title: Toxoplasma and HFF, ribosome footprinting, replicate 1

city: Cambridge

first: Sebastian

last: Lourido

address: 455 Main Street

institute: Whitehead Institute

description: Library name: ribosome_footprints_rep1

data_processing:
Reads from both sequencing runs were treated as single-end for compatibility. Adapters were trimmed with cutadapt (v3.7) and options -u 4 -a NNNNCTGTCTCTTATACACATCTCCGAGC --match-read-wildcards --minimum-length=15 and --nextseq-trim=20 or -q 20 for NovaSeq and HiSeq reads, respectively.
STAR (v2.7.1a) was used to map reads to a metagenome of T. gondii, H. sapiens, size markers, and spike-in sequences with settings --outFilterType BySJout --outSAMattributes All --alignIntronMax 25000 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1.
A custom Toxoplasma transcriptome annotation was generated to include representative 5′ UTR isoforms expressed in our data. For ToxoDB, Markus et al. 2021 Tz TSS and Bz TSS transcript isoforms, 5′ UTRs were split into windows of three nt with bedtools makewindows, and total RNA coverage was calculated across these windows for each model using bedtools coverage -counts -s. We calculated cumulative read coverage and D for each model, where D is the ks.test statistic from comparison of a normalized, even distribution against read coverage for the model normalized to the UTR length and total cumulative sum. D values were compared for all models for a given gene, and the model with the lowest D value was selected as the representative isoform, except in the following cases: 1) In cases where the difference between D values was less than 0.05, we selected the model with the longest length. 2) In cases where all models had a D value greater than 0.4, the result was deemed inconclusive, and the 5′ UTR was excluded from further analyses. RPKM was calculated from counts generated with featureCounts, and transcripts with RPKM > 5 in both replicates were considered expressed. CDS and 3′ UTR annotations were used directly from ToxoDB models. In cases where there are multiple annotated CDS isoforms, the longest isoform was selected. The GFF file was updated with the new UTRs.
For the H. sapiens transcriptome annotation, canonical transcripts were identified from the UCSC genome browser knownCanonical option, and the H. sapiens transcriptome was filtered to include just the canonical transcript for each gene. The transcript with the longest CDS was selected for genes with multiple canonical transcripts or no canonical transcripts.
The spliced transcriptome fasta for Toxoplasma was created using gffread -w. Genome-aligned reads were re-aligned to spliced H. sapiens and T. gondii transcriptomes with STAR options --outFilterMismatchNmax 2 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate.
Total mRNA and ribosome footprint reads mapping to the CDS of each transcript, excluding the first and last three codons, were counted with featureCounts and parameters GTF.featureType="CDS", useMetaFeatures=F, readShiftType = "downstream", readShiftSize = 12, read2pos = 5, strandSpecific = 1. Ribosome footprint and mRNA RPKM were calculated for each gene using DESeq2, and translation efficiency (ribosome footprint RPKM / mRNA RPKM) was calculated for each biological replicate and the average taken.
Assembly: ToxoDB Release 68 and HostDB Release 68
Supplementary files format and content: CDS_raw_counts.xlsx is an Excel spreadsheet that contains CDS counts (excluding the first and last 3 codons) generated with featureCounts. One tab contains Toxoplasma data and one tab contains host cell data.
Supplementary files format and content: RPKM_and_TE.xlsx is an Excel spreadsheet that contains RPKM values for the CDS of each transcript, and a separate tab with translation efficiency (TE). Separate tabs are provided for Toxoplasma and host data.
Supplementary files format and content: Toxoplasma_gondii_ME49_updated_5UTRs.gff is the GFF that contains updated 5' UTR models and remaning gene annotations from ToxoDB.
Library strategy: Ribo-Seq

organism:
Toxoplasma gondii
Homo sapiens

source_name: T gondii: ME49, H sapiens: human foreskin fibroblast

growth_protocol: T. gondii were grown in human foreskin fibroblasts (HFFs) at 37°C and 5% CO2 and maintained in DMEM supplemented with 3% heat-inactivated fetal bovine serum and 10 ug/mL gentamicin.

extract_protocol:
Dishes of HFFs with intracellular tachyzoites were placed on ice, and washed with ice-cold PBS with 100 ug/mL cycloheximide twice. 1 mL lysis buffer (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 ug mL-1 cycloheximide, 500 U mL-1 RNaseIn Plus (Promega), and cOmplete Protease Inhibitor Cocktail (1 tablet per 10 mL buffer, Roche)) was added, and a cell lifter was used to dissociate HFFs with intracellular parasites from the dish, combining both dishes into the 1 mL sample. Lysates were passed through a 27-gauge needle 3 times, then 30-gauge needle 3 times, before incubating on ice for 5-10 minutes. Debris was pelleted by centrifugation at 4°C 1300xg for 10 minutes, and supernatant was transferred to fresh tubes. Samples were flash-frozen in liquid nitrogen and stored at -80°C.
For ribosome profiling, RNase I (Thermo Fisher) concentration was empirically tested, after which 40 U per 1 OD260 was used. Sucrose gradient preparation, fractionation, collection of 80S ribosomes, and RNA fragment purification were performed as described in Xiang and Bartel 2021. For matched RNA-seq, probes for depletion of Toxoplasma rRNAs from total RNA samples were designed through NEB, and an equal ratio of human and Toxoplasma probes (2 uL each per reaction) were used for rRNA depletion with the NEBNext rRNA Depletion Kit (Human/Mouse/Rat, NEB, E6310L). Spike-in of GFP, Renilla luciferase, and Firefly luciferase mRNAs were added to the total RNA samples. Total RNA was fragmented with RNA Fragmentation Buffer (2 mM EDTA, 12 mM Na2CO3, 88 mM NaHCO3) by incubating at 95°C for 20 minutes followed by ethanol precipitation. Ribosome footprint and total RNA libraries were processed in parallel according to an established protocol (Subtelny et. al 2014).

value: T gondii:ME49, H sapiens:human foreskin fibroblast

value: T gondii:ME49/dKu80/dHXGPRT/TIR1


title: AB_65, small RNA, Colorectal

status: Public on Jul 15 2025

type: SRA

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

library_source: transcriptomic

data_processing:
The libraries were normalized, pooled, and denatured. Pooled libraries were loaded on Illumina NovaSeq SP lane using Xp protocol per manufacturer's recommendations.
Base-calling was performed with RTA v.3.4.4. Program bcl2fastq2 was used to demultiplex and generate fastq reads. Raw fastq files were subjected to cutadapt for  adapter trimming. Trimmed Reads were aligned to human genome 38 using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count data for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Rectus abdominis muscle

growth_protocol: Not Applicable

extract_protocol:
RNA extraction was performed using the Trizol method and Qiagen RNAeasy midi kit (Mississauga, ON). The optical density (OD) 260/280 ratio was measured using Nanodrop, and RNA integrity number (RIN) was assessed using Agilent Bio-analyzer 2100 for all the samples.
Libraries were genrated using NEBNext Multiplex Small RNA library Prep kit for Illumina as per the manufacturer's recommendations.

treatment_protocol: Not Applicable

tag: tissue

value: Rectus abdominis muscle

tag: cell line

value: Skeletal muscle tissue


title: PCKS_adenine_vehicle_4

city: Bern

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

country: Switzerland

institute: University Hospital Bern

data_processing:
Basecalling and demultiplexing were performed using Illumina bcl2fastq (v2.20.0).
Sequence data quality was assessed using FastQC (v0.11.8).
Counts for each gene were estimated using featureCounts (v1.5.1).
Assembly: Reads were aligned to the Ensembl GRCm38 reference genome using STAR (v2.7.9a).
Supplementary files format and content: tab-delimited text file contains raw counts for each sample.

organism: Mus musculus

source_name: kidney

extract_protocol:
RNA was extracted using Qiagen midi RNA extraction kit and purified.
Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA.

tag: strain

tag: Sex

value: male

value: kidney

tag: biol rep

tag: disease

tag: treatment


title: AB_64, small RNA, Colorectal


title: THP-1-derived macrophages, si-SLC40A1-2, biol rep 2

city: Guangzhou

first: Xinyu

last: Pan

address: No. 135 West Xingang Road, Haizhu District

country: China

institute: Sun Yat-Sen University Department of Biochemistry

description:
Library name: sample8
column name in counts.txt: s22

data_processing:
Paired-end RNA-seq reads were quality- and adapter-trimmed using Cutadapt (v1.18).
Cleaned reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters.
Aligned reads were filtered using SAMtools (v1.6) to retain uniquely mapped reads with mapping quality of at least 20, then sorted and indexed.
Gene-level read counts were quantified using featureCounts (v2.0.6)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using a standard poly(A) mRNA enrichment protocol and sequenced using paired-end reads.

treatment_protocol:
THP-1 cells were treated with 50 ng/mL phorbol 12-myristate 13-acetate (PMA) for 48 hours to induce differentiation into macrophage-like cells.
Differentiated cells were then transfected with either SLC40A1-targeting siRNA (two independent sequences) or negative control siRNA using Lipofectamine RNAiMAX reagent according to the manufacturer's instructions.

tag: cell type

value: macrophage

tag: genotype

value: SLC40A1 knockdown

value: PMA-induced differentiation + si-SLC40A1-2 transfection


title: PCKS_adenine_FGF23_3


title: PCKS_adenine_vehicle_3


title: AB_69, small RNA, Pancreas


title: THP-1-derived macrophages, si-NC, biol rep 1

description:
Library name: sample1
column name in counts.txt: NC1

value: WT

value: PMA-induced differentiation + si-NC transfection


title: THP-1-derived macrophages, si-SLC40A1-1, biol rep 3

description:
Library name: sample6
column name in counts.txt: s13

value: PMA-induced differentiation + si-SLC40A1-1 transfection


title: PCKS_adenine_FGF23_2


title: PCKS_adenine_vehicle_2


title: PCKS_adenine_FGF23_1


title: AB_63, small RNA, Pancreas


title: AB_61, small RNA, Colorectal


title: kidneyAdria_adriamycin.FGF23_3

value: BALB/c

value: female


title: kidneyAdria_adriamycin.FGF23_4


title: kidneyAdria_adriamycin.FGF23_1


title: HCC827-compound2(5μM)-24h

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

description: Library name: fpkm_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Non-small cell lung cancer cell


title: HCC827-compound1(5μM)-24h

description: Library name: fpkm_1


title: HCC827-CON

description: Library name: fpkm_CON

value: DMSO


title: AB_59, small RNA, Colorectal


title: AB_60, small RNA, Colorectal


title: CD45 Cells, treated

city: Augusta

first: Kendra

last: Fick

address: 1410 Laney Walker BLVD CN1109N

country: USA

institute: Medical College of Georgia

description:
Library name: F5446
10X Genomics

library_source: transcriptomic single cell

data_processing:
Data processing was done in 10x Genomics Cell Ranger
Assembly: mouse mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: Liver

