: Ton_FRC_50_ng_mL_48hr; R3

description: Library name: Sample 6 RNA


title: Ton_FRC_10_ng_mL_48hr; R1

description: Library name: Sample 1 RNA


title: genotype: CNAG_00460, librarydate: 2017-10-03, sample: 1444

description: Library name: sample_1444


title: genotype: CNAG_00460, librarydate: 2020-10-05, sample: 706

description: Library name: sample_706


title: genotype: CNAG_00460, librarydate: 2018-10-23, sample: 126

description: Library name: sample_126


title: Macrophages T_sup; R3

description: Library name: Sample 6 RNA

data_processing:
To improve mapping rate and accuracy, RNA-seq reads were trimmed using Trimmomatic to remove adaptors, low-quality bases at the ends, and reads shorter than 36 bases after trimming, with quality control performed via FastQC both before and after trimming. The trimmed reads were aligned to the hg38 reference genome using STAR.
Read quantification was conducted with Salmon using the “salmon quant” command. Samples with fewer than 2 million transcript counts mapped to the reference genome were excluded from further analysis. DESeq2 was used for differential gene expression analysis
Assembly: hg38
Supplementary files format and content: macrophages_salmon.cnts.csv

source_name: Blood

extract_protocol:
Peripheral blood-derived monocytes were isolated from cryopreserved peripheral blood mononuclear cells obtained from 3 different healthy donors (Stemcell) using pan-monocyte isolation kit (Miltenyi) with autoMACS Neo cell separator (Miltenyi) according to the manufacturer’s instructions. Cells were cultured in ImmunoCult SF Macrophage medium (Stemcell) containing 50 ng/mL of recombinant human M-CSF (Stemcell) in temperature-responsive polymer-treated UpCell plates (Thermo Fisher) for 4 days, followed by either supplementation with 50 ng/mL of recombinant human IFN-gamma (Stemcell) or replacement with supernatant of exhausted T-cells (Tex sup) for an additional 2 days. For Tex sup production, a serial killing assay was conducted using healthy donor-derived CAR T cells and HT cell line, starting at a 1:1 ratio in IMDM (Gibco) supplemented with 10% FBS (Gibco). HT cells were added every 2 days along with medium exchange. The supernatant was collected on day 10 and then cryopreserved until use. Tex sup and ImmunoCult SF macrophage medium were mixed at a 1:1 ratio and supplemented with 50 ng/mL rhM-CSF.
RNA was extracted using RNeasy micro kit (QIAGEN) according to the manufacturer’s protocol after washing the cells with PBS, followed by library preparation for RNAseq. Illumina NovaSeq 6000 platform, using the PE100 S4 flow cell for paired-end sequencing with a 200-cycle v1.5 kit.

value: Blood

value: Peripheral blood-derived monocytes

value: human M-CSF + supernatant of exhausted T-cells


title: Macrophages T_MCSF; R2

description: Library name: Sample 8 RNA

value: human M-CSF


title: Macrophages T_MCSF; R1

description: Library name: Sample 7 RNA


title: Macrophages T_MCSF; R3

description: Library name: Sample 9 RNA


title: genotype: CNAG_00332, librarydate: 2020-09-10, sample: 2065

description: Library name: sample_2065

value: deletion CNAG_00332

value: 90 min


title: FOXN3.A1loop_453

value: GST-tagged protein


title: FOXN3.A1loop_448


title: FOXN2.T154A_369


title: FOXN2.T154A_368


title: Macrophages T_sup; R1

description: Library name: Sample 4 RNA


title: Macrophages IFN; R1

description: Library name: Sample 1 RNA

value: human M-CSF + IFN-gamma


title: genotype: CNAG_00332, librarydate: 2020-10-05, sample: 676

description: Library name: sample_676


title: genotype: CNAG_00332, librarydate: 2021-01-13, sample: 1778

description: Library name: sample_1778


title: PBMC, Scale, sample F5B

description:
Library name: scale_F5B
Combined sequencing from a NextSeq 2000 run and a deeper NovaSeq run

value: PBMC

value: Scale Biosciences Single Cell RNA kit


title: Macrophages IFN; R3

description: Library name: Sample 3 RNA


title: Macrophages IFN; R2

description: Library name: Sample 2 RNA


title: PBMC, Scale, sample F5A

description:
Library name: scale_F5A
Combined sequencing from a NextSeq 2000 run and a deeper NovaSeq run


title: genotype: CNAG_00332, librarydate: 2021-01-13, sample: 1777

description: Library name: sample_1777


title: PBMC, Scale, sample F1B

description:
Library name: scale_F1B
Combined sequencing from a NextSeq 2000 run and a deeper NovaSeq run


title: PBMC, Scale, sample F1A

description:
Library name: scale_F1A
Combined sequencing from a NextSeq 2000 run and a deeper NovaSeq run


