title: Post-infusion scTCR for CAR-T from Patient 048 on D28

description:
Post_scTCR_048-d28-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: TB64RL

status: Public on Apr 03 2025

type: SRA

city: New York

first: Andrei

middle: V.

last: Tkatchenko

state: NY

department: Edward S. Harkness Eye Institute

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
The FASTQ raw data files generated by the Illumina sequencing system were imported into Partek Flow software package (Partek), libraries were separated based on their barcodes, adapters were trimmed and remaining sequences were subjected to pre-alignment quality control using the Partek Flow pre-alignment QA/QC module
After the assessment of various quality metrics, bases with the quality score < 34 were removed (≤ 5 bases) from each end.
Sequencing reads were then mapped to the mouse reference genome Genome Reference Consortium Mouse Build 38 (GRCm38/mm10, NCBI) using the STAR aligner resulting in 98.12 ± 0.06% mapped reads per library, which covered 30.1 ± 1.7% of the genome.
Aligned reads were quantified to transcriptome using the Partek E/M annotation model and the NCBI’s RefSeq annotation file to determine read counts per gene/genomic region.
The generated read counts were normalized by the total read count and subjected to the Gene Specific Analysis (GSA) to detect differentially expressed genes
Assembly: mm10
Supplementary files format and content: Tab-delimited text file including matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Left eye retina

extract_protocol:
The retinae were washed in RNAlater (Thermo Fisher Scientific) for 5 min., frozen in liquid nitrogen, and stored at -80°C. To isolate RNA, tissue samples were homogenized at 4°C in a lysis buffer using Bead Ruptor 24 tissue homogenizer (Omni). Total RNA was extracted from each tissue sample using miRNAeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Illumina sequencing libraries were constructed from 1 μg of total RNA using the TruSeq Stranded Total RNA LT kit with the Ribo-Zero Gold ribosomal RNA depletion module (Illumina).

treatment_protocol: Myopia was induced in mice by applying a plastic goggle holding a -20D lens onto one of the eyes and refractive development of the treated eye was compared to that of the contralateral eye which was not treated with a lens. On the first day of the experiment (P24), animals were anesthetized via intraperitoneal injection of ketamine and xylazine and goggles were attached to the skin surrounding the eye. Goggles were removed and the refractive state of both treated and control eyes was assessed using an automated infrared photorefractor after 10 days of treatment.

tag: strain

tag: tissue

value: Retina

tag: age

value: postnatal day 34

tag: genotype

value: wild type


title: TB61RL


title: Eye_ALAN_Male4

city: Edinburgh

first: Violeta

last: Trejo-Reveles

address: Old College, South Bridge, Edinburgh

country: United Kingdom

institute: The University of Edinburgh

description: Library name: 140EA

data_processing:
Raw fastq files were processed by trimming using trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) with the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; SLIDINGWINDOW:10:30; LEADING:28; TRAILING:28; MINLEN:75. After trimming the quality of the reads was checked using FASTQC
Reads were aligned using STAR aligner version 2.7.11a (https://github.com/alexdobin/STAR), with the ENSEMBL green anole (Anolis carolinensis) genome and gtf (AnoCar2.0v2, Anolis_carolinensis.AnoCar2.0v2.112.gtf) as references. BAM files were counted using featurecounts (https://subread.sourceforge.net/).
Assembly: AnoCar2.0v2
Supplementary files format and content: csv files contain ether raw counts for each sample

organism: Anolis carolinensis

source_name: Eye

growth_protocol: Twenty-four free-living adult green anole lizards (Anolis carolinensis; twelve of each sex) were captured in the breeding season, in May 2024, on the urban campus of Trinity University in San Antonio, Texas, USA, during daylight hours. Green anole lizards were collected by using a dental floss loop attached to an extendable fishing pole or by hand and were transported individually to the Trinity University vivarium in cotton bags. On the day of capture, the body mass of each anole was measured to the nearest 0.1 g using a Pesola spring scale and snout-vent length measured to the nearest mm using a clear plastic ruler (Males: range 52-69mm, average 62mm; Females: range 51-57mm, average 55mm). Each individual was given a unique identification number on the lower jaw using a non-toxic permanent marker.

extract_protocol:
RNAeasy kit
Library construction performed by BGI Genomics

treatment_protocol: Each anole was  randomly assigned to one of three treatment groups: Midday, Midnight, or ALAN. Sex was determined by the presence of hemipenes and the size of the dewlap; four anoles of each sex were assigned to each treatment group

value: Eye

tag: Sex

value: male

value: WT

tag: treatment

value: ALAN

tag: batch


title: Eye_ALAN_Female1

description: Library name: 141EA

value: Female


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 116 on D21

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

description:
Post_scRNA_TotalSeq_116-d21-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv

library_source: transcriptomic single cell

data_processing:
The RNA-seq and paired Total-seq reads were aligned to the GRCh38 reference genome, which was modified with the CAR transgene sequence used in axicabtagene ciloleucel, and quantified using the cellranger count (10x Genomics, version 6.0.0). The filtered gene/feature-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. In two patients with fewer CAR-T cells where hashtag multiplexing was used, cellranger multi pipeline was used to demultiplex and quanity.
The TCR-seq reads from each sample were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10x Genomics, version 6.0.0). The results were then aggregated using the cellranger aggr function, with the source patient (donor) and timepoint (origin) of each sample supplied in the metadata to guide the clonotype assignment. The resultant clonotype and filtered contig annotation data were used for downstream analyses. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions for paired productive TCRα and TCRβ chains.
Assembly: GRCh38
Supplementary files format and content: scRNA and Totalseq -- mtx: final merged raw count matrices of scRNA and Totalseq (ADT); csv: row and column names; metadata
Supplementary files format and content: scTCR -- csv: aggregated clonotype results from cellranger vdj

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
scRNA-Seq and OTHER (TotalSeq, scTCR, and Hastag-Multiplex for 2 patients with fewer CAR-T)
Cryopreserved patient biospecimens were thawed in warm RPMI+10% FBS and washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Next, Fc receptors were blocked by incubation with Human TruStain FcX (BioLegend, 422301) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-anti-CD3E (clone SK7), CITE-seq antibodies, and Alexa Fluor 647-labeled antigen-tetramers at 3 nM final concentration for CAR-detection. Subsequently, cells were incubated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) diluted 1:1000 in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media. Infusion products were partitioned and analyzed directly. Peripheral blood mononuclear cells were subject to fluorescence-activated cell sorting before single-cell partitioning and analysis.
T cells were partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). From the resulting barcoded nucleic acids, TCR-seq libraries were prepared via the Chromium Single-Cell Human TCR Amplification Kit (10x Genomics, 1000252). Sequencing libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via a high-sensitivity D5000 screentape (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq-6000).