extract_protocol:
Livers were harvested and underwent single cell suspension. CD45 cells were isolated from the samples using mouse CD45 positive selection beads before sequencing. Cells were resuspended in PBS + 5% FBS.
Library was performed according to manufacturer instructions (Chromium Next GEM Single Cell 3' Reagent Kits v3.1)

value: Liver

value: BALB/C

value: CD45 cells

value: 10mg/kg F5446 suspended in 10% Cremophor


title: kidneyAdria_control.FGF23_3

value: healthy


title: CD45 Cells, untreated

description:
Library name: Control
10X Genomics

value: 10% Cremophor


title: kidneyAdria_control.FGF23_2

value: kidney


title: AB_58, small RNA, Pancreas

value: Rectus abdominis muscle

value: Skeletal muscle tissue


title: kidneyAdria_control.FGF23_4


title: kidneyAdria_adriamycin.vehicle_4


title: MAS

city: Cincinnati

first: Kairavee

last: Thakkar

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: MAS

data_processing:
Following sequencing, libraries were processed using Cell Ranger (v7.0.1) followed by SoupX (v 1.5.0) for ambient mRNA removal using contamination fraction set to 0.1 and Seurat (v4.1.1) for integrated analysis of the three samples to determine cell clusters. Prior to integration, cells with mitochondrial percent more than 10 were removed and e ach sample was normalized by ScTransform method. Clusters were determined using the first 30 principal components and resolution set to 0.25.Differential expression and gene regulatory prediction analysis were performed using the software cellHarmony (adjusted p <0.05 and absolute fold change >1.2).
Assembly: Mm10 (mm10-2020-A)
Supplementary files format and content: Processed files for each treatment (MAS, Control, Resolution) are provided as h5 file.

source_name: peripheral blood neutrophils

extract_protocol:
Complete blood count was performed on Hemavet 950 FS (Drew Scientific Inc). For scRNA-seq and cytokine release assays, peripheral blood neutrophils were isolated from whole 5 blood by magnetic negative selection with Neutrophil Isolation Kit, mouse (Miltenyi Biotec, Germany).
Isolated blood neutrophils from 4 mice per conditions were pooled and resuspended at 700-1,200 cells/ μl in DPBS containing 0.5 U/μl of Protector RNase inhibitor (Roche, Basel, Switzerland ). 16,000 cells per sample were sequenced with 10x Genomics (Pleasanton, CA, USA) version Chromium NextGEM (Chemistry: 3’v3 Assay). Barcoded libraries were sequenced using the Illumina NovaSeq platform.

treatment_protocol: All studies were approved by Institutional Animal Care and Use Committees (IACUC ’s at CCHMC or The Children’s Hospital of Philadelphia. Six to ten week old female C57BL/6J mice (Jackson Laboratory) were injected intraperitoneally on days 0, 2, 4, 7 and 9 with vehicle (DPBS) or 50 μ g CpG ODN1826 (InvivoGen, San Diego, CA). Mice were sacrificed one day after the last injection (MAS) or allowed to recover for three weeks before sacrifice (resolution).

value: peripheral blood neutrophils

value: intraperitoneal injection on days 0, 2, 4, 7 and 9 with vehicle (DPBS) or 50 μ g CpG ODN1826


title: kidneyAdria_adriamycin.vehicle_2


title: kidneyAdria_adriamycin.vehicle_1


title: AB_62, small RNA, Colorectal


title: AB_57, small RNA, Colorectal


title: AB_56, small RNA, Colorectal


title: AB_55, small RNA, Pancreas


title: kidneyAdria_control.vehicle_4


title: PCKS_adenine_vehicle_1

value: male


title: Resolution

description: Library name: Resolution

value: 3 week recovery after MAS injection


title: kidneyAdria_adriamycin.FGF23_2

value: BALB/c

value: female


title: kidneyAdria_control.vehicle_3


title: AB_54, small RNA, Colorectal


title: kidneyAdria_control.vehicle_2


title: AB_52, small RNA, Colorectal


title: kidneyNTS_control.vehicle_4


title: AB_48, small RNA, Colorectal


title: kidneyNTS_control.vehicle_2


title: 171_D24_309

city: Gaithersburg

first: Binbin

last: Wang

state: MD

address: 408 Suffield Dr

institute: NATIONAL CANCER INSTITUTE, NIH

description:
Library name: 171_D24_309
NonResponder

data_processing:
RNAseq data was process with STAR
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

molecule: polyA RNA

source_name: Blood

extract_protocol:
Mice were bled via retro-orbital puncture using heparinized EDTA-coated glass capillary tubes. Blood was immediately transferred into microcentrifuge tubes containing TRIzol reagent (Thermo Fisher Scientific) for RNA stabilization. Samples were processed according to the manufacturer's instructions for RNA extraction.
RNA libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

value: Blood


title: kidneyNTS_antiGBM.FGF23_2

value: anti-GBM


title: kidneyNTS_control.FGF23_3


title: kidneyAdria_control.vehicle_1


title: kidneyNTS_control.vehicle_3


title: 176_D24_319

description:
Library name: 176_D24_319
NonResponder


title: kidneyNTS_control.FGF23_2


title: AB_53, small RNA, Pancreas


title: kidneyNTS_control.vehicle_1


title: kidneyNTS_antiGBM.vehicle_2


title: kidneyNTS_antiGBM.FGF23_1


title: Control

description: Library name: Control


title: ERRg CUT&RUN

city: London

first: Monika

last: Moissidis

address: New Hunt's House, Newcomen St

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Raw sequencing reads were trimmed using TrimGalore (v0.6.6) to remove adapters and low-quality reads
The trimmed fastq files were aligned to the mm10 genome using bowtie (v2.2.9) with the following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
PCR duplicates were removed from sam files using Picard (v2.6.0), and bam and fragment bed files generated using samtools (v1.3.1) and bedtools (v2.25.0), selecting for fragment lengths under 1000 bp
Fragment bed files were converted to bedgraph files with bedtools genomecov
Peaks were called on fragment bedgraph files using SEACR (Sparse Enrichment Analysis for CUT&RUN; v1.3) as follows: SEACR_1.3.sh input_bedgraph 0.005 non stringent out_name
Assembly: mm10
Supplementary files format and content: Bed files containing called peak ranges and correspondong bedgraph signal

molecule: genomic DNA

source_name: Cortex

extract_protocol:
Preparation of nuclei suspension: The somatosensory cortex was dissected from P12 WT C57BL/6 mice in ice-cold buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine). Cortices were homogenized by a Dounce homogenizer in the presence of 0.3% IGEPAL. The homogenate was then filtered through a 40 µm strainer (Fisher Scientific #11597522), centrifuged at 4°C for 5 min at 500 g, and the pellet was washed twice with 1% BSA solution. The pelleted nuclei were resuspended in CUT&RUN Wash buffer (20mM Tris-HCl pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.1% BSA), and the shape of the nuclei was verified using Tryptan Blue and a hemacytometer. All steps were performed on ice and using LoBind pipette tips.
CUT&RUN: Nuclei were incubated with 2 μg of mouse anti-PGC-1⍺ antibody (Millipore #ST1202, three replicates) or 2 μg of mouse anti-ERR𝛾 antibody (R&D Systems #PP-H6812-00, one replicate) in CUT&RUN Wash buffer for 10min with rotation at 4°C. 2 μg of rabbit anti-mouse IgG secondary antibodies (Abcam #ab6709) were then added to the nuclei solution, which was left to rotate for 10min at 4°C. Nuclei were then incubated without washing step with pA-MNase (1.6 µg/µl) at 4 °C with rotation for an additional 10 min. Nuclei were then washed and resuspended with CUT&RUN wash buffer. DNA-tethered cleavage was induced by adding CaCl2 at a final concentration of 2 mM on ice water for 10 min. The reaction was stopped by adding Stop buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/ml RNAse A (Thermo Scientific #EN0531), 40 µg/ml glycogen (Thermo Scientific #R0561)) at a 1-to-1 ratio. The shape of the nuclei was again verified using Tryptan Blue and a hemacytometer. To release the DNA fragments of interest, nuclei were incubated at 37 °C for 20 min. Solubilized chromatin of interest was separated from nuclei by centrifugation at 16,000 g at 4°C for 5 min and then digested with SDS (0.1% final concentration) and Proteinase K (0.2 mg/ml final concentration) at 70°C for 10 min. Released DNA fragments were then extracted with phenol:chloroform:isoamylalcohol (25:24:1) and 13,000 rpm centrifugation for 15 min at room temperature. The aqueous upper layer was transferred to a fresh tube, and NaCl was added at a final concentration of 250 mM. An equal volume of isopropanol was further added, and the DNA was left to precipitate for 2 h at -80°C. Precipitated DNA was then pelleted by centrifugation (13,000rpm for 15 min at 4°C), washed with 70% ice-cold EtOH, and resuspended in distilled water.
Libraries for sequencing were prepared using the NEBNext Ultra II library prep kit (New England Biolabs) following the protocol and thermocycling temperatures therein. Briefly, DNA ends from fragments harvested from the CUT&RUN experiment were repaired, 5’ ends phosphorylated and 3’ ends A tailed prior to ligation with NEBNext Adaptor, UNG was then used to linearize the ligated adapter. SPRIselect beads were used to deplete the unligated adaptor. Adaptor-ligated libraries were then barcoded by PCR following the manufacturer's recommended protocol. Libraries were amplified for between (11-13) cycles and purified using SPRIselect beads prior to quantitation using Qubit and HS DNA tapestation. Individually barcoded libraries were then pooled and sequenced on an Illumina NextSeq 2000 instrument.

