title: SI Apc Kras/+ Pik3ca Slc7a5 Rep5

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (either 2x36 cycles, paired end (Apc, Apc Kras/+, Apc Kras/+ Pik3ca/+, Apc Kras/+ Pten, Apc Pik3ca/+, Apc Pten)  or 2x74bp paired end (Apc Pik3ca, Apc Kras/+ Pik3ca, Apc Pik3ca Slc7a5, Apc Kras/+ Pik3ca Slc7a5)).

treatment_protocol: Induction of genetic recombination was performed by 2 x 80mg/kg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues  were harvested after 3 or 4 days, as noted.

value: Small Intestine

value: Female

tag: time point

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R SLC7A5fl/fl


title: SI Apc Kras/+ Pik3ca Slc7a5 Rep6

status: Public on Jul 19 2024

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: Sex

tag: genotype


title: heart biopsy_NR_TH47

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

organism: Homo sapiens

source_name: heart biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: heart biopsy

tag: mmdx (abmr, tcmr, mixed, pabmr, nr)

value: NR


title: 2-hour refed, beta-cells, DT-treated mouse_13

city: Geneva

first: Marta

last: Perez Frances

state: Geneva

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

data_processing:
All sequencing data were uploaded to and aligned on the Galaxy project against Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b (PMID: 23104886) n 2-pass mapping mode.
Aligned data were counted using HTSeq version 0.9.1  in union mode.
Analyses were performed in a pair-wise manner between the four conditions analyzed using DESeq2 version 1.28.1
For each pairwise comparison, genes were discarded if they had fewer than 5 counts per sample on average. After calculating differential expression between groups, log2 fold changes were shrunken using the normal estimator
Genes were considered to be differentially expressed if the absolute shrunken log2 fold changes were equal to or above 1, and adjusted p-values were equal to or below 0.05.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-separated values files (.tsv) containing gene and sample names

source_name: pancreatic beta-cells

extract_protocol:
RNA extraction from pancreatic beta-cells was performed using the Qiagen RNeasy Micro Kit. . RNA was extracted as described above and assessed for quality by Agilent bioanalyzer prior to library generation and sequencing.
Reverse transcription and cDNA amplification were performed using the SMARTer Ultra Low RNA kit (Clontech). cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq4000 platform with single-end 100-bp.

treatment_protocol: β-cells were FAC-sorted from one-month post-ablation and control mice, either under fasting or fasting plus 2-hour refed condition.

tag: cell type

value: pancreatic beta-cells

value: Male

value: GluDTR+, SstDTR htz, PpyDTR htz

tag: strain

value: Mix background

tag: age

value: 3 months old

tag: treatment 1

value: Diphtheria toxin (DT)

tag: time after_treatment_1

value: One month post ablation

tag: treatment 2

value: 8h-fasting + 2h refed


title: heart biopsy_pABMR_TH48

value: pABMR


title: telencephalon, WT- PBS injected

city: New York

first: Caghan

last: Kizil

department: Neurology & TAUB Institute

country: USA

institute: Columbia University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: telencephalon

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH7.5, at 28°C (±1°C) in groups of 20 animals per 2.8L.

extract_protocol:
Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue (Invitrogen, Cat No. S34857) and Dycle Ruby (Invitrogen, Cat. No. V10309) were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

treatment_protocol: WT-AB and abca7 +/- knock-out lines were injected with Amyloid-beta 42 peptide, and PBS as control as descibed (Bhatatrai et al. 2016).

value: telencephalon

value: WT-AB

tag: treatment

value: PBS


title: 2-hour refed, beta-cells, DT-treated mouse_17


title: telencephalon, WT-Ab42 injected

description: 10x Genomics


title: 2-hour refed, beta-cells, DT-treated mouse_14


title: CH455A2C

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: single cell RNA-sequencing

data_processing:
FASTQs were generated using cellranger v6.0 mkfastq with default parameters
Raw counts were generated by aligning FASTQs from two separate runs to achieve sequencing saturation. Reads were aligned to the human reference genome build GRCh38 using cellranger count v6.0 with default parameters
cellranger count files were input into Seurat v4 using R v4.2.1 for downstream analysis
PIK3CA genotyping results from long-read sequencing were added to the provided Seurat object (MCAPobj.rds) in the metadata column 'snp'
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: snp_data.txt contains information about the PIK3CA (NM_006218.4:c.3139C>T;p.His1047Tyr) variant calling in single cells; there are five column headers: 1) 10x cell barcode; 2) chromosome 3 PIK3CA c.3139 coordinate; 3) reference allele; 4) alternate allele; 5) depth of coverage at this site.

molecule: polyA RNA

source_name: in vitro expansion of skin biopsy of affected tissue

growth_protocol: Skin biopsy tissue from the right trunk was morcellated, digested in collagenase at 37C for 1 hour then pelleted in a centrifuge at 900 RPM x 10 minutes. The pellet was resuspended in alpha-MEM with 20% FBS, 1.5% L-glutamine, 1% penicillin streptomycin, and 1ml fungizone, plated in a T25, and incubated T25 at 37C and 5% CO2. Flasks were passaged with trypsin-EDTA

extract_protocol:
Cells were collected from culture media
10X Genomics Chromium Single Cell 3' dual-index kit v3.1 was used according to manufacturer's protocol

tag: age at_surgery

value: 3 years (at the time of biopsy)

value: M


title: SI Apc Kras/+ Pik3ca Slc7a5 Rep3

value: Small Intestine

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R SLC7A5fl/fl


title: mitoDMS KO2

city: Boston

first: Silvi

last: Rouskin

state: MA

address: 77 Ave Louis Pasteur

department: Microbiology

institute: Harvard

description: DMS treated isolated human LRPPRC KO mitochondria Bioreplicate 2

data_processing:
CutAdapt
Bowtie 2
DREEM
Supplementary files format and content: Population Average Reactivities from the Heavy and Light strand, .txt files

source_name: HEK 293

growth_protocol: HEK-293T cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS), 5 mL 100X antibiotic/antimycotic, 1 mM sodium pyruvate, 1 mM sodium formate, and 50 g/ml uridine, and 1x GlutaMAX (ThermoFisher Scientific; Waltham, MA) at 37°C under 5% CO2 in 1 L of liquid culture.

extract_protocol:
RNA was extracted following the Trizol manufacturer’s specifications. The aqueous phase was transferred to a new tube, and an equal volume of 100% isopropanol and 3 μL of glycogen were added to precipitate the RNA. The samples were incubated at -80 oC overnight and centrifuged at 15,000 xg for 45 min, at 4 °C. RNA was resuspended in 50 μL of RNAse-free water and quantified by measuring absorbance at a wavelength of 260 nm with Nanodrop (ThermoFisher Scientific).
Sequencing libraries were generated using the xGen Broad-range RNA library prep kit from IDT, following the manufacturer's specifications, with the following modifications. The RNA fragmentation step was conducted by combining 1 μg of RNA with 1 μL of reagent F1, 4 μL of F3, and 2 μL of F4, and incubating at 95 °C for 2 min. The samples were immediately placed on ice and combined with a mixture of 1 μL 10 mM TGIRTIII reverse transcriptase (RT), 1 μL R1 reagent, and 1 μL 0.1 M DTT. This RNA:RT mixture was incubated for 30 min at room temperature before adding 2 μL of reagent F2, and then placed in a thermocycler for 10 min at 20°C, 10 min at 42 °C, and 60 min at 55 °C. The thermocycler was programmed to pause at 55°C, at which point 1 μL of 4M NaOH was added and programmed to continue at 95°C for 3 minutes. At this point, the sample was removed from the thermocycler and placed on ice, and 1 μL of 4M HCl and 27 μL of low EDTA TE were added. After the indexing PCR, the indexed libraries were resolved on an 8% TBE gel for 55 min at 180 V and size-selected for products ~300 nt. The products were sequenced with NovaSeq6000 system (paired-end run,150 cycles).

treatment_protocol: Mitochondria were isolated and resuspended in 1 mL of STE buffer (0.32 M sucrose, 1 mM EDTA, and 10 mM Tris-HCl, pH 7.4). 3 mg of freshly prepared mitochondria were pelleted by centrifugation at 10,000 xg for 10 min at 4 °C. The pellet was resuspended in 150 μL of Na-cacodylate buffer (300 mM Na-cacodylate, 6 mM MgCl2, and 0.32 M sucrose) that had been preheated to 37 °C and incubated for 3 min at 37 °C. A freshly prepared and preheated mixture of 150 μL of the Na-cacodylate buffer plus 3 μL of DMS was added to the mitochondria, resulting in a final DMS concentration of 1%. Mitochondria were incubated for 5 min at 37 °C with gentle shaking. To quench the DMS reaction, 180 μL of beta-mercaptoethanol was added to the mitochondria, the solution was mixed by pipetting up and down several times, and the sample was centrifuged at 10,000 xg for 10 min at 4 °C. The mitochondrial pellet was washed twice in 1 mL of a glycerol buffer (10% glycerol, 0.15 mM MgCl2, 10 mM Tris-HCl pH 6.8), following the same centrifugation conditions indicated above.