value: PBMC

tag: disease

value: Diffuse Large B-Cell Lymphoma

tag: cell type

value: CAR-T


title: MB68SR

description: small RNA

data_processing:
The FASTQ raw data files generated by the Illumina sequencing system were imported into Partek Flow software package (Partek), libraries were separated based on their barcodes, adapters were trimmed and remaining sequences were subjected to pre-alignment quality control using the Partek Flow pre-alignment QA/QC module
After the assessment of various quality metrics, bases with the quality score < 35 were removed (90 bases from 3’ end).
Sequencing reads were then mapped to the mouse reference genome Genome Reference Consortium Mouse Build 38 (GRCm38/mm10, NCBI) using the Bowtie aligner.
Aligned reads were quantified to microRNA transcriptome using the Partek E/M annotation model and the NCBI’s miRBase mature microRNAs version 22 deduplicated annotation file to determine read counts per microRNA.
The generated read counts were normalized using quantile normalization and subjected to the Gene Specific Analysis (GSA) to detect differentially expressed microRNAs.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file including matrix table with normalized gene counts for every microRNA and every sample

source_name: Right eye RPE/choroid/sclera

extract_protocol:
The retinae were washed in RNAlater (Thermo Fisher Scientific) for 5 min., frozen in liquid nitrogen, and stored at -80°C. To isolate RNA, tissue samples were homogenized at 4°C in a lysis buffer using Bead Ruptor 24 tissue homogenizer (Omni). Small RNA fractions were extracted from each tissue sample using miRNAeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Illumina sequencing libraries were constructed from 50 ng of small RNA using the TruSeq Small RNA Library Prep Kit (Illumina)

value: RPE/choroid/sclera


title: cHet IP biol rep 1

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

description: biol rep 1

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases, and undetermined bases with default parameter.
Sequence quality of IP and input samples were also verified using fastp.
HISAT2 (http://daehwankimlab.github.io/hisat2) was used to map reads to the reference genome of Mus musculus.
Assembly: mm10
Supplementary files format and content: A composite Excel file "genes_fpkm_expression" contains fpkm values of all six samples.
Library strategy: m6A-seq

source_name: Limb buds

extract_protocol:
Total RNA was prepared with TRIzol Reagent (Thermo Fisher, 15596026)
NEB Next Ultra II RNA Library Prep by Illumina following manufacturer's protocols.

value: Limb buds

value: Limb bud cells

value: Mettl14 wt/flox

value: Mettl14 hetero as control


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 116 on D10

description:
Post_scRNA_TotalSeq_116-d10-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: Eye_ALAN_Male1

description: Library name: 137EA


title: MB68SL

description: small RNA

source_name: Left eye RPE/choroid/sclera


title: E16.5_negative_control

city: Nanjing

first: Zhao

last: Chunjie

state: Jiangsu

address: Hunan Road Street

department: School of Medicine

country: China

institute: Southeast University

library_source: genomic

data_processing:
Raw fastq reads were trimmed by Cutadapt to trim adapter and low-quality sequence, and then high-quality sequencing data (clean reads) were obtained. We utilized Bowtie2 to align clean reads with mouse genome (mm10), followed by a quality assessment of the alignment results to accomplish secondary data quality control. Model-based Analysis of ChIP-Seq (MACS2) was used for peak calling. Based on the peak calling results from individual samples, we used the MAnorm to perform a differential analysis of peaks across three samples, aiming to identify sample-specific peaks and shared peaks within three groups. Bigwig file, which is used for the display of dense and continuous data as a graph, was generated by the bamCoverage command in deepTools.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

source_name: ganglionic eminences

extract_protocol:
Cells were washed with 500 μl of wash buffer and centrifuged at 600 g for 5 min at RT. The cell pellets were resuspended in 100 μl of wash buffer. Concanavalin A-coated magnetic beads were washed twice with binding buffer. Next, 10 μl of activated beads were added and incubated at RT for 10 min. Bead-bound cells were resuspended in 50 μl of antibody buffer (antibody buffer, 5% digitonin). Then, 1 μg of primary antibody (rabbit polyclonal anti-FOXG1 antibody) or nothing was added and incubated at 4° overnight. The primary antibody was removed using a magnet stand. Secondary antibody (1 μg, goat anti-rabbit) was diluted in 50 μl of Dig-wash buffer [10× wash buffer (-), 50× protease inhibitor cocktail, ddH2O, 5% digitonin] and cells were incubated at RT for 1 h. Cells were washed three times with Dig-wash buffer to remove unbound antibodies. The Hyperactive pA/G-Transposon (2 µM; 2 µl) was diluted in 98 μl of Dig300 buffer [10× Dig-300 buffer (-), 5% digitonin, 50× protease inhibitor cocktail, ddH2O]. The cells were incubated with Dilute 100 μl of the pA/G-Tnp transposons at RT for 1 h. The cells were washed three times with Dig-300 buffer. Then, the cells were resuspended in 50μl of diluted TTBL (5xTrueprep Tagment Buffer L, Dig300 buffer) and incubated at 37° C for 1 h. Add 5 μl of Proteinase K, 100 μl of Buffer L/B, and 20 μl of DNA Extract Beads to each sample, fully mix by vortexing, and incubate at 55°C for 10 min. For library amplification, 15μl Fragmented DNA after purification was mixed with 25μl 2x CAM (CUT&Tag Amplification Mix), and 5 μl of uniquely barcoded i5 and i7 primers from TruePrep Index Kit V2 for Illumina. A total of 50 μl of the sample was placed in a thermocycler and subjected to the following program: 72°C for 3 min; 95°C for 3 min; 11 cycles of 98°C for 10 s, 60°C for 5s; 72°C for 1 min and hold at 4°C. To purify the PCR products, 100μl VAHTS DNA Clean Beads were added and incubated at RT for 10 min. The libraries were washed twice with 80% ethanol and eluted in 22 μl of ddH2O.
The libraries were sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

value: ganglionic eminences

value: wild-type


title: Eye_ALAN_Male3

description: Library name: 139EA


title: cHet input biol rep 1

description: biol rep 1


title: MB66SR

description: small RNA

value: postnatal day 34


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 048 on D28

description:
Post_scRNA_TotalSeq_048-d28-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 048 on D21

description:
Post_scRNA_TotalSeq_048-d21-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: Eye_ALAN_Male2