tag: age

value: Cortex

tag: antibody

value: Antibodies against ERR𝛾

value: Neurons

value: WT


title: AB_47, small RNA, Colorectal


title: 170_D24_303

description:
Library name: 170_D24_303
NonResponder


title: PGC1a  CUT&RUN replicate 2

value: Antibodies against PGC-1𝛼


title: AB_45, small RNA, Pancreas


title: kidneyAdria_control.FGF23_1

value: healthy


title: Ppargc1a mutant batch 3

description: 10X Genomics

data_processing:
Illumina BCL output files were de-multiplexed into FASTQ format files. FASTQ files were then processed with the Cell Ranger count pipeline (v7.0.1), specifying --include-introns=false but otherwise using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated value and matrix files

extract_protocol:
Preparation of single-cell suspension. Lhx6-Cre;Ppargc1a+/+ and Lhx6-Cre;Ppargc1aF/F animals, injected in both hemispheres with AAV8-hSyn-dio-tdTomato viruses at P1, were processed separately in three control and three mutant batches. For each animal, the somatosensory cortex of both hemispheres was dissociated into a single-cell suspension. Mice were deeply anesthetized with sodium pentobarbital by intraperitoneal injection and transcardially perfused with ice-cold oxygenated cutting solution (87mM NaCl, 2.5mM KCl, 1.25mM NaH2PO4, 26 mM NaHCO3, 75mM sucrose, 20mM D-glucose, 0.5mM CaCl2*2H2O, 4mM MgSO4*7H2O). The brain was extracted and incubated for three minutes in an ice-cold oxygenated cutting solution. The somatosensory cortex was then dissected into chunks in icy oxygenated cutting solution, and the tissue was dissociated using the Papain Dissociation System (Worthington #LK003160). After 30 minutes of incubation at 37°C with papain solution, the tissue chunks were washed with an oxygenated cutting solution and were manually and slowly dissociated using a 10mL pipette and a 1mL pipette tip. All solutions used during this process were oxygenated for at least 10 minutes with 95% O2 and 5% CO2. After papain incubation, all steps were performed on ice and using low retention filter tips (VWR). Oxygenation and a short time of dissection are crucial for the viability of the cells in suspension. After dissociation, small tissue chunks may remain, and these were discarded by filtering through a 100µm cell strainer (Fisher Scientific #11587522). The debris was removed by overlaying the single-cell suspension on top of a 10% Percoll solution (Sigma #P4937, diluted in oxygenated cutting solution and 1.5M NaCl). After a 10-min 500g centrifugation at 4°C, the pelleted single-cells were resuspended in cutting solution with 2% BSA, filtered through a 70µm cell strainer (Fisher Scientific #11597522), and transferred into a FACS tube (Falcon #352063) precoated with 3% BSA overnight.
Fluorescence-activated cell sorting. Samples were sorted at 4°C on BD FACS Aria II or Aria III Cell sorters for no longer than 40 min and using a 130 µm nozzle to increase cell viability. DAPI was added to the single-cell suspension to discard dead cells. Viable tdTomato+ single cells were collected into 1 ml of cutting solution with 2% BSA in LoBind tubes (SLS #Z666505) precoated with 3% BSA overnight. Collection tubes were centrifugated for 5 min at 4°C at 500 g, and the supernatant was discarded until 45 µl were left in the tube. Cells were resuspended, and cell number and viability were assessed using Trypan Blue and a hemacytometer for cell counts. We only carried out single-cell RNA-sequencing in experiments with viability above 60%. Between 3,000-5,000 cells were loaded for each sample onto a 10X Genomic single-cell chip/machine for single-cell capture and cDNA library preparation. RNA-seq was performed in an Illumina NextSeq 2000 platform.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-AmRNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an IluminaTruSeq Read 1primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR. The amplified cDNA was enzymatically fragmentedand appropriatesize fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction P5,P7,i7 and i5sample indexandIluminaTruSeqRead2 primer sequence were addedvia end repair, A-tailing, adaptor ligation and PCR.

value: Lhx6-Cre;Ppargc1a f/f


title: 168_D24_302

description:
Library name: 168_D24_302
NonResponder


title: PGC1a  CUT&RUN replicate 1


title: Ppargc1a mutant batch 2

description: 10X Genomics


title: AB_44, small RNA, Pancreas

value: Rectus abdominis muscle


title: kidneyNTS_antiGBM.FGF23_3

value: kidney


title: 167_D24_7225

description:
Library name: 167_D24_7225
NonResponder


title: AB_43, small RNA, Colorectal

value: Skeletal muscle tissue


title: AB_46, small RNA, Pancreas


title: 169_D24_306

description:
Library name: 169_D24_306
NonResponder


title: 175_D24_318

description:
Library name: 175_D24_318
NonResponder


title: AB_51, small RNA, Colorectal


title: 178_D24_325

description:
Library name: 178_D24_325
NonResponder


title: Ppargc1a control batch 2

description: 10X Genomics

value: Lhx6-Cre;Ppargc1a +/+


title: Ppargc1a control batch 3

description: 10X Genomics


title: Ppargc1a control batch 1

description: 10X Genomics


title: 165_D24_7223

description:
Library name: 165_D24_7223
NonResponder


title: AB_42, small RNA, Pancreas


title: 177_D24_324

description:
Library name: 177_D24_324
NonResponder


title: AB_41, small RNA, Pancreas


title: Ppargc1a mutant batch 1

description: 10X Genomics


title: mKate+/top 15% mNG, RNA sequencing, biorep 2

state: MA

description:
Library name: top RNA rep2
targeted RNA sequencing of reporter

data_processing:
Reads were trimmed using cutadapt, and paired-end reads were merged into one sequence with fastq-join.
All unique reads from any sample with length 170-190 nucleotides were identified. UTR sequences were used for downstream analysis if they were detected in both DNA replicates of unsorted parasites and the input plasmid library.
Exact matches were used to count UTR reads and UMIs from RNA sequencing.
DESeq2 was usedto compare the DNA read counts with deduplicated RNA read counts for each UTR. UTRs with adjusted p < 0.05 were excluded from further analysis
We required UTRs to have at least 25 reads in each bulk replicate, and a sum of at least 25 reads across all 4 sorted bins in each replicate. For each sample, reads were normalized to counts per million (cpm), and for each bin, UTRs were normalized to their corresponding bulk cpm.
Assembly: bulk_input_unique_sequences.fasta
Supplementary files format and content: bulk_input_unique_sequences.fasta is the FASTA file that contains all unique sequences common across the DNA sequencing of both bulk parasite samples and the input library. This reference file was used to generate counts of UTRs identified in the remaining samples.
Supplementary files format and content: MPRA_score_data.txt is a tab-delmited file and contains the sequence and MPRA score for each UTR that passed RNA expression and read count filters. The values given for each sample are counts per million normalized to the bulk read counts for that replicate.
Supplementary files format and content: Processed data files ending in "Counted.txt" are raw counts for each MPRA UTR sequence.

organism: Toxoplasma gondii

growth_protocol: T. gondii were grown in human foreskin fibroblasts (HFFs) at 37°C and 5% CO2

extract_protocol:
DNA and RNA were extracted with the DNA/RNA Allprep Mini kit (QIAGEN)
For RNA, samples were treated with Turbo DNase (Ambion) and reverse-transcribed with Superscript III (Invitrogen) and an mNG-specific primer which contains an 8-nucleotide unique molecular identifier. RNA clean-up was performed with RNAClean XP beads (Beckman Coulter) before library amplification from the constant region of the 5' UTR and the adapter added during RT. Amplification primers added barcodes and adapters for sequencing.
For DNA, samples were amplified from parasite gDNA or the plasmid library (for input) with primers targeting the constant region of the 5' UTR and the 5' end of mNG. Amplification primers added barcodes and adapters for sequencing.

treatment_protocol: If still intracellular, parasites were mechanically released from host cells with a cell lifter and passage through a 27g needle. Parasites were then passed through a 5 uM filter to remove host cell debris. Parasites for FACS were resuspended in PBS + 2% IFS and sorted on a BD FACS Aria II. Sorted parasites and bulk populations were pelleted and frozen at -80°C until library preparation.

value: population transfected with pTub1-UTR library-mNG/pMIC2-mKate2-P2A-DHFR


title: mKate+/top 15% mNG, RNA sequencing, biorep 1

description:
Library name: top RNA rep1
targeted RNA sequencing of reporter


title: mKate+/middle 15% mNG, RNA sequencing, biorep 1

description:
Library name: middle RNA rep1
targeted RNA sequencing of reporter


title: 164_D24_7218

description:
Library name: 164_D24_7218
NonResponder


title: AB_40, small RNA, Colorectal


title: mKate+/bottom 15% mNG, RNA sequencing, biorep 2

description:
Library name: bottom RNA rep2
targeted RNA sequencing of reporter


title: kidneyAdria_adriamycin.vehicle_3


title: 163_D24_330

description:
Library name: 163_D24_330
NonResponder


title: 166_D24_7224

description:
Library name: 166_D24_7224
NonResponder


title: mKate+/mNG- sorted, RNA sequencing, biorep 2

description:
Library name: negative RNA rep2
targeted RNA sequencing of reporter


title: AB_39, small RNA, Pancreas


title: mKate+/bottom 15% mNG, RNA sequencing, biorep 1

description:
Library name: bottom RNA rep1
targeted RNA sequencing of reporter


title: mKate+/mNG- sorted, RNA sequencing, biorep 1

description:
Library name: negative RNA rep1
targeted RNA sequencing of reporter


title: 162_D24_329

description:
Library name: 162_D24_329
NonResponder


title: mKate+/middle 15% mNG, RNA sequencing, biorep 2

description:
Library name: middle RNA rep2
targeted RNA sequencing of reporter


title: 161_D24_328

description:
Library name: 161_D24_328
NonResponder


title: AB_37, small RNA, Colorectal


title: bulk population, RNA sequencing, biorep 2

description:
Library name: bulk RNA rep2
targeted RNA sequencing of reporter


title: mKate+/top 15% mNG, DNA sequencing, biorep 1

description:
Library name: top DNA rep1
targeted DNA sequencing of reporter integrated into genomic DNA


title: bulk population, RNA sequencing, biorep 1

description:
Library name: bulk RNA rep1
targeted RNA sequencing of reporter


title: AB_38, small RNA, Colorectal


title: mKate+/top 15% mNG, DNA sequencing, biorep 2

description:
Library name: top DNA rep2
targeted DNA sequencing of reporter integrated into genomic DNA


title: mKate+/middle 15% mNG, DNA sequencing, biorep 2

description:
Library name: middle DNA rep2
targeted DNA sequencing of reporter integrated into genomic DNA


title: 159_D24_321

description:
Library name: 159_D24_321
NonResponder


title: 160_D24_323

description:
Library name: 160_D24_323
NonResponder


title: AB_36, small RNA, Pancreas


title: mKate+/middle 15% mNG, DNA sequencing, biorep 1

description:
Library name: middle DNA rep1
targeted DNA sequencing of reporter integrated into genomic DNA


title: AB_35, small RNA, Colorectal


title: kidneyNTS_antiGBM.vehicle_3

value: male


title: 158_D24_320

description:
Library name: 158_D24_320
NonResponder


title: mKate+/bottom 15% mNG, DNA sequencing, biorep 2

description:
Library name: bottom DNA rep2
targeted DNA sequencing of reporter integrated into genomic DNA


title: 172_D24_312

description:
Library name: 172_D24_312
NonResponder


title: mKate+/bottom 15% mNG, DNA sequencing, biorep 1

description:
Library name: bottom DNA rep1
targeted DNA sequencing of reporter integrated into genomic DNA


