title: gDNA - Tracer mESC - Day5

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 5

extract_protocol:
gDNA was extracted from isolated Cas9-GFP+ Tracer mESCs at different days after Cas9-GFP activation for downstream intBCs library preparation. Briefly, 1x105-1x106 cell pellets from the indicated days were collected and lysed in 200µl Lysis buffer (10mM Tris-HCl pH=8.0; 10mM NaCl; 10mM EDTA; 0.5% SDS; 300 µg/mL Proteinase K) overnight at 55°C. The following day phenol:chloroform (Thermo, 15593031) extraction followed by precipitation overnight at -80°C (2.5V EtOH, 1/10V 5M NaCl and 1/100V molecular biology grade Glycogen (Thermo, R0561)) was performed to isolate gDNA. gDNA concentrations were measured using Qubit™ dsDNA HS- Kit (Thermo, Q32851) and same amount of input material was used for each sample for intBCs library preparation.
Isolated gDNA from Tracer mESCs and prepared cDNA from Tracer mESCs and individual Tracer TLS were used for Amplicon-seq intBCs library preparation. 200ng gDNA and 100ng cDNA were used as input material. Two subsequent PCR reactions were carried on to prepare the NGS library: (i) in the first step the input material was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.55x-0.8x) was performed and purified intBCs amplicons were eluted in 30µl EB buffer; (ii) in the second step, the whole eluate from the previous PCR reaction was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a AMPure XP beads (Beckman, A63881) cleanup (0.8x) was performed to purify amplicons libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using paired end sequencing (500 cycles kit; 250/250) on a Miseq platform at a minimum of 50 million fragments per sample.

value: LSL-Cas9-GFP-Tracer BC library

value: mESC


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C06_S318]

status: Public on Mar 05 2024

type: SRA

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

country: USA

institute: Tufts University

description:
hillockCounts.csv
sc_manju_hillock_newest_Seurat.rds

library_source: transcriptomic

data_processing:
FASTQ files were aligned using STAR to MM10 annotation
Aligned reads were then processed using Cufflinks
Downstream analysis was performed using Seurat v4.0
Assembly: mm10
Supplementary files format and content: a concatenated count file of all single cells, and a processed Rdata, Seurat object

molecule: total RNA

organism: Mus musculus

source_name: trachea

extract_protocol:
Cells were FACS plated into lysis buffer in 96 well plates, according to the SMART-Seq2 protocol
RNA libraries were made according to SMART-Seq2 protocols

tag: tissue

value: trachea

tag: cell type

value: hillock

tag: genotype

tag: phenotype

value: hillock structure


title: total RNA-seq from sample_011

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
Quality control with FastQC version 0.11.8
Unique Molecular Identifiers extraction with UMI-tools version 1.1.1
Adapter trimming with cutadapt version 2.10
Read aligning to the reference genome with STAR version 2.7.7a
Read deduplication with UMI-tools version 1.1.1
Quantification of gene expression with featureCounts version 1.6.4
Batch correction for the GC content and randomization_batch with ComBat_seq from the sva package version 3.38.0
Normalization with vst from DESeq2 version 1.30.1
Assembly: GRCh38.p12
Supplementary files format and content: raw_counts.tsv contains the output of featureCounts (unfiltered raw counts)
Supplementary files format and content: normalized_data.tsv contains the batch corrected and normalized data with low-count genes and genes that are heavily influenced by the GC content filtered out

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Blood was collected in the morning under fasted conditions, peripheral blood mononuclear cells (PBMCs) were extracted and stored at in the gas phase of liquid nitrogen. The RNA was extracted automatically with the chemagic 360 instrument by using the chemagic RNA Kit according to the manufacturer’s instructions and 25µl eluate stored in a PCR plate at -80°C until further processing.
200ng RNA was used for rRNA depletion with the RiboCop rRNA Depletion Kit V1.3. 10µl of the depleted RNA was used for library preparation with the Lexogen CORALL total RNA-Seq Library Prep Kit with UDIs 12 nt Sets A1-A4. The library was sequenced on an NovaSeq 6000 using an S4 200 flow cell with paired-end 100bp reads.

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: E

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C12_S324]


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C05_S317]


title: LEC Tie1 KO Replicate1

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
RNA sequencing reads were mapped to mouse genome mm10 using TopHat.
Reads were counted on the exons of mm10 genes using htseq.
Differential gene expression analysis was performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Dermal lymphatic endothelial cells

growth_protocol: Cells were FACS sorted from fresh E18.5 embryonic skin samples

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were sorted directed to lysis buffer

value: Dermal lymphatic endothelial cells

value: Tie1 knockout

tag: treatment

value: 0.5% Doxycycline water


title: cDNA - Tracer mESC - Day1

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 1

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference: "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomics.
The reads that did not align to the reference were further processed using the reference and algorithms from the Cassiopeia tool. First, the reads were aligned to the reference (“PCT48”) using the Smith-Waterman algorithm with parameters -gapopen 20 and -gapextend. Next, the intBC cut site information per barcode was determined using the callAlleles-PCT48.pl script. intBC patterns were classified based on the code from the indel table into Deletion&Insertion (I and D), Deletion (D), Insertion (I) or uncut. Barcodes that did appear in the known barcode list were assigned to the closest barcode if the edit distance was less than 4 and otherwise remove.
genome build: mm10
processed data files format and content: Matrix with cutsite label, frequency (coverage), cellBC and cut information for the three target sites.
Library strategy: Amplicon-seq

molecule: polyA RNA

growth_protocol:
All cell lines used are male and derived from an F1G4 genetic background (Nagy et al). Mouse embryonic stem cells (mESCs) have been cultured as previously described (Veenvliet, Bolondi et al 2020; Bolondi et al 2021). Briefly, mESCs were routinely maintained on 6cm plates (Corning 430166) gelatinized with 0.1% gelatin (1:20 dilution of 2% gelatin (Sigma G1393) in tissue-culture grade H2O) and coated with mitotically inactive primary mouse embryo fibroblasts (3-4x104cells/cm²) with standard mESC medium containing 15% FCS and 1000 U/ml leukemia inhibitory factor (LIF, Chemicon ESG1107) at 37°C and 5% or 7.5%  CO2. mESCs were split every second day with a dilution suitable to the proliferation velocity (between 1:5 and 1:9). ES+LIF medium was refreshed daily. For splitting, media was aspirated and cells were washed once with PBS and trypsinized (Tryspin-EDTA (0.05%) (Gibco 25300054)) for 5-10 minutes at 37°C. Trypsin was neutralized by 3ml ES+LIF and cells centrifuged for 5 minutes at 1000 rpm, after which the pellet was resuspended in ES+LIF. For freezing of mESCs, cell pellets were resuspended in ES medium with 20% FCS, and mixed in a 1:1 ratio with ES freezing medium. Cells were frozen down o/n in the –80 °C and transferred to liquid nitrogen the next day.
Trunk-Like Structures (TLS) have been generated as previously described (Veenvliet, Bolondi et al 2020; Bolondi et al 2021) with some modifications to induce Cas9-based molecular recording. Briefly, mESCs were trypsinized on the feeder plate as described above and washed with ES+LIF. Cells were pelleted by centrifugation at 1000rpm for 5 minutes at room temperature and resuspended in 2ml ES+LIF. On three gelatinized (0.1% gelatin) wells of a 6-well plate, cells were sequentially plated for 25 minutes, 20 minutes and 15 minutes during which cells were kept in the incubator at 37°C and 5% or 7.5% CO2. With each transfer, cells were triturated to maintain a single cell suspension. Feeder-freed mESCs were then washed once in 5ml pre-heated (37°C) PBS containing MgCl2 and CaCl2 (Sigma D8662) and once in pre-incubated (37°C, 5% or 7.5% CO2) 5ml NDiff227 (Takara Y40002). mESCs were then pelleted by centrifugation for 5 minutes at 1000rpm and resuspended in 500µl of NDiff227. 10µl of the cell suspension was mixed with 10µl of Trypanblue (Bio-Rad 1450021) for automated cell counting with Luna Automated Cell Counter. 1x106 live cells were then used for nucleofection using the Amaxa 4D-Nucleofector X Kit for mESCs (Lonza V4XP-3012) in combination with 10µg of Cre-expressing plasmid DNA (Addgene #13775) using the manufacturer instruction and the CG-104 program. Nucleofected cells were then washed with 10ml pre-warmed N2Diff227, resuspended in 1ml N2Diff227 and counted again using the automated cell counting with Luna Automated Cell Counter. 500 cells were then plated in a volume of 30 to 40µl NDiff227 into each well of a 96-well round bottom, low attachment plate (Costar 7007 ultra-low attachment 96 well plate (7007)). Cells were then allowed to aggregate for 48 h. After these 48h cells were pulsed with 3µM CHIR99021 (CHIR, Merck Millipore) in 150µl NDiff227. After 72h, medium was refreshed by removing 150µl of the old media and adding the same volume of new, pre-incubated (37°C and 5% or 7.5% CO2) NDiff227. At 96h, structures were then embedded in 5% Growth-Factor-Reduced Matrigel (MG) (Corning 356231). To this end, fresh NDiff227 medium was pre-incubated for at least 20 minutes at 37°C and 5% or 7.5% CO2. Pre-incubated medium was then put on ice for 5 minutes, after which MG was added to achieve a final concentration of 5% in the culture wells. Medium was then put at room temperature for 5 minutes, during which 150µl of old medium was removed from the aggregates. New medium with MG (150µl) was then added, and the cultures were returned to the incubator and further cultured at 37°C and 5% or 7.5% CO2. Tracer TLS cultures were allowed to settle for at least 30 minutes before proceeding to further experimentation. For Tracer TLS treated with CHIR+LDN (Tracer TLSCL), 5µM CHIR together with 600nM LDN was added prior to MG and left from 96h to 120h.

extract_protocol:
RNA was extracted from isolated Cas9-GFP+ Tracer mESCs at different days after Cas9-GFP activation or from individual Tracer TLS at day 5 post aggregation for downstream intBCs library preparation. Briefly, RNA was extracted from 1x105 isolated Cas9-GFP+ Tracer mESCs or individual Tracer TLS using RNeasy Plus Micro Kit (Qiagen) and RNA concentration and quality was measured using Qubit™ RNA HS (Thermo, Q32852). cDNA synthesis was performed using 1μg total RNA (for Tracer mESCs) or all extraced RNA (for individual Tracer TLS) using the RevertAid First Strand cDNA Synthesis Kit (Thermo, K1622), following the manufacturer’s instructions. OligoT were used as primers first strand cDNA synthesis.
Isolated gDNA from Tracer mESCs and prepared cDNA from Tracer mESCs and individual Tracer TLS were used for Amplicon-seq intBCs library preparation. 200ng gDNA and 100ng cDNA were used as input material. Two subsequent PCR reactions were carried on to prepare the NGS library: (i) in the first step the input material was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.55x-0.8x) was performed and purified intBCs amplicons were eluted in 30µl EB buffer; (ii) in the second step, the whole eluate from the previous PCR reaction was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a AMPure XP beads (Beckman, A63881) cleanup (0.8x) was performed to purify amplicons libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using paired end sequencing (500 cycles kit; 250/250) on a Miseq platform at a minimum of 50 million fragments per sample.

tag: strain


title: BMDM of Ncoa6-KO, control, 1

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

data_processing:
The quality of the sequencing data was verified using MultiQC software.
Sequence alignment and quantification were performed using the STAR (ver. 2.7.3a)–RSEM (ver. 1.3.3) pipeline.
The expected counts were imported by using the tximport package.
The DESeq2 R package was used to calculate normalized count data from RNA sequencing data by regularized log transformation and to conduct differential gene expression analyses.
Assembly: GRCm38, release number 101
Supplementary files format and content: tab-delimited text files include expected counts values for each Sample

source_name: BMDM

growth_protocol: To generate BMDMs, bone marrow cells were harvested from the tibia and femur of mice and then differentiated by culture in RPMI 1640 medium containing murine M-CSF (20 ng mL-1) for 6 days.