description: Library name: 138EA


title: Eye_Midnight_Female3

description: Library name: 135EA

value: Midnight


title: E16.5_FOXG1_replicate2


title: Eye_Midnight_Female4

description: Library name: 136EA

value: Eye


title: cHet input biol rep 2

description: biol rep 2


title: MB65SR

description: small RNA

value: wild type


title: Post_TotalSeq_049-d90-CART

data_processing:
The RNA-seq and paired Total-seq reads were aligned to the GRCh38 reference genome, which was modified with the CAR transgene sequence used in axicabtagene ciloleucel, and quantified using the cellranger count (10x Genomics, version 6.0.0). The filtered gene/feature-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. We obtained a total of 32,741 cells from 13 samples with on average 97,036 reads per cell and a median of 1979 genes per cell.
The TCR-seq reads from each sample were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10x Genomics, version 6.0.0). The results were then aggregated using the cellranger aggr function, with the source patient (donor) and timepoint (origin) of each sample supplied in the metadata to guide the clonotype assignment. The resultant clonotype and filtered contig annotation data were used for downstream analyses. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions for paired productive TCRα and TCRβ chains. TCR clonality overlap and tracing analyses were carried out using the immunarch package (version 0.6.7).
Assembly: GRCh38
Supplementary files format and content: final merged raw count matrices of scRNA and Totalseq
Supplementary files format and content: final R object of combined scTCR data

extract_protocol:
Cryopreserved patient biospecimens were thawed in warm RPMI+10% FBS and washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Next, Fc receptors were blocked by incubation with Human TruStain FcX (BioLegend, 422301) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-anti-CD3E (clone SK7), CITE-seq antibodies, and Alexa Fluor 647-labeled antigen-tetramers at 3 nM final concentration for CAR-detection. Subsequently, cells were incubated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) diluted 1:1000 in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media. Infusion products were partitioned and analyzed directly. Peripheral blood mononuclear cells were subject to fluorescence-activated cell sorting before single-cell partitioning and analysis.
T cells were partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). From the resulting barcoded nucleic acids, TCR-seq libraries were prepared via the Chromium Single-Cell Human TCR Amplification Kit (10x Genomics, 1000252). Sequencing libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via a high-sensitivity D5000 screentape (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq-6000).

tag: disease state

value: Blood PBMCs

tag: molecule type

value: ADT (feature barcode)


title: E16.5_Dlx5/6-Cre-IRES-EGFP; Foxg1fl/fl

data_processing:
The damultiplenxing, barcoded processing, gene counting and aggregation were made using the cell Ranger softwrare v5.0.0  (http://support.10xgenomics. com/single-cell-gene-expression/softwrare/pipelines/latest/what/-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
E16.5 ganglion eminences (GEs) from Dlx5/6-Cre-IRES-EGFP; Foxg1fl/fl and Foxg1fl/fl mice were dissected and immediately submerged in/rinsed with fresh ice-cold Hanks’ balanced salt solution. GEs were subsequently dissected and dissociated into a single-cell suspension using the Papain Cell Dissociation Kit. In brief, subpallium tissues were dissociated in papain reagent containing 0.1% DNaseI at 37 ℃ with a shaking speed of 50 rpm for about 10 min. After re-adding the digestion solution, a second collection was performed following an additional 20 min of digestion to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution. Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue to check the viability of Countess® II Automated Cell Counter.
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Nova seq 6000.

value: Dlx5/6-Cre-IRES-EGFP; Foxg1fl/fl


title: Post_TotalSeq_049-d12-CART


title: T4_unt_4

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Mapping and quantification were perfromed with STAR and Salmon (nf-core/rnaseq version 3.12.0) on the mouse genome mm10 with reverse strand setting and default parameters.
Raw counts were normalized using TMM method from EdgeR (v.4.0.16) and voom from limma (v.3.58.1).
Genes were filtered out if average TPM < 1 or average counts < 5 per sample. Uncharacterized, predicted and pseudogenes were also filtered out to keep a matrix of counts  with n=11’838 genes.
Assembly: mm10
Supplementary files format and content: tab-separated text file with raw count matrix
Supplementary files format and content: tab-separated text file with tpm matrix
Supplementary files format and content: tab-separated text file with log normalized filtered gene expression matrix

source_name: Tumor

growth_protocol: Neutrophils were isolated from the BM, spleen and tumor of H16sc-IS1-tumor-bearing mice treated with anti-IL1RAP (n=4) or matching isotype control (n=4) for 7 days.

extract_protocol:
Total RNA was isolated with the miRNeasy micro Kit (Qiagen), according to the manufacturer’s instructions. RNA quality was controlled on the TapeStation 4200 (Agilent), which confirmed their integrity.
Libraries for mRNA-seq were prepared with the Stranded mRNA Ligation method (Illumina), according to manufacturer’s instructions, starting from 60ng RNA. Libraries, all bearing unique dual indexes, were subsequently loaded at 100 pM on a Novaseq 6000 flow cell (Illumina) and sequenced according to manufacturer’s instructions, yielding pairs of 60 nucleotides reads.

treatment_protocol: Neutrophil isolation was performed on single cell suspensions, using the Mouse Anti-Ly-6G UltraPure MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions.

value: Tumor

value: Neutrophils

value: tumor-bearing

tag: replicate

value: Untreated


title: Eye_Midnight_Female2

description: Library name: 134EA

value: Female

value: WT


title: Post_TotalSeq_049-d28-CART

value: Diffuse Large B-Cell Lymphoma


title: MB64SR

description: small RNA

value: RPE/choroid/sclera


title: MB61SL

description: small RNA


title: T4_IL1rap_4


title: Eye_Midnight_Female1

description: Library name: 133EA


title: T3_unt_3


title: E16.5_Foxg1fl/fl

value: ganglionic eminences


title: E16.5_FOXG1_replicate1

value: wild-type


title: Post_TotalSeq_049-d21-CART


title: MB64SL

description: small RNA

value: postnatal day 34


title: MB66SL

description: small RNA


title: MB61SR

description: small RNA


title: Eye_Midnight_Male4

description: Library name: 132EA

value: male

value: Midnight


title: Post_TotalSeq_033-d28-CART


title: Post_TotalSeq_034-d21-CART


title: Eye_Midnight_Male3

description: Library name: 131EA

value: Eye


title: T2_unt_2


title: Eye_Midday_Female4

description: Library name: 128EA

value: Midday


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 048 on D14

description:
Post_scRNA_TotalSeq_048-d14-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv

value: PBMC

value: CAR-T


title: Eye_Midday_Female3

description: Library name: 127EA


title: T2_IL1rap_2

value: Tumor


title: Eye_Midnight_Male2

description: Library name: 130EA


title: Post_TotalSeq_034-d08-CART

value: Blood PBMCs

value: ADT (feature barcode)