title: kidneyNTS_antiGBM.vehicle_4


title: AB_34, small RNA, Pancreas


title: kidneyNTS_control.FGF23_1


title: 157_D24_316

description:
Library name: 157_D24_316
NonResponder


title: mKate+/mNG- sorted, DNA sequencing, biorep 1

description:
Library name: negative DNA rep1
targeted DNA sequencing of reporter integrated into genomic DNA


title: AB_50, small RNA, Pancreas


title: AB_33, small RNA, Colorectal


title: mKate+/mNG- sorted, DNA sequencing, biorep 2

description:
Library name: negative DNA rep2
targeted DNA sequencing of reporter integrated into genomic DNA


title: AB_49, small RNA, Pancreas


title: bulk population, DNA sequencing, biorep 1

description:
Library name: bulk DNA rep1
targeted DNA sequencing of reporter integrated into genomic DNA


title: 156_D24_313

description:
Library name: 156_D24_313
NonResponder


title: bulk population, DNA sequencing, biorep 2

description:
Library name: bulk DNA rep2
targeted DNA sequencing of reporter integrated into genomic DNA


title: 155_D24_310

description:
Library name: 155_D24_310
NonResponder


title: AB_32, small RNA, Colorectal


title: AB_31, small RNA, Pancreas


title: c3 replicat 3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Leptospira interrogans

source_name: bacterial cells

extract_protocol:
Total RNA was extracted from biofilm or planktonic cells. Cells were collected by centrifugation for 15 min at 3000xg at 4°C and resuspended in 1mL TRIzol
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit following manufacturer's protocol

value: bacterial cells

value: Manilae strain L500

value: serovar Manilae strain L500


title: input library, DNA sequencing

description:
Library name: input plasmid library
targeted DNA sequencing of plasmid library

library_source: other

molecule: other


title: 173_D24_314

description:
Library name: 173_D24_314
NonResponder

value: Blood


title: kidneyNTS_antiGBM.vehicle_1

value: anti-GBM


title: 174_D24_317

description:
Library name: 174_D24_317
NonResponder


title: c3 replicat 2

value: Manilae strain L499

value: serovar Manilae strain L499


title: c3 replicat 1

value: Manilae strain L498

value: serovar Manilae strain L498


title: AB_30, small RNA, Colorectal


title: c3p16 replicat 4

value: Manilae strain L497

value: serovar Manilae strain L497


title: 153_D24_305

description:
Library name: 153_D24_305
NonResponder


title: c3p16 replicat 3

value: Manilae strain L496

value: serovar Manilae strain L496


title: AB_29, small RNA, Colorectal

value: Rectus abdominis muscle

value: Skeletal muscle tissue


title: 152_D24_304

description:
Library name: 152_D24_304
NonResponder


title: AB_28, small RNA, Pancreas


title: c3p16 replicat 2

value: Manilae strain L495

value: serovar Manilae strain L495


title: AB_27, small RNA, Colorectal


title: 151_D24_7222

description:
Library name: 151_D24_7222
NonResponder


title: 150_D24_7220

description:
Library name: 150_D24_7220
NonResponder


title: GoT_AML20-Rel

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

description:
Library name: GoT_AML20-Rel
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.

data_processing:
FASTQs were aligned to reference genome GRCh38 using CellRanger 5.0.1. Mutation status for single cells was ascertained by performing a pileup on each mutation while tabulating cell barcodes and UMIs (automatically stored in BAM file by CellRanger) in both the GoT and gene expression libraries. Cells were assigned Mutant if one or more mutant UMIs was detected. Due to allelic dropout, increased stringency was applied for wildtype cells. Cells were assigned as wildtype if 2 or more UMIs had only wildtype alleles.
Assembly: GRCh38 - default CellRanger reference
Supplementary files format and content: seurat object in rds format

source_name: MNCs

extract_protocol:
Samples from AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, CH-01, CH-02 were processed as follows. Frozen bone marrow and peripheral blood samples were thawed under standard procedures and prepared for sorting by flow cytometry. Briefly, cryopreserved samples were thawed and transferred to 15 ml conical tubes containing 10 ml of RPMI media with 10% fetal bovine serum (FBS) and 0.1mL of a 1 mg/mL DNAse I solution. Cells were centrifuged at 300 x g for 4 minutes at 4°C, and supernatant was removed. Cells were resuspended in FACS buffer and incubated with Fc blocker for 15 minutes. Next, cells were stained with PE-conjugated CD45, and FITC-conjugated CD3, CD19, and CD56 to enable lymphoid-depleted sorting. Cells were stained for 15 minutes and resuspended in FACS-DAPI to enable enrichment for live cells. Cells were then sorted for DAPI-, CD3-/CD19-/CD56- cells using the BD Influx at the Weill Cornell Medicine flow cytometry core.
Sorted cells were processed using the 10X Genomics Chromium controller with the Single Cell Gene Expression 5’ V1 protocol (except sample CH-05 which was processed on 5’ V2 after V1 was discontinued). The 5’ kit was selected to maximize genotyping efficiency because most mutations, including IDH1, IDH2, NRAS, and SRSF2, were closer to the 5’ end of the mRNA. Single cell gene expression libraries were sequenced on a Nova-seq 6000 with R1:R2:I1 27:176:8bp paired end format where R1 contains the 10X barcode and UMI, R2 contains the transcript sequence, and I1 the sample index. Single cell genotyping was applied to 13 patients/donors (AML-01, AML-02, AML-03, AML-04, AML-05, AML-06, AML-16, AML-17, AML-18, AML-19, AML-20, CH-01, CH-02). Somatic mutations detected by clinical targeted DNA sequencing informed the design of multiplexed single cell genotyping using Genotyping of Transcriptomes (GoT).25 GoT targets were prioritized to capture mutations representative of distinct subclones with greater than 5% VAF in targeted DNA sequencing and sufficient gene expression in 10X data. Cells were profiled using the 5’ 10X Genomics kit to maximize GoT efficiency, as most mutations were within 1000bp of the 5’ end (IDH1/2, NRAS, NPM1, and SRSF2) (Figures S4B and S4C). GoT libraries were prepared for IDH1, IDH2, NRAS, NPM1, FLT3 and SRSF2 as described in Nam et al.25 We did not genotype DNMT3A which is often clonal and co-occurring within the same cells as IDH mutations, due to technical limitations of low gene expression (Average expression in single cell data: 0.19; comparable to IDH1 0.15) and >2000 base pair mutation distance from 5’ end. Primers used for GoT are provided in Table S1. GoT Libraries were pooled and sequenced on Illumina MiniSeq 300 cycle mid-output kit in 147:8:147 paired end configuration or spiked in at 1-2% of gene expression library sequencing runs on NovaSeqX Plus with configuration as described above.

value: MNCs


title: GoT_AML20-Dx

description:
Library name: GoT_AML20-Dx
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML20_R1

description:
Library name: GoT_AML20_R1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML19_R1

description:
Library name: GoT_AML19_R1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML20_Dx

description:
Library name: GoT_AML20_Dx
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML20_CR

description:
Library name: GoT_AML20_CR
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: 154_D24_308

description:
Library name: 154_D24_308
NonResponder


title: 148_D24_327

description:
Library name: 148_D24_327
Responder


title: AB_25, small RNA, Colorectal


title: 149_D24_7203

description:
Library name: 149_D24_7203
NonResponder


title: AB_26, small RNA, Pancreas


title: GoT_AML19_Dx

description:
Library name: GoT_AML19_Dx
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_24, small RNA, Pancreas


title: GoT_AML19-Dx

description:
Library name: GoT_AML19-Dx
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: 147_D24_322

description:
Library name: 147_D24_322
Responder


title: GoT_AML19_CR

description:
Library name: GoT_AML19_CR
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML19-CR

description:
Library name: GoT_AML19-CR
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_23, small RNA, Pancreas


title: GoT_AML18_R_2

description:
Library name: GoT_AML18_R_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: 146_D24_315

description:
Library name: 146_D24_315
Responder


title: GoT_AML18_R_1

description:
Library name: GoT_AML18_R_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_22, small RNA, Colorectal


title: 145_D24_311

description:
Library name: 145_D24_311
Responder


title: AB_21, small RNA, Pancreas


title: 144_D24_7229

description:
Library name: 144_D24_7229
Responder


title: GoT_AML20-CR

description:
Library name: GoT_AML20-CR
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML19-Rel

description:
Library name: GoT_AML19-Rel
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML18_Dx_2

description:
Library name: GoT_AML18_Dx_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_20, small RNA, Pancreas


title: GoT_AML18_Dx_1

description:
Library name: GoT_AML18_Dx_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML18_CR_2

description:
Library name: GoT_AML18_CR_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: 143_D24_7228

description:
Library name: 143_D24_7228
Responder


title: 142_D24_7227

description:
Library name: 142_D24_7227
Responder


title: GoT_AML17_Rel_1

description:
Library name: GoT_AML17_Rel_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML17_Dx_2

description:
Library name: GoT_AML17_Dx_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_19, small RNA, Pancreas


title: GoT_AML17_CR_2

description:
Library name: GoT_AML17_CR_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML17_Dx_1

description:
Library name: GoT_AML17_Dx_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML17_Rel_2

description:
Library name: GoT_AML17_Rel_2
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: GoT_AML18_CR_1

description:
Library name: GoT_AML18_CR_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: AB_17, small RNA, Pancreas


title: GoT_AML17_CR_1

description:
Library name: GoT_AML17_CR_1
GoT libraries for corresponding GEX libraries. Some run in duplicate. Multiple mutation libraries are pooled together based on belonging to the same GEX library.


title: 141_D24_7226

description:
Library name: 141_D24_7226
Responder


title: AB_16, small RNA, Pancreas


title: AB_15, small RNA, Colorectal


title: Wildtype neurons

city: Oxnard

first: Abril

last: Morales

state: CA

address: 1300 East Pleasant Valley Road, Spc 119

institute: University of California, Los Angeles

description: Library name: R18_unt

data_processing:
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the human genome hg38.108. In Partek Flow, read counts were normalized by median ratio for targeted use in DESeq2.
Assembly: hg38
Supplementary files format and content: Normalized-Gene-Counts.txt

source_name: neurons

extract_protocol:
RNA was extracted and isolated using Rneasy Mini plus kit (Qiagen).
Libraries for RNA-Seq were prepared with KAPA mRNA-Seq Hyper Prep Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeqX+ for a PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina BCL Convert v4.2.7 software.