tag: cell line

value: HEK 293

value: LRPPRC KO,1 percent DMS


title: heart biopsy_NR_TH46

value: heart biopsy

value: NR


title: SI Apc Kras/+ Pik3ca Slc7a5 Rep2

value: Male


title: heart biopsy_NR_TH49


title: heart biopsy_NR_TH44


title: heart biopsy_TCMR_TH45

value: TCMR


title: mitoDMS KO1

description: DMS treated isolated human LRPPRC KO mitochondria Bioreplicate 1

value: LRPPRC KO,1percent DMS


title: 2-hour refed, beta-cells, control mouse_12

value: pancreatic beta-cells

value: GluDTR+, SstDTR htz, PpyDTR htz

value: Mix background

value: 3 months old

value: Control

value: One month post ablation

value: 8h-fasting + 2h refed


title: 2-hour refed, beta-cells, DT-treated mouse_15

value: Diphtheria toxin (DT)


title: SI Apc Kras/+ Pik3ca Slc7a5 Rep4

value: Small Intestine

value: Female

value: Day 3


title: 8-hour fasting, beta-cells, DT-treated mouse_11

value: 8-hour fasting


title: SI Apc Pik3ca Slc7a5 Rep6

value: Day 4

value: vilCreER Apcfl/fl Pik3caH1047R/H1047R SLC7A5fl/fl


title: mitoDMS WT1

description: DMS treated isolated human WT mitochondria, Bioreplicate 1

value: HEK 293

value: 1percent DMS


title: mitoDMS WT2

description: DMS treated isolated human WT mitochondria, Bioreplicate 2


title: 8-hour fasting, beta-cells, DT-treated mouse_10

value: Male


title: heart biopsy_Mixed_TH42

value: heart biopsy

value: Mixed


title: SI Apc Pik3ca Slc7a5 Rep5


title: heart biopsy_NR_TH43

value: NR


title: SI Apc Pik3ca Slc7a5 Rep4


title: 8-hour fasting, beta-cells, DT-treated mouse_8

value: pancreatic beta-cells

value: GluDTR+, SstDTR htz, PpyDTR htz

value: Mix background

value: 3 months old


title: heart biopsy_TCMR_TH41

value: TCMR


title: SI Apc Pik3ca Slc7a5 Rep3

value: Small Intestine


title: SI Apc Pik3ca Slc7a5 Rep2

value: Female


title: 8-hour fasting, beta-cells, DT-treated mouse_6

value: Diphtheria toxin (DT)

value: One month post ablation


title: SI Apc Kras/+ Pik3ca Slc7a5 Rep1

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R SLC7A5fl/fl


title: SI Apc Kras/+ Pik3ca Rep6

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R


title: SI Apc Pik3ca Slc7a5 Rep1

value: Day 4

value: vilCreER Apcfl/fl Pik3caH1047R/H1047R SLC7A5fl/fl


title: 8-hour fasting, beta-cells, control mouse_4

value: Male

value: Control

value: 8-hour fasting


title: heart biopsy_pABMR_TH37

value: heart biopsy

value: pABMR


title: heart biopsy_ABMR_TH40

value: ABMR


title: heart biopsy_pABMR_TH38


title: heart biopsy_ABMR_TH39


title: SI Apc Kras/+ Pik3ca Rep5


title: H9-Ectoderm Day 6, WDR5B-FLAG, rep2

city: Santa Barbara

first: Jeffrey

middle: K.

last: Bailey

state: CA

department: Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute

institute: University of California, Santa Barbara

library_source: genomic

data_processing:
Initial analysis steps including read quality control and adapter trimming (trimgalore 0.6.7, fastqc 0.11.9, cutadapt 3.4), alignment to hg38 (bwa-mem 0.7.17), marking and filtering out duplicate reads, filtering out reads in blacklisted regions (hg38-blacklist.v2.bed) (Amemiya et al., 2019), and filtering out improperly mapped reads (picard 2.27.4, samtools 1.15.1, bedtools 2.30.0) were performed using the nf-core/chipseq Nextflow pipeline v2.0.0 with default parameters (Ewels et al., 2020).
Peak calling was performed using MACS3 3.0.0b1 with thresholds of q<0.05 or p<0.001 as indicated. Results were saved as narrowPeak files.
Peak set overlap analysis was conducted using DiffBind 3.8.4 [DOI: 10.18129/B9.bioc.DiffBind] (Stark et al., 2011), and peak annotation of promoters was performed using ChIPSeeker 1.34.1 [DOI: 10.18129/B9.bioc.ChIPseeker] (Yu et al., 2015).
Assembly: hg38
Supplementary files format and content: narrowPeak (p<0.001 threshold, except IgG samples)
Supplementary files format and content: narrowPeak (q<0.05 threshold, except IgG samples)
Library strategy: Cut & Run

molecule: genomic DNA

source_name: H9 (WiCell, WA09)

growth_protocol: Neural ectoderm cells were differentiated for 6 days prior to CUT&RUN in DMEM/F12 medium containing 1X B-27, 1X N-2, 10mM nicotinamide, 10µM SB431542, and 5µM DMH1.

extract_protocol:
CUT&RUN was performed using a similar protocol to those previously described (Skene et al., 2018; Kong et al., 2021).  Immediately prior to lifting the cells, magnetic concanavalin A (Con A) beads (Bangs Laboratories, #BP531) were activated by rinsing twice in cold binding buffer (20mM HEPES pH7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and stored on ice in binding buffer equivalent to the original bead volume.  Con A beads were always mixed by gentle pipetting or flick mixing rather than by vortexing.  Cells were rinsed with 1X PBS, lifted with 0.25% Trypsin, and quenched with 2-3 volumes of growth media.  Cell count and viability were determined using a NucleoCounter NC-200, and 3x10^6 cells per sample (ARPE-19) to 6x10^6 cells per sample (neural ectoderm) were pelleted, washed once with 1X PBS, washed once with wash buffer (20mM HEPES pH7.5 and 150mM NaCl supplemented with 1:100 spermidine [Cell Signaling Technology, 27287] and 1:200 protease inhibitor cocktail [Cell Signaling Technology, 7012]), and resuspended in wash buffer of the same composition.  Activated Con A beads were added to the cell suspension, and binding was achieved by end-over-end mixing at room temperature for 15min.  Cells bound to Con A beads were resuspended in antibody buffer (wash buffer supplemented with 2mM EDTA, and 0.01% digitonin [Millipore-Sigma, 300410]) and aliquoted into equal portions.  Antibodies or IgG were added, and incubations were conducted at 4C overnight.  Following antibody binding, beads were washed twice with wash buffer supplemented with 0.01% digitonin and incubated for 10min at room temperature with 1:25 pAG-MNase (EpiCypher CUTANA pAG-MNase for CUT&RUN, 15-1016) diluted in wash buffer of the same composition.  Beads were washed twice with wash buffer containing 0.01% digitonin, and pAG-MNase digestion was performed at 4C for 2h in wash buffer supplemented with 0.01% digitonin and 2mM CaCl2.  Digestion was stopped by addition of 2X stop buffer (340mM NaCl, 20mm EDTA, 4mm EGTA) supplemented with 0.01% digitonin, 1:200 of 10mg/ml RNAse A (Cell Signaling Technology, #7013), and 50pg per sample of S. cerevisiae spike-in normalization DNA (Cell Signaling Technology, 36598S).  Samples were incubated at 37C for 15min with gentle agitation to release DNA, supernatant was separated from magnetic Con A beads into a fresh tube, and samples were diluted with an equal volume of 0.1X TE buffer (1mM Tris-HCl pH7.5, 0.1mM EDTA).  Samples were stored at -20C prior to DNA purification. DNA purification of CUT&RUN samples was performed by Phenol:Chloroform:Isoamyl Alcohol extraction as previously described (Skene et al., 2018).  Briefly, samples were thawed, supplemented with 1:100 of 10% SDS, 1:100 of 20mg/ml proteinase K, and incubated for 10min at 70C.  One sample volume of UltraPure Phenol:Chloroform:Isoamyl Alcohol 25:24:1 v/v (Thermo Fisher Scientific, 15593031) was added and samples were mixed by full-speed vortexing, transferred to phase-lock tubes (Qiagen, 129046), and centrifuged at room temperature for 5min at 16,000g.  One sample volume of chloroform was added, mixed by inversion, and samples were centrifuged at room temperature for 5min at 16,000g.  The aqueous upper phase was removed into a fresh microfuge tube containing 4µg glycogen (Millipore-Sigma, 10901393001), 2.5 volumes of ice cold 100% ethanol were added, and samples were mixed by vortexing followed by incubation on ice for 10min.  Samples were centrifuged at 4C for 10min at 16,000g, supernatant was gently discarded, samples were washed with 5 volumes of ice cold 100% ethanol, centrifuged at 4ºC for 2min at 16,000g, supernatant was gently discarded, and pellets were allowed to air dry for 5-10min.  After excess liquid had evaporated, pellets were resuspended in 0.1X TE buffer, transferred to fresh tubes, and stored at -20C.
Libraries were constructed by DNA end repair, A-tailing, Illumina adapter ligation, size selection, PCR amplification, and quantification by qPCR.  Both library construction and 150bp paired-end sequencing on an Illumina NovaSeq 6000 were performed by Novogene Corporation Inc. (Beijing, China).

value: H9 ESC-derived neural ectoderm

value: H9 (WiCell, WA09)

value: CRISPR-Cas9 WDR5B-FLAG tagged

tag: cut&run antibody

value: FLAG (Cell Signaling #14793)


title: 8-hour fasting, beta-cells, control mouse_3

value: pancreatic beta-cells

value: GluDTR+, SstDTR htz, PpyDTR htz

value: Mix background

value: 3 months old


title: heart biopsy_NR_TH35

value: NR


title: SI Apc Kras/+ Pik3ca Rep4

value: Small Intestine

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R


title: 8-hour fasting, beta-cells, DT-treated mouse_9

value: Male

value: Diphtheria toxin (DT)

value: One month post ablation


title: heart biopsy_NR_TH34

value: heart biopsy


title: H9-Ectoderm Day 6, WDR5B-FLAG, rep1


title: 8-hour fasting, beta-cells, DT-treated mouse_7

value: 8-hour fasting


title: 8-hour fasting, beta-cells, control mouse_2

value: Control


title: 8-hour fasting, beta-cells, control mouse_5


title: heart biopsy_ABMR_TH33

value: ABMR


title: H9-Ectoderm Day 6, WDR5, rep2

value: H9 ESC-derived neural ectoderm

value: H9 (WiCell, WA09)

value: CRISPR-Cas9 WDR5B-FLAG tagged

value: WDR5 (Bethyl #A302-429A)


title: SI Apc Kras/+ Pik3ca Rep2


title: 8-hour fasting, beta-cells, control mouse_1

value: pancreatic beta-cells

value: GluDTR+, SstDTR htz, PpyDTR htz

value: Mix background


title: MICE40

city: Bialystok

first: Andrzej

last: Eljaszewicz

state: Podlaskie

address: Jana Kilinskiego 1

department: Centre for Regenerative Medicine

country: Poland

institute: Medical University of Bialystok

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (bbduk; minlength=30, qtrim=rl, trimq=15)
Reads were then mapped to the reference genome of Mus musculus (GRCm38) using STAR aligner version 2.5.3a with parameters --quantMode GeneCounts --runThreadN 4
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
Lung lobes were stored in RNA later solution (Invitrogen) for 48 hours to stabilize RNA. Next, tissues were disrupted using TissueRuptor II (Qiagen) in RNeasy Lysis Buffer (Qiagen). Total RNA was isolated by using the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen). Only the RNA with proper RNA integrity, namely RIN>8, was subjected to cDNA library establishment according to TruSeq Stranded Total RNA protocol (Illumina), followed by the quality confirmation (Agilent Technologies 2100 Bioanalyzer). The expected length of the final product was assumed at 260 base pairs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: female

value: wild type

value: lung lobe challenged with 10 micrograms of house-dust mite (HDM) extract for 5 days each week and affected by short-term effects of MSC administration


title: H9-Ectoderm Day 6, WDR5, rep1


title: heart biopsy_ABMR_TH36


title: MICE39


title: H9-Ectoderm Day 6, IgG, rep2

value: Rabbit IgG (Cell Signaling #66362)


title: SI Apc Kras/+ Pik3ca Rep1

value: Small Intestine

value: Female

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R


title: MICE38


title: SI Apc Pik3ca Rep6

value: Male

value: Day 4

value: vilCreER Apcfl/fl Pik3caH1047R/H1047R


title: heart biopsy_ABMR_TH32

value: heart biopsy

value: ABMR


title: H9-Ectoderm Day 6, IgG, rep1

value: H9 ESC-derived neural ectoderm

value: H9 (WiCell, WA09)

value: CRISPR-Cas9 WDR5B-FLAG tagged


title: SI Apc Pik3ca Rep5


title: ARPE-19 WDR5B-FLAG, CUT&RUN, FLAG, rep2

source_name: ARPE-19 (ATCC, CRL-2302)

growth_protocol: ARPE-19 cells were grown in Lonza XVIVO10 medium and harvested on day 8 post-seeding.