title: genotype: CNAG_00193, librarydate: 2021-01-13, sample: 1787

description: Library name: sample_1787

value: deletion CNAG_00193


title: MTBP_FUCCI, anti-GFP, Late S, replicate 2

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_LateS_replicate2

data_processing:
The initial processing of Cut&Run sequencing data was carried out systematically using a tailored Snakemake pipeline (doi.org/10.5281/zenodo.8329766).
Trimmomatic (0.35) was used to trim reads, excising bases with quality scores below 20 at both the leading and trailing ends, as well as internal bases with an average quality score lower than 15 within a 4-base pair window.
To remove adapter remnants shorter than 6 bases, Cutadapt (3.7) was employed with a quality cutoff of 20 and a mismatch rate of 20%. Reads shorter than 25 base pairs were filtered out after each trimming stage.
The processed reads were aligned to a GRCh38 - hg38 human genome assembly with Drosophila melanogaster (dm6) and E. Coli (ASM886v2) genome sequence using bowtie2 (2.3.1). Default settings were used, with the inclusion of the --dovetail flag to allow dovetailed paired reads during alignment.
Alignment processing and filtering was performed using samtools (1.1.4) to eliminate reads with a quality score less than 10, those with an unmapped mate pair, or duplicates.
Potential spike-in reads aligning to either the D. melanogaster or E. coli genomes were also removed.
Alignments or peaks overlapping problematic genomic regions (ENCODE blacklist ENCFF356LFX) were removed during downstream analysis.
Narrow peak calling was conducted on individual replicates using macs2 (2.2.7.1), applying an FDR threshold of 0.05 and a minimum fold change cutoff of 1.
BigWig coverage files were generated using deepTools (bamCoverage -b {input.bam} -o {output.bw} --effectiveGenomeSize 2913022398 --binSize 50 --smoothLength 150 --blackListFileName hg38-blacklist.v2.bed --centerReads). The blacklist file (hg38-blacklist.v2.bed) was obtained from ENCODE (DOI: 10.5281/zenodo.1491733).
Normalized BigWig files were generated using deepTools (bamCompare --smoothLength 150 --minFragmentLength 50 --ignoreForNormalization "chrX chrM chrY" --maxFragmentLength 1000 --minMappingQuality 20 --effectiveGenomeSize 2913022398 --scaleFactorsMethod "None" --normalizeUsing "CPM" --operation "log2" --binSize 50 --blackListFileName hg38-blacklist.v2.bed --centerReads -b1 {input.tx_bam} -b2 {input.in_bam}. The untagged HCT116 sample, processed in parallel, served as the input control for normalization of each replicate.
Assembly: hg38
Supplementary files format and content: .narrowPeak files have peak data for each replicate
Supplementary files format and content: Bigwig files ending in "_50_150.bw" were prepared using deeptools bamCoverage.
Supplementary files format and content: Normalized bigwig files ending in "_50_150_bkgrndNorm.bw" were prepared using deeptools bamCompare.
Library strategy: CUT&Run

source_name: HCT 116 MTBP-miniAID-mClover FUCCI

growth_protocol: tFucci(CA)2.1/pCSII-CMV (Riken BRC DNA Bank #RDB15453; doi: 10.1016/j.molcel.2017.10.001) was introduced into the HCT-116 mClover cell lines from Wittig et al., 2021. Cells were grown in McCoy's 5A medium (Corning 10-050-CV) with 10% Fetal Bovine Serum. HCT-116 mClover cells expressing Fucci fluorescent proteins were synchronized with double thymidine block at 2mM then released for 1.5hr or 4.5hr for S phase timepoints for sorting. Cells were plated at 2.5x10^6 in 10cm^2 dishes and collected after 48hrs for G1 and G2 sorting.

extract_protocol:
Cut&Run was performed as described by Skene et al., 2018 (https://doi.org/10.1038/nprot.2018.015) with adapted steps for 1% fixation for 2min and a modified wash buffer according to Epicypher CUTANA Cross-linking protocol v1.9. Each sample used 600,000 cells and protein A-MNase digest step used 40min incubation.
Libraries were prepared using KAPA Hyper Prep Kit (Ref# 7962347001-KK8502) following the manufacturer's protocol. Adapters used were IDT for Illumina TruSeq UDI indexes (Ref# 20020178). Library amplification was performed using 13-16x cycles. Samples were sequenced on Illumina NovaSeq 6000 platform for PE150 sequencing.

tag: cut&run antibody

value: HCT 116 MTBP-miniAID-mClover FUCCI

tag: cell cycle_phase

value: Late S

value: homozygous knockin; FUCCI

tag: Sex

value: Male


title: Macrophages T_sup; R2

description: Library name: Sample 5 RNA


title: MTBP_FUCCI, anti-GFP, Late S, replicate 1

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_LateS_replicate1


title: genotype: CNAG_00193, librarydate: 2020-10-30, sample: 2312

description: Library name: sample_2312

value: yeast


title: MTBP_FUCCI, anti-GFP, Early S, replicate 2

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_EarlyS_replicate2

value: Early S


title: genotype: CNAG_00193, librarydate: 2020-09-10, sample: 2078

description: Library name: sample_2078

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: FOXN2.T151N_448


title: FOXN2.T151N_458


title: FOXN2.T151A_458


title: MTBP_FUCCI, anti-GFP, Early S, replicate 1

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_EarlyS_replicate1


title: FOXN2.T151A_448


title: MTBP_FUCCI, anti-GFP, G1, replicate 2

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_G1_replicate2


title: FOXN2.ref_458


title: FOXN2.ref_448


title: MTBP_FUCCI, anti-GFP, G2, replicate 1

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_G2_replicate1


title: genotype: CNAG_00193, librarydate: 2017-10-03, sample: 1441

description: Library name: sample_1441


title: HCT116_FUCCI, anti-GFP, replicate 1

description: Library name: HCT116FUCCI_replicate1

source_name: HCT 116 FUCCI

value: HCT 116 FUCCI

value: WT; FUCCI


title: HCT116_FUCCI, anti-GFP, replicate 2

description: Library name: HCT116FUCCI_replicate2


title: FOXN2.ref_369


title: MTBP_FUCCI, anti-GFP, G2, replicate 2

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_G2_replicate2


title: genotype: CNAG_00156, librarydate: 2015-11-16, sample: 2282

description: Library name: sample_2282

value: deletion CNAG_00156


title: genotype: CNAG_00156, librarydate: 2015-11-16, sample: 2281

description: Library name: sample_2281


title: genotype: CNAG_00156, librarydate: 2015-11-16, sample: 2280

description: Library name: sample_2280


title: FOXN2.P153L_369


title: genotype: CNAG_00156, librarydate: 2020-10-05, sample: 682

description: Library name: sample_682


title: LAM1158A

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

institute: Zhejiang University - University of Edinburgh

description:
Library name: LAM1158A
FFPE spatial transcrtiptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomic Sapce Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes. Were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz:list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.pgn.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: features.tsv.gz:list of gene IDs
Library strategy: Spatial Transcriptomics

source_name: pulmonary LAM

extract_protocol:
Human LAM tissues were fixed with formalin and embedded with paraffin and 5 𝞵m section were cut with paraffin sectioning machine.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Reagent kit FFPE v2 according to the manufacturer's instructions.