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions (Invitrogen). The RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, R11490). To assess the integrity of the total RNA, samples were run on the TapeStation RNA system (Agilent Technologies, Santa Clara, CA, USA, 5067-5576). Only high-quality RNA preparations with RIN greater than 7.0 were used for RNA library construction.
RNA-seq libraries were prepared according to the TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E (Illumina) and were then submitted for paired-end (2×100 bp) sequencing on an Illumina NovaSeq system (Illumina, Inc., San Diego, CA, USA) by Macrogen Incorporated (https://www.macrogen.com/).

treatment_protocol: Mouse BMDMs were stimulated with medium only or primed with LPS (100 ng ml-1) for 4 hours, followed by MSU (200 μg ml-1) for 2 hours.

value: BMDM


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C04_S316]


title: total RNA-seq from sample_009

value: male


title: gDNA - Tracer mESC - Day4

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 4

library_source: genomic

molecule: genomic DNA


title: cDNA - Tracer mESC - Day0

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 0


title: total RNA-seq from sample_019

value: F


title: Tracer TLS Explant Multiseq 3 - Multiseq barcodes

description: Multiseq barcodes library of the Tracer TLS explant pool

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
Processed using the deMULTIplex R pacakge for MULTI-seq sample barcode FASTQ alignment. In brief: The R functions found in 'MULTIseq.Align.Suite.R' can be used to convert MULTI-seq sample barcode FASTQ files into a sample barcode UMI count matrix. Think of this pipeline as 'CellRanger' for sample barcode data. This pre-processing pipeline can be split into four distinct steps: (1) Split raw FASTQs into cell barcode, UMI, and sample barcode sequences associated with a user-defined set of cell barcodes; (2) Remove reads that do not align with >1 mismatch to any MULTI-seq sample barcode reference sequence; (3) Remove reads representing duplicated UMIs on a cell-by-cell basis; (4) Convert this parsed read table to a sample barcode UMI count matrix.
Assembly: mm10
Supplementary_files_format_and_content:  TSV file with "<final.calls>\t<cellBC>\t<MultiSeqBCseq>\t<MultiSeqGroup>" represeting an entry for every cell containing a label for a MultiSeqGroup (final.calls), the cell barcode, the MultiSeq barcode sequence and the assigend MultiSeq group.
Library strategy: Amplicon-seq

organism: synthetic construct

growth_protocol: For the explant experiments, Tracer TLS and TLSCL have been derived as previously described. To this end, 500 cells per well have been seeded for these experiments. At day 5 TLS and TLSCL have been imaged using the Zeiss Celldiscoverer 7 with incubator chamber temperature set at 37°C and CO2 content at 5%. Next, the most posterior ends from eight TLS and eight TLSCL have been manually dissected using microdissection forceps under a stereomicroscope and each explant transferred in a well of an Ibidi 8-well glass-bottom plates (Ibidi 80827) using a p10 pipette with minimal transferring volume. The anterior portion of each structure has been subjected to single cell RNA sequencing. The dissection was carried out to include most of the posterior end, paying attention not to include any somite. Pre-incubated NDiff227 medium (see “Generation of Tracer Trunk-Like Structures” section) was then put on ice for 5 minutes, after which MG was added to a concentration of 5%. Medium was then put at room temperature for 5 minutes. MG-supplemented medium (200µl) was then added in each well containing an explant, and each of the explant was repositioned in the center of each well and imaged using the Zeiss Celldiscoverer 7 with incubator chamber temperature set at 37°C and CO2 content at 5%. Explant cultures were then returned to the incubator and further cultured at 37°C and 5% or 7.5% CO2 for 24h. The following day, outgrowths from the explants were imaged and used for single cell RNA sequencing.

extract_protocol:
Single-cell RNAseq (scRNA-seq) experiments have been performed as previously described (Veenvliet, Bolondi et al 2020). Briefly, Tracer TLS were generated as described above. Two individual 120h TLS (Tracer TLS 1 and 2) were selected based on the presence of one axis of elongation, clear formation of a neural tube domain and segmentation. Individual structures were picked with a p200 with the pipette tip cut-off at the 50µl mark, and serially washed through pipette transferring (cut 200µl tip) in wells filled with 200µl of 1xPBS/0.4%BSA (5 transfers) to get rid of the Matrigel. Each structure was then dissociated in 200µl TrypLE Express (Gibco) for 25 minutes at 37ºC, with pipetting every 5 minutes intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40µm. Cells were washed twice with 1ml 1xPBS/0.4%BSA with centrifugation steps performed for 5 minutes at 1200rpm in low DNAbind Eppendorf tubes. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3.1; one structure per reaction). Single-cell libraries were generated according to the manual, with one modification: fewer PCR cycles (n=8) were ran than recommended during cDNA amplification or library generation/sample indexing to increase library complexity. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were sequenced with a minimum of 400 million paired end fragments according to parameters described in the manual.
Lineage tracing barcodes (intBCs) libraries were prepared for all samples via PCR amplification from the double stranded 10x cDNA. Briefly, 100ng of 10x cDNA was used to prepare 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 68ºC 30sec – 72ºC 40sec (10 cycles)/ 72ºC 2 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.45X/0.7X) was performed to purify the intBCs libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using asymmetric end sequencing (150 cycles kit; 28/91 FC-410-1002) on a Novaseq platform at a minimum of 100 million fragments per sample.

value: synthetic


title: BMDM of Ncoa6-KO, LPS/MSU, 1

value: LPS / MUS


title: gDNA - Tracer mESC - Day3

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 3

value: LSL-Cas9-GFP-Tracer BC library


title: gDNA - Tracer mESC - Day2

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 2

value: mESC


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C09_S321]

value: trachea


title: BMDM of WT, control, 2

value: WT


title: total RNA-seq from sample_010


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C11_S323]

value: hillock

value: hillock structure


title: mouse liver,KO,GW4064,GRO-Seq

city: HOUSTON

first: Ruoyu

last: Wang

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
GRO-Seq and RNA-Seq raw data were de-multiplexed by bcl2fastq, and quality-controlled with fastqc
Reads were mapped to mouse reference genome mm10 by STAR v2.7.3a.
For gene/mRNA quantification, mm10 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the RPKM value
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse liver

extract_protocol:
The RNAs from livers of fasted mice (n = 2/group, each group contains RNAs pooled from 2 mice) were prepared using the RNeasy mini prep kit (Qiagen). RNA quality was tested using an Agilent bioanalyzer by the Functional Genomics Core at the Roy J. Carver Biotechnology Center, UIUC.
Ribosomal RNA was removed with the Ribozero Human/Mouse/Ratkit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq

treatment_protocol: C57BL/6 mice were fasted overnight and treated with 30 mg/kg GW4064 or vehicle for 1 h.

value: mouse liver

value: FXR KO

tag: time

value: 1 hour


title: gDNA - Tracer mESC - Day1

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 1


title: gDNA - Tracer mESC - Day0

description: Tracing BCs AmpliconSeq from Tracer mESCs gDNA at day 0


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C07_S319]

tag: tissue


title: Tracer TLS Explant Multiseq 2 - Multiseq barcodes


title: total RNA-seq from sample_012

tag: cell type

value: PBMCs

value: female

value: affected

value: D


title: BMDM of WT, control, 1

value: BMDM

tag: genotype


title: mouse liver, WT,GW4064,GRO-Seq


title: BMDM of Ncoa6-KO, control, 2


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C01_S313]

tag: phenotype


title: BMDM of WT, LPS/MSU, 2


title: DBA2 naïve, Bone marrow-derived Inflammatory monocytes, D3, rep3

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Workflow based on BBDuk/BBMap v 37.99
Sequence reads were trimmed for adaptor sequence and applying a length filtering, using BBDuk, with parameters: ktrim=r k=23 hdist=1 minlen=50
Trimmed sequence reads were mapped to GRCm38/mm10 using BBMap, with parameters: maxindel=100000 intronlen=10 ambig=random qin=33 sam=1.3
The bam files were sorted using samtools v 1.8
The read count was perforned using Subread/featureCounts v 1.5.2, with parameters: -T 8 -g gene_id -p -s 0
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Inflammatory monocytes

growth_protocol: LN4K1 cells were cultured using MEM media and KAL-LN2-E1 cells cultured with DMEM media and supplemented with 10% FBS and Penicillin-Streptomycin.

extract_protocol:
RNA was harvested using Rneasy micro kit.
RNA libraries for RNAseq were prepared with SMARtr Ultra low RNA amp+ NexteraXT/ NON Stranded library kit following manufactuer's protocols.

treatment_protocol: LN4K1 cells (3x10^5 cells/mouse) were intravenously injected in 100uL in DBA2 mice. KAL-LN2-E1 cells (5x10^5 cells/mouse) were orthotopically injected into the lung of FVB mice. After tumor development, inflammatory monocytes were isolated from lungs, lung tumors and LN metastases using the EasyStep Mouse Monocyte Isolation Kit (StemCell) and sorted using CD45, CD11b, Ly6C, Ly6G, live/dead antibodies. The sorted IM populations were further used for RNA isolation.