value: Retinal pigmented epithelium

value: ARPE-19 (ATCC, CRL-2302)

value: WDR5B-FLAG stable expression

value: FLAG (Cell Signaling #14793)


title: MICE37

value: lung

value: female

value: wild type

value: lung lobe challenged with 10 micrograms of house-dust mite (HDM) extract for 5 days each week and affected by short-term effects of MSC administration


title: SI Apc Pik3ca Rep4

value: Small Intestine

value: Female


title: SI Apc Kras/+ Pik3ca Rep3

value: Male

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/H1047R


title: heart biopsy_NR_TH29

value: heart biopsy

value: NR


title: ARPE-19 WDR5B-FLAG, CUT&RUN, FLAG, rep1


title: MICE36


title: heart biopsy_TCMR_TH30

value: TCMR


title: heart biopsy_Mixed_TH31

value: Mixed


title: SI Apc Pik3ca Rep3

value: Day 4

value: vilCreER Apcfl/fl Pik3caH1047R/H1047R


title: ARPE-19 WDR5B-FLAG, CUT&RUN, IgG, rep2

value: Retinal pigmented epithelium

value: ARPE-19 (ATCC, CRL-2302)

value: WDR5B-FLAG stable expression

value: Rabbit IgG (Cell Signaling #66362)


title: MICE30

value: lung

value: female

value: wild type

value: lung lobe challenged with 10 micrograms of house-dust mite (HDM) extract for 5 days each week and affected by long-term effects of MSC administration


title: MICE29


title: ARPE-19 WDR5B-FLAG, CUT&RUN, IgG, rep1


title: MICE28


title: heart biopsy_NR_TH27


title: ARPE-19 WDR5-FLAG, CUT&RUN, FLAG, rep2

value: WDR5-FLAG stable expression

value: FLAG (Cell Signaling #14793)


title: SI Apc Pik3ca Rep1

value: Small Intestine

value: Female


title: heart biopsy_Mixed_TH28

value: heart biopsy


title: SI Apc Pten Rep4

value: Male

value: vilCreER Apcfl/fl Ptenfl/fl


title: MICE27


title: ARPE-19 WDR5-FLAG, CUT&RUN, FLAG, rep1


title: ARPE-19 WDR5-FLAG, CUT&RUN, IgG, rep2


title: MICE26


title: SI Apc Pik3ca Rep2

value: Day 4


title: MICE20

value: lung lobe challenged with 10 micrograms of house-dust mite (HDM) extract for 5 days each week


title: SI Apc Pten Rep2


title: SI Apc Pten Rep1


title: PTEN Haplo

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description:
9771_SS_gene_count.txt
9771-SS-0009_S1_L005_R1_001.fastq.gz

data_processing:
trim adapters with fastp
Align with STAR
featureCounts for counting
edgeR for calling DEGs
Assembly: hg38 or mm10
Supplementary files format and content: txt/rds file containing raw counts

source_name: PBMC monocytes

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit (Cat# 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC monocytes

tag: disease

value: PTEN Haplo


title: MICE19


title: heart biopsy_NR_TH25

value: NR


title: heart biopsy_TCMR_TH26

value: TCMR


title: heart biopsy_NR_TH22


title: SI Apc Pik3ca/+ Rep4

value: vilCreER Apcfl/fl Pik3caH1047R/+


title: MICE18

value: lung

value: female


title: SI Apc Pten Rep3


title: healthy donor 2

description:
9771_SS_gene_count.txt
9771-SS-0005_S1_L005_R1_001.fastq.gz

value: healthy


title: heart biopsy_NR_TH24


title: heart biopsy_TCMR_TH21


title: healthy donor 1

description:
9771_SS_gene_count.txt
9771-SS-0001_S1_L005_R1_001.fastq.gz


title: MICE17

value: wild type


title: heart biopsy_NR_TH20


title: SI Apc Pik3ca/+ Rep3


title: SI Apc Pik3ca/+ Rep2


title: K562

first: Christina

last: Sharkey

address: 99 Brookline Ave Rm 389

department: Urology

institute: Beth Israel Deaconess Medical Center

data_processing:
library strategy: Iso-CUT&MAP (Isolated cell-based Cut Under Target and Mapping Apoptotic Protein-binding sequences)
The Skewer is used to filter raw data. The procedure for data trimming is in the following: (1) Discard the reads with low quality (proportion of low quality bases larger than 50%); (2) Discard the reads with N ratio (unsure base) larger than 15%; (3) Discard the reads with adaptor at the 5’-end; (4) Discard the reads without adaptor and inserted fragment at the 3’-end; (5) Trim the adapter sequence at the 3’-end; (6) Discard the reads whose length are less than 18nt after trimming. base-calling : Illumina CASAVA v1.8 software. read alignment software: BWA
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: .bw

growth_protocol: K562 (lymphoblast cells from chronic myelogenous leukemia) cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum and 1% Antibiotic-Antimycotic solution (Corning Cellgro, Manassas, VA).

extract_protocol:
After immune cell, target cells and (NF-kB) conjugated beads were co-encapsulated and incubated for 6 hours- time needed to observe sufficient killing of K562 by NK92 cells- the antibody coated beads, capturing the transcription factor interacting with the DNA from the dead target cell (Transcription factor + DNA complex), were pulled out from the droplets using a magnetic rack (0.5-0.7 mL tube Magnetic Rack, Amazon) for 10 minutes. The beads were washed with 0.1M MES buffer pH 5.2 (Coupling Buffer) and a simple DNA isolation protocol was performed using a DNA Clean & ConcentratorTM-5 (Cat# D4014, Zymo Research Corporation).
After the DNA samples quality control: (1) The DNA fragments are repaired, dA-tailed. (2) The DNA fragments with A tail are ligated to sequencing adaptors. (3) The final DNA library is obtained by size selection and PCR amplification. ChIP DNA has two kinds of lib our internal kit, provided with enough DNA amount. The other is low input, which applies kit preparation workflow. One is based on regular input and applies our internal kit, provided with enough DNA amount. The other is low input, which applies kit called NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. Both workflows of library construction are as following graph.

treatment_protocol: To obtain optimal droplet sizes the oil to aqueous flow rates were generally maintained at a ratio of 4:1 in the device. The oil phase consisted of Fluorinert® FC-40 (Sigma, St. Louis, MO) supplemented with 2% w/w surfactant (008-FluoroSurfactant, Ran Biotechnologies, Beverly, MA). The water-in-oil droplets were generated upstream using a flow-focusing junction. The aqueous phase consisted of NK cells and tumor cells with beads mixed before reaching a flow-focusing junction at 200 μl per hour. FC-40 with 2% surfactant Span-80 was used as a continuous phase at 1000 μl per hour. The oil and aqueous phase were pumped into the microfluidic device using three syringe pumps. Under the flow-focusing geometry dimensions, droplets having a diameter in the range of 150 to 200 μm were generated. These generated droplets were collected in a sterile 15ml tube containing mineral oil to prevent evaporation The collected droplets encapsulating NK cells and tumor cells with beads were incubated at 37 °C 5% C02 for 6 hrs.

tag: chip antibody

value: NF-kB (ChIpAB+ NF-kB p65)

value: lymphoblast cells


title: heart biopsy_NR_TH19


title: MICE16


title: SI Apc Pik3ca/+ Rep1

value: Small Intestine

tag: time point


title: heart biopsy_NR_TH23

tag: tissue

value: heart biopsy


title: HeLa cells, ITPRIPL2 knockdown, biol rep 4

city: Maastricht

first: Mike

last: Gerards

address: Paul-Henri Spaaklaan 1

department: Maastricht Centre for Systems Biology (MaCSBio)

country: Netherlands

institute: Maastricht University

description:
HeLa_RawCounts.txt
HeLa4_ITPRIPL2

data_processing:
Raw reads were processed and mapped to the hg38 reference genome using the Galaxy platform and RNA STAR.
Aligned reads were converted to transcript counts in Galaxy.
Assembly: hg38
Supplementary files format and content: RawCounts

source_name: HeLa

growth_protocol: nHDF and HeLa cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) according to manufacturer's protocol. 1 ug of total RNA was used for mRNA enrichement (Nex Poly(A) Beads 2.0) before the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer) following manufacturer's protocols.

treatment_protocol: Cell were treated with gene specific or non-targetting esiRNAs to induce knockdown. For this esiRNAs were combined with RNAiMAX in OptiMEM medium with a concentration of 50 ng esiRNA/ml culture medium and incubated for 72 hours before RNA isolation.