value: pulmonary LAM


title: LAM1158B

description:
Library name: LAM1158B
FFPE spatial transcrtiptome sequencing


title: LAM1069A

description:
Library name: LAM1069A
FFPE spatial transcrtiptome sequencing


title: LAM1159B

description:
Library name: LAM1159B
FFPE spatial transcrtiptome sequencing


title: LAM1159A

description:
Library name: LAM1159A
FFPE spatial transcrtiptome sequencing


title: LAM1069B

description:
Library name: LAM1069B
FFPE spatial transcrtiptome sequencing


title: genotype: CNAG_00068, librarydate: 2020-09-10, sample: 2071

description: Library name: sample_2071

value: deletion CNAG_00068

value: 90 min


title: MTBP_FUCCI, anti-GFP, G1, replicate 1

description: Library name: HCT116MTBP-miniAID-mCloverFUCCI_G1_replicate1


title: genotype: CNAG_00193, librarydate: 2017-10-03, sample: 1439

description: Library name: sample_1439


title: LAM939A

description:
Library name: LAM939A
FFPE spatial transcrtiptome sequencing


title: genotype: CNAG_00828, librarydate: 2020-10-07, sample: 1079

description: Library name: sample_1079

value: deletion CNAG_00828


title: FOXN2.L119P_369

value: GST-tagged protein


title: genotype: CNAG_00068, librarydate: 2021-01-13, sample: 1782

description: Library name: sample_1782


title: genotype: CNAG_00068, librarydate: 2020-10-30, sample: 2302

description: Library name: sample_2302


title: FOXN2.ref_368


title: FOXN2.P153L_368


title: LAM939B

description:
Library name: LAM939B
FFPE spatial transcrtiptome sequencing


title: FOXN2.K179E_458


title: FOXN2.L119P_368


title: genotype: CNAG_00068, librarydate: 2016-06-09, sample: 1997

description: Library name: sample_1997


title: genotype: CNAG_00068, librarydate: 2016-06-09, sample: 1995

description: Library name: sample_1995


title: FOXN2.K179E_448


title: genotype: CNAG_00039, librarydate: 2018-01-16, sample: 2562

description: Library name: sample_2562

value: deletion CNAG_00039


title: Resistant HCC827 cells, (HCC827-OsiR), replicate 2

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
RNA-seq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for all samples

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Nucleospin RNA mini kit (MN).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R Kit by Macrogen company

treatment_protocol: Cells were became resistant to osimertinib by treating them with escalating doses of the drug, starting from 2 nM up to 1.5 µM.

value: lung adenocarcinoma

value: Res

value: Osimertinib


title: Resistant HCC827 cells, (HCC827-OsiR), replicate 3


title: FOXN1.ref_470


title: genotype: CNAG_00791, librarydate: 2017-06-12, sample: 1626

description: Library name: sample_1626

value: deletion CNAG_00791


title: Resistant HCC827 cells, (HCC827-OsiR), replicate 1


title: FOXN1.ref_458


title: FOXN1.ref_469


title: genotype: CNAG_00039, librarydate: 2018-01-16, sample: 2540

description: Library name: sample_2540


title: HCC827 cells, control, replicate 3

value: WT

value: Vehicle


title: FOXN1.ref_454


title: HCC827 cells, control, replicate 2


title: genotype: CNAG_00039, librarydate: 2018-01-26, sample: 1732

description: Library name: sample_1732

value: yeast


title: FOXN1.ref_450


title: HCC827 cells, control, replicate 1


title: FOXN1.ref_453


title: genotype: CNAG_00068, librarydate: 2016-06-09, sample: 1996

description: Library name: sample_1996

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: hESC_DE_hom_3, RNAseq

city: Storrs

first: Laijun

last: Lai

state: Connecticut

address: 1390 Storrs Road

institute: University of Connecticut

data_processing:
Quality control of raw reads was conducted using FastQC. The reads were trimmed using Trimmomatic. Afterward, the paired-end raw reads were aligned to the human reference genome (hg38) using HISAT2 and sorted by Samtools. Mapped reads were performed using htseq-count.
Assembly: hg38
Supplementary files format and content: Microsoft excel comma separated values file includes the raw counts for each sample

source_name: hESCs H9

growth_protocol: hESCs were cultured with mTeSR™ Plus medium (STEMCELL Technologies, Vancouver, Canada) in culture plates coated Corning™ Matrigel™ hESC-Qualified Matrix (Corning, Tewksbury, MA).

extract_protocol:
Total RNA was isolated from cells by the NucleoSpin RNA, Mini kit (Macherey-Nagel, USA).
RNA-seq libraries were prepared using an RNA-seq preparation kit (Illumina, Inc.).An Illumina NovaSeq 6000 was used for sequencing.

value: hESCs H9

value: hESC-derived definitive endoderm

value: homozygous


title: genotype: CNAG_00039, librarydate: 2018-01-26, sample: 1710

description: Library name: sample_1710


title: hESC_DE_hom_2, RNAseq


title: FOXN1.ref_422


title: genotype: CNAG_00068, librarydate: 2018-08-14, sample: 372

description: Library name: sample_372


title: genotype: CNAG_00031, librarydate: 2021-03-10, sample: 2666

description: Library name: sample_2666

value: deletion CNAG_00031


title: hESC_DE_hom_1, RNAseq


title: hESC_DE_het_3, RNAseq

value: heterozygous


title: genotype: CNAG_00031, librarydate: 2021-03-10, sample: 2665

description: Library name: sample_2665

value: 90 min


title: FOXN1.ref_455


title: hESC_DE_het_1, RNAseq


title: FOXN1.ref_383


title: hESC_DE_wt_3, RNAseq

value: wild type


title: genotype: CNAG_00031, librarydate: 2021-01-13, sample: 1773

description: Library name: sample_1773


title: hESC_DE_wt_2, RNAseq


title: FOXN1.ref_382

value: GST-tagged protein


title: hESC_DE_wt_1, RNAseq


title: FOXN1.N3loop_470


title: genotype: CNAG_00000, librarydate: 2021-10-26, sample: 3208

description: Library name: sample_3208


title: hESC_DE_hom_3, ATACseq

data_processing:
Raw sequencing data was first filtered by fastp, low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with MarkDuplicates to eliminate duplication bias introduced in library preparation and sequencing. Reads were first mapped to the reference genome of hg38 using Bowtie2 with default parameters. The MACS2 was used for peak calling. The ChIPseeker was used for peak annotation and peak distribution analysis.
Assembly: hg38
Supplementary files format and content: NarrowPeak