value: Inflammatory monocytes

tag: disease state

value: healthy


title: mouse liver, WT,DMSO,GRO-Seq

value: Vehicle


title: BMDM of Ncoa6-KO, LPS/MSU, 2

value: LPS / MUS


title: Library2_plasmid

city: Palo Alto

first: Chris

last: Hsiung

state: CA

address: 3181 Porter Dr

institute: Arc Institute

description: 6-plex crRNA plasmid library

data_processing:
Library 1: Reads were mapped to crRNA constructs using sgcount (https://noamteyssier.github.io/sgcount/), requiring perfect match to the reference sequence.
Library 2: First, reference construct sequences were created by interspersing provided spacer and constant regions. Each construct is then given a unique construct id (CID). Each CID is then split into R1 and R2 reference sequences, which are constructed by taking the first three and last three spacer-construct pairs of the reference sequence respectively. The R2 sequence is then reverse complemented for matching against the R2 sequencing reads. Next, two hashmaps are created for the R1 and R2 spacer-construct pairs respectively, which map the R1/R2 sequences to a set of corresponding CIDs. Finally, for each R1/R2 sequencing pair, each k-mer (k = length of R1/R2 respective construct sequence) in the sequence is mapped against their respective R1/R2 hashmap. If both sequencing pairs are able to be mapped to a CID set, then the intersection of their sets is their original construct, and the total count of that CID is incremented. We implemented the above algorithm as the `casmap constructs` command in a package written in Rust, available at https://github.com/noamteyssier/casmap.
Starting from read counts, the cell fitness scores were calculated using custom scripts in R as detailed in the associated publication. For Library 1, data from a single T0 sample was used to calculate the fitness score for both replicates due to an unexpected global loss of sequencing read counts for one of two originally intended T0 replicate samples. For each screen replicate in Library 2, data from two separate sequencing library preps from the same Round 1 PCR material subjected to separate Round 2 PCR’s and sequenced on separate runs were pooled together for analysis.
Assembly: crRNA library reference for each screen
Supplementary files format and content: Lib1_Counts.txt contains counts table for Library 1.
Supplementary files format and content: Lib1_FitnessScore.txt contains the cell fitness scores (gamma) for Library 1.
Supplementary files format and content: Lib2_Counts.txt containsn counts table for Library 2.
Supplementary files format and content: Lib2_FitnessScore.txt contains the cell fitness scores (gamma) for Library 2.
Supplementary files format and content: README_DescriptionScreenProcessedFiles.txt contains detailed description of the contents of all processed data files

source_name: plasmid

growth_protocol: K562 cells were cultured at 37deg. C with 5% CO2 in tissue culture incubators. Culture media consists of RPMI-1640 (Gibco cat# 22400121) containing 25 mM HEPES, 2mM L-glutamine, and supplemented with 10% FBS (VWR), 100 units/mL streptomycin, and 100 mg/mL penicillin. During the screen, K562 cells were cultured in flasks in a shaking incubator and the culture media was supplemented with 0.1% Pluronic F-127 (Thermo Fisher P6866).

extract_protocol:
Genomic DNA was isolated using the NucleoSpin Blood XL Maxi kit (Machery-Nagel 740950.50)
crRNA inserts were amplified from genomic DNA isolated from screens using 16 cycles of first round PCR using pooled 0-8nt staggered forward and reverse primers, treated with ExoSAP-IT (Thermo Fisher 78201.1.ML), followed by second round of PCR to introduce Illumina unique dual indices and adaptors. Sequencing primer binding sites, unique dual indices, P5 and P7 adaptor sequences are from Illumina Adaptor Sequences Document # 1000000002694 v16. PCR amplicons were subject to size selection by magnetic beads (SPRIselect, Beckman B23318) prior to sequencing on an Illumina NovaSeq6000 using SP100 kit (PE100) for Library 1 or SP500 kit (PE250) for Library 2. Sequencing of plasmid libraries were performed similarly, except 7 cycles of amplification were each used for Round 1 and Round 2 PCR. The size distribution of the final library was measured on an Agilent TapeStation system. We noted that even after magnetic bead selection of Round 2 PCR-amplified Library 2 plasmid library (colonies from which were Sanger sequencing verified) and genomic DNA from screens, smaller sized fragments from non-specific PCR amplification during Illumina sequencing library preparation persisted. This might contribute to the fraction of reads that could not be mapped to our reference 6-plex array. Thus, these unmapped reads do not necessarily reflect recombination of the crRNA library constructs, though the latter could contribute as well.

treatment_protocol: Library 1 screen: K562 cells engineered by piggyBac transposition to constitutively express denAsCas12a-KRAB or multiAsCas12a-KRAB were transduced with lentivirally packaged Library 1 constructs at MOI = ~0.15. Transduced cells were then selected using 1ug/ml puromycin for 2 days, followed by washout of puromycin. On Day 6 after transduction, initial (T0) time point was harvested, and the culture was split into 2 replicates that are separately cultured henceforth. 10 days later (T10), the final time point was harvested (8.6 total doublings for multiAsCas12a-KRAB cells, 9.15 total doublings for denasCas12a-KRAB cells). A cell coverage of >500x was maintained throughout the screen. Library 2 screen: K562 cells engineered by piggyBac transposition to constitutively express multiAsCas12a-KRAB were transduced with lentivirally packaged Library 2 constructs at MOI = ~0.15. The screen was carried out similarly as described for Library 1 screen, except the screen was carried out for 14 days (T14) or 13.5 total doublings and maintained at a cell coverage of >2000x throughout.

tag: cell line

value: plasmid


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C03_S315]

value: trachea


title: total RNA-seq from sample_008

tag: age

tag: Sex

tag: bmi


title: total RNA-seq from sample_005

tag: status

tag: plate

tag: row

value: C


title: Tracer TLS Explant Multiseq 1 - Multiseq barcodes

value: synthetic

value: LSL-Cas9-GFP-Tracer BC library


title: Tracer TLS Explant Multiseq 3 - Lineage tracing

description: Lineage barcodes library of the Tracer TLS explant pool

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
FASTQ files were processed using the Cassiopeia python package for  preprocessing for phylogeny-inference algorithms. In brief: the steps of the Cassiopeia pipeline are 1) converts FASTQ files into an unmapped BAM, 2) collapses reads together into UMIs, 3) aligns sequences onto the reference target site sequence, and finally 4) calls alleles and lineage information at specific sites within the aligned target site.
Assembly: mm10
Supplementary_files_format_and_content: TSV of indel information for each target site in each cell barcode.
Library strategy: Amplicon-seq


title: enAsCas12aKRAB-gCH134

description: gCH134 = crCD55-4_crB2M-1_crB2M-3_crKIT-2_crKIT-3_crCD81-1

data_processing:
fastq files were generated by MinKNOW application.
BAM files were generated by alignment to the reference genomic regions in allregions_formanuscript.fasta using the MinKNOW application.
Bam files for each sample were merged using samtool merge (samtools v1.6). Merged bam files were filtered for alignments that overlap the start and end coordinates of the protospacer region of the Cas12a crRNA using bamtools filter -region (bamtools v2.5.1). Filtered bam files were loaded into the Integrative Genomics Viewer 2.17.0 for visualization of individual read alignments. pysamstats –fasta –type variation (pysamstats v1.1.2) was used to extract per base total read coverage and deletion counts. The fraction of aligned reads harboring a deletion at each base was plotted using custom scripts in R.
Assembly: hg19
Supplementary files format and content: Output of pysamstats as tab-delimited text file.
Supplementary files format and content: allregions_formanuscript.fasta contains sequences used for read alignment, consisting of genomic regions spanning Cas9-based sgRNA enrichment target sites.

growth_protocol: K562 cells were cultured at 37deg. C with 5% CO2 in tissue culture incubators. Culture media consists of RPMI-1640 (Gibco cat# 22400121) containing 25 mM HEPES, 2mM L-glutamine, and supplemented with 10% FBS (VWR), 100 units/mL streptomycin, and 100 mg/mL penicillin.

extract_protocol:
Genomic DNA was harvested from 20 million cells using the Qiagen Genomic Tips Kit (cat #10243).
We used a custom protocol adapted from the Nanopore Cas9 Sequencing Kit user’s manual (SQK-CS9109, though this kit was not actually used) to enrich for genomic DNA surrounding crRNA target sites for Nanopore sequencing using Kit 14 chemistry. Except where specified below, reagents are from the Nanopore Ligation Sequencing Kit V14 (SQK-LSK114). To summarize in brief, synthetic spCas9 Alt-R crRNAs targeting ~15-20kb regions surrounding target sites of crCD55-4, crCD81-1, crKIT-2, crKIT-3, crB2M-1, and crB2M3 were designed according to instructions for the Nanopore Cas9 Sequencing Kit and ordered from IDT. At least two guides were used to target the (+) strand upstream of the Cas12a crRNA target sites, and at least two guides were used to target the (-) strand downstream of the target sites. Synthetic spCas9 guides were pooled and annealed with spCas9 tracrRNA (IDT Cat # 1072532) by heating to 95deg. C for 5min and cooling on the bench at room temperature, followed by assembly into ribonucleoprotein complexes by incubating the following mixture at room temperature for 30min: 10ul annealed crRNA:tracrRNA pool (100uM), 10ul 10x NEB rCutSmart Buffer (NEB B6004S), 79.2ul nuclease-free water, and 0.8ul HiFi Cas9 (62uM, S. pyogenes HiFi Cas9 nuclease V3 IDT Cat#1081060). 5ug of genomic DNA was dephosphorylated in a 30ul reaction volume using 15U of Quick calf intestinal phosphatase (NEB cat #M0525) and 3ul of 10x rCutsmart Buffer (NEB B6004S), incubated for 37deg. C for 10min, 80deg. C for 2min, and hold at 20deg. C. The entire volume of dephosphorylated genomic DNA is then mixed with 10ul of Cas9 ribonucleoprotein, 1ul 10mM dATP, and 1ul Taq polymerase for a total of 42ul, incubated at 37deg. C for 20min, 72 deg. C for 5min, and held at 4deg. C. The reaction is then cleaned up using 21ul (0.5X) AMPure XP using two washes with 200ul 80% ethanol, and eluted in 61ul of water. Adapters ligation was set up as follows: 60ul DNA eluate, 25ul Ligation Buffer, 10ul NEBNExt Quick T4 DNA Ligase (NEB E6056S), and 5ul Ligation Adapter, and incubated for 40min at room temperature. The entire ligation reaction was subjected to AMPure XP bead clean up using 40ul (0.4X) of AMPure beads, two washes with Long Fragment Buffer, and eluted in 15ul Elution Buffer. Size distribution and concentration of library was checked by Agilent Tapestation Genomic DNA ScreenTape Analysis. ~75ng-560ng of each library per flow cell was each run on 1 or 2 flow cells on a Promethion P2 Solo, yielding ~100k reads per flow cell run over 40h-72h.
Nanopore sequencing of genomic DNA

treatment_protocol: K562 cells piggyBAC-engineered to constitutively express the indicated fusion protein constructs were lentivirally transduced with the crRNA construct at MOI < 0.13, sorted for transduced cells based on GFP reporter fluorescence, and cultured for total of 16 days after crRNA transduction.