value: HeLa

value: Cervical cancer epithelial cell

value: ITPRIPL2 esiRNAs

value: ITPRIPL2 KD


title: heart biopsy_NR_TH18


title: HeLa cells, ITPRIPL2 knockdown, biol rep 3

description:
HeLa_RawCounts.txt
HeLa3_ITPRIPL2


title: SI Apc Kras/+ Pten Rep4

tag: Sex

value: Female

value: Day 3

value: vilCreER Apcfl/fl KrasG12D/+ Ptenfl/fl


title: heart biopsy_NR_TH17

value: NR


title: HeLa cells, ITPRIPL2 knockdown, biol rep 2

description:
HeLa_RawCounts.txt
HeLa2_ITPRIPL2

tag: genotype


title: SI Apc Kras/+ Pten Rep3


title: HeLa cells, ITPRIPL2 knockdown, biol rep 1

description:
HeLa_RawCounts.txt
HeLa1_ITPRIPL2


title: ds2, 2w, left, snRNAseq

city: Buenos Aires

first: Ariel

last: Chernomoretz

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the STARsolo software v2.7.4a (https://github.com/alexdobin/STAR). For QC, filtering, normalization, and doublet exclusion the scran R package v.1.24.0, scDblFinder v1.10.0 were used. Scripts for preprocessing and analyzing data with detailed descriptions are available here: https://github.com/chernolabs/NeuronalSwitch.
Assembly: mm10
Supplementary files format and content: Count matrix in market matrix format, nuclei barcodes as tab-delimited text file and feature names as tab-delimited text file.
Supplementary files format and content: tab file with 26716 nuclei metadata ("nuclei_id": unique identifier for single nuclei, "sample_id", "seuratLT": partition estimated by seurat label transfer function, "seuratLT_refined": refined partition based on seuratLT labeling, "ptime"), all cohorts included, and log-normalized expression values for 14220 genes

molecule: nuclear RNA

source_name: Dentate Gyrus

extract_protocol:
Mice were deeply anesthetized (ketamine/xylazine, as described above), brains were carefully removed and placed into ice cold Earl’s balanced salt solution (EBSS, in mM: 117 NaCl, 5.4 KCl, 1 NaH2PO4, 26 NaHCO3, 5.6 glucose, 1.8 CaCl2 .2H2O and 0.8 MgSO4) with trehalose 5% v/v and kynurenic acid 0.8 mM. Dissection solution was equilibrated in 95% O2/5% CO2 before use. The brain was cut along the longitudinal fissure and the regions posterior to lambda were cut off. Under a dissection microscope and upon removal of the diencephalon, the medial side of the hippocampus was exposed. The dentate gyrus was isolated by inserting a sharp-needle tip and sliding it superficially along the septotemporal axis of the hippocampus. The dissected tissue was placed in a 0.5 ml microcentrifuge tube with a minimal amount of media, flash-freezed on dry ice and stored at -80ºC until use. Nuclei were isolated as previously described with several modifications. Dounce tissue grinder and pestles were sequentially washed with 100% EtOH, RNAse Zap (Sigma, Cat # R2020), 2-3 rounds with RNAse-free water, and finally rinsed with EZ Lysis Buffer (Sigma, Cat # NUC-101). All material and buffers were chilled on ice. The tissue was transferred to a chilled dounce prefilled with 2 ml ice-cold EZ Lysis Buffer and homogenized slowly with 20-25 strokes of pestle A, followed by 20 strokes with pestle B. Suspension was transferred to a chilled tube and incubated on ice 5 min. Then the suspension was centrifuged at 500 × g for 5 min at 4°C and the supernatant was removed. The pellet was resuspended in 4 ml ice-cold EZ Lysis Buffer and after a second round of ice incubation and centrifugation, the isolated nuclei were resuspended in 4 ml ice-cold Nuclei Suspension Buffer (NSB) (1x RNase-free molecular-biology grade PBS, 0.1% molecular-biology grade BSA 100 μg/ml and 0.2U/μl RNase inhibitor). Finally, nuclei were centrifuged at 500 × g for 5 min at 4°C and after removing the supernatant were resuspended in 1ml NSB-Ruby (final Ruby concentration 1:500) and filtered twice through a 35-μm cell strainer to remove as many debris as possible. Nuclei were kept on ice until sorting (Harvard University, Bauer Core Facility, BD FACSAria II) into 96 well plates, pre-coated with BSA to reduce adherence and improve recovery, containing with ~10-20 μl of rich-NSB (with final 2U/μl of RNase inhibitor and 1% BSA). The final nuclei concentration was determined using a C-chip Neubauer counting chamber and Trypan Blue (1:2 final dilution). Nuclei were immediately loaded for single-cell GEM formation (10x Genomics, single cell RNA sequencing 3ʹ, Chromium v3.1)
Dataset sampling for snRNA-seq experiments was carried out within a minimal time interval, processing two time points in a single experiment each day to minimize batch effects. For each time point, four dentate gyri (left or right hemispheres) from male and female mice were pooled. For snRNA-seq, nuclei were loaded in the 10x Genomics chips aiming to recover 2,000–10,000 nuclei. cDNA amplification and library construction were done following 10x Genomics protocols. Libraries were generated using Chromium v3.1, quantified in BioAnalyzer and sequenced on an Illumina HiSeq 2500. Samples were sequenced to a depth of 40–70,000 reads per cell.
snRNA-Seq

value: Dentate Gyrus

value: adult born Granule Cells

tag: cohort

tag: hemisphere

value: L


title: TGFB1_48h_3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with R (v 4.2.2.). Gene expression profiling was performed using arrays of Mouse430_2 from Affymetrix. A Custom CDF Version 25 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: hepatocyte isolated from male DBA/2J mice (8-12 weeks old)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary hepatocytes were isolated from livers of male DBA/2J mice (8-12 weeks old) using collagenase perfusion. Hepatocytes were plated on collagen-coated 6-well plates at a density of 3x105 cells/well in Williams' medium E supplemented with 10% FBS, 2mM L-glutamine, 1% penicillin/streptomycin and 100nM dexamethasone. Hepatocytes were allowed to attach, and medium was exchanged after 4h with Williams medium E supplemented with 2mM L-glutamine and 1% penicillin/streptomycin.

extract_protocol: After cytokine treatment, cultured cells were washed twice with PBS. Next, total RNA was isolated using the Total RNA Kit, peqGOLD (Cat No. 13-6834-02) or the InviTrap®Spin Universal RNA Mini Kit from Stratec (1060100300, Birkenfeld, Germany) according to manufacturers´ instructions. RNA concentration was measured with the Infinite M200 microplate reader (Tecan, Switzerland).

treatment_protocol: 5ng/mL recombinant TGF-β1 was added to serum-free culture medium for 1, 6, 24 and/or 48 hours. Control conditions included cells maintained for the same period in a serum-free medium without TGF-beta1.

value: 5ng/mL recombinant TGF-β1

tag: time


title: heart biopsy_ABMR_TH16

tag: mmdx (abmr, tcmr, mixed, pabmr, nr)

value: ABMR


title: SI Apc Kras/+ Pten Rep1

value: Male


title: HeLa cells, non-targetting control, biol rep 4

description:
HeLa_RawCounts.txt
HeLa4_GFP

tag: cell type

value: non-targetting (GFP) esiRNAs

value: control


title: HeLa cells, non-targetting control, biol rep 3

description:
HeLa_RawCounts.txt
HeLa3_GFP


title: SI Apc Kras/+ Pik3ca/+ Rep3

value: Small Intestine

value: vilCreER Apcfl/fl KrasG12D/+ Pik3caH1047R/+


title: HeLa cells, non-targetting control, biol rep 2

description:
HeLa_RawCounts.txt
HeLa2_GFP

value: HeLa

value: Cervical cancer epithelial cell


title: no_TGFB1_0h_3


title: TGFB1_24h_3


title: heart biopsy_Mixed_TH15

value: heart biopsy

value: Mixed


title: TGFB1_1h_3


title: heart biopsy_Mixed_TH14


title: SI Apc Kras/+ Pik3ca/+ Rep2

value: Female

value: Day 3


title: HeLa cells, non-targetting control, biol rep 1

description:
HeLa_RawCounts.txt
HeLa1_GFP


title: heart biopsy_NR_TH12

value: NR


title: TGFB1_48h_2


title: SI Apc Kras/+ Pten Rep2

value: vilCreER Apcfl/fl KrasG12D/+ Ptenfl/fl


title: heart biopsy_Mixed_TH13


title: nHDF cells, ITPRIPL2 knockdown, biol rep 4

description:
nHDF_RawCounts.txt
nHDF4_ITPRIPL2

source_name: Normal Human DermalFibroblasts (wild type)

value: nHDF

value: Fibroblast

value: ITPRIPL2 esiRNAs

value: ITPRIPL2 KD


title: SI Apc Kras/+ Pik3ca/+ Rep1

value: Male


title: nHDF cells, ITPRIPL2 knockdown, biol rep 3

description:
nHDF_RawCounts.txt
nHDF3_ITPRIPL2


title: TGFB1_24h_2

value: 5ng/mL recombinant TGF-β1


title: SI Apc Kras/+ Rep4

value: vilCreER Apcfl/fl KrasG12D/+


title: SI Apc Kras/+ Pik3ca/+ Rep4

value: Small Intestine


title: TGFB1_6h_3


title: SI Apc Kras/+ Rep3


title: heart biopsy_TCMR_TH8

value: TCMR


title: heart biopsy_Mixed_TH9


title: TGFB1_6h_2


title: heart biopsy_pABMR_TH11

value: pABMR


title: TGFB1_1h_2


title: no_TGFB1_0h_2


title: nHDF cells, ITPRIPL2 knockdown, biol rep 1

description:
nHDF_RawCounts.txt
nHDF1_ITPRIPL2


title: SI Apc Kras/+ Rep2


title: nHDF cells, ITPRIPL2 knockdown, biol rep 2

description:
nHDF_RawCounts.txt
nHDF2_ITPRIPL2


title: heart biopsy_NR_TH10


title: heart biopsy_NR_TH7


title: SI Apc Kras/+ Rep1


title: nHDF cells, non-targetting control, biol rep 4

description:
nHDF_RawCounts.txt
nHDF4_GFP

value: non-targetting (GFP) esiRNAs

value: control


title: SI Apc Rep3

value: Day 4

value: vilCreER Apcfl/fl


title: heart biopsy_NR_TH5

value: heart biopsy


title: nHDF cells, non-targetting control, biol rep 3

description:
nHDF_RawCounts.txt
nHDF3_GFP


title: SI Apc Rep2

value: Female


title: TGFB1_24h_1


title: nHDF cells, non-targetting control, biol rep 2

description:
nHDF_RawCounts.txt
nHDF2_GFP


title: TGFB1_1h_1


title: TGFB1_6h_1


title: Control_pooled_smrt3

city: Solna

first: Saida

last: Hadjab

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Smartseq3-express
adata_drg_smrt3_WT.h5ad

data_processing:
For 10x snMultiomics, the raw fastq files were processed with Cell Ranger Arc software v2.0.2
For smartseq3, the raw fastq files were process with zUMIs software v2.9.7
Assembly: mm10
Supplementary files format and content: For 10x snMultiomics, the processed files are in h5 (count matrices) and tsv (ATAC fragments) formats.  The files with .h5 format contain the count matrices for both GEX and ATAC modalities within the same file. The atac_peak_annotation.tsv files contain the annotation of the peaks regions in the ATAC count matrices found in .h5 files.
Supplementary files format and content: For smartseq3, the processed files are in h5ad format (count matrix)

source_name: Dorsal Root Ganglia (all DRGs)

extract_protocol:
For snMultiomic: L4-L6 DRGs from mice were collected at 14 days after CCI injury or without injury, and then immediately put on dry ice. Nuclei were extracted from frozen DRG according to a published protocal by the Allen Institute for Brain Science. Pooled nuclei suspension were used for snMultiomic sequencing.
For smartseq3, all DRGs from mice were collected and immediately put on dry ice. Nuclei were extracted from frozen DRG according to a published protocal by the Allen Institute for Brain Science. Nuclei suspension was incubated with anti-NeuN PE conjugated antibody and DAPI. Single NeuN+ and DAPI+ nuclei were sorted into each well of a 384 well plate RNA-for smartseq3 sequencing.
Library was performed according to the manufacter’s instructions (Single Cell Multiome ATAC + Gene Expression protocal, 10x Genomics)
10x snMultiomics

value: Dorsal Root Ganglia (all DRGs)

value: WT

value: Control, Pooled (4 mice)


title: SI Apc Rep1


title: no_TGFB1_0h_1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 6

status: Public on Jul 18 2024

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts, normalized fragments-per-kilobase-per-million-mapped (FPKM), or normalized transcripts-per-million-mapped (TPM).