extract_protocol:
hESC-DE cells were collected from cultures and 50,000 cells for each sample were lysed using an adjusted lysis buffer based on the Omni-ATAC protocol, followed by a transposition reaction with hyperactive Tn5 transposase. The DNA fragments were purified using a MinElute Reaction Cleanup Kit (Qiagen, Germantown, MD).
Library construction was performed according to the manufacturer’s recommendations of the Nextera DNA Prep Kit. Libraries were purified using AMPure XP beads to remove primer dimers. The library quality was evaluated using the TapeStation D1000 ScreenTape.


title: genotype: CNAG_00000, librarydate: 2021-06-08, sample: 2912

description: Library name: sample_2912


title: hESC_DE_hom_1, ATACseq


title: genotype: CNAG_00000, librarydate: 2021-06-08, sample: 2911

description: Library name: sample_2911


title: FOXN1.N3loop_469


title: hESC_DE_het_3, ATACseq


title: hESC_DE_het_2, ATACseq


title: FOXN1.I278V_458


title: hESC_DE_het_1, ATACseq


title: genotype: CNAG_00000, librarydate: 2021-05-06, sample: 2816

description: Library name: sample_2816


title: hESC_DE_het_2, RNAseq


title: FOXN1.I278V_453


title: hESC_DE_wt_3, ATACseq


title: genotype: CNAG_00000, librarydate: 2021-04-28, sample: 2800

description: Library name: sample_2800


title: hESC_DE_wt_1, ATACseq


title: genotype: CNAG_00000, librarydate: 2021-04-28, sample: 2799

description: Library name: sample_2799


title: TICRR, thymidine-mimosine-doxycycline, anti-GFP, replicate 2

data_processing:
The initial processing of Cut&Run sequencing data was carried out systematically using a tailored Snakemake pipeline (doi.org/10.5281/zenodo.8329766).
Trimmomatic (0.35) was used to trim reads, excising bases with quality scores below 20 at both the leading and trailing ends, as well as internal bases with an average quality score lower than 15 within a 4-base pair window.
To remove adapter remnants shorter than 6 bases, Cutadapt (3.7) was employed with a quality cutoff of 20 and a mismatch rate of 20%. Reads shorter than 25 base pairs were filtered out after each trimming stage.
The processed reads were aligned to a GRCh38 - hg38 human genome assembly with Drosophila melanogaster (dm6) and E. Coli (ASM886v2) genome sequence using bowtie2 (2.3.1). Default settings were used, with the inclusion of the --dovetail flag to allow dovetailed paired reads during alignment.
Alignment processing and filtering was performed using samtools (1.1.4) to eliminate reads with a quality score less than 10, those with an unmapped mate pair, or duplicates.
Potential spike-in reads aligning to either the D. melanogaster or E. coli genomes were also removed.
Alignments or peaks overlapping problematic genomic regions (ENCODE blacklist ENCFF356LFX) were removed during downstream analysis.
Log2 normalized bigwigs were generated for every replicate anti-GFP Cut&Run done on each mClover-tagged cell line. Background values were calculated from anti-GFP Cut&Run done in parallel on the untagged parental cell line. Normalized Cut&Run signal was calculated using Deeptools (3.4.3) bamCompare with the following settings:  --smoothLength 150, --binSize 50,  --minFragmentLength 50, --minMappingQuality 20, --ignoreForNormalization chrX chrM chrY, --effectiveGenomeSize 2913022398, --scaleFactorsMethod None, --normalizeUsing CPM, --operation log2, --blackListFileName ENCFF356LFX (ENCODE ENCSR636HFF), --centerReads.
Density readings were calculated in genomic windows for all Cut&Run samples. Two controls were conducted for each replicate: rabbit anti-goat-IgG Cut&Run was performed on each tagged cell line, and anti-GFP Cut&Run was carried out concurrently on the parental, untagged cell line. Coverage files were generated using Deeptools (version 3.4.3) bamCoverage with the following settings: --effectiveGenomeSize 2913022398, --normalizeUsing CPM, --binSize 50, --smoothLength 150, --blackListFileName ENCFF356LFX (ENCODE ENCSR636HFF), and --centerReads.
Assembly: GRCh38
Supplementary files format and content: For all samples, 50_150.bw files are provided with read counts per million calculated for 150-base pair windows at 50-base pair intervals across GRCh38.
Supplementary files format and content: For replicates of each tagged cell line, 50_150_bkgrndNorm.bw files with Log2 normalized signals across GRCh38 are provided.
Library strategy: Cut&Run

source_name: HCT-116 TICRR-mClover-XLoneGemininT25D

growth_protocol: The HCT-116 cells used for the control or to generate knock-in cell lines were acquired from ATCC and were grown in McCoy's 5A medium (Corning 10-050-CV) with 10% Fetal Bovine Serum. Cells were plated at a density of 700,000 per well in 6cm 2 plates and allowed to recover overnight.

extract_protocol:
Cut&Run was performed as described by Skene et al., 2018 (https://doi.org/10.1038/nprot.2018.015). Each sample used 300,000 cells and included a modified wash buffer and fixation steps adapted from CUTANA Cross-linking Protocol v1.9 from Epicypher. Samples were fixed with 1% fresh paraformaldehyde for 2 min and quenched with 2.5M Glycine at 1:20 dilution before proceeding to wash steps. Overnight incubation at 55C with 2uL proteinase-K (20mg/mL) and 1.6uL 10% SDS per sample was used to reverse cross-links before DNA purification.
Libraries were prepared using KAPA Hyper Prep Kit (Ref# 7962347001-KK8502) following the manufacturer's protocol. Adapters used were IDT for Illumina TruSeq UDI indexes (Ref# 20020178). Library amplification was performed using 13-16x cycles. Samples were sequenced on Illumina NovaSeq 6000 platform for PE150 sequencing.