value: neurons


title: MECP2 mutant neurons

description: Library name: R15_unt


title: MECP2 mutant neurons with NAD treatment

description: Library name: R15_NAD


title: 139_D24_7210

description:
Library name: 139_D24_7210
Responder


title: 138_D24_7208

description:
Library name: 138_D24_7208
Responder


title: 137_D24_7206

description:
Library name: 137_D24_7206
Responder


title: AB_18, small RNA, Colorectal


title: AB_13, small RNA, Pancreas


title: Flag-OGT IAV (PR8 strain) Input sample, Replicate 1

city: Columbus

first: Weidong

last: Wu

state: Ohio

address: 2255 Kenny Rd

institute: Ohio State University

description: Library name: T13022_8-G8_N

data_processing:
Raw Reads were quality-controlled, trimmed, and filtered using fastp (v0.23.2), followed by alignment to  IAV referenece genome (NCBI accession number: GCF_000865725.1) or human genome (GRCh38.99) using Hisat2. Furthermore, Human and IAV counts were normalized using Counts Per Million (CPM)
Assembly: GRCh38
Supplementary files format and content: csv formatted files including the sample name, counts, and related metadata.

growth_protocol: 293T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
1.Add 1 ml Trizol into each sample (Total 8 samples, including IP and Input samples) 2. Add 0.2 ml chloroform into each sample. Shake the tubes between two racks vigorously. 3. Centrifuge at highest speed for 28 min at 4 °C. 4. Pipetting 0.35 ml from upper aqueous phase and add into new 1.5-ml tube. Add the same volume of isopropanol (2-propanol). Shake gently. 5. Centrifuge at highest speed for 10 min at 4 °C. 6. Dump the liquid. Add 1 ml 70% ETOH. 7. Centrifuge at highest speed for 2 min at 4 °C. 8. Dump the liquid. Centrifuge again at highest speed for 1 min at 4 °C. 9. Vacuum the rest liquid. Be careful and do not suck up RNA samples. Rest the tube at RT without lid for 10 min. 10. Add 20 ul sterile H2O to resolve RNA sample. 11. Measure the concentration.
Purified RNA were subjected to RNA quality control test using Qubit Flex Fluorometer and Agilent 2100 Bioanalyzer. 100 ng total RNA was used for RNA-Seq Library preparation with QIAseq® FastSelect™ RNA Library Kit. Briefly, ribosomal RNA (rRNA) depletion was carried out using the QIAseq FastSelect rRNA HMR Kit (334387, Qiagen), following the manufacturer's instructions. cDNA synthesis was performed using the QIAseq Low Input RNA Library Kit (334205, Qiagen), employing both the N6-T RT Primer (random hexamer) and the ODT-T RT Primer (oligo-dT primer). Library amplification/indexing were carried out with QIAseq UX Index kit UDI-A (331815, Qiagen), which incorporates unique 10-base dual indices (UDIs) into each library. The final library quality control test was again conducted using the Qubit Flex Fluorometer and the Agilent 2100 Bioanalyzer.

treatment_protocol: We transfected 293T cells with pFlag-OGT plasmid (Flag empty plasmid as control) for 24 h and infected the cells with influenza virus (no infection as control) for 16 h, then harvest the cells for the immunoprecipitation (IP) assay.

value: kidney

value: Embryonic kidney cell line

value: Transfected with pFlag-OGT and infected with IAV (PR8 strain) Input sample


title: Flag-OGT IAV (PR8 strain) IP sample, Replicate 1

description: Library name: T13018_4-G8_IP

value: Transfected with pFlag-OGT and infected with IAV (PR8 strain) IP sample


title: Flag-OGT Mock Input sample, Replicate 1

description: Library name: T13020_6-GM_N

value: Transfected with pFlag-OGT and Mock Input sample


title: Flag empty vector Mock Input sample, Replicate 1

description: Library name: T13019_5-FM_N

value: Transfected with Flag empty vector and Mock Input sample


title: Flag empty vector IAV (PR8 strain) Input sample, Replicate 1

description: Library name: T13021_7-F8_N

value: Transfected with Flag empty vector and infected with IAV (PR8 strain) Input sample


title: Flag-OGT Mock IP sample, Replicate 1

description: Library name: T13016_2-GM_IP

value: Transfected with pFlag-OGT and Mock IP sample


title: 135_D24_7202

description:
Library name: 135_D24_7202
Responder

value: Blood


title: Flag empty vector Mock IP sample, Replicate 1

description: Library name: T13015_1-FM_IP

value: Transfected with Flag empty vector and Mock IP sample


title: AB_12, small RNA, Colorectal


title: AB_11, small RNA, Colorectal


title: 20190809_tcon_4

city: Minneapolis

first: Michael

last: Zaiken

state: MN

address: East River Parkway

department: Pediatrics

institute: University of Minnesota

description: Library name: 20190809_tcon_4

data_processing:
Data preprocessing was done using STAR 2.7.9a with Gencode 38 as the gene model for alignmnet
Assembly: GRCh38
Supplementary files format and content: Array of genes vs sample table. Counts are Log transformed and TMM normalized across all samples

source_name: PMBCs

extract_protocol:
Total RNA was extracted from the sorted cells using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer's protocol.
cDNA was synthesized using Takara SmartSeq v4 reagents. Full length cDNA was fragmented to a mean size of 200bp with a Covaris R230 ultrasonicator and Illumina sequencing libraries were prepared from 2ng of sheared cDNA using IDT DNAseq library prep reagents on a Beckman Coulter Biomek i7 according to manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Uniquely dual indexed libraries were pooled in equimolar ratios and evaluated for cluster efficiency and pool balance with shallow sequencing on an Illumina MiSeq.

value: PMBCs

value: Tcon

value: IL2 Non-Responsive

tag: batch


title: 134_D24_7201

description:
Library name: 134_D24_7201
Responder


title: 140_D24_7221

description:
Library name: 140_D24_7221
Responder


title: 20190418_treg_9

description: Library name: 20190418_treg_9

value: Treg


title: 133_D17_325

description:
Library name: 133_D17_325
NonResponder


title: 20190418_treg_8

description: Library name: 20190418_treg_8

value: IL2 Responsive


title: AB_10, small RNA, Colorectal

value: Rectus abdominis muscle

value: Skeletal muscle tissue


title: 20190418_treg_7

description: Library name: 20190418_treg_7


title: AB_8, small RNA, Colorectal


title: 132_D17_324

description:
Library name: 132_D17_324
NonResponder


title: 20190418_treg_3

description: Library name: 20190418_treg_3


title: AB_14, small RNA, Colorectal


title: AB_9, small RNA, Pancreas


title: 136_D24_7205

description:
Library name: 136_D24_7205
Responder


title: 20190418_treg_4

description: Library name: 20190418_treg_4


title: Flag empty vector IAV (PR8 strain) IP sample, Replicate 1

description: Library name: T13017_3-F8_IP

value: kidney

value: Transfected with Flag empty vector and infected with IAV (PR8 strain) IP sample


title: 131_D17_319

description:
Library name: 131_D17_319
NonResponder


title: 20190418_treg_2

description: Library name: 20190418_treg_2


title: 130_D17_318

description:
Library name: 130_D17_318
NonResponder


title: 20190418_treg_11

description: Library name: 20190418_treg_11


title: 20190418_treg_12

description: Library name: 20190418_treg_12


title: AB_6, small RNA, Pancreas


title: 20190418_treg_10

description: Library name: 20190418_treg_10


title: 20190418_treg_1

description: Library name: 20190418_treg_1


title: 129_D17_317

description:
Library name: 129_D17_317
NonResponder


title: 20160717-cm84388-treg

description: Library name: 20160717-cm84388-treg


title: 128_D17_314

description:
Library name: 128_D17_314
NonResponder


title: AB_5, small RNA, Pancreas


title: 20160717-cm84388-tcon

description: Library name: 20160717-cm84388-tcon


title: AB_4, small RNA, Pancreas


title: 20160717-cm82393-treg

description: Library name: 20160717-cm82393-treg


title: 127_D17_312

description:
Library name: 127_D17_312
NonResponder


title: AB_3, small RNA, Pancreas


title: 20160717-cm76381-tcon

description: Library name: 20160717-cm76381-tcon


title: 20160715-cm81903-tcon

description: Library name: 20160715-cm81903-tcon


title: 126_D17_309

description:
Library name: 126_D17_309
NonResponder


title: 20160715-cm77388-treg

description: Library name: 20160715-cm77388-treg


title: 125_D17_303

description:
Library name: 125_D17_303
NonResponder


title: AB_2, small RNA, Colorectal


title: 20160715-cm77090-treg

description: Library name: 20160715-cm77090-treg


title: 20160715-cm77388-tcon

description: Library name: 20160715-cm77388-tcon


title: AB_1, small RNA, Colorectal


title: AB_7, small RNA, Pancreas


title: 20160715-cm77090-tcon

description: Library name: 20160715-cm77090-tcon


title: AB_84, Pancreas

data_processing:
The libraries were normalized, pooled, and denatured. Pooled libraries were loaded on Illumina NovaSeq S4 lane using Xp protocol per manufacturer's recommendations.
Base-calling was performed with RTA v.3.4.4. Program bcl2fastq2 was used to demultiplex and generate fastq reads. Raw fastq files were subjected to cutadapt for  adapter trimming. Trimmed Reads were aligned to human genome 38 using STAR v.2.7.3a.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count data for each sample

source_name: Skeletal muscle tissue

extract_protocol:
RNA extraction was performed using the Trizol method and Qiagen RNAeasy midi kit (Mississauga, ON). The optical density (OD) 260/280 ratio was measured using Nanodrop, and RNA integrity number (RIN) was assessed using Agilent Bio-analyzer 2100 for all the samples.
NEB Next RNA First-strand synthesis and NEBNext Ultra Directional RNA Second strand synthesis were used. Remaining steps were performed using NEBNext Ultra II DNA library Prep kit  for Illumina.