title: T3_IL1rap_3

value: Neutrophils

value: tumor-bearing


title: MB68RR

description: small RNA

source_name: Right eye retina

value: retina

value: wild type


title: MB65SL

description: small RNA

value: RPE/choroid/sclera


title: Post_scRNA_049-d90-CART

value: Diffuse Large B-Cell Lymphoma

value: mRNA


title: Eye_Midday_Female2

description: Library name: 126EA

value: Female

value: WT


title: T1_IL1rap_1


title: MB65RR

description: small RNA

value: postnatal day 34


title: Eye_Midnight_Male1

description: Library name: 129EA

value: Eye

value: male

value: Midnight


title: S4_unt_4

source_name: Spleen

value: Spleen

value: Untreated


title: Post_scRNA_049-d12-CART

value: Blood PBMCs


title: MB64RR

description: small RNA


title: Post_TotalSeq_033-d21-carT

value: ADT (feature barcode)


title: Post_scRNA_034-d21-CART


title: MB66RR

description: small RNA


title: MB68RL

description: small RNA


title: MB66RL

description: small RNA


title: T1_unt_1

value: Tumor

value: Neutrophils


title: Eye_Midday_Female1

description: Library name: 125EA

value: Midday


title: S3_unt_3

value: tumor-bearing


title: Post_scRNA_049-d28-CART


title: Eye_Midday_Male1

description: Library name: 121EA


title: Post_scRNA_033-d28-CART


title: MB61RL

description: small RNA

value: retina

value: wild type


title: Post_scRNA_049-d21-CART

value: Diffuse Large B-Cell Lymphoma

value: mRNA


title: Eye_Midday_Male4

description: Library name: 124EA

value: WT


title: S2_IL1rap_2


title: S4_IL1rap_4


title: Eye_Midday_Male3

description: Library name: 123EA


title: MB65RL

description: small RNA

value: postnatal day 34


title: S1_unt_1


title: Ovary_ALAN_Female1

description: Library name: 117OA

source_name: Ovary

value: Ovary

value: Female

value: ALAN


title: MB64RL

description: small RNA


title: Eye_Midday_Male2

description: Library name: 122EA

value: Eye

value: male


title: Post_scRNA_034-d08-CART

value: Blood PBMCs


title: MB61RR

description: small RNA


title: P58 RNA-seq

city: Vienna

first: Dietmar

last: Pils

address: Spitalgasse 23

department: Dept. of General Surgery

country: Austria

institute: Medical Univ. of Vienna

description:
Library name: 15053
P58

library_source: other

data_processing:
Mapped to the human genome and transcriptome (HG19)
with the RNA Seq Unified Mapper RUM v2.0.4.
Counting in fragments into the gene model from the GENCODE Project v18
http://www.gencodegenes.org/) using htseq-count (HTSeq v0.5.4p2)
Assembly: HG19
Supplementary files format and content: Raw read counts for all samples with ENSEMBL gene identifiers (GENCODE v18); tab-delimited

molecule: other

source_name: HGSOC

extract_protocol:
miRNeasy Mini Kit (Qiagen, Hilden, Germany)
NEXTflex RNA-Seq and Barcoding Kits (Bioo Scientific, Austin, TX, USA)
Ribo-Zero™ rRNA Removal Kit (Epicentre, Madison, WI, USA)

value: HGSOC

value: EpCAM+

tag: histology

value: serous

tag: figo

value: IIIC

tag: grade

tag: spread type


title: Post_scRNA_033-d21-carT


title: S2_unt_2

value: Spleen

value: Neutrophils

value: tumor-bearing

value: Untreated


title: Ovary_ALAN_Female3

description: Library name: 119OA


title: P24 RNA-seq

description:
Library name: 15609
P24

value: IIIb


title: Ovary_ALAN_Female2

description: Library name: 118OA

value: WT


title: S3_IL1rap_3


title: Testes_ALAN_Male2

description: Library name: 114TA

source_name: Testes

value: Testes


title: P16 RNA-seq

description:
Library name: 15605
P16

value: IIIc


title: P8 RNA-seq

description:
Library name: 15054
P8


title: M58 RNA-seq

description:
Library name: 15050
M58


title: BM3_IL1rap_3

source_name: Bone marrow

value: Bone marrow


title: Ovary_ALAN_Female4

description: Library name: 120OA

value: Ovary

value: Female

value: ALAN


title: Testes_ALAN_Male4

description: Library name: 116TA

value: male


title: blood_25w_depressed_ID_2070

type: RNA

city: Brescia

first: Maria Grazia

last: Di Benedetto

address: Via Pilastroni 4

country: Italy

institute: IRCCS Centro San Giovanni di Dio Fatebenefratelli

description: Gene expression data from 25th gestational week pregnant depressed woman

hyb_protocol: Hybridization was performed on Human Gene 2.1 ST Array Strips (Affymetrix), according to GeneChip WT PLUS Reagent kit (ThermoFisher Scientific) protocol, number 703174 - MAN0018137 rev A.0

scan_protocol: Scanning was performed according to GeneChip WT PLUS Reagent kit (ThermoFisher Scientific) protocol (number 703174 - MAN0018137 rev A.0), scanned on GeneAtlasTM software. The data were collected by a laser scanning technique (Agilent Technologies, Palo Alto, CA, USA), and the pixel levels were analyzed with commercial software (Affymetrix).

data_processing: The Affymetrix CEL file were imported into the Partek Genomic Suite software and the analysis followed a specific pipeline. After importing the samples and giving attributes, the quality assessment and control were performed (QA/QC analysis). The data were firstly explored with the Principal Components Analysis (PCA) to find similarities and differences between the samples. Background correction was conducted using Robust Multi-strip Average (RMA) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm to integrate probe intensities to compute the expression levels for each gene transcript.

label: Biotin

source_name: pregnant depressed woman, transcript from blood at 25 gestational week

label_protocol: Biotin based labeling was performed according to GeneChip WT PLUS Reagent kit (ThermoFisher Scientific) protocol, number 703174 - MAN0018137 rev A.0

extract_protocol: Isolation of total RNA from blood PAXgene tubes was performed using the PAXgene blood miRNA kit according to the manufacturer’s protocol (PreAnalytiX, Hombrechtikon, CHE).