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B09_S309]

value: hillock

value: hillock structure


title: TBL-blastoids-2

city: beijing

first: yuxin

last: luo

address: NO.49 Huanyuanbei Road Haidian District

country: China

institute: Peking University Third Hospital

description: Sample 3

library_source: transcriptomic single cell

data_processing:
We use STAR v2.5.1b1 to align reads to the 10x Genomics pre-built mm10 reference genome and utilized CellRanger v3.0.2 software for blastocysts (288 cells) and EPS- blastoids (3528 cells) datasets with default setting for de-multiplexing to generate feature-barcode matrix.
The R package Seurat v4.3.0 was used to read and analyze feature-barcode matrix following the steps: First, we filtered the cells that have unique feature counts over 5000 for TBLCs and TBL-blastoids according to quality control matrix plots (1079, 4262 in total and 4387 cells in the TBLCs, ctrl TBL-blastoids and H2O2 treated TBL-blastoids group passed the filter, respectively);
Then UMI counts were normalized with NormalizeData function using defalult settings. Seurat’s RunUMAP function was used to do non-linear dimension reduction and cluster with resolution setting as 0.2.
Differentially expressed genes in the clusters between blastocysts and EPS-blastoids were determined by the FindMarkers function using a bimodal likelihood ratio test. For the differentially expressed genes, we tested weather each had enriched GO terms in biological process and molecular functions using the ToppGene Suite3. Unsupervised clustering analysis (UCA) was performed using the R package ComplexHeatmap v2.8.0.
Assembly: mm10
Supplementary files format and content: processed tsv files contain information on barcodes and gene annotations; the processed mtx files contain gene umi counts

source_name: synthetic embryos (blastocyst-like structures)

growth_protocol: TBLCS were dissociated into single cells by incubation with TrypLE Express (Thermo Fisher Scientific, 12604-013). Cell resuspension was transferred into a 0.2% gelatin-coated plate and incubated at 37℃ for 40 min to separate irradiated MEF. The supernatant was collected, filtered through a 40 µm cell strainer, and counted using the TC-10 counter (Bio-Rad, 1450001). AggreWell 400 (STEMCELL Technologies, 34415) was prepared following the manufacturer’s instructions. TBL-blastoid basal medium is composed of 25% TSC basal medium, 25% N2B27 basal medium (see above), and 50% KSOM. The KSOM medium contains: NaCl (95 mM), KCl (2.5 mM), KH2PO4 (0.35 mM), MgSO4 (0.2 mM), NaHCO3 (25 mM), CaCl2 (1.71 mM), Na2-EDTA (0.01 mM), L-glutamine (1.0 mM), Na lactate (10 mM), Na pyruvate (0.2 mM), glucose (5.56 mM), essential amino acid (EAA; 10.0 mL/l), non-essential amino acid (NEAA; 5.0 mL/l), and bovine serum albumin (BSA) (4 g/L). Approximately 6,000 cells (five cells per microwell for 1200 microwells in 24-well AggreWell400 culture plate) were resuspended in TBL-blastoid basal medium supplemented with 2 mM ROCK inhibitor Y-27632 (Reagents Direct, 53-B80-50), 12.5 ng/mL rhFGF4 (R&D, 235F4025), 0.5 mg/mL heparin (Sigma-Aldrich, H3149), 3 mM GSK3 inhibitor CHIR99021 (Tocris, 4423), 5 ng/mL BMP4 (Proteintech, HZ-1040), and 0.5 mM A83-01 (Axon Medchem, 1421) and seeded into one well of the 24-well AggreWell plate (Stem Cell Technologies, 07010). The plate was centrifuged at 300 g for one min and transferred into the cell incubator. The day of cell seeding was marked as day 0 of the process. Medium was removed 24 h later (day 1) and replaced with fresh medium without Y-27632 and supplemented with 200 nM LPA (Sigma-Aldrich, L7260). In the modified protocol, on day 4, the medium was replaced with fresh medium without LPA. Starting from day 5, blastoids were manually picked up using a mouth pipette (Sigma-Aldrich, A5177) under a stereomicroscope. analysis or downstream experiments.

extract_protocol:
TBLCS were dissociated into single cells by incubation with TrypLE Express (Thermo Fisher Scientific, 12604-013). TBL-blastoids were manually picked up using mouthpipette and  washed three times. ~10,000 TBLCs and ~500 TBL-blastoids were harvested and dissciated with a homemade enzyme mix composed of 0.5X versene (Lonza, 17711E), 0.5X Acumax (Innovative Cell Tech, AM105), and 0.05X Dnase (STEMCELL Tech, 07900) at 37°C for 30min with agitation. Dissociated cells were spinned down and wash with PBS + 0.04% BSA for three times and resupended in the same buffer. Cell density was determined by a TC10 cell counter (Biorad, 1450001).
Dissociated cells (~1500 cells for TBLCs, ~2000 cells for ctrl TBL-blastoids, and ~4000 for H2O2 treated TBL-blastoids) were loaded into the Chromium single cell controller (10xGenomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. The library was generated using the Chromium Single Cell 3' Reagent Kits according to the manufacturer’s manual. The two libraries were pooled and sequenced using Nextseq 500 (150 cycles, high output).

treatment_protocol: TBLCs were treated with 1 mM/L H2O2 for 1 h to establish the senescent state, and then replace the fresh medium for 24 h.

value: mixed

value: mixed (ICM/EPI like cells, PrE like cells, TE like cells and some uncertain cells)


title: total RNA-seq from sample_002

value: PBMCs

value: male

value: A

tag: column

tag: rin

tag: gc content


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B11_S311]


title: total RNA-seq from sample_006

value: female

value: affected

tag: randomization batch


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C02_S314]


title: total RNA-seq from sample_007

value: E


title: BMDM of WT, LPS/MSU, 1

tag: strain

value: BMDM

value: WT

tag: treatment


title: TBL-blastoids-1

description: Sample 2

tag: tissue

value: synthetic embryos (blastocyst-like structures)

tag: cell type


title: denAsCas12aKRAB-gCH134


title: total RNA-seq from sample_004


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B08_S308]

value: trachea

tag: genotype

tag: phenotype


title: H2O2 DEC-3

data_processing:
Sequencing reads were filtered and mapped to the mouse genome build mm10 using the HISAT2 alignment program. De novo transcriptome assembly and transcript and gene abundance calculations were performed using the StringTie assembler. The expression values of each gene were normalized using FPKM.
Differentially expressed genes (DEGs) were calculated using the R package ballgown. DEGs were deemed significant if they passed the following cutoff parameters: FPKM > 1, absolute value of log2 ratio > 1, and Q-value (adjusted p value) < 0.05.
Gene ontology (GO) and KEGG pathway analyses were performed using Fisher’s exact test, and the false discovery rate (FDR) was controlled by the BH method.
Principle components analysis was performed using the R package ade4. Cluster analysis was performed using the R package pvclust. Heatmaps were generated using the R package pheatmap.
Assembly: mm10
Supplementary files format and content: processed xlxs file includes FPKM values for each Sample

source_name: decidua like structure

extract_protocol:
Total RNA was isolated from decidua-like tissues or embryo-like tissues derived from decidua-like tissues collected at day 3 after transplantation using the TRIzol (Thermo Fisher Scientific, 15596026) method.
RNA-Seq libraries were constructed using the Illumina Smart-Seq2 using Nextera XT DNA sample preparation kit (Illumina, FC-131-1096) and Nextera XT 24-index kit (Illumina, FC-131-1001), and 2x150 bp pair-end sequencing was performed on an Illumina HiSeq X ten.

value: decidua like structure

tag: cell line


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B10_S310]


title: Tracer TLS Explant Multiseq 1 - Lineage tracing


title: Tracer TLS Explant Multiseq 2 - Lineage tracing


title: H2O2 TBL-blastoids

description: Sample 4

value: 1 mM/L H2O2 for 1 h


title: total RNA-seq from sample_003

tag: age

value: F


title: H2O2 DEC-2


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B06_S306]

value: hillock


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B12_S312]

value: hillock structure


title: total RNA-seq from sample_001

tag: Sex

value: B


title: H2O2 DEC-1

value: mixed


title: G2-3

city: Houston

first: Ronald

last: DePinho

state: TX

address: 515 Holcombe Blvd

department: Cancer Biology

institute: MD Anderson

data_processing:
library strategy: Whole genome sequencing
Raw sequencing reads were mapped to the mm10 reference genome using BWA-MEM
copy number calls (segment file) of all the samples against the tail sample were generated using HHMcopy
The weighted genome instability index (WGII) (Dewhurst et al., 2014) was used to quantitatively characterize portion of the genome with copy number alterations (log2 scores >=0.2; log2 scores <=-0.2) as a measure of chromosomal instability
Assembly: mm10
Supplementary files format and content:
Weighted_genome_instability_index.txt contains percentage of instable genome for all the samples
All_Segments.seg.txt includes quantified the copy number data across all the genome of all the samples.