source_name: spleen

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacture’s protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

value: spleen

tag: age in_days_post_conception


title: nHDF cells, non-targetting control, biol rep 1

description:
nHDF_RawCounts.txt
nHDF1_GFP

value: nHDF

value: Fibroblast


title: heart biopsy_NR_TH6

value: NR


title: heart biopsy_NR_TH4


title: heart biopsy_NR_TH3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 4

value: Male


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 5


title: heart biopsy_NR_TH1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 3


title: Dp16; spleen; sample 4


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 2


title: Dp16; spleen; sample 5


title: Dp16; spleen; sample 6


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); spleen; sample 1


title: Dp16; spleen; sample 3


title: heart biopsy_NR_TH2


title: Dp16; spleen; sample 1


title: TGFB1_48h_1

value: 5ng/mL recombinant TGF-β1


title: Dp16; spleen; sample 2


title: Wild-type; spleen; sample 4

value: wild-type C57BL/6J


title: Wild-type; spleen; sample 6


title: Wild-type; spleen; sample 5


title: Wild-type; spleen; sample 2


title: Wild-type; spleen; sample 1


title: Dp16; liver; sample 6

source_name: liver

value: liver

tag: age in_weeks_post-birth


title: Wild-type; spleen; sample 3

tag: treatment


title: Dp16; liver; sample 3


title: Dp16; liver; sample 1


title: Dp16; liver; sample 5


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 6


title: Dp16; liver; sample 2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 4


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 2


title: Wild-type; liver; sample 6


title: Wild-type; liver; sample 5


title: Wild-type; liver; sample 2


title: Wild-type; liver; sample 1


title: Wild-type; liver; sample 3


title: Wild-type; liver; sample 4


title: Dp16; kidney; sample 6

source_name: kidney

value: kidney


title: Dp16; kidney; sample 2


title: Dp16; kidney; sample 4


title: Dp16; kidney; sample 5


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 6


title: Dp16; kidney; sample 3


title: Dp16; kidney; sample 1


title: Dp16; liver; sample 4


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample 5


title: Wild-type; kidney; sample 5


title: Wild-type; kidney; sample 6


title: Wild-type; kidney; sample 3


title: Wild-type; kidney; sample 4


title: ARPE-19 WDR5-FLAG, CUT&RUN, IgG, rep1

value: Retinal pigmented epithelium

value: ARPE-19 (ATCC, CRL-2302)

value: WDR5-FLAG stable expression

value: Rabbit IgG (Cell Signaling #66362)


title: Wild-type; kidney; sample 1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 5

source_name: brain cortex

value: brain cortex

value: Female

tag: age in_weeks


title: Wild-type; kidney; sample 2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 5


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 4


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 6


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); cortex; sample 1


title: Dp16; cortex; sample 2


title: Dp16; cortex; sample 4


title: Dp16; cortex; sample 1


title: Dp16; cortex; sample 5


title: Dp16; cortex; sample 3


title: Dp16; cortex; sample 6


title: Wild-type; cortex; sample 5


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); kidney; sample 4


title: Wild-type; cortex; sample 6


title: Wild-type; cortex; sample 4


title: Wild-type; cortex; sample 2


title: Wild-type; cortex; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); hippocampus; sample 5

source_name: brain hippocampus

value: brain hippocampus


title: Wild-type; cortex; sample 1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); hippocampus; sample 4


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); hippocampus; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); hippocampus; sample 1


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); hippocampus; sample 2


title: Dp16; hippocampus; sample 6


title: Dp16; hippocampus; sample 5


title: Dp16; hippocampus; sample 4


title: Dp16; hippocampus; sample 3


title: Dp16; hippocampus; sample 2


title: Dp16; hippocampus; sample 1


title: Wild-type; hippocampus; sample 1


title: Wild-type; hippocampus; sample 4


title: Wild-type; hippocampus; sample 5


title: Mac_C-3

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
The read quality was assessed with FastQC software.
The reads were mapped to the mouse genome (Mus musculus GRCm38; Ensembl release 98) by using STAR software, version 2.6.1c.
Transcript abundance estimates were calculated using the featureCounts software.
Expression normalization and differential gene expression calculations were performed in DESeq2 software.
Assembly: GRCm38
Supplementary files format and content: tab delimited text file containing raw read counts

source_name: peritoneal lavage

growth_protocol: ID8 cells were grown in DMEM media with 1% ITS, 1x Penicillin and streptomycin, 4% FBS. PMJ2R cells were cultured in DMEM with 4 mM Glutamine,1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 5 mM HEPES and 5$ FBS.

extract_protocol:
After treatment, ID8 cells were trypsinized, washed with cold PBS, and centrifuged at 1500 rpm for 5 minutes. The pellet was then flash-frozen. PMJ2R cells were centrifuged at 1500 rpm for 5 min at 4 °C and washed with cold PBS. The pellet was then flash-frozen in liquid nitrogen. ID8 and PMJ2R pellets were submitted to the genomics core at the University of Kansas Medical Center for mRNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both ID8 cells and PMJ2R cell line were treated with 5 nM rebastinib for 6h. Cell pellet was submiited to the genomics core for RNA extraction and sequencing.

value: peritoneal lavage

value: C57BL6J  with v-raf and v-myc oncogenes

value: macrophage

value: Control


title: Mac_R-2

value: 5nM rebastinib for 6h


title: Mac_R-3


title: Mac_C-2


title: Mac_R-1


title: ID8_C-3

source_name: ovarian epithelium

value: ovarian epithelium

value: C57BL6J wildtype

value: epithelial


title: Wild-type; hippocampus; sample 6

value: wild-type C57BL/6J

value: Male


title: ID8_C-2


title: Mac_C-1


title: Wild-type; hippocampus; sample 3


title: ID8_C-1


title: ID8_R-1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 2 gastruloids replicate 2

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

data_processing:
For data analysis, adapter and bad quality bases were removed from fastq files using cutadapt version 1.18  (Martin, 2011) (-q 30 -m 15 and sequences for -a and -A were adapted to the library).
Filtered reads were aligned on mm10 using STAR version 2.7.10a (Dobin et al, 2013) with the ENCODE parameters and a custom gtf (https://doi.org/10.5281/zenodo.7510406). Coverages were also obtained by STAR.
FPKM were computed with cufflinks version 2.2.1 (Roberts et al, 2011; Trapnell et al, 2010) using --max-bundle-length 10000000 --multi-read-correct --library-type "fr-firststrand" -b mm10.fa --no-effective-length-correction -M mm10_chrM.gtf.
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample)

source_name: gastruloid

extract_protocol:
Gastruloids were collected and RNA was extracted as in (Beccari et al, 2018).
Most of Llibraries were prepared with ISML kit from Illumina but two replicates of HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 at 120h were prepared with the TruSeq Stranded mRNA kit from Illumina.

value: gastruloid

tag: library

tag: stage (h_after_agregation)


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 2 gastruloids replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10):Del(CBS7-10) gastruloids replicate 1


title: Wild-type; hippocampus; sample 2


title: RNA-seq of 144h HoxB Del/Del(i9-13) gastruloids replicate 1

value: HoxB Del/Del(i9-13)


title: RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 3


title: RNA-seq of 168h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1


title: RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1


title: RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10):Del(CBS7-10) gastruloids replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 4


title: ID8_R-3


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1


title: RNA-seq of 96h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1


title: ID8_R-2


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS8-10) gastruloids replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS7-10)  gastruloids replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS5-10) gastruloids replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS7-10)  gastruloids replicate 2


title: RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS8-10) gastruloids replicate 1


title: CTCF CUT&RUN of HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS8-10) mESC

data_processing:
Adapter and bad quality bases were removed from fastq files using cutadapt version 4.1 (Martin, 2011)(-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-q 30 -m 15).
Filtered reads were aligned on the in silico mutant genome using bowtie2 version 2.4.5 (Langmead & Salzberg, 2012)with adapted parameters (--very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000).
No filtering for mutlimap reads was performed as sequences are duplicated between both alleles of chromosome 11.
PCR duplicates were removed with Picard MarkDuplicates version 2.27.4 (Broad Institute).
Filtered BAM file was converted to BED with BEDTools version 2.30.0 (Quinlan & Hall, 2010).
Coverage was computed with macs2 version 2.2.7.1 (Zhang et al, 2008) (--nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B) and then normalized to the million reads in peaks.
Assembly: mm10_HoxB_deli9-13insCBS5-10_del
Supplementary files format and content: *bw = coverage normalized to million reads in peaks
Supplementary files format and content: *narrowPeak.gz = peak obtained by macs2
Library strategy: CUT&RUN

source_name: mESC

extract_protocol:
Each ESC per genotype were washed into fresh PBS before dissociation. The dissociation was performed in 0.5mL StemPro Accutase (Gibco A1110501), 5min at 37°C. Cells were resuspended into 2mL of ESC media and span at 300g for 2min.
Then, 0.5x106 cells were processed according to the CUT&RUN protocol55. First, cells were resuspended into 1mL of Wash Buffer (WB: 20mM HEPES-KOH pH7.5, 150 mM NaCl, 0.5mM Spermidin (Sigma S2626)) and bound to Concanavalin A-coated beads (BioMagPlus 86057) into Digitonin Wash Buffer (DWB) using a ﬁnal concentration of 0.02% digitonin (Apollo APOBID3301) into WB. Second, cells were incubated with 0.5µg/100μl of anti-CTCF antibody (Active Motif 61311) in DWB at 4°C for 2hr. The pA-MNase was produce by the Protein Production and Structure Core Facility at EPFL and added at 0.5 μl/100 μl in Digitonin Wash Buffer for 1hr at 4°C. Third, cells were digested in Low Calcium Buffer (100mM CaCl2 into DWB). Reaction was stopped using cold 2X STOP Buffer (340mM NaCl, 4mM EGTA, 20mM EDTA, 0.02% Digitonin, 50µg RNase A (10mg/mL), 50µG Glycogen (5mg/mL)) for 5min. Finally, targeted chromatin was released for 30 min at 37 °C, then precipitated into 70% EtOH and stored at -20°C until sequencing libraries generation. Sequencing libraries were prepared with KAPA HyperPrep reagents (07962347001) with 2.5µl of adapters at 0.3µM and ligated for 1 h at 20 °C. Then, DNA was cleaned and size selected using 1:1 ratio of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. The DNA was ampliﬁed for 16 cycles. Post-ampliﬁed DNA was cleaned and size selected using 1:1 ratio followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5 M NaCl.