value: blood

tag: timing of collection

value: 25 gestational week

tag: psychological profile group

value: depressed

value: female


title: blood_25w_depressed_ID_2064

tag: tissue


title: blood_25w_depressed_ID_2046


title: BM4_IL1rap_4


title: blood_25w_depressed_ID_2069


title: A9 RNA-seq

description:
Library name: 15049
A9

value: HGSOC

value: EpCAM+

value: serous


title: Testes_ALAN_Male3

description: Library name: 115TA


title: Liver_ALAN_Female4

description: Library name: 112LA

source_name: Liver

value: Liver


title: M5 RNA-seq

description:
Library name: 15606
M5


title: BM3_unt_3

value: Neutrophils

value: tumor-bearing

value: Untreated


title: S1_IL1rap_1

value: Spleen


title: BM4_unt_4

value: Bone marrow


title: P55 RNA-seq

description:
Library name: 15052
P55

value: IIa


title: blood_25w_depressed_ID_2056


title: blood_25w_depressed_ID_2041


title: BM2_unt_2


title: BM2_IL1rap_2


title: Testes_ALAN_Male1

description: Library name: 113TA

value: Testes

value: WT


title: A8 RNA-seq

description:
Library name: 15048
A8

value: IIIc


title: Liver_ALAN_Female3

description: Library name: 111LA

value: Female

value: ALAN


title: A6 RNA-seq

description:
Library name: 15047
A6


title: blood_25w_depressed_ID_2037

value: blood

value: 25 gestational week

value: depressed


title: BM1_unt_1


title: Liver_ALAN_Female2

description: Library name: 110LA


title: S62 RNA-seq

description:
Library name: 15046
S62

value: HGSOC

value: EpCAM+

value: IIIC


title: Liver_ALAN_Female1

description: Library name: 109LA

value: Liver


title: BM1_IL1rap_1

value: Neutrophils

value: tumor-bearing


title: P41 RNA-seq

description:
Library name: 15045
P41

value: serous

value: IIC


title: Imp_ctrl_3

data_processing:
Mapping and quantification were perfromed with STAR and Salmon (nf-core/rnaseq version 3.12.0) on the mouse genome mm10 with reverse strand setting and default parameters.
Raw counts were normalized using TMM method from EdgeR (v.4.0.16) and voom from limma (v.3.58.1).
Genes were filtered out if average TPM < 0.78 or average counts < 5 per sample. Uncharacterized, predicted and pseudogenes were also filtered out to keep a matrix of counts  with n=11’813 genes.
Assembly: mm10
Supplementary files format and content: tab-separated text file with raw count matrix
Supplementary files format and content: tab-separated text file with tpm matrix
Supplementary files format and content: tab-separated text file with log normalized filtered gene expression matrix

growth_protocol: H16sc-IS1, and H16sc-ImP cancer cell lines were derived from skin squamous cell carcinomas of K14HPV16/H2b mice. H16sc-IS1 cancer cells were cultured in RPMI (Gibco), 10% FBS (Gibco), penicillin/streptomycin (100 U/mL penicillin, 100 μg/mL streptomycin; Gibco). H16sc-ImP cancer cells were cultured in DMEM (Gibco), 10% FBS (Gibco), 1% penicillin/streptomycin (100 U/mL penicillin, 100 μg/mL streptomycin; Gibco).

extract_protocol:
Total RNA from H16sc-IS1, Control H16sc-ImP and ILs-OE H16sc-ImP cancer cells was isolated with the miRNeasy mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quality was controlled on the TapeStation 4200 (Agilent), which confirmed their integrity.
Libraries for mRNA-seq were prepared with the Stranded mRNA Ligation method (Illumina), according to manufacturer’s instructions, starting from 900ng RNA. Libraries, all bearing unique dual indexes, were subsequently loaded at 100 pM on a Novaseq 6000 flow cell (Illumina) and sequenced according to manufacturer’s instructions, yielding pairs of 60 nucleotides reads.

treatment_protocol: Mouse Il1a (ORF [NM_010554.4]), mouse Il33 (ORF [NM_133775.3]) and mouse Il1f8 (ORF [NM_027163.4]) were overexpressed under the EF1A promoter in H16sc-ImP cancer cells by lentiviral transduction. Expression vectors and control constructs were custom made by VectorBuilder. Lentivirus production and p24 titration (ELISA) were performed at the Gene Therapy Core Facility, EPFL, Switzerland. Cancer cells were plated at 4x104 cells/well in a 24-well plate and incubated at 37oC overnight. The next day, when cells had reached 30-40% confluency, viral particles were added to cells (200 TU/cell) for overnight incubation at 37oC with 8 μg/ml of polybrene. The following day, media was changed and cells allowed to recover for 48 hours before antibiotic selection was initiated with puromycin (2 μg/ml for Il1a), G418 (300 μg/ml for Il33), or blasticidin (4 μg/ml for Il1f8). Co-expression of ILs was achieved through 3 successive rounds of transduction.

value: Tumor

value: Cancer cells

value: No


title: blood_25w_depressed_ID_2040

value: female


title: Liver_ALAN_Male4

description: Library name: 108LA

value: male

value: WT


title: blood_25w_depressed_ID_2035

value: blood


title: Liver_ALAN_Male2

description: Library name: 106LA

value: ALAN


title: Imp_ctrl_2


title: P27 RNA-seq

description:
Library name: 15044
P27

value: IIIA


title: Imp_OE_3

value: OE-ILs

value: lentiviral transduction


title: M39 RNA-seq

description:
Library name: 15041
M39

value: HGSOC

value: EpCAM+

value: IIIC


title: M54 RNA-seq

description:
Library name: 15042
M54

value: IV


title: Liver_ALAN_Male1

description: Library name: 105LA

value: Liver


title: Imp_ctrl_1


title: M35 RNA-seq

description:
Library name: 15040
M35

value: serous

value: IIIB


title: Imp_OE_2

value: Tumor

value: Cancer cells


title: blood_25w_depressed_ID_2033

value: 25 gestational week

value: depressed

value: female


title: Ventral skin_ALAN_Female4

description: Library name: 104VA

source_name: Ventral skin

value: Ventral skin

value: Female

value: WT


title: M28 RNA-seq

description:
Library name: 15039
M28

value: IIIc


title: Imp_OE_1

value: OE-ILs

value: lentiviral transduction


title: LT2_IS1_3

value: No


title: Ventral skin_ALAN_Female3

description: Library name: 103VA

value: ALAN


title: Ventral skin_ALAN_Female2

description: Library name: 102VA


title: Liver_ALAN_Male3

description: Library name: 107LA

value: male


title: P42 RNA-seq

description:
Library name: 15037
P42

value: HGSOC

value: EpCAM+


title: Ventral skin_ALAN_Male4

description: Library name: 100VA


title: LT2_IS1_1


title: GA, KD_RT, rep3

city: Wuhan

first: Xiaohui

last: Zhang

address: Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Gastrocnemius muscle

growth_protocol: Xenograft models were established by injecting subcutaneously 5 × 105 WT MDA-MB-231/Rab27a KD cells with an equal volume of Matrigel on left flank of NOD/SCID/IL2Rγ-null (NSG) mice. All mice were housed in a specific pathogen-free (SPF)  environment under a 12 h light/dark cycle at a relative humidity of 50-60% and room temperature of 22.2 ± 1.1°C, and allowed free access to food and water.