source_name: Colon Adenoma

extract_protocol:
Qiagen DNEasy
PCR library

value: Colon Adenoma

value: Apcmin;mTERTLSL/LSL


title: multiAsCas12aKRAB-gCH134


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B07_S307]


title: TBLCs

description: Sample 1

source_name: 2-cell embryos

value: 2-cell embryos

value: TBLCs

value: totipotent cells


title: Parental-nocrRNA


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B05_S305]


title: G2-3-tail

source_name: Tail

value: Tail


title: pooledCells_scADT3

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Universitätsklinikum Erlangen

description: 10x Genomics

data_processing:
The three sequencing samples were processed separately via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics), the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics), and customized feature barcode references.
Supplementary files format and content: comma-separated value files and matrix files

source_name: PBMC

extract_protocol:
PBMCs were thawed from cryopreserved stocks and rested overnight at 1x106cells/mL in cRPMI medium. For each donor, individual dextramer cocktails were prepared directly before staining. For each cocktail, 1µL per 5x106 cells of HLA-matched dCODE dextramers® (immudex) and 100 µM d-biotin (1/10 of total dextramer volume) were pre-mixed in FACS-buffer to block free binding sites. 5x106PBMCs per donor and timepoint were recovered and first stained with 50µL of individual dextramer cocktails for 30min on ice. Afterwards, a cocktail of surface antibodies, individual hashtag antibodies (2.5µL per 5x106PBMCs of TotalSeq-C anti-human hashtag antibodies 1–8, Biolegend, 394661, 394663, 394665, 394667, 394669, 394671, 394673, 394675), and TotalSeq-C antibodies (0.078µg per 5x106PBMCs anti-human CD45RA (Biolegend, 304163), 0.277µg per 5x106PBMCs anti-human CCR7 (Biolegend, 353251), 0.25µg 5x106PBMCs anti-human CXCR3 (Biolegend, 353251)) were added. For three samples, instead of individual TotalSeq-C antibodies, the TotalSeq-C Human Universal Cocktail, V1.0 (Biolegend, 399905) was added. The day of the experiment, three vials of this universal cocktail were rehydrated in 18µL of FACS-buffer each, incubated for 5min an RT, vortexed, and centrifuged at maximum speed for 30sec at RT. One vial was used to stain 5x106 PBMCs. Samples were incubated for an additional 30min on ice. Up to 8 samples were pooled prior to the sort and could be distinguished by individual CD45 color-barcoding at the sorter and by individual TotalSeq-C anti-human hashtag antibodies in the scRNAseq dataset. Single, live, CD4+ or CD8+, dextramer-positive lymphocytes were sorted in previously FCS-coated 1.5mL tubes filled with FACS-buffer. Additionally, single, live, CD4+ or CD8+, dextramer-negative lymphocytes were sorted from 3 donors, as a framework for CD4- and CD8-T cell phenotypic clusters. Cells were sorted on a FACS Aria II cell sorter (BD). Immediately after sorting, cells were loaded to a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX, VDJ and CITEseq libraries according to the manufacturer’s instructions (10X Genomics, 1000263, 1000256, 1000252, 1000286, 1000250, 1000215, 1000190). Libraries were sent to Novogene and sequenced on an Illumina NovaSeq platform with PE150 strategy.
Library construction was performed according to manufacturer's instructions (10x Genomics) for 5' GEX, VDJ and CITEseq, V2 chemistry dual index

value: PBMC

value: T cells

value: SARS-CoV-2 vaccination

tag: adt/hto

value: see barcodes_202310_3.csv


title: pooledCells_scADT2

description: 10x Genomics

value: see barcodes_202310_1.csv


title: G2-2


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B03_S303]

value: trachea


title: pooledCells_scVDJ1

description: 10x Genomics


title: pooledCells_scADT1

description: 10x Genomics


title: ctrl DEC-1

value: decidua like structure

value: ctrl


title: pooledCells_scVDJ2

description: 10x Genomics


title: pooledCells_scVDJ3

description: 10x Genomics


title: G2-1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B04_S304]

value: hillock

value: hillock structure


title: ctrl DEC-2

value: mixed


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B01_S301]


title: G0-3

value: Colon Adenoma

value: Apcmin;mTERTLSL/+


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-B02_S302]


title: ctrl DEC-3


title: pooledCells_scGEX2

description: 10x Genomics


title: pooledCells_scGEX3

description: 10x Genomics


title: G0-2


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A12_S300]


title: ctrl EMB-2

source_name: embryonic like structure

value: embryonic like structure


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A11_S299]


title: P7_cortex_Xenium_biol 3

type: RNA

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Division of Neurology

country: Canada

institute: The University of British Columbia

description: mouse brain gene panel

hyb_protocol: Sections were incubated in a probe solution for 22 hours at 50°C for hybridization. The probe solution contained a set of 347 gene-targeting probes (described in methods) in TE buffer (Fisher). The rest of the Xenium workflow for fresh frozen tissue (fixation, permeabilization, ligation, amplification, etc) was performed as recommended by 10x Genomics.

scan_protocol: Full sections were imaged and analyzed using the Xenium Analyzer, software v1.7.6.0.

data_processing: Output files (transcripts, cell boundaries, features, etc) were generated directly by the Xenium onboard analysis pipeline (analysis v1.7.1.0).

label: Gene targeting probes

source_name: CD1, M/F, Postnatal day 7, brain, cortex

label_protocol: Single cell spatial transcriptomics was performed using a panel targeting 347 mRNA transcripts. 247 of these probes were from the mouse brain panel designed by 10x Genomics (10xgenomics.com/products/xenium-panels).

extract_protocol: Brains were dissected from CD1 mice at postnatal day 7 and were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections.

value: Postnatal mouse brain cortex


title: pooledCells_scGEX1

description: 10x Genomics


title: P7_cortex_Xenium_biol 2

description: mouse brain gene panel


title: ctrl EMB-1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A09_S297]


title: Adult_DM_PV_LpWF, replicate 5, bulkRNAseq

city: Baltimore

first: Haolong

last: Zhu

state: Maryland

address: 3520 San Martin Drive

institute: Carnegie Institution for Science

description:
PV_LpWF_R5
Illumina RiboZero TruSeq

data_processing:
Nextflow (v22.10.1) workflow revision 3.11.1 was used for data processing.
Assembly: scRNA-seq: BDGP6.22.Ensembl.98 with the addition of a GFP CDS sequence on an artificial chromosome.
Assembly: RNA-seq: BDGP6.22 Ensemble.98
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files.
Supplementary files format and content: RNA-seq: Salmon output quantification file

organism: Drosophila melanogaster

source_name: Adult proventriculus

growth_protocol: Flies were cultured on standard laboratory food unless otherwise specified. Adult mated female flies were used for the experiments.

extract_protocol:
Drosophila proventriculus tissues were dissected in cold PBS. RNA was extracted using the Qiagen RNeasy Mini Kit (50) (Cat#74104) and Qiagen RNase-Free DNase Set (50) (Cat#79254) and following the manufacturer’s protocols.
Library was constructed using the Illumina RiboZero TruSeq with the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 48 Samples kit (Cat#20020596) following the manufacturer’s protocols. The indexes used are from the TruSeq RNA Single Indexes Set A, 12 Indexes, 48 Samples kit (Cat#20020492).

value: Adult proventriculus

value: Canton-S

value: Flies were reared axenically. During adulthood, Lactiplantibacillus plantarum (LpWF), one of the core gut microbiome species in Drosophila melanogaster was supplemented to the fly culture to establish a stable gut microbiome colonization.


title: Control_SVZreplicate 1-4

city: Nagoya

first: Yuji

last: Nakamura

address: Kawasumi 1, Mizuho-cho, Mizuho-ku

department: Department of Pediatrics and Neonatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38 or GRCh38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Assembly: GRCh38
Supplementary files format and content: count matrix:CSV

source_name: Cerebral organoids

extract_protocol: Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55°C cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.

value: Cerebral organoids

value: iPS cell line derived from control individual

value: Neural progenitor cells

value: WT


title: G0-1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A10_S298]

data_processing:
FASTQ files were aligned using STAR to MM10 annotation
Aligned reads were then processed using Cufflinks
Downstream analysis was performed using Seurat v4.0
Assembly: mm10
Supplementary files format and content: a concatenated count file of all single cells, and a processed Rdata, Seurat object

source_name: trachea

extract_protocol:
Cells were FACS plated into lysis buffer in 96 well plates, according to the SMART-Seq2 protocol
RNA libraries were made according to SMART-Seq2 protocols

value: trachea


title: P7_cortex_Xenium_biol 1

description: mouse brain gene panel


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A08_S296]


title: ctrl EMB-3


title: Adult_DM_PV_LpWF, replicate 4, bulkRNAseq

description:
PV_LpWF_R4
Illumina RiboZero TruSeq


title: Patient_SVZ_replicate 1-4

value: iPS cell line derived from affected individual


title: H9 cells, sicontrol#1

city: Changsha

first: caiping

last: ren

address: 110 Xiangya Road,

institute: Central South University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM, FPKM, Count values for each Sample

source_name: human embryonic stem cells (H9) treated by sicontrol

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: sicontrol


title: Drug_rIL7, Visium [D15_IL7_Visium]

first: Hye Hyeon

last: Eum

address: 222, Banpo-daero, Seocho-gu

institute: The Catholic University of Korea

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were performed using the spaceranger software v1.1.0 with mm10-2020-A reference genome.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv
Library strategy: 10X visium

organism: Mus

source_name: tissue specimen

extract_protocol:
Total RNA capture from the tissue and cDNA amplification were performed according to the manufacter’s instructions (Spatial 3' v1 protocol, 10x Genomics). Briefly, the OCT embedded tissues were cryosectioned to a thickness of 10um. The cryosectioned tissues were H&E stained on a Visium Spatial Gene Expression Slide, then followed by permeablilization, reverse transcription, second strand synthesis, denaturation, and cDNA amplification.
Library was generated according to the manufacter’s instructions (Spatial 3' v1 protocol, 10x Genomics).

treatment_protocol: For the rIL7 treatment group, 10ug of recombinant mouse IL7 (rIL7) was intraperitoneally (i.p.) treated at day 11 and day 13 post-transplantation.

value: tissue specimen

value: balb/c

value: 6-8 weeks old


title: Adult_DM_PV_LpWF, replicate 3, bulkRNAseq

description:
PV_LpWF_R3
Illumina RiboZero TruSeq


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A07_S295]

value: hillock

value: hillock structure


title: H9 cells, siHNRNPA1#1

source_name: human embryonic stem cells (H9) treated by siHNRNPA1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A06_S294]


title: Adult_DM_PV_GF, replicate 5, bulkRNAseq

description:
PV_GF_R5
Illumina RiboZero TruSeq

value: Flies were reared axenically.


title: Drug_Control, Visium [D15_PBS_Visium]

description: 10x Genomics


title: Adult_DM_PV_LpWF, replicate 2, bulkRNAseq

description:
PV_LpWF_R2
Illumina RiboZero TruSeq


title: Drug_rIL7, scRNA-seq [D15_IL7_5P]

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were performed using the cellranger software v3.1.0 with mm10-3.0.0 reference genome (for NAÏVE, D7_PBS, D7_CT26, and D14_CT26) or v5.0.0 multi pipeline with mm10-2020-A and vdj-GRCm38-alts-ensembl-5.0.0 reference genomes (for D15_PBS and D15_IL7).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

extract_protocol:
Single cell suspension was generated from the tissue following the manufacturer's recommentations (Tissue dissociation kit, mouse, Miltenyi). Total RNA capture and cDNA amplification were performed according to the manufacter’s instructions (Single Cell 3' Gene Expression v3 or Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics). Briefly, the dissociated cells were loaded onto the 10x Chromium system targeting 5,000 cells (for NAÏVE, D7_PBS, D7_CT26, and D14_CT26) or 10,000 cells (for D15_PBS and D15_IL7). For each single cell, total RNA from the cell lysate contained in gel bead-in-emulsion (GEM) was captured with UMI and 10x barcoded gel bead and then reverse transcribed to cDNA. The barcoded cDNAs were pooled and amplified.
Library was generated according to the manufacter’s instructions (Single Cell 3' Gene Expression v3 or Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics).