treatment_protocol: Cells were synchronized in G1 by treating with 2mM Thymidine (Sigma T1895) for 22 hours followed by a wash in 1xPBS and a 6 hour release. At 2 hours into the release 1ug/mL doxycycline was added for a 16 hour dox treatment to express degradation-resistant Geminin(T25D). After the 6 hour release 0.5mM mimosine was added for 12 hours before cell collection.

value: HCT-116 TICRR-mClover-XLoneGemininT25D

value: Male

tag: antibody dilution


title: TICRR, thymidine-mimosine-doxycycline, anti-GFP, replicate 1


title: hESC_DE_hom_2, ATACseq


title: hESC_DE_wt_2, ATACseq


title: TICRR, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 2


title: genotype: CNAG_00000, librarydate: 2021-03-10, sample: 2662

description: Library name: sample_2662

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: gzipped tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.


title: hESC_DE_het_4, ATACseq


title: FOXN1.E359K_454


title: TICRR, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 1


title: FOXN1.E333K_458


title: genotype: CNAG_00000, librarydate: 2021-03-10, sample: 2661

description: Library name: sample_2661


title: MTBP, thymidine-mimosine-doxycycline, anti-GFP, replicate 2

source_name: HCT-116 MTBP-mClover-XLoneGemininT25D

value: HCT-116 MTBP-mClover-XLoneGemininT25D


title: FOXN1.E333K_450


title: MTBP, thymidine-mimosine-doxycycline, anti-GFP, replicate 1


title: FOXN1.D313N_422


title: MTBP, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 2


title: genotype: CNAG_00000, librarydate: 2021-01-13, sample: 1771

description: Library name: sample_1771


title: MTBP, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 1


title: genotype: CNAG_00000, librarydate: 2021-01-13, sample: 1770

description: Library name: sample_1770


title: HCT116, thymidine-mimosine-doxycycline, anti-GFP, replicate 2

value: WT; Tg(Xlone-GemininT25D)


title: FOXN1.E359K_455


title: genotype: CNAG_00000, librarydate: 2018-01-16, sample: 2549

description: Library name: sample_2549


title: HCT116, thymidine-mimosine-doxycycline, anti-GFP, replicate 1


title: HCT116, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 2


title: FOXN1.I278V_450


title: FOXN1.D313N_382


title: HCT116, thymidine-mimosine-NoDoxControl, anti-GFP, replicate 1


title: FOXN1.D313N_383


title: G1_TICRR_IgG_50_replicate3

data_processing:
The initial processing of Cut&Run sequencing data was carried out systematically using a tailored Snakemake pipeline (doi.org/10.5281/zenodo.8329766).
Trimmomatic (0.35) was used to trim reads, excising bases with quality scores below 20 at both the leading and trailing ends, as well as internal bases with an average quality score lower than 15 within a 4-base pair window.
To remove adapter remnants shorter than 6 bases, Cutadapt (3.7) was employed with a quality cutoff of 20 and a mismatch rate of 20%. Reads shorter than 25 base pairs were filtered out after each trimming stage.
The processed reads were aligned to a GRCh38 - hg38 human genome assembly with Drosophila melanogaster (dm6) and E. Coli (ASM886v2) genome sequence using bowtie2 (2.3.1). Default settings were used, with the inclusion of the --dovetail flag to allow dovetailed paired reads during alignment.
Alignment processing and filtering was performed using samtools (1.1.4) to eliminate reads with a quality score less than 10, those with an unmapped mate pair, or duplicates.
Potential spike-in reads aligning to either the D. melanogaster or E. coli genomes were also removed.
Alignments or peaks overlapping problematic genomic regions (ENCODE blacklist ENCFF356LFX) were removed during downstream analysis.
Narrow peak calling was conducted on individual replicates using macs2 (2.2.7.1), applying an FDR threshold of 0.05 and a minimum fold change cutoff of 1.
Assembly: GRCh38
Supplementary files format and content: For all samples, 50_150.bw files are provided with read counts per million calculated for 150-base pair windows at 50-base pair intervals across GRCh38.
Supplementary files format and content: For replicates of each tagged cell line, 50_150_bkgrndNorm.bw files with Log2 normalized signals across GRCh38 are provided.
Supplementary files format and content: For replicates of each tagged cell line, .narrowPeak files with GRCh38 peaks called using MACS2 are provided.
Library strategy: Cut&Run

source_name: HCT 116 TICRR-miniAID-mClover (RRID:CVCL_C7SS)

growth_protocol: The HCT-116 cells used for the control or to generate knock-in cell lines were acquired from ATCC and were grown in McCoy's 5A medium (Corning 10-050-CV) with 10% Fetal Bovine Serum. HCT-116 cells were plated at 10x10^6 into a T175 flask for G1 and 5x10^6 into a T75 flask for cycling samples.

extract_protocol:
Cut&Run was performed as described by Skene et al., 2018 (https://doi.org/10.1038/nprot.2018.015). Each sample used 100,000 cells and protein A-MNase digest step used 40min incubation.
Libraries were prepared using KAPA Hyper Prep Kit (Ref# 7962347001-KK8502) following the manufacturer's protocol. Adapters used were IDT for Illumina TruSeq UDI indexes (Ref# 20020178). Library amplification was performed using 13-16x cycles. Samples were sequenced on Illumina NovaSeq 6000 platform for PE150 sequencing.

treatment_protocol: Cells were synchronized in G1 by arresting in nocodazole (100ng/mL) for 4hrs followed by mitotic shakeoff and 2hr release before collection. Cycling cells were passaged two consecutive days before collection to obtain an asynchronously cycling population.

value: homozygous knockin

value: Anti-Goat IgG (Jackson ImmunoResearch Labs Cat# 305-005-045, RRID:AB_2339379)


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2472

description: Library name: sample_2472

value: WT


title: G1_TICRR_IgG_50_replicate2

value: HCT 116 TICRR-miniAID-mClover (RRID:CVCL_C7SS)


title: FOXJ3.V162A_373

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.