tag: cell line

value: mESC

tag: antibody

value: CTCF (61311, Active Motif)


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 3

value: HoxB Del/Del(i9-13):Ins(CBS5-10)


title: RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 1


title: CTCF CUT&RUN of HoxB Del/Del(i9-13):Ins(CBS5-10) mESC


title: CMO mulitplexing library on WT gastruloids at 96h other replicates

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

library_source: other

data_processing:
Gene expression librairies were analysed similarly for standard 10x and CellPlex samples to generate the cell-gene expression matrices. For both Mapping, demultiplexing of cell barcode and quantification was performed using rna_STARsolov2.7.10b on the mm10 reference genome, and a modified gtf file based on Ensembl v102, with the parameters: --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'Gene Expression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000. Then DropletUtils v1.10.0 was used to remove barcodes which were not corresponding to cells (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01). Cell multiplexing oligo (CMO) librairies which identify the sample of origin in multiplexed experiments were quantified using CITE-seq-Count v1.4.455 --cell_barcode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 --bc_collapsing_dist 1 --umi_collapsing_dist 2 --expected_cells 24000 --whitelist '3M-february-2018.txt' --max-error 2.
Individual 10x gene expression librairies, were analysed using Seurat v4.3. We first filtered out barcodes with less than 200 identified gene and genes identified in less than three cells. For CMO libraries, the demultiplexing by barcode was done in R using counts from CITE-seq-Counts. Cell barcodes with less than 5 CMO UMI and absent in the seurat object were discarded. Then sample attribution was performed using demuxmix using the total number of UMI per cell. Cells which were not classified by demuxmix as singlet (negative, unsure, doublet) were excluded from the analysis.
Low quality cells and potential doublets were removed by computing the mean UMI content and the percentage of mitochondrial genes and filtering out barcodes with less than 0.4 times the mean UMI or more than 2.5 times the mean UMI. Only barcodes between 0.05 and 8 percent of mitochondrial UMI were kept. Matrices were normalised and the cell cycle score (using the 2019 updated gene list from Seurat) from these filtered libraries were computed. Then we merged the different samples using the merge command by Seurat. The combined Seurat object was then normalised, 2000 variable features were identified and the data was scaled and regressed by cell cycle score, and percentage of mitochondrial reads. Principal component were then computed using variable genes falling within the 5th and 80th percentile of expression to limit batch effect as performed here. UMAP and k-nearest neighbors were then computed using 30 principal components. The resolution to cluster the data was chosen by ensuring that no cluster was missed, and that no duplicated clusters were found. Cluster annotation was performed manually. Marker identification was done using a maximum of 400 cells per identity to limit the impact of widely variable cluster sizes in the ability to identify markers, these also required a difference of 20% in the proportion of expressing cells and a logFC >0.5.
For RNA velocity analysis, Velocyto v0.17.1759 was used with the run10x command on the BAM files generated by STARsolo. Then, velocyto.R v0.6 was used to identify the velocity using the RunVelocity function with the settings: spliced.average = 0.2, unspliced.average = 0.02, deltaT = 1, kCells = 20, fit.quantile = 0.02. RNA velocity was then displayed on the UMAP embedding with the show.velocity.on.embedding.cor function with the setting: n = 300, scale='sqrt', cell.colors = ac(subset.seurat$FateColor, alpha=0.5), cex=0.8, arrow.scale = 5, show.grid.flow=TRUE, min.grid.cell.mass = 0.5, grid.n=40, arrow.lwd = 1, do.par = F, cell.border.alpha = 0.
Scoring of cells based on this list of genes up- /down-regulated in Snai1-/- was performed with the addModuleScore by Seurat. All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: loom: output of velocyto (quantification of spliced and unspliced)
Supplementary files format and content: tar.gz: output of STARsolo or CITE-seq-Counts (translated) as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)
Supplementary files format and content: RDS: R object with everything to redo the plots
Supplementary files format and content: CMO.Samples.csv: comma separated text file with for each Library (first column), the different samples (second column), with their barcodes (third column). A sample to NA indicates that it has not been used into this study

molecule: other

source_name: Gastruloids

extract_protocol:
Gastruloids were collected, pooled in a 1.7 ml Eppendorf tube and washed twice in 1 ml of PBS. The number of gastruloids used in each condition was chosen to ensure that more than 300 000 cells were obtained. They were then dissociated in 100 µl of Accutase (Stempro) for 5 min at 37°C. Full dissociation was completed using mechanical dissociation and verified to ensure the absence of doublet cells. Cells were then resuspended in 200 µl of PBS and counted on a Countess 3 automated cell counter (Invitrogen). All centrifugations were done at 400g for 5 minutes. Some samples were then analysed with the standard 10x genomics pipeline (Chemistry v3 and v3.1), while others also included a CellPlex procedure to multiplex samples (see Supplementary Table 6 for list of samples and the method used). For the sample treated with the normal 10x procedure, after counting, dissociated cells were diluted in PBS BSA 0.04% (Millipore, A1595) to 1x106 cells/ml. For samples treated with the CellPlex multiplexing approach, cells were pelleted and incubated for 5 minutes in 50 µl of cell multiplexing oligos (3' CellPlex Kit Set A, PN-1000261) at room temperature. They were then washed three times with 1ml of PBS 1% BSA and finally they were resuspended in 110 µl of PBS 1% BSA and counted. The multiplexed samples were then pooled in equal proportions for each targeted sample. Both CellPlex and standard 10x Genomics sample were then filtered using a 40 µm cell strainer (Flowmi, BAH136800040).
The pool of cells was counted and subjected to single cell RNA-seq following manufacturer’s recommendation similarly as non-CellPlex samples (protocol CG000388 Rev A). For standard 10x samples, we aimed for a recovery of c.a. 6000 cells per sample while for multiplexed single cell RNA-seq we aimed for a recovery of maximum 24 000 cells as more doublet can be resolved with this method. cDNA preparations were performed according to 10x Genomics recommendations, amplified for 10–12 cycles and verified on fragment analyser. Both cell multiplexing oligo, and gene expression libraries were sequenced on a HiSeq 4000 (ref 15065681 v03) or a Novaseq (Illumina protocol #1000000106351 v03) with the cbot2 chemistry.

value: Gastruloids

tag: Stage

value: WT

tag: multiplexing

value: CellPlex

tag: 10x well

tag: background


title: CMO mulitplexing library on WT gastruloids at 144h

tag: tissue

tag: genotype


title: CMO mulitplexing library on WT and Snai1 KO gastruloids at 72h

description: Pool_72h.WT.rep2.3.vs.Snai1KO.rep1.2.CMO

value: Snai1 WT and KO


title: RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 2


title: CMO mulitplexing library on WT gastruloids at 96h


title: CMO mulitplexing library on WT gastruloids at 120h


title: CMO mulitplexing library on WT gastruloids at 168h and mESC at 0h

source_name: mESC and gastruloids

value: mESC and gastruloids

value: 0h and 168h


title: scRNA-seq on WT gastruloids at 120h replicate 5


title: Colletotrichum camelliae △CcCp1 treated rep3

city: Changchun

first: Shouan

last: Liu

address: Xian Da Road

country: China

institute: Jilin University

description:
Colletotrichum camelliae △CcCp1 treated sample 3
CPm3

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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

organism: Camellia sinensis

source_name: leaf

growth_protocol: The tea plant Longjing43 were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark.The plants were watered once a week and kept growing for about 2 years.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TheColletotrichum camelliae CCA and △CcCp1 were grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were spray infected with 1*106 spores mL-1. The buffer without any spores were sprayed as untreated control (CK). All leaves were harvest at 24 hours and frozen at -80℃ for RNA sequencing.

value: leaf

tag: developmental stage

value: 2 years old tea plant

tag: cultivar

value: Colletotrichum camelliae deltaCcCp1 treated


title: scRNA-seq on Snai1.KO gastruloids at 96h clone 2 replicate 1

value: Snai1 KO


title: Colletotrichum camelliae CCA treated rep3

description:
Colletotrichum camelliae CCA treated sample 3
CC3

value: Colletotrichum camelliae CCA treated


title: Colletotrichum camelliae △CcCp1 treated rep1

description:
Colletotrichum camelliae △CcCp1 treated sample 1
CPm1


title: scRNA-seq on Snai1.KO gastruloids at 120h clone 2 replicate 1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS5-10) gastruloids replicate 2


title: scRNA-seq on WT gastruloids at 96h replicate 6


title: Colletotrichum camelliae CCA treated rep1

description:
Colletotrichum camelliae CCA treated sample 1
CC1

value: Colletotrichum camelliae  CCA treated


title: Colletotrichum camelliae CCA treated rep2

description:
Colletotrichum camelliae CCA treated sample 2
CC2


title: scRNA-seq on WT gastruloids at 168h replicate 1


title: Colletotrichum camelliae △CcCp1 treated rep2

description:
Colletotrichum camelliae △CcCp1 treated sample 2
CPm2


title: CK rep2

description:
uninfected control samples replicate 2
CK2

value: control


title: CK rep3

description:
uninfected control samples replicate 3
CK3


title: Multiplexed scRNA-seq on WT gastruloids at 144h


title: CK rep1

description:
uninfected control samples replicate 1
CK1


title: Multiplexed scRNA-seq on WT gastruloids at 120h


title: LNC-Iso2-R1881-2_S17_L001_R1_001.fastq.gz

city: Syracuse

first: Leszek

last: Kotula

state: New York

address: 750 East Adams Str

institute: Upstate Medical University

description: Sample 17

data_processing:
Primary analysis was performed on Partek Flow Genomic Analysis Software
Reads were aligned to the Homo sapiens genome (hg38) using STAR – 2.7.3a
Alignments were quantified using Partek E/M
Quantified alignments were normalized with CPM counts per million), followed by addition of 0.0001 for all samples
Assembly: Homo sapiens genome (hg38)
Supplementary files format and content: Tab-separated values matrix file containing raw read counts (Gene_counts.txt) and normalized read counts (Normalized_counts.txt) are provided

source_name: LNCaP

growth_protocol: Adherent cultures were grown in DMEM at 37C with 5% CO2

extract_protocol:
Qiagen Qiashredder and RNAeasy Extraction Kit
Illumina TruSeq Stranded mRNA Library Prep kit, using 1 microgram total RNA as input. Sequencing was performed using 2 x 101 bp paire-end reads.