title: 124_D17_306

description:
Library name: 124_D17_306
NonResponder


title: 123_D17_302

description:
Library name: 123_D17_302
NonResponder


title: AB_83, Colorectal


title: 20160429-cm85212-treg

description: Library name: 20160429-cm85212-treg


title: 20160429-cm85212-tcon

description: Library name: 20160429-cm85212-tcon


title: 20160715-cm74375-treg

description: Library name: 20160715-cm74375-treg


title: 122_D17_7225

description:
Library name: 122_D17_7225
NonResponder


title: AB_82, Pancreas


title: 121_D17_7224

description:
Library name: 121_D17_7224
NonResponder


title: 20160717-cm82393-tcon

description: Library name: 20160717-cm82393-tcon


title: 20160429-cm83673-treg

description: Library name: 20160429-cm83673-treg


title: 20190809_tcon_3

description: Library name: 20190809_tcon_3


title: 20160429-cm83673-tcon

description: Library name: 20160429-cm83673-tcon


title: 120_D17_7223

description:
Library name: 120_D17_7223
NonResponder


title: 20160427-cm82528-treg

description: Library name: 20160427-cm82528-treg


title: AB_80, Colorectal


title: 20160427-cm82528-tcon

description: Library name: 20160427-cm82528-tcon


title: 119_D17_7218

description:
Library name: 119_D17_7218
NonResponder


title: 20160427-cm78680-treg

description: Library name: 20160427-cm78680-treg


title: 20160427-cm78680-tcon

description: Library name: 20160427-cm78680-tcon


title: 20160427-cm78001-treg

description: Library name: 20160427-cm78001-treg


title: AB_78, Pancreas


title: AB_79, Pancreas


title: 20160429-cm85083-treg

description: Library name: 20160429-cm85083-treg


title: 117_D17_329

description:
Library name: 117_D17_329
NonResponder


title: 20160427-cm78001-tcon

description: Library name: 20160427-cm78001-tcon


title: 116_D17_328

description:
Library name: 116_D17_328
NonResponder


title: AB_76, Colorectal


title: 115_D17_323

description:
Library name: 115_D17_323
NonResponder


title: 20160429-cm85083-tcon

description: Library name: 20160429-cm85083-tcon


title: AB_77, Colorectal


title: 114_D17_321

description:
Library name: 114_D17_321
NonResponder


title: AB_81, Colorectal


title: AB_74, Colorectal


title: AB_75, Pancreas


title: 113_D17_320

description:
Library name: 113_D17_320
NonResponder


title: 118_D17_330

description:
Library name: 118_D17_330
NonResponder


title: AB_73, Colorectal


title: 112_D17_316

description:
Library name: 112_D17_316
NonResponder


title: AB_72, Colorectal


title: 111_D17_313

description:
Library name: 111_D17_313
NonResponder


title: AB_71, Colorectal


title: AB_70, Colorectal


title: 109_D17_308

description:
Library name: 109_D17_308
NonResponder


title: AB_69, Pancreas


title: Renal cell carcinoma_MCF14

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

organism: Rattus norvegicus

source_name: normal kidney cortex

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: Male wild-type and BRCA2+/- rats at 5 weeks of age were injected intraperitonealy with Fe-NTA by the dose of 5 mg iron/kg for the first two times then 7 for the last three times for the first week. The treatment for next 9 weeks was by the dose of 10 mg iron/kg weight, five times per week and by 10 mg iron/kg for three times for the last week. The rats were euthanized when they were dying.

value: Jcl:SD BRCA2+/-

value: normal kidney cortex

value: Fe-NTA, 3 months


title: Renal cell carcinoma_MCF1


title: 108_D17_305

description:
Library name: 108_D17_305
NonResponder


title: 5929-607140_1-Day_S1_PBS_ROI-006_Secretory

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

institute: Kansas University Medical Center

description: Library name: DSP-1001660006710-B-G06

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 ) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

value: PBS

tag: patient

tag: roi

tag: days

tag: segment

value: Secretory

tag: nuclei

tag: area


title: Renal cell carcinoma_MCF13

tag: tissue


title: Renal cell carcinoma_MCF3


title: 5929-607140_1-Day_S1_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660006710-B-G05

value: Ciliated


title: 5929-607140_1-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006710-B-G04


title: Renal cell carcinoma_MCF2


title: Renal cell carcinoma_MCF12


title: AB_68, Colorectal


title: 5929-607140_1-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006710-B-G02


title: 107_D17_304

description:
Library name: 107_D17_304
NonResponder

value: Blood


title: 110_D17_310

description:
Library name: 110_D17_310
NonResponder


title: AB_67, Colorectal


title: 5929-607140_1-Day_S1_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660006710-B-G01


title: 106_D17_7222

description:
Library name: 106_D17_7222
NonResponder


title: Renal cell carcinoma_WCF7

value: Jcl:SD wild-type


title: 5929-607140_1-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006710-B-F12


title: Renal cell carcinoma_MCF16


title: Renal cell carcinoma_MCF7


title: 5929-607140_1-Day_S1_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660006710-B-G03


title: 5929-607140_1-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006710-B-F11


title: AB_66, Pancreas


title: 104_D17_7203

description:
Library name: 104_D17_7203
Responder


title: 5929-607140_1-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006710-B-F09


title: 105_D17_7220

description:
Library name: 105_D17_7220
NonResponder


title: 5929-607140_1-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006710-B-F08


title: 5929-607140_1-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006710-B-F07


title: 103_D17_327

description:
Library name: 103_D17_327
Responder


title: 5929-608036_14-Day_S3_PBS_ROI-009_Secretory

description: Library name: DSP-1001660006710-B-F06


title: 102_D17_322

description:
Library name: 102_D17_322
Responder


title: 5929-608036_14-Day_S3_PBS_ROI-007_Secretory

description: Library name: DSP-1001660006710-B-F04


title: AB_62, Colorectal


title: Renal cell carcinoma_WCF1


title: Renal cell carcinoma_WCF20


title: Renal cell carcinoma_WCF8


title: Renal cell carcinoma_WCF24


title: Renal cell carcinoma_WCF19


title: Renal cell carcinoma_WCF2


title: 101_D17_315

description:
Library name: 101_D17_315
Responder


title: Renal cell carcinoma_WCF25


title: AB_61, Colorectal


title: 5929-608036_14-Day_S3_OVCAR3_ROI-004_Ciliated

description: Library name: DSP-1001660006710-B-E12


title: 99_D17_7229

description:
Library name: 99_D17_7229
Responder


title: AB_63, Pancreas


title: 5929-608036_14-Day_S3_OVCAR3_ROI-006_Secretory

description: Library name: DSP-1001660006710-B-F03


title: AB_64, Colorectal


title: 5929-607140_1-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006710-B-F10


title: AB_65, Colorectal


title: 5929-608036_14-Day_S3_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006710-B-E08


title: 5929-608036_14-Day_S3_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006710-B-E10


title: 100_D17_311

description:
Library name: 100_D17_311
Responder


title: AB_60, Colorectal


title: AB_59, Colorectal


title: 5929-608036_14-Day_S3_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006710-B-E09


title: 5929-608036_14-Day_S3_PBS_ROI-008_Secretory

description: Library name: DSP-1001660006710-B-F05


title: 5929-608036_14-Day_S3_OVCAR3_ROI-005_Secretory

description: Library name: DSP-1001660006710-B-F02


title: 5929-608036_14-Day_S3_OVCAR3_ROI-004_Secretory

description: Library name: DSP-1001660006710-B-F01


title: 5929-608036_14-Day_S3_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006710-B-E11


title: 98_D17_7228

description:
Library name: 98_D17_7228
Responder


title: AB_58, Pancreas


title: 97_D17_7227

description:
Library name: 97_D17_7227
Responder


title: 5929-608036_14-Day_S3_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006710-B-E07


title: 5929-608036_14-Day_S3_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006710-B-E06


title: AB_57, Colorectal


title: 5929-607836_14-Day_S2_OVCAR3_ROI-009_Ciliated

description: Library name: DSP-1001660006710-B-E04


title: AB_56, Colorectal


title: 5929-607836_14-Day_S2_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660006710-B-E03


title: 95_D17_7221

description:
Library name: 95_D17_7221
Responder


title: 5929-607836_14-Day_S2_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660006710-B-E02


title: AB_55, Pancreas


title: 5929-607836_14-Day_S2_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660006710-B-D12


title: 5929-607836_14-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660006710-B-D11


title: 5929-607836_14-Day_S2_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660006710-B-E01


title: 94_D17_7210

description:
Library name: 94_D17_7210
Responder


title: 92_D17_7205

description:
Library name: 92_D17_7205
Responder


title: AB_52, Colorectal


title: AB_54, Colorectal


title: 93_D17_7208

description:
Library name: 93_D17_7208
Responder


title: 5929-607836_14-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660006710-B-D10


title: 5929-607836_14-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660006710-B-D08


title: AB_53, Pancreas


title: 5929-607836_14-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660006710-B-D09


title: 5929-607836_14-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660006710-B-D06


title: 5929-607836_14-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660006710-B-D05


title: 91_D17_7202

description:
Library name: 91_D17_7202
Responder


title: 5929-607836_14-Day_S2_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660006710-B-D04


title: 5929-607836_14-Day_S2_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660006710-B-E05


title: AB_51, Colorectal


title: 5929-607836_14-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660006710-B-D07


title: 96_D17_7226

description:
Library name: 96_D17_7226
Responder


title: AB_50, Pancreas


title: 90_D17_7201

description:
Library name: 90_D17_7201
Responder


title: 89_D9_325

description:
Library name: 89_D9_325
NonResponder


title: AB_49, Pancreas


title: 5929-607836_14-Day_S2_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660006710-B-D02


title: 88_D9_324

description:
Library name: 88_D9_324
NonResponder


title: AB_48, Colorectal


title: DSP-1001660006710_NTC

description: Library name: DSP-1001660006710-B-A01

source_name: NTC

value: NTC


title: 5929-607836_14-Day_S2_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660006710-B-C12


title: 87_D9_319

description:
Library name: 87_D9_319
NonResponder


title: 021355_14-Day_S3_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-G11


title: AB_47, Colorectal


title: 021355_14-Day_S3_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-G10


title: AB_46, Pancreas


title: 021355_14-Day_S3_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-G09


title: 86_D9_318

description:
Library name: 86_D9_318
NonResponder


title: 85_D9_317

description:
Library name: 85_D9_317
NonResponder


title: 021355_14-Day_S3_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-G08


title: AB_45, Pancreas


title: 021355_14-Day_S3_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-G07


title: AB_44, Pancreas


title: 5929-607140_14-Day_S3_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-G06


title: 5929-607140_14-Day_S3_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-G04


title: 5929-607140_14-Day_S3_PBS_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-G05


title: AB_43, Colorectal


title: 5929-607836_14-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660006710-B-D03


title: 82_D9_309

description:
Library name: 82_D9_309
NonResponder


title: 5929-607836_14-Day_S2_FT240_ROI-001_Secretory

description: Library name: DSP-1001660006710-B-D01


title: 5929-607836_14-Day_S5_OVCAR3_ROI-009_Ciliated

description: Library name: DSP-1001660010858-A-G01


title: 5929-607140_14-Day_S3_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-G03


title: AB_42, Pancreas


title: 5929-607836_14-Day_S5_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660010858-A-F12


title: 5929-607836_14-Day_S5_OVCAR3_ROI-008_Ciliated

description: Library name: DSP-1001660010858-A-F11


title: AB_41, Pancreas


title: 80_D9_306

description:
Library name: 80_D9_306
NonResponder


title: 5929-607836_14-Day_S5_OVCAR3_ROI-007_Ciliated

description: Library name: DSP-1001660010858-A-F09


title: 84_D9_314

description:
Library name: 84_D9_314
NonResponder


title: AB_40, Colorectal


title: 5929-607836_14-Day_S5_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-F08