title: Patient 3, ST

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

description: 10x Visium Spatial Transcriptomics

data_processing:
Space Ranger (Version 1.2, 10× Genomics) was applied to verify the capture areas of detected sections by comparing Visium ST sequencing data with brightfield images. Reads of each spot were segregated referred to spatial barcodes. Quality evaluation of raw reads were conducted by FastQC (Version 0.11.9) according to parameters including the number of spots, reads, genes detected and unique molecular identifier (UMI) counts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every spot
Library strategy: Spatial Transcriptomics

source_name: OSF-associated OSCC

extract_protocol:
All OCT-embedded tissues were sectioned into 10 μm slices and placed on the Capture Area (6.5 mm × 6.5 mm) of Visium Spatial slides (Visium Spatial Gene Expression Slide, 10× Genomics, Pleasanton, CA) by a cryostat microtome (Leica Microsystem). The prepared slides were stored at a dry environment for fixation and staining.  Sections incubated by pre-chilled methanol (Millipore Sigma, Darmstadt, Germany) and isopropanol (Millipore Sigma) were stained by Mayer’s hematoxylin (Dako, Agilent, Santa Clara, CA) for 7 min, Bluing buffer (Dako) for 2 min, Eosin Y solution (Millipore Sigma) diluted 1:10 in Tris-base (ThermoFisher Scientific, 0.45 M, pH 6.0) for 1min, respectively. Slides were fully rinsed by Milli-Q water (Corning, Corning, NY) after each staining. Images of all Capture Areas in the fiducial frames were taken in the bright-field and imported into 3DHISTECH software.  After placed in the Slide Cassette, each well of the sections were uniformly covered with 70 μl permeabilization enzyme (10× Genomics). Sections were incubated at 37℃ following a time gradient (3, 6, 12, 18, 24, 30 min). Each well of tissue sections, after the removal of permeabilization enzyme by pipette, were rinsed with 100 μl 0.1× SSC (Sigma-Aldrich, St. Louis, MO).
Reverse transcription was conducted by Bio-Rad PCR instrument (MyCycler, Bio-Rad, Hercules, CA) in accordance with the protocol of 10× Genomics (Protocol # CG000238). cDNAs in the supernatant, released during reverse transcription, were collected for second strand synthesis, denaturation, in vitro transcription and adaptor ligation. The products of a second reverse transcription were applied in the construction of spatial transcriptomic libraries, which was sequenced on the Illumina NovaSeq 6000 platform with over 4, 000 spots per sample and over 60, 000 reads per spots.

value: OSF-associated OSCC


title: Adult_DM_PV_LpWF, replicate 1, bulkRNAseq

description:
PV_LpWF_R1
Illumina RiboZero TruSeq

value: Adult proventriculus


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A05_S293]

first: Brian

last: Lin

address: 136 Harrison Avenue


title: ATRA+MRT

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

institute: Kanazawa University

description: Probe analysis data, which are binary format files generated by Affymetrix Power Tools

hyb_protocol: Labeled DNA (5.5 μg) was hybridized to the Affymetrix GeneChip Array (Clariom S Assay human, Thermo Fisher Scientific) at 45 ℃ for 16 hrs.

scan_protocol: Slides were washed, stained on a GeneChip Fluidics Station 450 (Thermo Fisher Scientific), and scanned with a GCS3000 Scanner (Thermo Fisher Scientific).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix GeneChip Command Console software (Thermo Fisher Scientific).

label: biotin

label_protocol: cDNA was then fragmented and biotin-labeled with terminal deoxynucleotidyl transferase using GeneChip WT Terminal Labeling kit (Thermo Fisher Scientific).

growth_protocol: RPMI1640 supplemented with 10% FBS

extract_protocol: Total RNA was extracted using RNesy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: HL-60 cells were treated with 1 mM MRT68921 and/or 1 mM all-trans retinoic acid (ATRA) for 48 hours.

tag: agent

value: ATRA+MRT

tag: neoplastic type

value: leukemia


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A03_S291]

institute: Tufts University


title: Drug_Control, scRNA-seq [D15_PBS_5P]

description: 10x Genomics


title: Adult_DM_PV_GF, replicate 4, bulkRNAseq

description:
PV_GF_R4
Illumina RiboZero TruSeq

value: Canton-S


title: ATRA

value: ATRA


title: Patient 1, ST

description: 10x Visium Spatial Transcriptomics


title: RH41_BMS986_500nM_RNAseq

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and 1% Pen/Strep/Glut.

extract_protocol:
To isolate RNA, RH4 or RH5 cells were washed with PBS, then lysed on ice with RLT using the RNeasy mini kit (Qiagen). PDXs were directly lysed with RLT.  For HiChIP, the Dovetail MNase HiChIP kit (Catalogue #21007) was used. Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-RNA Pol2 antibody (Santa Cruz Biotechnology, Mouse mAb #sc-47701 X). On-bead bridge incorporation and religation was performed, followed by reversal of crosslinks, proteinase K treatment, and DNA purification.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For in vitro RNA-seq and HiChIP experiments, RH4 and RH5 cells were treated with DMSO, ARV771, or JQ1 for six hours at 100nM.


title: Panicle late_rep3 [PL3]

city: Saskatoon

first: Sateesh

last: Kagale

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council Canada

data_processing:
Basecalls performed using CASAVA
Short Illumina reads were filtered using Trimmomatic by trimming adapter and low quality sequences and removing reads shorter than 75 bp
De novo transcriptome assembly was performed with Trinity.
Transcript abundance was estimated using Kallisto, and the transcripts per million (TPM) values were generated
Genome_build: Trinity.cdhit.fasta.longest.filtered.fasta
Supplementary_files_format_and_content: Matrix table with TPM values for each sample

organism: Panicum sumatrense

source_name: Panicle late

growth_protocol: Seeds of Little millet, Panicum sumatrense, genotype JK-8, were obtained from the University of Agricultural Sciences, Bengaluru, India. Plants were grown in a growth chamber at the Agriculture and Agri-Food Canada, Saskatoon, Canada. Growth chamber was set at 12 hours day/night light photoperiod and 25 °C day/20 °C night temperatures.

extract_protocol:
Total RNA was extracted from 100 mg of harvested tissues using RNeasy Plant Mini Kit (Qiagen) or Triazol (Sigma-Aldrich) and  purified using the RNeasy MinElute cleanup kit (Qiagen) according to manufacturer's protocol. Purified RNA was quantified using a NanoDrop ND‐100 spectrophotometer (Thermo Scientific), and its integrity evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies)
TruSeq RNA sequencing libraries were constructed following the manufacturer’s instructions (Illumina, http://www.illumina.com/)

value: Panicle late


title: Drug_rIL7, scTCR-seq [D15_IL7_TCR]

description: 10x Genomics


title: Adult_DM_PV_GF, replicate 3, bulkRNAseq

description:
PV_GF_R3
Illumina RiboZero TruSeq


title: RH41_BMS986_50nM_RNAseq


title: Panicle late_rep2 [PL2]


title: Drug_Control, scTCR-seq [D15_PBS_TCR]

description: 10x Genomics


title: Adult_DM_PV_GF, replicate 2, bulkRNAseq

description:
PV_GF_R2
Illumina RiboZero TruSeq


title: Patient 4, ST

description: 10x Visium Spatial Transcriptomics


title: Adult_DM_PV_GF, replicate 1, bulkRNAseq

description:
PV_GF_R1
Illumina RiboZero TruSeq


title: Patient 2, ST

description: 10x Visium Spatial Transcriptomics


title: RH41_DMSO_RNAseq

value: DMSO


title: Panicle mid_rep3 [PM3]

source_name: Panicle mid

value: Panicle mid


title: Adult_DM_SG, replicate 1, bulkRNAseq

description:
SG_R1
Illumina PolyA TruSeq

source_name: Adult salivary gland

extract_protocol:
Drosophila salivary gland tissues were dissected in cold PBS. RNA was extracted using the TRIzol Reagent (Cat#15596026) and following the manufacturer’s protocols.
Library was constructed using the Illumina PolyA TruSeq with the  TruSeq Stranded mRNA Library Prep, 48 Samples kit (Cat#20020594) following the manufacturer’s protocols. The indexes used are from the TruSeq RNA Single Indexes Set A, 12 Indexes, 48 Samples kit (Cat#20020492).

value: Adult salivary gland

value: Flies were reared axenically. Lactiplantibacillus plantarum (LpWF), one of the core gut microbiome species in Drosophila melanogaster was supplemented to the fly culture during fly adulthood.


title: RH5_BMS986_500nM_080222_CWRU


title: RH5_BMS986_50nM_080222_CWRU


title: Panicle late_rep1 [PL1]


title: Adult_DM_SG, replicate 3, bulkRNAseq

description:
SG_R3
Illumina PolyA TruSeq


title: Adult_DM_SG, replicate 2, bulkRNAseq

description:
SG_R2
Illumina PolyA TruSeq


title: D7_CT26, scRNAseq [D7_CT26]

description: 10x Genomics

value: tissue specimen


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-A01_S289]

city: Boston

value: trachea


title: Control, scRNAseq [NAIVE]

description: 10x Genomics

value: balb/c

value: 6-8 weeks old


title: Mock, scRNAseq [D7_PBS]

description: 10x Genomics


title: RH5_DMSO_RNAseq

value: DMSO from BMS-986158 experiment


title: Panicle mid_rep1 [PM1]


title: Panicle mid_rep2 [PM2]


title: Adult_DM_Crop, replicate 3, bulkRNAseq

description:
Crop_R3
Illumina RiboZero TruSeq

source_name: Adult crop

extract_protocol:
Drosophila crop tissues were dissected in cold PBS. RNA was extracted using the Qiagen RNeasy Mini Kit (50) (Cat#74104) and Qiagen RNase-Free DNase Set (50) (Cat#79254) and following the manufacturer’s protocols.
Library was constructed using the Illumina RiboZero TruSeq with the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 48 Samples kit (Cat#20020596) following the manufacturer’s protocols. The indexes used are from the TruSeq RNA Single Indexes Set A, 12 Indexes, 48 Samples kit (Cat#20020492).

value: Adult crop

value: Flies were reared axenically. During fly adulthood, Lactiplantibacillus plantarum (LpWF), one of the core gut microbiome species in Drosophila melanogaster, was supplemented to the fly culture to establish a stable gut microbiome colonization.