extract_protocol: GST fusion proteins were expressed by in vitro transcription and translation.


title: G1_TICRR_GFP_replicate3


title: G1_TICRR_GFP_replicate2


title: FOXJ3.V162A_372


title: G1_TICRR_GFP_replicate1


title: G1_MTBP_IgG_50_replicate3

source_name: HCT 116 MTBP-miniAID-mClover (RRID:CVCL_C7SR)


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2452

description: Library name: sample_2452

value: yeast

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: G1_MTBP_IgG_50_replicate2

value: HCT 116 MTBP-miniAID-mClover (RRID:CVCL_C7SR)


title: FOXJ3.ref_457

source_name: in vitro trancription and translation


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2451

description: Library name: sample_2451


title: G1_MTBP_GFP_replicate2


title: G1_MTBP_GFP_replicate1


title: FOXJ3.ref_417


title: FOXJ3.ref_454


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2450

description: Library name: sample_2450


title: G1_MTBP_GFP_replicate3


title: G1_HCT116_IgG_50_replicate3

source_name: HCT 116 (RRID:CVCL_0291)

value: HCT 116 (RRID:CVCL_0291)


title: G1_HCT116_IgG_50_replicate2


title: genotype: CNAG_00000, librarydate: 2020-10-30, sample: 2288

description: Library name: sample_2288


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2473

description: Library name: sample_2473


title: genotype: CNAG_00000, librarydate: 2020-10-30, sample: 2286

description: Library name: sample_2286


title: G1_HCT116_GFP_replicate2


title: genotype: CNAG_00000, librarydate: 2016-10-04, sample: 2471

description: Library name: sample_2471


title: G1_HCT116_GFP_replicate1


title: FOXJ3.ref_416


title: genotype: CNAG_00000, librarydate: 2015-11-16, sample: 2276

description: Library name: sample_2276


title: Cycling_TICRR_IgG_50_replicate3

value: Asynchronous


title: genotype: CNAG_00000, librarydate: 2015-11-16, sample: 2275

description: Library name: sample_2275


title: Cycling_TICRR_GFP_replicate3


title: Cycling_TICRR_GFP_replicate2


title: Cycling_TICRR_GFP_replicate1


title: genotype: CNAG_00000, librarydate: 2015-11-16, sample: 2274

description: Library name: sample_2274


title: Cycling_MTBP_IgG_50_replicate3


title: genotype: CNAG_00000, librarydate: 2017-11-13, sample: 2182

description: Library name: sample_2182


title: Cycling_MTBP_IgG_50_replicate2


title: Cycling_MTBP_GFP_replicate3


title: G1_HCT116_GFP_replicate3


title: FOXJ3.ref_372


title: genotype: CNAG_00000, librarydate: 2016-06-09, sample: 2016

description: Library name: sample_2016


title: Cycling_MTBP_GFP_replicate1


title: Cycling_HCT116_IgG_50_replicate3


title: genotype: CNAG_00000, librarydate: 2016-06-09, sample: 2015

description: Library name: sample_2015


title: Cycling_HCT116_GFP_replicate2


title: FOXJ3.N3wingH1face_416


title: Cycling_HCT116_IgG_50_replicate2


title: Cycling_TICRR_IgG_50_replicate2


title: genotype: CNAG_00000, librarydate: 2016-06-09, sample: 1994

description: Library name: sample_1994


title: Cycling_HCT116_GFP_replicate1


title: Cycling_MTBP_GFP_replicate2


title: DNA from FFPE Meningioma Sample PT20-P

value: DNA from FFPE Meningioma

value: U

value: Primary

value: NRM


title: TICRR, anti-IgG, 50, replicate 3

data_processing:
The initial processing of Cut&Run sequencing data was carried out systematically using a tailored Snakemake pipeline (doi.org/10.5281/zenodo.8329766).
Trimmomatic (0.35) was used to trim reads, excising bases with quality scores below 20 at both the leading and trailing ends, as well as internal bases with an average quality score lower than 15 within a 4-base pair window.
To remove adapter remnants shorter than 6 bases, Cutadapt (3.7) was employed with a quality cutoff of 20 and a mismatch rate of 20%. Reads shorter than 25 base pairs were filtered out after each trimming stage.
The processed reads were aligned to a GRCh38 - hg38 human genome assembly with Drosophila melanogaster (dm6) and E. Coli (ASM886v2) genome sequence using bowtie2 (2.3.1). Default settings were used, with the inclusion of the --dovetail flag to allow dovetailed paired reads during alignment.
Alignment processing and filtering was performed using samtools (1.1.4) to eliminate reads with a quality score less than 10, those with an unmapped mate pair, or duplicates.
Potential spike-in reads aligning to either the D. melanogaster or E. coli genomes were also removed.
Alignments or peaks overlapping problematic genomic regions (ENCODE blacklist ENCFF356LFX) were removed during downstream analysis.
Narrow peak calling was conducted on individual replicates using macs2 (2.2.7.1) with the following settings:  -f BAMPE, -g 2913022398, -q 0.05, and --fe-cutoff 1. For each mClover-knockin sample, peaks were called using Cut&Run with anti-GFP on both the knockin sample and the parental, untagged cell line as a control.
Log2 normalized bigwigs were generated for every replicate anti-GFP Cut&Run done on each mClover-tagged cell line. Background values were calculated from anti-GFP Cut&Run done in parallel on the untagged parental cell line. Normalized Cut&Run signal was calculated using Deeptools (3.4.3) bamCompare with the following settings:  --smoothLength 150, --binSize 50,  --minFragmentLength 50, --minMappingQuality 20, --ignoreForNormalization chrX chrM chrY, --effectiveGenomeSize 2913022398, --scaleFactorsMethod None, --normalizeUsing CPM, --operation log2, --blackListFileName ENCFF356LFX (ENCODE ENCSR636HFF), --centerReads.
Density readings were calculated in genomic windows for all Cut&Run samples. Two controls were conducted for each replicate: rabbit anti-goat-IgG Cut&Run was performed on each tagged cell line, and anti-GFP Cut&Run was carried out concurrently on the parental, untagged cell line. Coverage files were generated using Deeptools (version 3.4.3) bamCoverage with the following settings: --effectiveGenomeSize 2913022398, --normalizeUsing CPM, --binSize 50, --smoothLength 150, --blackListFileName ENCFF356LFX (ENCODE ENCSR636HFF), and --centerReads.
Assembly: GRCh38
Supplementary files format and content: For all samples, 50_150.bw files are provided with read counts per million calculated for 150-base pair windows at 50-base pair intervals across GRCh38.
Supplementary files format and content: For replicates of each tagged cell line, 50_150_bkgrndNorm.bw files with Log2 normalized signals across GRCh38 are provided.
Supplementary files format and content: For replicates of each tagged cell line, .narrowPeak files with GRCh38 peaks called using MACS2 are provided.
Library strategy: Cut&Run