title: 79_D9_302

description:
Library name: 79_D9_302
NonResponder


title: 5929-607836_14-Day_S5_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010858-A-F07


title: AB_38, Colorectal


title: 5929-607836_14-Day_S5_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010858-A-F05


title: 5929-607836_14-Day_S5_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-F06


title: AB_39, Pancreas


title: 83_D9_312

description:
Library name: 83_D9_312
NonResponder


title: 78_D9_7225

description:
Library name: 78_D9_7225
NonResponder


title: 76_D9_7223

description:
Library name: 76_D9_7223
NonResponder


title: 77_D9_7224

description:
Library name: 77_D9_7224
NonResponder


title: 5929-607836_14-Day_S5_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-F02


title: 81_D9_303

description:
Library name: 81_D9_303
NonResponder


title: 5929-607836_14-Day_S5_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010858-A-F01


title: 5929-607836_14-Day_S5_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660010858-A-G02


title: AB_37, Colorectal


title: 5929-607836_14-Day_S5_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010858-A-F03


title: 75_D9_7218

description:
Library name: 75_D9_7218
NonResponder


title: 5929-607836_14-Day_S5_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660010858-A-E11


title: AB_36, Pancreas


title: 5929-607836_14-Day_S5_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-E12


title: AB_35, Colorectal


title: 5929-607836_14-Day_S5_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660010858-A-F10


title: 74_D9_330

description:
Library name: 74_D9_330
NonResponder


title: 5929-607836_14-Day_S5_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-E10


title: 5929-607836_14-Day_S5_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010858-A-E09


title: 73_D9_329

description:
Library name: 73_D9_329
NonResponder


title: 021355_14-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-E08


title: 021355_14-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-E07


title: AB_33, Colorectal


title: 021355_14-Day_S2_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-E06


title: 5929-607836_14-Day_S5_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-F04


title: 72_D9_328

description:
Library name: 72_D9_328
NonResponder


title: AB_32, Colorectal


title: 021355_14-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-E04


title: 021355_14-Day_S2_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-E05


title: 021355_14-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-E03


title: 71_D9_323

description:
Library name: 71_D9_323
NonResponder


title: AB_31, Pancreas


title: 5929-607140_1-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-E02


title: 5929-607140_1-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010858-A-E01


title: AB_30, Colorectal


title: 70_D9_321

description:
Library name: 70_D9_321
NonResponder


title: 69_D9_320

description:
Library name: 69_D9_320
NonResponder


title: 5929-607140_1-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010858-A-D11


title: 5929-607140_1-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-D12


title: 5929-607140_1-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-D10


title: AB_28, Pancreas


title: AB_29, Colorectal


title: 5929-607140_1-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010858-A-D09


title: 5929-607140_1-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-D08


title: 67_D9_313

description:
Library name: 67_D9_313
NonResponder


title: 5929-607140_1-Day_S2_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010858-A-D07


title: 68_D9_316

description:
Library name: 68_D9_316
NonResponder


title: AB_27, Colorectal


title: AB_34, Pancreas


title: 5929-607140_1-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-D06


title: AB_26, Pancreas


title: 5929-607140_1-Day_S2_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-D04


title: 65_D9_308

description:
Library name: 65_D9_308
NonResponder


title: 66_D9_310

description:
Library name: 66_D9_310
NonResponder


title: 5929-607140_1-Day_S2_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660010858-A-D05


title: 64_D9_305

description:
Library name: 64_D9_305
NonResponder


title: 5929-608036_14-Day_S1_OVCAR3_ROI-007_Secretory

description: Library name: DSP-1001660010858-A-C12


title: 5929-608036_14-Day_S1_OVCAR3_ROI-009_Secretory

description: Library name: DSP-1001660010858-A-D02


title: AB_24, Pancreas


title: 5929-608036_14-Day_S1_OVCAR3_ROI-008_Secretory

description: Library name: DSP-1001660010858-A-D01


title: AB_23, Pancreas


title: 5929-608036_14-Day_S1_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-C10


title: 62_D9_7222

description:
Library name: 62_D9_7222
NonResponder


title: 5929-608036_14-Day_S1_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-C09


title: 5929-608036_14-Day_S1_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-C11


title: AB_22, Colorectal


title: 5929-608036_14-Day_S1_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-C08


title: 61_D9_7220

description:
Library name: 61_D9_7220
NonResponder


title: 5929-608036_14-Day_S1_FT240_ROI-003_Ciliated

description: Library name: DSP-1001660010858-A-C07


title: 60_D9_7203

description:
Library name: 60_D9_7203
NonResponder


title: 5929-608036_14-Day_S1_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-C06


title: AB_20, Pancreas


title: 5929-607140_1-Day_S2_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010858-A-D03


title: AB_21, Pancreas


title: 5929-608036_14-Day_S1_FT240_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-C04


title: AB_25, Colorectal


title: 59_D9_327

description:
Library name: 59_D9_327
Responder


title: 5929-607140_14-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-C02


title: AB_19, Pancreas


title: 5929-608036_14-Day_S1_FT240_ROI-001_Ciliated

description: Library name: DSP-1001660010858-A-C03


title: 58_D9_322

description:
Library name: 58_D9_322
Responder


title: AB_18, Colorectal


title: 5929-607140_14-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-C01


title: 5929-607140_14-Day_S2_FT240_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-B12


title: 63_D9_304

description:
Library name: 63_D9_304
NonResponder


title: 57_D9_315

description:
Library name: 57_D9_315
Responder


title: 5929-607140_14-Day_S2_FT240_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-B11


title: AB_17, Pancreas


title: 5929-607140_14-Day_S2_PBS_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-B09


title: 5929-607140_14-Day_S2_FT240_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-B10


title: 56_D9_311

description:
Library name: 56_D9_311
Responder


title: 55_D9_7229

description:
Library name: 55_D9_7229
Responder


title: 5929-607267_1-Day_S4_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010858-A-B06


title: 5929-607267_1-Day_S4_PBS_ROI-010_Secretory

description: Library name: DSP-1001660010858-A-B08


title: 5929-608036_14-Day_S1_FT240_ROI-002_Ciliated

description: Library name: DSP-1001660010858-A-C05


title: 5929-607267_1-Day_S4_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010858-A-B05


title: AB_15, Colorectal


title: 54_D9_7228

description:
Library name: 54_D9_7228
Responder


title: AB_14, Colorectal


title: AB_13, Pancreas


title: 53_D9_7227

description:
Library name: 53_D9_7227
Responder


title: 5929-607267_1-Day_S4_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010858-A-B02


title: 5929-607267_1-Day_S4_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010858-A-B04


title: 5929-607267_1-Day_S4_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010858-A-B03


title: AB_12, Colorectal


title: 5929-607267_1-Day_S4_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010858-A-B01


title: 51_D9_7221

description:
Library name: 51_D9_7221
Responder


title: AB_11, Colorectal


title: 5929-607267_1-Day_S4_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010858-A-A11


title: 5929-607267_1-Day_S4_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010858-A-A10


title: 52_D9_7226

description:
Library name: 52_D9_7226
Responder


title: 5929-607267_1-Day_S4_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010858-A-A12


title: 50_D9_7210

description:
Library name: 50_D9_7210
Responder


title: 5929-607267_1-Day_S4_PBS_ROI-010_Ciliated

description: Library name: DSP-1001660010858-A-B07


title: AB_16, Pancreas


title: 5929-607267_1-Day_S4_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010858-A-A08


title: 49_D9_7208

description:
Library name: 49_D9_7208
Responder


title: 5929-607267_1-Day_S4_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010858-A-A09


title: 48_D9_7206

description:
Library name: 48_D9_7206
Responder


title: 5929-607267_1-Day_S4_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010858-A-A04


title: 5929-607267_1-Day_S4_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010858-A-A03


title: 5929-607267_1-Day_S4_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010858-A-A06


title: AB_8, Colorectal


title: 5929-607267_1-Day_S4_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010858-A-A05


title: AB_10, Colorectal


title: 46_D9_7202

description:
Library name: 46_D9_7202
Responder


title: 5929-607267_1-Day_S4_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010858-A-A02


title: AB_6, Pancreas


title: 5929-606950_1-Day_S2_FT240_ROI-010_Secretory

description: Library name: DSP-1001660010837-B-D07


title: 45_D9_7201

description:
Library name: 45_D9_7201
Responder


title: AB_7, Pancreas


title: 5929-607267_1-Day_S4_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010858-A-A07


title: 5929-606950_1-Day_S2_FT240_ROI-010_Ciliated

description: Library name: DSP-1001660010837-B-D06


title: DSP-1001660010858_NTC

description: Library name: DSP-1001660010858-A-A01


title: AB_5, Pancreas


title: AB_9, Pancreas


title: 5929-606950_1-Day_S2_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010837-B-D05


title: 5929-606950_1-Day_S2_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010837-B-D04


title: 5929-606950_1-Day_S2_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010837-B-D03


title: 43_D4_324

description:
Library name: 43_D4_324
NonResponder


title: AB_4, Pancreas


title: AB_3, Pancreas


title: 5929-606950_1-Day_S2_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010837-B-D02


title: 42_D4_319

description:
Library name: 42_D4_319
NonResponder


title: 5929-606950_1-Day_S2_PBS_ROI-007_Secretory

description: Library name: DSP-1001660010837-B-D01


title: 5929-606950_1-Day_S2_PBS_ROI-007_Ciliated

description: Library name: DSP-1001660010837-B-C12


title: 47_D9_7205

description:
Library name: 47_D9_7205
Responder


title: AB_2, Colorectal


title: 41_D4_318

description:
Library name: 41_D4_318
NonResponder


title: 5929-606950_1-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010837-B-C11


title: 5929-606950_1-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010837-B-C10


title: AB_1, Colorectal


title: 5929-606950_1-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010837-B-C09


title: 5929-606950_1-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010837-B-C08


title: 44_D4_325

description:
Library name: 44_D4_325
NonResponder


title: 5929-606950_1-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010837-B-C07


title: iPSC multiome ATAC

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

institute: ETH Zurich

description: 10x Genomics Multiome RNA+ATAC

library_source: genomic single cell

data_processing:
ParseBio snRNAreads were aligned against the human genome (hg38, sourced from Parse Biosciences) by split-pipe (v1.0.4, Parse Biosciences)
10x Multiome reads were aligned against the human genome (hg38, sourced from 10x Genomics) by Cell Ranger ARC (v2.0.0, 10x Genomics)
scRNA-seq samples were loaded into scanpy. Next, cells were filtered on quality using the following thresholds: minimum number of genes = 750 and minimum number of UMI counts = 1000. Furthermore, cells that were more than 5 standard deviations in log1p(total_counts), log1p(number of genes) and percentage of counts in top 20 genes were also removed. Next, we removed cells that showed too high percentage of mitochondrial reads (5% for NGN2-iNs, 6% for ASCL1/DLX2 post-patterned iNs, 8% for ASCL1/DLX2 pre-patterned iNs). Finally, we used Scrublet to remove predicted doublets.
Assembly: hg38
Supplementary files format and content: scRNA-seq data is represented by adata objects (Scanpy), containing raw expression values for both the ParseBio snRNA and 10x multiome samples. Treatment information and analysis results are given as .tsv files.
Supplementary files format and content: 10x multiome ATAC processed data is given by fragment files