title: UAS-Alk.DN, Alk inhibition with C155-Gal4  promoter Neg 2 replicate 1

city: Göteborg

first: Vimala

last: Anthonydhason

address: Medicinaregatan 9 a-b

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

data_processing:
FastQC, Bowtie2, Sam Tools, BED Tools and Deep Tools
Assembly: Drosophila melanogaser
Supplementary files format and content: GATC coordinates were extracted and merged to determine the log-fold differences between the control and dominant negative groups.
Library strategy: Targeted DamID (TaDa)

source_name: Third instar larval CNS

extract_protocol: Genome binding/occupancy profiling by high throughput sequencing

value: Third instar larval CNS


title: UAS-Alk.DN, Alk inhibition with C155-Gal4  promoter Neg 1 replicate 2


title: CRT513_veh_3_RNAseq

value: vehicle (10% DMSO + 40% PEG-300 + 5% Tween-80 + 45% Saline)


title: Adult_DM_PV, replicate 3, scRNAseq

description:
HZ9
10x Genomics

data_processing:
Cell Ranger software (v6.0.1) from the 10x Genomics was used for demultiplexing, barcoded processing, gene counting, and data aggregation.
Assembly: scRNA-seq: BDGP6.22.Ensembl.98 with the addition of a GFP CDS sequence on an artificial chromosome.
Assembly: RNA-seq: BDGP6.22 Ensemble.98
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files.
Supplementary files format and content: RNA-seq: Salmon output quantification file

source_name: Adult proventriculus and associated tissue

extract_protocol:
Drosophila proventriculus tissues were dissected in cold PBS. Samples were dissociated with a combined mechanical and enzymatic (8-10mg/ml Gibco Collagenase, Type IV, powder, Cat#17104019) dissociation. Samples were filtered (BD 20um syringe, Cat#340595) and washed. RNA extraction and library construction were performed using the 10X Genomics products including the Chromium Next GEM Single Cell 3’ Kit v3.1. (PN1000128), the Chromium Next GEM Chip G Single Cell Kit (PN1000127), and the Single Index Kit T Set A (PN1000213), and following the manufacturer’s protocols (CG000204 Rev D). See the method session for more details.
Library was constructed using the Chromium Next GEM Single Cell 3’ Kit v3.1. (PN1000128), the Chromium Next GEM Chip G Single Cell Kit (PN-1000127), and the Single Index Kit T Set A (PN1000213), and following the manufacturer’s protocols (CG000204 Rev D).

value: Flies were reared with conventional microbiome. Lactiplantibacillus plantarum (LpWF), one of the core gut microbiome species in Drosophila melanogaster was supplemented to the fly culture during fly adulthood (72 hours before the dissection).


title: CRT513_BMS986158_3_RNAseq


title: Panicle early_rep3 [PE3]

source_name: Panicle early

value: Panicle early


title: Vegetative stem_rep2 [VS2]

source_name: Vegetative stem

value: Vegetative stem


title: D14_CT26, scRNAseq [D14_CT26]

description: 10x Genomics


title: Adult_DM_Crop, replicate 2, bulkRNAseq

description:
Crop_R2
Illumina RiboZero TruSeq

value: Canton-S


title: Panicle early_rep2 [PE2]


title: UAS-Alk.DN, Alk inhibition with C155-Gal4  promoter Neg 1 replicate 1


title: Vegetative stem_rep1 [VS1]


title: Adult_DM_Crop, replicate 1, bulkRNAseq

description:
Crop_R1
Illumina RiboZero TruSeq


title: CRT513_BMS986158_1_RNAseq


title: CRT513_veh_2_RNAseq


title: CRT513_veh_1_RNAseq


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 3 replicate 1


title: Panicle early_rep1 [PE1]


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 3 replicate 2


title: CRT513_BMS986158_2_RNAseq


title: UAS-Alk.DN, Alk inhibition with C155-Gal4  promoter Neg 2 replicate 2


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 2 replicate 2


title: RH5_JQ1_6h_RNAseq


title: Adult_DM_PV, replicate 2, scRNAseq

description:
HZ8
10x Genomics

value: Adult proventriculus and associated tissue

value: Flies were reared with conventional microbiome. Lactiplantibacillus plantarum (LpWF), one of the core gut microbiome species in Drosophila melanogaster was supplemented to the fly culture during fly adulthood (24 hours before the dissection).


title: Crown meristem_rep3 [CM3]

source_name: Crown meristem

value: Crown meristem


title: RH5_ARV771_6h_RNAseq


title: Crown meristem_rep2 [CM2]


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 1 replicate 2


title: Crown meristem_rep1 [CM1]


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 2 replicate 1


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_315

city: Bethesda

first: Avindra

last: Nath

address: 10 Center Drive

institute: NIH/NINDS

data_processing:
Illuminasoftware bcl2fastq v.2.17
RNA sequences were subjected to quality control  through FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Adapters were removed using Trimmomatic: https://github.com/timflutre/trimmomatic
Alignment to the human genome (GRCh38) using STAR
Gene expression levels were quantified using FeaturesCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression levels for each sample

source_name: Blood

extract_protocol:
RNA was extracted from PBMC’s of participants using miRNeasy Micro Kit (QIAGEN).
Dual index libraries were constructed with at least one unique index per each patient library using the TruSeq Stranded Total RNA HT Kit (Illumina).

value: Blood

value: Female


title: RH4_JQ1_6h_RNAseq


title: Dam-PolII expression with C155-Gal4  promoter Ctrl 1 replicate 1


title: Young root_rep2 [YR2]

source_name: Young root

value: Young root


title: Young root_rep1 [YR1]


title: Young leaf_rep2 [YL2]

source_name: Young leaf

value: Young leaf


title: Adult_DM_PV, replicate 1, scRNAseq

description:
HZ6
10x Genomics

value: Flies were reared with conventional microbiome.


title: Young leaf_rep1 [YL1]


title: BJIKT3

city: Daejeon

first: Heerim

last: Yeo

address: 99, Daehak-ro, Yuseong-gu

institute: Chungnam National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: H460 tumor tissue

growth_protocol: H460 cells were grown in RPMI 1640 medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2. Human PBMC-Injected H460 Tumor-Bearing Mice were established by subcutaneous injection of H460 cells (1 × 10^6 cells) into MHC I/II dKO NSG mice infused with human PBMC.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, California, USA). RNA quality was assessed by Agilent TapeStation 4000 system (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., Wilmington, Delaware, USA).
Library construction was performed using the QuantSeq 3' mRNA-Seq Library Preparation Kit (Lexogen, Inc., Vienna, Austria) according to the manufacturer's instructions.  High-throughput sequencing was performed by single-end 75 sequencing using the NextSeq 550 (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: The mice were administered a daily oral dose of 450 mg/kg BJIKT and/or received 10 mg/kg of pembrolizumab via intraperitoneal injection every three days.

value: H460 tumor tissue

value: tumor cells

value: MHC I/II dKO

value: BJIKT monotherapy

tag: time

value: Day 23


title: Combined1

value: combined treatment


title: RH4_ARV771_6h_RNAseq


title: Combined3


title: Young leaf_rep3 [YL3]


title: BST2_24h_3

city: Kaifeng, Henan Province

first: Yanqing

last: Li

address: Jinming Avenue

institute: Henan University

description:
processed data file:
hKCs_BST2_gene_expression.xls

data_processing:
Base calling and the quality score of each base are calculated based on the phred-33 quality score standard by the sub-Pixel Registration algorithm according to the optical signal intensity of each lane
This project uses the filtering software SOAPnuke (Versionv1.5.2) developed by BGI independently for filtering. SOAPnuke   Official Websitehttps://github.com/BGI-flexlab/SOAPnuke The specific steps are as follows: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information:HISAT2 (Version：v2.0.4) ,Official Website：http://www.ccb.jhu.edu/software/hisat
Bowtie2 (v2.2.5) was used to compare clean reads to reference sequences for gene alignment with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200. And then RSEM (v1.2.8) was used to calculate gene and transcript expression levels with -p 8 --forward-prob 0.5 --paired-end.
Genome_build: GCF_000001635.26_GRCm38.p6 for Mus musculus GCF_000001405.39_GRCh38.p13 for Homo sapiens
Supplementary_files_format_and_content: FPKM values, Reads Count for each Sample

growth_protocol: phKCs were seeded into 24 well plates and cultured in KBM-Gold medium with KBM Gold SingleQuot KC supplement (Lonza, Basel, Switzerland). Cells were maintained in the above medium for 3 days before use.     Mouse trigeminal neurons (mTGNs) were isolated from postnatal d5 C57BL/6 mice after the mice after being deeply anesthetized by i.p. injection of a mixture of 0.2% xylazine, 1% ketamine, and 0.9% NaCl. The harvested ganglia were incubated with Hank’s balanced salt solution (HBSS) using collagenase I (10 mg/mL, Sigma) and dispase II (5 mg/mL, Sigma) for 30 minutes. Digests were washed with DMEM and the cell suspension was filtered through a 100-μm cell strainer and cultured in 24-well plates pre-coated with poly-L-lysine (Sigma) and laminin (Sigma) in medium consisting DMEM supplemented with 5% (v/v) FBS (Sigma), 100 U/ml penicillin, 100 μg/ml streptomycin in the presence of cytosine β-d-arabinofuranoside (Sigma) 10 µM, 1xB27, and nerve growth factor 50 ng/ml (Sigma) for 7 days

extract_protocol:
Remove the upper medium and wash it twice with cold PBS, frozen on ice, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol: phKCs were treated with IL-27(100 ng/ml) for 6h or BST2(250 ng/ml) for 24h; mTGNs were treated with IL-27(100 ng/ml) or BST2(500 ng/ml) for 6h

value: human primary keratinocytes

value: BST2 (250 ng/ml) treated


title: Plumule_rep3 [PU3]

source_name: Plumule

value: Plumule


title: ctrl_6h_3

value: untreated


title: Plumule_rep1 [PU1]


title: BJIKT1


title: Plumule_rep2 [PU2]


title: BST2_24h_2


title: BST2_24h_1


title: Pemb3

value: Pemb monotherapy


title: Radicle_rep3 [RD3]

source_name: Radicle

value: Radicle


title: Pemb1


title: hKCs_hIL27_2

description:
processed data file:
hKCs_IL27_gene_expression.xls

value: IL-27(100 ng/ml) treated


title: Combined2


title: hKCs_hIL27_1


title: BJIKT2


title: ctrl_6h_1


title: Control1

value: vehicle


title: hKCs_Ctrl_2


title: hKCs_hIL27_3


title: Radicle_rep2 [RD2]


title: Germinating seed_rep3 [GS3]

source_name: Germinating seed

value: Germinating seed


title: ctrl_6h_2


title: hKCs_Ctrl_3


title: Germinating seed_rep2 [GS2]


title: Germinating seed_rep1 [GS1]


title: Pemb2


title: hKCs_Ctrl_1


title: Radicle_rep1 [RD1]


title: Control3


title: Control2


title: Reaction_II_5_2

status: Public on Mar 04 2024

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Reaction_II_5_2
SBL 3_R_II_2