growth_protocol: The HCT-116 cells used for the control or to generate knock-in cell lines were acquired from ATCC and were grown in McCoy's 5A medium (Corning 10-050-CV) with 10% Fetal Bovine Serum. HCT-116 cells were plated at 2.5x10^6 in 10 cm2 dishes and collected after 48 hours.


title: TICRR, anti-IgG, 50, replicate 2


title: genotype: CNAG_00000, librarydate: 2015-08-10, sample: 1856

description: Library name: sample_1856

value: 90 min


title: genotype: CNAG_00000, librarydate: 2015-08-10, sample: 1855

description: Library name: sample_1855


title: DNA from FFPE Meningioma Sample PT19-P

value: T


title: FOXJ3.N3wingH1face_417

value: GST-tagged protein


title: FOXJ3.N3wing_417


title: FOXJ3.ref_373


title: genotype: CNAG_00000, librarydate: 2015-08-10, sample: 1854

description: Library name: sample_1854


title: TICRR, anti-IgG, 50, replicate 1

value: Male


title: DNA from FFPE Meningioma Sample PT18-P

value: S


title: Cycling_HCT116_GFP_replicate3


title: DNA from FFPE Meningioma Sample PT17-P

value: R


title: genotype: CNAG_00000, librarydate: 2018-07-06, sample: 1763

description: Library name: sample_1763

value: WT


title: genotype: CNAG_00000, librarydate: 2018-01-26, sample: 1719

description: Library name: sample_1719


title: FOXJ3.N3wing_416


title: TICRR, anti-GFP, 250, replicate 2

value: HCT 116 TICRR-miniAID-mClover (RRID:CVCL_C7SS)

value: homozygous knockin


title: TICRR, anti-GFP, 250, replicate 3


title: DNA from FFPE Meningioma Sample PT16-P

value: Q


title: TICRR, anti-GFP, 250, replicate 1


title: DNA from FFPE Meningioma Sample PT15-P

value: P


title: DNA from FFPE Meningioma Sample PT13-R1

value: M

value: MRM


title: genotype: CNAG_00000, librarydate: 2017-10-03, sample: 1450

description: Library name: sample_1450

value: yeast

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_00000, librarydate: 2017-10-03, sample: 1449

description: Library name: sample_1449


title: TICRR, anti-GFP, 1000, replicate 3

value: Asynchronous


title: FOXJ3.K98N_457


title: FOXI2.W88L_423


title: FOXJ3.H1face_454


title: TICRR, anti-GFP, 1000, replicate 2


title: DNA from FFPE Meningioma Sample PT12-P

value: DNA from FFPE Meningioma

value: L

value: Primary


title: FOXJ3.H1face_457

value: GST-tagged protein


title: DNA from FFPE Meningioma Sample PT13-P


title: FOXI2.ref_455


title: genotype: CNAG_00000, librarydate: 2018-01-26, sample: 1697

description: Library name: sample_1697

value: 90 min


title: FOXI2.W88L_426


title: genotype: CNAG_00000, librarydate: 2017-10-03, sample: 1448

description: Library name: sample_1448


title: DNA from FFPE Meningioma Sample PT11-P

value: K


title: FOXI2.ref_450


title: FOXI2.ref_461


title: FOXI2.ref_426


title: FOXJ3.K98N_454


title: TICRR, anti-GFP, 1000, replicate 1

value: Male


title: FOXI2.ref_436


title: MTBP, anti-IgG, 50, replicate 3

value: HCT 116 MTBP-miniAID-mClover (RRID:CVCL_C7SR)

value: Anti-Goat IgG (Jackson ImmunoResearch Labs Cat# 305-005-045, RRID:AB_2339379)


title: genotype: CNAG_00000, librarydate: 2017-10-03, sample: 1447

description: Library name: sample_1447

value: WT


title: genotype: CNAG_00000, librarydate: 2019-10-23, sample: 1327

description: Library name: sample_1327


title: genotype: CNAG_00000, librarydate: 2018-05-25, sample: 1333

description: Library name: sample_1333


title: DNA from FFPE Meningioma Sample PT10-P

value: J


title: genotype: CNAG_00000, librarydate: 2017-11-01, sample: 1109

description: Library name: sample_1109


title: MTBP, anti-IgG, 50, replicate 2-1

value: homozygous knockin


title: FOXI2.ref_451


title: DNA from FFPE Meningioma Sample PT09-R1

value: I


title: MTBP, anti-GFP, 250, replicate 3


title: DNA from FFPE Meningioma Sample PT09-P

value: MRM


title: FOXI2.ref_423


title: DNA from FFPE Meningioma Sample PT08-R2

value: H


title: MTBP, anti-GFP, 250, replicate 2


title: genotype: CNAG_00000, librarydate: 2019-11-10, sample: 976

description: Library name: sample_976

value: yeast

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_00000, librarydate: 2020-10-07, sample: 1041