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon reaching approximately 800 mm3, tumors were locally irradiated with a single dose of 10 Gy using a clinical linear accelerator (Varian Medical Systems). Radiation was delivered at a dose rate of 6 Gy/min with 6 MV X-rays. Mice were sacrificed 3 days post-IR and the contralateral GA muscle was sampled.

value: Gastrocnemius muscle

value: raidotherapy


title: Ventral skin_ALAN_Female1

description: Library name: 101VA


title: blood_25w_depressed_ID_2031

value: blood


title: blood_25w_depressed_ID_2034

value: 25 gestational week


title: blood_25w_depressed_ID_2029

value: depressed


title: M53 RNA-seq

description:
Library name: 15034
M53

value: serous

value: IIIC


title: M16 RNA-seq

description:
Library name: 15032
M16


title: GA, KD_RT, rep2


title: P12 RNA-seq

description:
Library name: 15035
P12


title: blood_25w_depressed_ID_2030

value: female


title: blood_25w_depressed_ID_2028


title: blood_25w_depressed_ID_2021


title: blood_25w_depressed_ID_2020


title: Ventral skin_ALAN_Male3

description: Library name: 99VA

value: Ventral skin

value: WT


title: Ventral skin_ALAN_Male2

description: Library name: 98VA


title: P53 RNA-seq

description:
Library name: 15038
P53


title: blood_25w_depressed_ID_2016


title: S25 RNA-seq

description:
Library name: 15030
S25

value: IIIc


title: Ventral skin_ALAN_Male1

description: Library name: 97VA


title: GA, KD_RT, rep1


title: blood_25w_depressed_ID_2009


title: S21 RNA-seq

description:
Library name: 15029
S21


title: LT2_IS1_2

value: Tumor

value: Cancer cells


title: Dorsal skin_ALAN_Female4

description: Library name: 96DA

source_name: Dorsal skin

value: Dorsal skin

value: Female

value: ALAN


title: M25 RNA-seq

description:
Library name: 15027
M25

value: HGSOC

value: EpCAM+


title: GA, KD_CT, rep3

value: Gastrocnemius muscle

value: control


title: blood_25w_depressed_ID_2010

value: blood

value: 25 gestational week


title: blood_25w_depressed_ID_2007

value: depressed


title: blood_25w_depressed_ID_2008


title: GA, KD_CT, rep2


title: GA, KD_CT, rep1


title: Dorsal skin_ALAN_Female1

description: Library name: 93DA


title: M21 RNA-seq

description:
Library name: 15026
M21

value: serous


title: A25 RNA-seq

description:
Library name: 15024
A25


title: GA, RT, rep2

growth_protocol: Xenograft models were established by injecting subcutaneously 5 × 105 WT MDA-MB-231 cells with an equal volume of Matrigel on left flank of NOD/SCID/IL2Rγ-null (NSG) mice. All mice were housed in a specific pathogen-free (SPF)  environment under a 12 h light/dark cycle at a relative humidity of 50-60% and room temperature of 22.2 ± 1.1°C, and allowed free access to food and water.

value: raidotherapy


title: S54 RNA-seq

description:
Library name: 13933
S54

value: IV


title: A21 RNA-seq

description:
Library name: 15023
A21


title: blood_25w_depressed_ID_2003

value: female


title: GA, RT, rep1


title: A54 RNA-seq

description:
Library name: 13932
A54


title: Dorsal skin_ALAN_Male2

description: Library name: 90DA

value: male

value: WT


title: Dorsal skin_ALAN_Male1

description: Library name: 89DA


title: GA, CT, rep3


title: blood_25w_depressed_ID_2004


title: Dorsal skin_ALAN_Female3

description: Library name: 95DA


title: blood_25w_depressed_ID_1042


title: GA, RT, rep3


title: GA, CT, rep2


title: blood_25w_depressed_ID_1048


title: blood_25w_depressed_ID_1031


title: blood_25w_depressed_ID_1035


title: Brain _ALAN_Female4

description: Library name: 88BA

source_name: Brain

value: Brain


title: blood_25w_depressed_ID_2068


title: A42 RNA-seq

description:
Library name: 13930
A42

value: IIIB


title: GA, CT, rep1


title: S41 RNA-seq

description:
Library name: 13929
S41

value: IIC


title: Brain _ALAN_Female2

description: Library name: 86BA

value: Female

value: ALAN


title: Brain _ALAN_Female1

description: Library name: 85BA


title: GDNF_Pos_NCAM1_Pos_2_S11

city: Durham

first: Dorothy

middle: Anna

last: Sipkins

state: North Carolina

address: 905 S. LaSalle St.

institute: Duke University

data_processing:
RNA concentration was evaluated by Qubit and the integrity was assessed by 2100 Bioanalyzer.
Sequencing was conducted using the Illumina Nextseq1000 platform with 150-bp paired-end.
Raw reads were mapped to the mouse reference transcriptome, GRCm39 from Ensembl, using Kallisto version 0.46.2. The quality of the reads and the Kallisto mapping was assessed using FastQC and MultiQC.
After read mapping, the raw data were analyzed using DEsep2 package in R studio by the Duke Center for Genomic and Computational Biology core.
Assembly: mm10
Supplementary files format and content: The text file includes raw counts for each sample

growth_protocol: EO771-tdT-LM2 cells were treated with Glucose deprived media (10mg/dl Glucose +1% FBS ) for 30 minutes and seeded into 12 well plates.

extract_protocol:
RNA was extracted using a Quick-RNA miniPrep kit (Zymo Research). Each condition had triplicates.
library preparation, and sequencing was conducted by the Duke Center for Genomic and Computational Biology core. RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: GDNF (Peprotech, 200ng/ml) and/or anti-NCAM1 (Sigma, 2.5ug/ml) treated the cells for 24 hours in glucose deprived media.