treatment_protocol: DMSO or R1881 1nM was applied for 48 hours

value: LNCaP

value: Iso2 Rescue


title: LNC-Iso2-untreated-3_S15_L001_R1_001.fastq.gz

description: Sample 15

value: untreated


title: scRNA-seq on WT gastruloids at 120h replicate 2


title: scRNA-seq on Snai1.KO gastruloids at 120h clone 1 replicate 2


title: LNC-Iso2-R1881-1_S16_L001_R1_001.fastq.gz

description: Sample 16


title: scRNA-seq on Snai1.KO gastruloids at 96h clone 1 replicate 2


title: LNC-Iso2-untreated-2_S14_L001_R1_001.fastq.gz

description: Sample 14


title: LNC-KO15-R1881-3_S12_L001_R1_001.fastq.gz

description: Sample 12

value: KO


title: scRNA-seq on WT gastruloids at 120h replicate 1

value: Gastruloids


title: LNC-KO15-R1881-2_S11_L001_R1_001.fastq.gz

description: Sample 11


title: LNC-KO15-R1881-1_S10_L001_R1_001.fastq.gz

description: Sample 10


title: LNC-Iso2-untreated-1_S13_L001_R1_001.fastq.gz

description: Sample 13


title: LNC-Iso2-R1881-3_S18_L001_R1_001.fastq.gz

description: Sample 18


title: Multiplexed scRNA-seq on WT gastruloids at 96h

value: WT


title: LNC-KO15-untreated-3_S9_L001_R1_001.fastq.gz

description: Sample 9


title: scRNA-seq on WT gastruloids at 96h replicate 2


title: LNC-KO15-untreated-2_S8_L001_R1_001.fastq.gz

description: Sample 8


title: scRNA-seq on WT gastruloids at 96h replicate 1


title: S2.Myc.IKK.1

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

description: Plasmablast

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw illumina text files were read into R(version3.4) and normalised using the lumi package

source_name: FACS purified

label_protocol: Standard Illumina  protocol

growth_protocol: Cells were grown at 1x106/mL in B-cell media (DMEM high glucose with Glutamax (Gibco), supplemented with Fetal Bovine Serum (GE Healthcare), non-essential aminoacids (Gibco), HEPES buffer (Gibco), sodium pyruvate (Gibco), Penicillin-Streptomycin (Gibco), and 2-Mercaptoethanol (Sigma-Aldrich), at 37 °C in 5% CO2.

extract_protocol: AllPrep DNA/RNA Mini and Micro Kits (Qiagen)

treatment_protocol: B cells were stimulated with Lipopolysaccharide (LPS; Sigma-Aldrich) at a concentration of 10ug/mL.

tag: genotype/variation


title: S1.Myc.IKK1

description: Plasmablast


title: S2.Myc.IKK.2

description: Plasmablast


title: S1.Myc.IKK2

description: Plasmablast


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 2

value: gastruloid

value: HoxB Del/Del(i9-13):Ins(CBS5-10)


title: S2.IKK2.2

description: Plasmablast


title: Multiplexed scRNA-seq on WT gastruloids at 96h other replicates

value: CellPlex


title: S2.IKK2.1

description: Plasmablast


title: LNC-KO15-untreated-1_S7_L001_R1_001.fastq.gz

description: Sample 7


title: RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 2

value: HoxB Del/Del(i9-13)


title: Multiplexed scRNA-seq on WT and Snai1 KO gastruloids at 72h

value: Snai1 WT and KO


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 1


title: S1.IKK2.2

description: Plasmablast


title: S1.IKK2.1

description: Plasmablast


title: LNC-parent-R1881-3_S6_L001_R1_001.fastq.gz

description: Sample 6

value: parent


title: LNC-parent-R1881-2_S5_L001_R1_001.fastq.gz

description: Sample 5


title: RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 1


title: scRNA-seq on WT gastruloids at 48h replicate 1


title: scRNA-seq on WT gastruloids at 72h replicate 1


title: RNA-seq of E10.5 headless embryo Hoxb13hd homozygous replicate 3

data_processing:
For data analysis, adapter and bad quality bases were removed from fastq files using cutadapt version 1.18  (Martin, 2011) (-q 30 -m 15 and sequences for -a and -A were adapted to the library).
Filtered reads were aligned on mm10 using STAR version 2.7.10a (Dobin et al, 2013) with the ENCODE parameters and a custom gtf (https://doi.org/10.5281/zenodo.7510406). Coverages were generated by STAR.
FPKM were computed with cufflinks version 2.2.1 (Roberts et al, 2011; Trapnell et al, 2010) using --max-bundle-length 10000000 --multi-read-correct --library-type "fr-firststrand" -b mm10.fa --no-effective-length-correction -M mm10_chrM.gtf.
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified_E.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts_E.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample)

source_name: headless embryo

growth_protocol: Murine E9.5 and E10.5 mutant or wild-type littermate embryos were dissected to remove the head.

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen) following the manufacturer recommendation.
The E9.5 samples libraries are poly(A)-enriched and E10.5 are ribo-depleted. Both were prepared with stranded RNA TruSeq kits (Illumina).

value: headless embryo

value: Hoxb13hd homozygous

value: Ribo-depleted


title: Multiplexed scRNA-seq on WT gastruloids at 168h and mESC at 0h

value: mESC and gastruloids

value: 0h and 168h


title: LNC-parent-R1881-1_S4_L001_R1_001.fastq.gz

description: Sample 4

value: LNCaP


title: S2.Myc1

description: Plasmablast

value: Myc


title: LNC-parent-untreated-3_S3_L001_R1_001.fastq.gz

description: Sample 3

value: untreated


title: RNAseq of 96h Snai1 KO clone 2 gastruloids replicate2

data_processing:
Raw RNA-seq reads generated in this study were trimmed to remove Nextera adapters or bad quality bases (Cutadapt v4.043 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15). Mapping and counting were performed on filtered reads on the mouse genome mm10 with STAR version 2.7.8a44 with a custom gtf based on Ensembl version 10245 and ENCODE parameters. FPKM values were obtained by Cufflinks version 2.2.146,47 with options --no-effective-length-correction -b 'mm10.fa' --multiread-correct --library-type fr-firststrand --mask-file 'chrM_mm10.gtf' --max-bundle-length 10000000 --max-bundle-frags 1000000 (where chrM_mm10.gtf contains a transcript on each strand of the whole chrM). Uniquely mapped reads were filtered with bamFilter48 version 2.5.1. Coverages were computed with BEDTools49 version 2.30.0 for each strand using the '-scale' parameter to normalize to million uniquely mapped reads. Average between duplicates was performed with bigwigAverage v3.5.4 from deepTools50. All samples were of good quality and none were excluded from the analysis. Genes were called differentially expressed when they had both abs(log2fc) > 1 and padj < 0.05
All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: repX_both_strands.bw: normalized coverage (to million of uniquely mapped reads) with both strands combined
Supplementary files format and content: repX_negative_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on negative strand
Supplementary files format and content: repX_positive_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on positive strand
Supplementary files format and content: .bw: average of normalized coverage of the two or three replicates (96h_WT is the average of rep1, rep2 and rep3 while 96h_Snai1WT is the average of 96h_WT_rep4 and rep5)
Supplementary files format and content: tablesX.tar.gz: archive with two tables: AllCufflinks_Simplified.txt.gz: single table with all FPKM values from cufflinks and AllHTSeqCounts.txt.gz: single table with all counts from STAR
Supplementary files format and content: DESeq2_summary.txt: tabular separated text file where each row is a gene and columns indicates log2FC, padj and weather it was significant in each of the analysis
Supplementary files format and content: DESeq2_summary_long.txt: tabular separated text file where each row is a gene in a DESeq2 comparison. This format is more compatible with ggplot2.

extract_protocol:
Gastruloids were collected and pooled in a 2-ml Eppendorf tube at the indicated timepoints. After medium removal, gastruloids were washed once with PBS, pelleted and stored at −80 °C until RNA extraction. RNeasy Mini kit (Qiagen) with on-column DNase digestion was used for RNA extraction following manufacturer’s instructions. RNA quality was assessed on a Tapestation TS4200, all RNA samples showed quality number (RIN) above 9.5.
RNA-seq library preparation with Poly-A selection was performed with 1000 ng (for time course analysis) or 500 ng (for mutant gastruloid analysis) of RNA using the Illumina stranded mRNA ligation and following the manufacturer’s protocol 1000000124518 v01. Library quality was assessed with a Libraries were quantified by qubit DNA HS and profile analysis was done on TapeStation TS4200. Libraries were sequenced on HiSeq 4000 Illumina, with paired end 75 bp reads.

value: Snai1 KO

tag: replicate

tag: clone


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13):Hoxb13hd homozygous replicate 3

value: HoxB Del(i9-13):Hoxb13hd homozygous


title: LNC-parent-untreated-2_S2_L001_R1_001.fastq.gz

description: Sample 2

tag: treatment


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13):Hoxb13hd homozygous replicate 2


title: RNAseq of 96h Snai1 KO clone 2 gastruloids replicate1

value: Gastruloids


title: LNC-parent-untreated-1_S1_L001_R1_001.fastq.gz

description: Sample 1


title: S2.Myc2

description: Plasmablast


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13):Hoxb13hd homozygous replicate 1


title: RNA-seq of E10.5 headless embryo Hoxb13hd homozygous replicate 2


title: RNAseq of 96h Snai1 KO clone 1 gastruloids replicate2


title: RNA-seq of E10.5 headless embryo Hoxb13hd homozygous replicate 1


title: S1.Myc2

description: Plasmablast


title: RNAseq of 96h Snai1 KO clone 1 gastruloids replicate1


title: RNAseq of 96h WT gastruloids replicate5

value: WT


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13) homozygous replicate 3

value: HoxB Del(i9-13) homozygous


title: S2.Ctrl2

description: Plasmablast

value: Ctrl


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13) homozygous replicate 2


title: S1.Ctrl1

description: Plasmablast


title: S2.Ctrl1

description: Plasmablast


title: RNA-seq of E10.5 headless embryo wild-type replicate 3

value: wild-type


title: RNA-seq of E10.5 headless embryo HoxB Del(i9-13) homozygous replicate 1


title: RNAseq of 120h Cdh2 KO clone 2 gastruloids replicate2

value: Cdh2 KO


title: O: Control VS GE-0132

city: Elche

first: Víctor M.