description: Library name: sample_1041


title: DNA from FFPE Meningioma Sample PT08-R1

value: DNA from FFPE Meningioma


title: MTBP, anti-IgG, 50, replicate 2-2

value: Asynchronous


title: DNA from FFPE Meningioma Sample PT08-P

value: Primary


title: genotype: CNAG_00000, librarydate: 2020-09-02, sample: 827

description: Library name: sample_827


title: MTBP, anti-GFP, 1000, replicate 3


title: MTBP, anti-GFP, 250, replicate 1


title: genotype: CNAG_00000, librarydate: 2018-08-14, sample: 371

description: Library name: sample_371


title: FOXI2.R141L_436

value: GST-tagged protein


title: MTBP, anti-GFP, 1000, replicate 2


title: FOXI2.R141L_423


title: FOXI2.L178P_423


title: FOXI2.L178P_426


title: FOXI2.R141L_426


title: DNA from FFPE Meningioma Sample PT07-R1

value: G


title: genotype: CNAG_00000, librarydate: 2019-11-10, sample: 365

description: Library name: sample_365

value: 90 min


title: DNA from FFPE Meningioma Sample PT07-P


title: FOXI2.K184R_423


title: FOXI2.K184R_426


title: FOXI2.K140R_436


title: genotype: CNAG_00000, librarydate: 2017-09-07, sample: 176

description: Library name: sample_176


title: HCT116, anti-IgG, 50, replicate 3

value: HCT 116 (RRID:CVCL_0291)

value: Male


title: genotype: CNAG_00000, librarydate: 2012-01-30, sample: 2442

description: Library name: sample_2442


title: FOXI2.K140R_426


title: HCT116, anti-IgG, 50, replicate 2

value: Anti-Goat IgG (Jackson ImmunoResearch Labs Cat# 305-005-045, RRID:AB_2339379)


title: HCT116, anti-IgG, 50, replicate 1

value: WT


title: genotype: CNAG_00000, librarydate: 2012-01-30, sample: 2434

description: Library name: sample_2434


title: DNA from FFPE Meningioma Sample PT06-P

value: F


title: HCT116, anti-GFP, 250, replicate 3


title: genotype: CNAG_00000, librarydate: 2012-03-26, sample: 2418

description: Library name: sample_2418


title: DNA from FFPE Meningioma Sample PT05-R1

value: E


title: FOXI2.K140R_423


title: genotype: CNAG_00000, librarydate: 2012-03-26, sample: 2417

description: Library name: sample_2417


title: HCT116, anti-GFP, 250, replicate 2


title: MTBP, anti-GFP, 1000, replicate 1

value: HCT 116 MTBP-miniAID-mClover (RRID:CVCL_C7SR)

value: homozygous knockin


title: FOXI2.G171S_461


title: DNA from FFPE Meningioma Sample PT05-P

value: MRM


title: genotype: CNAG_00000, librarydate: 2012-03-26, sample: 2416

description: Library name: sample_2416

value: yeast


title: DNA from FFPE Meningioma Sample PT06-R2


title: DNA from FFPE Meningioma Sample PT04-P

value: D


title: HCT116, anti-GFP, 250, replicate 1


title: genotype: CNAG_00000, librarydate: 2012-01-03, sample: 2408

description: Library name: sample_2408

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: FOXI2.G171S_451


title: HCT116, anti-GFP, 1000, replicate 3

value: Asynchronous


title: HCT116, anti-GFP, 1000, replicate 2


title: DNA from FFPE Meningioma Sample PT03-P

value: DNA from FFPE Meningioma

value: C

value: Primary


title: DNA from FFPE Meningioma Sample PT06-R1


title: FOXI2.G171A_461

value: GST-tagged protein


title: FOXI2.E200K_436


title: FOXI2.E200K_426


title: FOXI2.G171A_451


title: HCT116, anti-GFP, 1000, replicate 1

value: HCT 116 (RRID:CVCL_0291)


title: DNA from FFPE Meningioma Sample PT02-R1

value: B


title: genotype: CNAG_00000, librarydate: 2012-01-03, sample: 2399

description: Library name: sample_2399

value: 90 min


title: genotype: CNAG_00000, librarydate: 2015-05-19, sample: 2351

description: Library name: sample_2351

value: WT


title: DNA from FFPE Meningioma Sample PT02-P


title: PBMCs, MS_13_t2 (scRNA-seq)

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

description: 10X Genomics

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of all samples , using 10X Cellranger v5.1.0 with default parameters.
Assembly: GRCh38-2020-A
Supplementary files format and content: raw read counts in gene-barcode matrix

growth_protocol: Cryopreserved PBMCs thawed for library preparation

extract_protocol:
10x Genomics Chromium Controller (gell bead emulsion formation and RNA capture)
Barcoded cDNA generation from bead-captured transcripts (10x Genomics Single-Cell Gene Expression Kit v3.1)

treatment_protocol: Samples were derived from people with CIS treated with atorvastatin or placebo

value: Blood

value: 6 month follow-up

value: PBMC

value: male

tag: age

value: 33 yo

tag: demographic information

value: NHW

value: atorvastatin


title: DNA from FFPE Meningioma Sample PT01-R1

value: A

value: MRM


title: FOXI2.E200K_423


title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2112

description: Library name: sample_2112

value: yeast

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: DNA from FFPE Meningioma Sample PT03-R1

value: DNA from FFPE Meningioma

value: C


title: PBMCs, LTNP_3_t2 (scRNA-seq)

description: 10X Genomics

value: female

value: 39 yo


title: genotype: CNAG_00000, librarydate: 2012-01-03, sample: 2407

description: Library name: sample_2407

value: 90 min


title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2111

description: Library name: sample_2111

value: WT


title: DNA from FFPE Meningioma Sample PT01-P

value: Primary


title: PBMCs, LTNP_3_t1 (scRNA-seq)

description: 10X Genomics

value: Blood

value: baseline diagnosis


title: PBMCs, MS_13_t1 (scRNA-seq)

description: 10X Genomics

value: PBMC

value: male


title: PBMCs, MS_12_t2 (scRNA-seq)

description: 10X Genomics

value: 3 month follow-up

value: 21 yo

value: NHW


title: FOXI2.D169E_436

value: GST-tagged protein


title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2101

description: Library name: sample_2101

value: yeast


title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2100

description: Library name: sample_2100

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: PBMCs, MS_12_t1 (scRNA-seq)

description: 10X Genomics

value: atorvastatin