source_name: NGN2-inducible iPSCs, 409B2 background

growth_protocol: All cells were cultured under standard conditions of 37°C and 5% CO2

extract_protocol:
For ParseBio, to obtain single cell suspension, induced neurons cultured in 12-well plates were washed with PBS and incubated with 300 μL accutase at 37°C for 5 min. Dissociation reaction were stopped with 700 μL PBS containing 0.04% BSA, and cells were gently trituated into single cell suspension. Cells were washed twice with 500 μL PBS containing 0.04% BSA before nuclei isolation. To isolate the nuclei from single cell suspension, cells were trituated ten times in 100 μL lysis buffer (10 mM Tris-Cl pH7.4, 3 mM NaCl, 10 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 0.2U/μL RNase inhibitor (Takara), 0.1% NP-40, 0.01% Digitonin (Invitrogen)) and incubate 2 min on ice. The isolated nuclei underwent two subsequent washes in 500 μL wash buffer (10 mM Tris-Cl pH7.4, 3 mM NaCl, 10 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 0.2U/μL RNase inhibitor). Isolated nuclei were fixed and cryopreserved for snRNA-seq according to the instructions provided by the manufacturer (Parse Biosciences).   For 10x Multiome, single-cell suspensions obtained from each NGN2-iN pre-patterning condition were divided into two distinct pools (Supplementary Table 1). Subsequently, each pool, along with the control NGN2-inducible iPSCs, underwent nuclei isolation individually following provider’s instruction (10x Genomics user guide CG000365).
Libraries were constructed according to the manufacter's instructions. For 10x Genomics user guide CG000338 was used.

treatment_protocol: Cells were treated with varying concentrations of BMP4, SHH, RA, XAV, CHIR, FGF8 and CycA on different media types and different timings

tag: cell line

value: NGN2-inducible iPSCs, 409B2 background


title: 5929-606950_1-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010837-B-C06


title: 39_D4_314

description:
Library name: 39_D4_314
NonResponder


title: iPSC multiome RNA

description: 10x Genomics Multiome RNA+ATAC


title: 38_D4_312

description:
Library name: 38_D4_312
NonResponder


title: 5929-606950_1-Day_S2_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010837-B-C04


title: 5929-606950_1-Day_S2_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010837-B-C03


title: 37_D4_309

description:
Library name: 37_D4_309
NonResponder


title: 5929-606950_1-Day_S2_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010837-B-C02


title: NGN2 prepatterning multiome RNA 2

description: 10x Genomics Multiome RNA+ATAC


title: 5929-606950_1-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010837-B-C01


title: 36_D4_303

description:
Library name: 36_D4_303
NonResponder


title: NGN2 prepatterning multiome ATAC 2

description: 10x Genomics Multiome RNA+ATAC


title: 5929-606950_1-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010837-B-B12


title: 35_D4_306

description:
Library name: 35_D4_306
NonResponder


title: 5929-606994_1-Day_S2_PBS_ROI-011_Secretory

description: Library name: DSP-1001660010837-B-B11


title: 5929-606994_1-Day_S2_PBS_ROI-011_Ciliated

description: Library name: DSP-1001660010837-B-B10


title: NGN2 prepatterning multiome RNA 1

description: 10x Genomics Multiome RNA+ATAC


title: NGN2 prepatterning multiome ATAC 1

description: 10x Genomics Multiome RNA+ATAC


title: 34_D4_302

description:
Library name: 34_D4_302
NonResponder


title: 5929-606994_1-Day_S2_PBS_ROI-010_Ciliated

description: Library name: DSP-1001660010837-B-B08


title: 40_D4_317

description:
Library name: 40_D4_317
NonResponder


title: ASCL1 pre

description: ParseBiosciences scRNA

source_name: ASCL1-DLX2-inducible iPSCs,  iLB-C-133bm-s4 background


title: 5929-606994_1-Day_S2_FT240_ROI-009_Secretory

description: Library name: DSP-1001660010837-B-B07


title: 5929-606950_1-Day_S2_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010837-B-C05


title: 33_D4_7225

description:
Library name: 33_D4_7225
NonResponder


title: 5929-606994_1-Day_S2_FT240_ROI-009_Ciliated

description: Library name: DSP-1001660010837-B-B06


title: 5929-606994_1-Day_S2_FT240_ROI-008_Secretory

description: Library name: DSP-1001660010837-B-B05


title: 5929-606994_1-Day_S2_FT240_ROI-008_Ciliated

description: Library name: DSP-1001660010837-B-B04


title: ASCL1 post

description: ParseBiosciences scRNA

value: ASCL1-DLX2-inducible iPSCs,  iLB-C-133bm-s4 background


title: 31_D4_7223

description:
Library name: 31_D4_7223
NonResponder


title: 32_D4_7224

description:
Library name: 32_D4_7224
NonResponder


title: 5929-606994_1-Day_S2_FT240_ROI-007_Ciliated

description: Library name: DSP-1001660010837-B-B02


title: 5929-606994_1-Day_S2_PBS_ROI-006_Secretory

description: Library name: DSP-1001660010837-B-B01


title: 5929-606994_1-Day_S2_FT240_ROI-007_Secretory

description: Library name: DSP-1001660010837-B-B03


title: 5929-606994_1-Day_S2_PBS_ROI-006_Ciliated

description: Library name: DSP-1001660010837-B-A12


title: 29_D4_329

description:
Library name: 29_D4_329
NonResponder


title: NGN2 post p1

description:
ParseBiosciences scRNA
NGN2_post_dr_clustered_raw_merged_meta.tsv


title: 5929-606994_1-Day_S2_PBS_ROI-005_Secretory

description: Library name: DSP-1001660010837-B-A11


title: 5929-606994_1-Day_S2_PBS_ROI-005_Ciliated

description: Library name: DSP-1001660010837-B-A10


title: mHAR123, scRNAseq

city: La Jolla

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

description: 10X Genomics

data_processing:
Demultiplexed raw sequencing reads were processed and mapped to the human genome (GRCh38) using Cell Ranger software (v7.0.1) with default parameters.
Filtered count matrices for each library were tagged with a library batch ID and combined across independent experiments using the Seurat package (version 4.4.0) in R.
To check the quality of the single cell data and to remove any multiplets, we performed Seurat based filtering of cells: number of detected features (nFeature_RNA) per cell (2000 to 10000) and percentage of mitochondrial genes expressed (<0.1).
Gene expression values were log normalized. Batch correction was performed using the ‘JackStraw’ functions in the Seurat package. To identify cell clusters, we employed UMAP. The ‘FindMarkers’ function (a Wilcoxon rank sum test) was used to determine differential gene expression between clusters (set at minimum expression in 25% of cells).
Single-cell pseudotime trajectories were constructed with the Monocle3 package (v1.3.4).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells were dissociated into single cell suspension using Accutase (Gibco) and dead cells were removed using the ClioCell Dead Cell Removal kit (Amsbio) following the manufacturers’ instructions. Viable cells were washed once in PBS and resuspended in 0.04% BSA in PBS for loading on the 10x Chromium chip.
Cell capturing, and library preparation was carried as per kit instructions (Chromium Next GEM Single Cell 3' HT v3.1). In brief, 20,000 cells (10,000 cells per loading well) were targeted for capture per sample. After cDNA synthesis and library amplification, the resultant libraries were size selected, pooled and sequenced using 2 x 100 paired-end sequencing protocol on an Illumina NovaSeq 6000 instrument.

treatment_protocol: hESCs from different genotypes were harvested and seeded as single cells at 6x104 cells per cm2. Once 80% confluent, the hESCs were cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gemini), 5 μM of Rock inhibitor, 1 μM Dorsomorphin and 10 μM SB431542 (STEMCELL Technologies) for 2 days. Colonies were then cut into a big chess pattern, and cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gibco), 1 μM Dorsomorphin and 10 μM SB431542 for 5 days under rotation (95 rpm) inside the 37°C incubator. Embryoid bodies were then replated on plates coated with hESC-qualified Matrigel (Corning) in DMEM/F12 media supplemented with N2 (1:200; Gemini), and Gem21 (1:100; Gemini) for 7 days.

value: human embryonic stem cells

value: replace hHAR123 with mHAR123

value: Differentiate into neural progenitor cells (NPCs)


title: 5929-606994_1-Day_S2_PBS_ROI-004_Secretory

description: Library name: DSP-1001660010837-B-A09


title: 28_D4_328

description:
Library name: 28_D4_328
NonResponder


title: 5929-606994_1-Day_S2_PBS_ROI-004_Ciliated

description: Library name: DSP-1001660010837-B-A08


title: 5929-606994_1-Day_S2_PBS_ROI-010_Secretory

description: Library name: DSP-1001660010837-B-B09


title: cHAR123, scRNAseq

description: 10X Genomics

value: replace hHAR123 with cHAR123


title: 5929-606994_1-Day_S2_OVCAR3_ROI-003_Secretory

description: Library name: DSP-1001660010837-B-A07


title: 5929-606994_1-Day_S2_OVCAR3_ROI-003_Ciliated

description: Library name: DSP-1001660010837-B-A06


title: 5929-606994_1-Day_S2_OVCAR3_ROI-002_Secretory

description: Library name: DSP-1001660010837-B-A05


title: HAR123-KO, scRNAseq

description: 10X Genomics


title: 26_D4_321

description:
Library name: 26_D4_321
NonResponder


title: NGN2 post p2


title: 5929-606994_1-Day_S2_OVCAR3_ROI-002_Ciliated

description: Library name: DSP-1001660010837-B-A04


title: 30_D4_7218

description:
Library name: 30_D4_7218
NonResponder


title: NGN2 pre

description: ParseBiosciences scRNA


title: 5929-606994_1-Day_S2_OVCAR3_ROI-001_Secretory

description: Library name: DSP-1001660010837-B-A03


title: hHAR123, scRNAseq

description: 10X Genomics

value: WT


title: 24_D4_316

description:
Library name: 24_D4_316
NonResponder


title: 5929-606994_1-Day_S2_OVCAR3_ROI-001_Ciliated

description: Library name: DSP-1001660010837-B-A02