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Mycobacterium leprae Gene Expression Microarray 8X15K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5188-5242). Hybridization was carried out in Agilent’s Hybridization oven at 65ºC for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5325 and 5188-5326)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Mycobacterium leprae

source_name: Human skin biopsy

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0424). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-2000

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations. The concentration and purity of the RNA was evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 2000). The integrity of the RNA was analyzed on the Bioanalyzer (Agilent; 2100 expert). We considered RNA to be of good quality based on the 260/280 values (Nanodrop) and optimal RNA integrity profile in Bioanalyzer.

tag: source

value: Human skin biopsy


title: Relapse 2_1

description:
Relapse 2_1
SBL 42_AT_1


title: Relapse 3_1

description:
Relapse 3_1
SBL 44_AT_1


title: Reaction_II_1

description:
Reaction_II_1
SBL 6_R_II


title: Relapse 4

description:
Relapse 4
SBL 43_AT


title: Reaction_II_4

description:
Reaction_II_4
SBL 2_R_II


title: Relapse 2_2

description:
Relapse 2_2
SBL 42_AT_2


title: Relapse 1 _1

description:
Relapse 1 _1
SBL 41_AT_1


title: Relapse 3_2

description:
Relapse 3_2
SBL 44_AT_2


title: Reaction_I_4_2

description:
Reaction_I_4_2
SBL 31_R_I_2


title: Reaction_II_6

description:
Reaction_II_6
SBL 5_R_II


title: Reaction_I_4_1

description:
Reaction_I_4_1
SBL 31_R_I_1


title: Relapse 1_2

description:
Relapse 1_2
SBL 41_AT_2


title: Reaction_I_5

description:
Reaction_I_5
SBL 32_R_I


title: Reaction_I_1

description:
Reaction_I_1
SBL 27_R_I


title: Reaction_I_3

description:
Reaction_I_3
SBL 30_R_I


title: Reaction_II_2

description:
Reaction_II_2
SBL 7_R_II


title: Reaction_II_3_2

description:
Reaction_II_3_2
SBL 8_R_II_2


title: Reaction_I_2_1

description:
Reaction_I_2_1
SBL 29_R_I_1


title: Paucibacillary 5_2

description:
Paucibacillary 5_2
SBL 21_Paucibacillary_2


title: Reaction_II_3_1

description:
Reaction_II_3_1
SBL 8_R_II_1


title: Paucibacillary 2_2

description:
Paucibacillary 2_2
SBL 18_Paucibacillary_2


title: Reaction_I_7

description:
Reaction_I_7
SBL 26_R_I


title: Reaction_I_6

description:
Reaction_I_6
SBL 25_R_I


title: Lepromatous leprosy 6

description:
Lepromatous leprosy 6
SBL 11_LL


title: Paucibacillary 5_1

description:
Paucibacillary 5_1
SBL 21_Paucibacillary_1


title: Paucibacillary 1

description:
Paucibacillary 1
SBL 17_Paucibacillary


title: Paucibacillary 4

description:
Paucibacillary 4
SBL 20_Paucibacillary


title: Reaction_I_2_2

description:
Reaction_I_2_2
SBL 29_R_I_2


title: tumor_IgG2a_mRNA_EXP_anti_CSF1R_batch3.1

city: South San Francisco

first: Xiangnan

last: Guan

state: California

address: 1 DNA WAY

institute: Genentech

description:
mouse_scSeq_anti-CSF1R_tumor_myeloid_metadata.rds
mouse_scSeq_anti-CSF1R_tumor_myeloid_RNA_raw_counts.rds
mouse_scSeq_anti-CSF1R_tumor_T_NK_metadata.rds
mouse_scSeq_anti-CSF1R_tumor_T_NK_RNA_raw_counts.rds

data_processing:
FASTQ files were aligned to the mouse transcriptome (mm10) and UMI counts were quantified to generate a gene–barcode matrix using the Cell Ranger pipeline (10x Genomics, v.6.1.1).
ADT hashtag expression were generated using the Cell Ranger pipeline (10x Genomics, v.6.1.1).
Downstream analyses including demultiplexing ADT hashtags and single cell processing were performed using the R package Seurat (v.3.2.2).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Seurat and R output files in .rds format.

source_name: tumor

extract_protocol:
Blood and tumours were collected from mice and processed for single-cell suspension preparation by enzymatic dissociation and/or red blood cell lysis as needed. Cells within each tissue and treatment group were hash-tagged (BioLegend TotalSeq C), pooled from different mice and labelled with fluorescent anti-CD45 antibodies and a viability dye.
Live CD45+ cells were sorted and processed according to the 10x Genomics’ protocol (CG000330_Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide_RevA) to generate 5′ single-cell RNA-seq and hashed libraries.
Single cell RNAseq + Hashing ADT (antibody-derived tag)

value: tumor

value: tumor CD45+

tag: library type

value: mRNA


title: tumor_IgG2a_ADT_EXP_anti_CSF1R_batch3.1

library_source: other

molecule: protein

value: ADT

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody, TotalSeq-C0302 anti-mouse Hashtag 2 Antibody, TotalSeq-C0303 anti-mouse Hashtag 3 Antibody, TotalSeq-C0304 anti-mouse Hashtag 4 Antibody, TotalSeq-C0305 anti-mouse Hashtag 5 Antibody


title: Lepromatous leprosy 2

description:
Lepromatous leprosy 2
SBL 13_LL


title: Paucibacillary 2_1

description:
Paucibacillary 2_1
SBL 18_Paucibacillary_1


title: Paucibacillary 3

description:
Paucibacillary 3
SBL 19_Paucibacillary


title: Healthy Control 3_2

description:
Healthy Control 3_2
SBL 38_HC_2

source_name: Human Skin Slit

value: Human Skin Slit


title: Lepromatous leprosy 4_2

description:
Lepromatous leprosy 4_2
SBL 16_LL_2


title: Healthy Control 2

description:
Healthy Control 2
SBL 34_HC


title: Healthy Control 5_2

description:
Healthy Control 5_2
SBL 40_HC_1


title: tumor_PDL1tg2b_ADT_EXP_anti_TIGIT_comboTx_batch2

description:
mouse_scSeq_anti-TIGIT_comboTx_tumor_myeloid_metadata.rds
mouse_scSeq_anti-TIGIT_comboTx_tumor_myeloid_RNA_raw_counts.rds
mouse_scSeq_anti-TIGIT_comboTx_tumor_T_NK_metadata.rds
mouse_scSeq_anti-TIGIT_comboTx_tumor_T_NK_RNA_raw_counts.rds


title: tumor_tigit2a_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: Lepromatous leprosy 5

description:
Lepromatous leprosy 5
SBL 9_LL


title: Lepromatous leprosy 4_1

description:
Lepromatous leprosy 4_1
SBL 16_LL_1


title: tumor_tigit2b_ADT_EXP_anti_TIGIT_comboTx_batch2


title: tumor_PDL1_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: tumor_PDL1_ADT_EXP_anti_TIGIT_comboTx_batch2


title: Lepromatous leprosy 1

description:
Lepromatous leprosy 1
SBL 10_LL


title: Healthy Control 4

description:
Healthy Control 4
SBL 39_HC


title: tumor_ctrl_ADT_EXP_anti_TIGIT_comboTx_batch2

value: ctrl


title: Healthy Control 1_2

description:
Healthy Control 1_2
SBL 33_HC_1


title: blood_PDL1tg2b_mRNA_EXP_anti_TIGIT_comboTx_batch2

description:
mouse_scSeq_anti-TIGIT_comboTx_blood_metadata.rds
mouse_scSeq_anti-TIGIT_comboTx_blood_metadata.rds

source_name: blood

value: blood

value: blood CD45+


title: tumor_PT_antiCSF1R_mRNA_EXP_anti_CSF1R_batch3.1


title: tumor_ctrl_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: blood_PDL1tg2b_ADT_EXP_anti_TIGIT_comboTx_batch2


title: Healthy Control 3_1

description:
Healthy Control 3_1
SBL 38_HC_1


title: blood_tigit2a_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: Healthy Control 1_1

description:
Healthy Control 1_1
SBL 33_HC_2


title: tumor_PT_antiCSF1R_ADT_EXP_anti_CSF1R_batch3.1


title: blood_tigit2a_ADT_EXP_anti_TIGIT_comboTx_batch2


title: blood_tigit2b_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: tumor_PT_mRNA_EXP_anti_CSF1R_batch3.1

value: PT


title: tumor_PT_ADT_EXP_anti_CSF1R_batch3.1


title: tumor_PDL1tg2a_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: blood_PDL1_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: tumor_PDL1tg2a_ADT_EXP_anti_TIGIT_comboTx_batch2


title: tumor_PDL1tg2b_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: tumor_tigit2a_ADT_EXP_anti_TIGIT_comboTx_batch2


title: tumor_tigit2b_ADT_EXP_anti_TIGIT_monoTx_batch1

description:
mouse_scSeq_anti-TIGIT_monoTx_tumor_myeloid_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_myeloid_RNA_raw_counts.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_T_NK_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_T_NK_RNA_raw_counts.rds


title: tumor_tigitlalapg_mRNA_EXP_anti_TIGIT_monoTx_batch1

value: tigitlalapg


title: Lepromatous leprosy 3

description:
Lepromatous leprosy 3
SBL 14_LL


title: tumor_tigitlalapg_ADT_EXP_anti_TIGIT_monoTx_batch1


title: tumor_tigit2b_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: Healthy Control 5_1

description:
Healthy Control 5_1
SBL 40_HC_2


title: tumor_ctrl_ADT_EXP_anti_TIGIT_monoTx_batch1


title: blood_tigitlalapg_mRNA_EXP_anti_TIGIT_monoTx_batch1

description:
mouse_scSeq_anti-TIGIT_monoTx_blood_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_blood_RNA_raw_counts.rds


title: blood_tigit2b_mRNA_EXP_anti_TIGIT_monoTx_batch1


title: blood_PDL1tg2a_ADT_EXP_anti_TIGIT_comboTx_batch2


title: blood_PDL1tg2a_mRNA_EXP_anti_TIGIT_comboTx_batch2


title: blood_tigitlalapg_ADT_EXP_anti_TIGIT_monoTx_batch1


title: blood_ctrl_mRNA_EXP_anti_TIGIT_monoTx_batch1


title: blood_ctrl_ADT_EXP_anti_TIGIT_monoTx_batch1


title: blood_PDL1_ADT_EXP_anti_TIGIT_comboTx_batch2


title: blood_tigit2b_ADT_EXP_anti_TIGIT_comboTx_batch2