last: Barberá

state: Not US or Canada

address: Camí de l'Almazara, 11

department: Laboratorio de Genética Molecular

country: Spain

institute: Hospital General Universitario de Elche

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5)

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: non-tumor brain RNA (pool from five donors)

label_protocol: Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling (version 6.5)

growth_protocol: The samples were not cultured or treated in cell culture, they were processed directly from the surgical resection specimen of the tumor.

extract_protocol: Total RNA isolation from human GBM biopsies was performed using the RNAqueous-Micro Kit (Ambion), following the manufacturer’s instructions. Normal human brain RNA was purchased from BioChain

tag: age

value: Pooled

tag: Sex

source_name: Untreated glioblastoma multiforme specimen 4

value: Female


title: S1.Ctrl2

description: Plasmablast


title: P: Control VS GE-0120

treatment_protocol: The samples were not cultured or treated in cell culture, they were processed directly from the surgical resection specimen of the tumor.

source_name: Untreated glioblastoma multiforme specimen 6


title: N: GE-0132 VS Control


title: RNAseq of 120h Cdh2 KO clone 1 gastruloids replicate2


title: RNAseq of 120h Cdh2 KO clone 2 gastruloids replicate1


title: RNA-seq of E10.5 headless embryo wild-type replicate 1

value: headless embryo

tag: library


title: L: GE-0134 VS GE-0127

source_name: Untreated glioblastoma multiforme specimen 8

value: Male

source_name: Untreated glioblastoma multiforme specimen 7


title: RNAseq of 96h WT gastruloids replicate4


title: RNAseq of 120h Cdh2 KO clone 1 gastruloids replicate1


title: coTAK-2 CD8

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: T cell

growth_protocol: CS1-CAR T cells were thawed and cultured in RPMI medium with 10% FBS, 50U/ml IL2, and 0.5ng/ml rhIL15.

extract_protocol:
Total RNA of sorted cells were exacted using Qiagen miRNAeasy kit.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

treatment_protocol: CS1-CAR T cells were treated with DMSO (Vehicle, Veh) or 0.1µM TAK-981 (TAK) for 16 h, then CD4+ and CD8+ subsets of CS1 CAR T cells treated were purified by FACS sorting after staining with CD4 and CD8 antibodies. In co-culture experiment, CS1-CAR T cells were treated with vehicle (Veh) or TAK-981 (0.1µM, TAK) for 16 h. CAR T were spin down and washed off compound, then CAR T cells were cultured with MM1S-Luc cells at 1:1 ratio for 24 h. Cell mixtures were harvested then CD4+ and CD8+ CAR T cells were purified by FACS sorting after staining with CD4 and CD8. In both experiments, CS1 CAR T cells generated from two individual donors were used as biological replicates.

tag: cell type

value: T cell

value: TAK-981, 0.1uM, 16h, then co-culture with MM1S for 24h


title: M: GE-0132 VS Control


title: coTAK-1 CD8


title: RNA-seq of E9.5 headless embryo HoxB Del(i9-13) homozygous replicate 3

value: poly(A)-enriched


title: coVeh-2 CD8

value: vehicle, co-culture with MM1S for 24h


title: RNA-seq of E10.5 headless embryo wild-type replicate 2

value: Ribo-depleted


title: RNAseq of 120h Cdh2 Het gastruloids replicate2

value: Cdh2 Het


title: RNA-seq of E9.5 headless embryo HoxB Del(i9-13) homozygous replicate 2


title: RNAseq of 120h Cdh2 Het gastruloids replicate1


title: J: GE-0127 VS GE-0134


title: RNA-seq of E9.5 headless embryo HoxB Del(i9-13) homozygous replicate 1


title: TAK-2 CD8


title: I: GE-0135 VS GE-0123

source_name: Untreated glioblastoma multiforme specimen 3

source_name: Untreated glioblastoma multiforme specimen 2


title: K: GE-0127 VS GE-0134


title: RNA-seq of E9.5 headless embryo wild-type replicate 3


title: RNA-seq of E9.5 headless embryo wild-type replicate 2


title: Veh-2 CD8

value: vehicle


title: TAK-1 CD8


title: RNAseq of 96h WT gastruloids replicate2

value: Gastruloids


title: Veh-1 CD8


title: RNAseq of 96h WT gastruloids replicate3

value: WT


title: RNAseq of 96h WT gastruloids replicate1


title: BMDM_WT_3

city: San Francisco

first: Robert

last: Raffai

state: California

address: 4150 Clement St

department: Surgery

institute: University of California San Francisco

data_processing:
Aligned with STAR v 2.7.5c
Assembly: GRCm38
Supplementary files format and content: gene by read counts table text file

source_name: Bone marrow

growth_protocol: Bone marrow cells were collected from male mice that are 6- to 12-week-old. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% GlutaMAX, and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA were collected using the Qiagen RNeasy Mini Kit.
Universal Plus mRNA-Seq library preparation kit

treatment_protocol:
Cells were treated with 25 ng/mL recombinant murine M-CSF every two days for six days total.
Upon differentiation into BMDM, cells were treated with 2 x 10^9 particles/mL of EKO-BMDM-exo, or WT-BMDM-exo, or PBS for 18 hours.

value: Bone marrow

value: Bone marrow derived macrophages

tag: treatment 1

value: Macrophage differentiation w/ M-CSF

tag: treatment 2

value: WT-BMDM-exo


title: BMDM_WT_2


title: RNAseq of 90h WT gastruloids replicate3

tag: Stage


title: G: GE-0123 VS GE-0135


title: coTAK-2 CD4


title: RNA-seq of E9.5 headless embryo wild-type replicate 1

value: wild-type


title: S1.Myc1

description: Plasmablast

value: Myc


title: coTAK-1 CD4


title: E: GE-0112T VS GE-0120

source_name: Glioblastoma multiforme specimen with adjuvant treatment 1

value: Female


title: F: GE-0120 VS GE-0112T

value: Male


title: RNAseq of 90h WT gastruloids replicate1


title: BMDM_WT_1


title: RNAseq of 84h WT gastruloids replicate3


title: B: GE-0112 VS GE-0117

source_name: Untreated glioblastoma multiforme specimen 1

source_name: Untreated glioblastoma multiforme specimen 5


title: BMDM_PBS_3

value: PBS


title: coVeh-2 CD4

value: T cell


title: C: GE-0117 VS GE-0112


title: D: GE-0112T VS GE-0120


title: Aptamers, DNA , pyoverdine

city: Ames

first: Marit

last: Nilsen-Hamilton

state: Iowa

address: 2437 Pammel Dr

department: BBMB

institute: Iowa State University

data_processing:
Raw data are demultiplexed and assigned to respective rounds by open source software AptaSuite. Barcodes ATCACG,TAGCTT,GGCTAC,AGTCAA,CTTGTA,CGATGT and ACAGTG were used to assign rounds1,4,6,7,8,9 and 10 respectively. Quality control was performed by allowing a zero-nucleotide mismatch between the reference and matched barcodes, and no mismatches between the reference and matched primers. Any reads not conforming to these standards were excluded from downstream analysis. Aptamer families (clusters) were consequently extracted from each round using AptaCluster. We performed a total of 10 iterations of locality sensitive hashing, sampling 40% of the indices in the randomized regions and allowing no more than 10 nucleotide mismatches between the seed sequence of a cluster to each remaining member
Supplementary files format and content: S_1501 summary.xlsx: conatins the information about barcodes, pool size , count of unique fraction, singletons and enriched species. Also conatins the seed sequences from top 10K clusters.
Supplementary files format and content: S1501_1.tar: conatins demultiplexed and clustered output analyzed by aptasuite program
Library strategy: SELEX

organism: synthetic construct

source_name: not applicable

extract_protocol:
SELEX was performed with PYO-Pf5 as target to select DNA aptamers. For the first round of selection libraries of 1015 DNA were used. The biotinylated capture oligos, which are complementary to the short constant region in the library sequence, were attached to streptavidin coated magnetic beads. The DNA libraries were first hybridized with oligos complementary to the PCR primer regions and then immobilized on the beads by hybridization with the capture oligos. The length of the capture oligo varied with the SELEX round as did the hybridization temperature and the oligo: PYO-Pf5 ratio . The bound oligos were captured using a magnet and purified by ethanol precipitation in the presence of 2 µL linear polyacrylamide (LPA) . Purified DNAs were amplified by low fidelity Taq polymerase. The ratio of DNA to PYO-Pf5 was reduced and the length of capture oligo increased in successive SELEX rounds to increase selection pressure .  Ten rounds of selection were performed, and two sequential rounds of counter selection were done after rounds 3 and 6. The targets for counter selection were enterobactin and ornibactin. All targets used in selection and counter-selection were the Fe3+-bound forms. PCR-amplified libraries were prepared for NGS using Nextera Illumina sequencing primers and the appropriate bar coding. Next generation sequencing was performed by  Novogene facility, Sacramento, California using HiSeq PE150 platform. The raw NGS data was demultiplexed and assigned to respective rounds by open-source software AptaSuite. Barcodes were used to assign DNA pools from different rounds of selection. A zero-nucleotide mismatch between the reference and matched barcodes, and zero mismatches between the reference and matched primers were criteria for demultiplexing.  Further analysis was done with the sequences that met this standard. Clustering was done with 10 iterations of locality sensitive hashing, sampling 55% of the indices in the randomized regions and allowing no more than 10 nucleotide mismatches between the seed sequence of a cluster to each remaining member. Clusters were extracted for further analysis and aptamer screening.
PCR amplified libraries were prepared for NGS using Nextera Illumina sequencing primers and the appropriate bar coding.

value: not applicable

tag: selex target


title: BMDM_PBS_2


title: TAK-2 CD4