tag: cell line

value: breast cancer cells

value: 0.2 ug/mL GDNF and 2.5 ug/mL anti-NCAM1


title: blood_25w_depressed_ID_2052


title: GDNF_Pos_NCAM1_Pos_3_S12

tag: genotype


title: GDNF_Pos_NCAM1_Pos_1_S10


title: S28 RNA-seq

description:
Library name: 13927
S28

value: HGSOC

value: EpCAM+

value: IIIc


title: Brain _ALAN_Male4

description: Library name: 84BA

tag: Sex


title: Dorsal skin_ALAN_Female2

description: Library name: 94DA

value: Dorsal skin

tag: treatment


title: S42 RNA-seq

description:
Library name: 13931
S42

value: serous


title: GDNF_Neg_NCAM1_Pos_3_S9

value: 0.1% BSA and 2.5 ug/mL anti-NCAM1


title: Brain _ALAN_Male3

description: Library name: 83BA

tag: batch


title: A28 RNA-seq

description:
Library name: 13926
A28


title: Brain _ALAN_Male2

description: Library name: 82BA


title: Brain _ALAN_Female3

description: Library name: 87BA


title: S24 RNA-seq

description:
Library name: 13925
S24

value: IIIb


title: GDNF_Neg_NCAM1_Pos_2_S8


title: blood_25w_depressed_ID_2044

value: blood

value: 25 gestational week

value: depressed

value: female


title: Brain _ALAN_Male1

description: Library name: 81BA

value: Brain

value: male

value: WT


title: GDNF_Neg_NCAM1_Pos_1_S7


title: blood_25w_depressed_ID_2048


title: blood_25w_depressed_ID_2039


title: A41 RNA-seq

description:
Library name: 13928
A41

value: IIC


title: S16 RNA-seq

description:
Library name: 13921
S16


title: blood_25w_depressed_ID_2047


title: blood_25w_depressed_ID_2038


title: GDNF_Pos_NCAM1_Neg_3_S6

value: breast cancer cells

value: 0.2 ug/mL GDNF and 2.5 ug/mL IgG


title: Ovary_Midnight_Female4

description: Library name: 80OA

value: Ovary

value: Female

value: Midnight


title: A16 RNA-seq

description:
Library name: 13920
A16

value: HGSOC

value: EpCAM+

value: IIIc


title: GDNF_Pos_NCAM1_Neg_2_S5


title: Ovary_Midnight_Female3

description: Library name: 79OA


title: GDNF_Pos_NCAM1_Neg_1_S4


title: blood_25w_depressed_ID_2045


title: S13 RNA-seq

description:
Library name: 13919
S13

value: serous

value: IIIC


title: blood_25w_depressed_ID_2023

value: blood

value: 25 gestational week


title: Ovary_Midnight_Female2

description: Library name: 78OA


title: blood_25w_depressed_ID_2018

value: depressed

value: female


title: MGG31, drug treatment, SGC-CK2-1, rep3

city: Los Angeles

first: Yuanzhong

last: Pan

state: California

address: 1002 Childs Way

institute: University of Southern California

description: Library name: MGG31-SGC-3

data_processing:
Raw reads in fastq format was processed with trimgalore to trim adaptor sequences, only paired reads were retained for downstream analysis
Quality control (QC) of trimmed and paried reads were done using fastqc
Paired reads that passed QC were mapped to hg38 assembly using hisat2
Mapped reads in bam format were processed using featureCounts to count number of reads for each gene
Assembly: hg38
Supplementary files format and content: tab-separated counts data, output from featureCounts in the Subread package

growth_protocol: GBM cells were cultured in complete neural media, which is composed of neurobasal medium (Gibco cat. 12348017), 1X B-27 supplement (Gibco cat. 17504044), 1X GlutaMax (Gibco cat. 35050061), 1X sodium pyruvate (Gibco cat. 11360070), 1% Penicillin-Streptomycin (Gibco cat. 15070063), 0.5 µg/mL FGF, and 0.5 µg/mL EGF.

extract_protocol:
Total RNA was extracted using TRIzol followed by column purification.
Poly-A selection and library preparation was performed at Azenta according to their standard RNA-seq service package

treatment_protocol: For onBME culture, Cultrex Basement Membrane Extract Type 2 (BME2, biotechne cat. 3532-005-02) were used per manufacturer’s protocol. In 24-well plates, 60 µL of matrix was coated on the bottom of each well, cured, and 100,000 resuspended single cells were added gently on top. For drug treatment, drugs were diluted in complete media to working concentration and added to cultured cells for 24 hours before RNA extraction.

value: glioblastoma stem cell


title: Testes_Midnight_Male4

description: Library name: 76TA

value: Testes

value: male

value: WT


title: Ovary_Midnight_Female1

description: Library name: 77OA


title: GDNF_Neg_NCAM1_Neg_2_S2

value: breast cancer cells

value: 0.1% BSA and 2.5 ug/mL IgG


title: blood_25w_depressed_ID_2013


title: MGG31, drug treatment, SGC-CK2-1, rep2

description: Library name: MGG31-SGC-2


title: GDNF_Neg_NCAM1_Neg_1_S1


title: GDNF_Neg_NCAM1_Neg_3_S3


title: A24 RNA-seq

description:
Library name: 13924
A24

value: IIIb


title: Testes_Midnight_Male3

description: Library name: 75TA

value: Midnight


title: MGG31, drug treatment, SGC-CK2-1, rep1

description: Library name: MGG31-SGC-1


title: Testes_Midnight_Male2

description: Library name: 74TA


title: blood_25w_history-only_ID_2067

description: Gene expression data from 25th gestational week pregnant history-only woman

source_name: pregnant history-only woman, transcript from blood at 25 gestational week

value: history-only


title: MGG31, drug treatment, CX3935, rep3

description: Library name: MGG31-CX4945-3


title: EO771-tdT-LM2_2

data_processing:
Sequencing was conducted using the Illumina NovaSeq 6000 platform on an S-Prime 50-bp paired-end flow cell. 33 million reads per sample were conducted.
Raw reads were mapped to the mouse reference transcriptome, GRCm39 from Ensembl, using Kallisto version 0.46.2.
The quality of the reads and the Kallisto mapping was assessed using FastQC and MultiQC. After read mapping, the data were imported into RStudio version 1.4.1106 and edgeR version 3.32.1 was used to calculate normalized log2 counts per million (CPM) and filtering was carried out to remove lowly expressed genes (genes with less than 1 CPM in at least 3 or more samples).
To identify differentially expressed genes (DEGs), precision weights were first applied to each gene based on its mean-variance relationship usingVOOM, then data were normalized using theTMM method inedgeR. Linear modeling and bayesian stats were employed viaLimmaversion 3.46.0 to find genes that were up- or down-regulated by 2-fold or more, with a false-discovery rate (FDR) of 0.05
Assembly: GRCm39 from Ensembl
Supplementary files format and content: est_counts, tpm, log2(fold change) values for each group

growth_protocol: EO771-tdT-Parental and EO771-tdT-LM2 were cultured in tissue culture treated flasks for 48 h to about 75% confluence.They were maintained in RPMI 1640 medium with 10% fetal bovine serum.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit (Qiagen). RNA QC, library preparation, and sequencing was conducted by the Duke Center for Genomic and Computational Biology core. RNA concentration was evaluated by Qubit and the integrity was assessed by 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols


title: Testes_Midnight_Male1

description: Library name: 73TA


title: EO771-tdT-LM2_1


title: A13 RNA-seq

description:
Library name: 13918
A13

value: HGSOC

value: EpCAM+


title: MGG31, drug treatment, CX3935, rep2

description: Library name: MGG31-CX4945-2


title: blood_25w_depressed_ID_2011


title: blood_25w_depressed_ID_2015


title: Liver_Midnight_Female4

description: Library name: 72LA

value: Liver

value: Female


title: blood_25w_history-only_ID_2026

value: blood


title: blood_25w_history-only_ID_2036

value: 25 gestational week


title: Liver_Midnight_Female3

description: Library name: 71LA


title: EO771-tdT-Parental_Ac6_3


title: blood_25w_history-only_ID_2022


title: Liver_Midnight_Female2

description: Library name: 70LA


title: EO771-tdT-Parental_Ac6_2


title: EO771-tdT-LM2_3


title: blood_25w_history-only_ID_2042


title: EO771-tdT-Parental_Ac6_1


title: MGG31, drug treatment, GO289, rep1

description: Library name: MGG31-GO289-1


title: Liver_Midnight_Female1

description: Library name: 69LA


title: Input_6 (eCLIP)

city: Frederick

first: Francesco

last: Tomassoni Ardori

state: MD

address: Building 560

institute: Mouse Cancer Genetics Program

description:
0131_Human_Hg38_WT_RBFOX1_IP_vs_WT_no_RBFOX1_IP.IDR.peaks.bed
0131_Minigene_WT_RBFOX1_IP_vs_WT_no_RBFOX1_IP.IDR.peaks.bed
0131_Minigene_WT_RBFOX1_IP_vs_mutant_RBFOX1_IP.IDR.peaks.bed

data_processing:
Trimming and filtering using umi_tools
Alignment and annotation using STAR
Peaks calling with CLIPper
Assembly: hg38 and custom minigene
Supplementary files format and content: Peaks comparison between 77-5 cells + Dox versus 77-5 cells for human assembly (0131_Human_Hg38_WT_RBFOX1_IP_vs_WT_no_RBFOX1_IP.IDR.peaks.bed)
Supplementary files format and content: Peaks comparirson between 77-5 cells + Dox versus 77-5 cells for custom rat and mouse Ntrk2 minegene (0131_Minigene_WT_RBFOX1_IP_vs_WT_no_RBFOX1_IP.IDR.peaks.bed)
Supplementary files format and content: Peaks comparison between 77-5 cells + Dox versus 32-1 + Dox cells for custom rat and mouse Ntrk2 minegene (0131_Minigene_WT_RBFOX1_IP_vs_mutant_RBFOX1_IP.IDR.peaks.bed)

source_name: BAC clone RP23-424E11

growth_protocol: 77-5 and 32-1 cells (T-Rex-293) were maintained in DMEM medium supplemented with 10% FBS  and 1% P/S

extract_protocol:
Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end seCLIP protocol
seCLIP protocol
Other, seCLIP protocol

treatment_protocol: Doxycycline (D3447, Millipore-Sigma) 0.5 mg/ml / 48h

value: BAC clone RP23-424E11

value: control


title: Liver_Midnight_Male4

description: Library name: 68LA


title: MGG31, drug treatment, control, rep3

description: Library name: MGG31-DMSO-3

value: glioblastoma stem cell

value: DMSO


title: MGG31, drug treatment, CX3935, rep1

description: Library name: MGG31-CX4945-1


title: MGG31, drug treatment, control, rep2

description: Library name: MGG31-DMSO-2


title: blood_25w_history-only_ID_2059

value: female


title: Input_4 (eCLIP)


title: Liver_Midnight_Male2

description: Library name: 66LA

value: male

value: WT


title: MGG31, drug treatment, GO289, rep3

description: Library name: MGG31-GO289-3


title: MGG31, drug treatment, control, rep1

description: Library name: MGG31-DMSO-1


title: blood_25w_history-only_ID_2057


title: Input_3 (eCLIP)


title: Liver_Midnight_Male1

description: Library name: 65LA


title: MGG31, drug treatment, GO289, rep2

description: Library name: MGG31-GO289-2


title: MGG31, onBME, rep3

description: Library name: MGG31-BME-3

value: basement membrane extract type 2


title: Input_2 (eCLIP)


title: Ventral skin_Midnight_Female4

description: Library name: 64VA

value: Ventral skin


title: blood_25w_history-only_ID_2066


title: blood_25w_history-only_ID_2043


title: blood_25w_history-only_ID_2012


title: Ventral skin_Midnight_Female3

description: Library name: 63VA

value: Midnight


title: MGG31, onBME, rep2

description: Library name: MGG31-BME-2


title: blood_25w_history-only_ID_2055

value: history-only


title: Input_5 (eCLIP)


title: Liver_Midnight_Male3

description: Library name: 67LA


title: MGG31, onBME, rep1

description: Library name: MGG31-BME-1


title: blood_25w_history-only_ID_1056


title: Ventral skin_Midnight_Female1

description: Library name: 61VA


title: 32-1_Dox_1 (eCLIP)

value: Rbfox1 expression

value: Doxycycline


title: MGG31, 2D, rep3

description: Library name: MGG31-2D-3


title: blood_25w_history-only_ID_2017


title: Ventral skin_Midnight_Female2

description: Library name: 62VA


title: blood_25w_history-only_ID_1050


title: MGG31, 2D, rep2

description: Library name: MGG31-2D-2


title: 77-5_Dox_2 (eCLIP)


title: Ventral skin_Midnight_Male4

description: Library name: 60VA


title: MGG31, 2D, rep1

description: Library name: MGG31-2D-1


title: Ventral skin_Midnight_Male3

description: Library name: 59VA


title: blood_25w_history-only_ID_2019


title: Ventral skin_Midnight_Male2

description: Library name: 58VA


title: T387, onBME, rep3

description: Library name: T387-BME-3


title: blood_25w_history-only_ID_1041


title: 77-5_2 (eCLIP)


title: Input_1 (eCLIP)


title: blood_25w_history-only_ID_1034


title: Ventral skin_Midnight_Male1

description: Library name: 57VA


title: T387, onBME, rep2

description: Library name: T387-BME-2


title: 32-1_Dox_2 (eCLIP)


title: 77-5_1 (eCLIP)


title: 77-5_Dox_3 (RNA-seq)

data_processing:
Trimming and filtering using Cutadapt
Alignment and annotation using STAR
Counts obtained using RSEM
Assembly: GRCh38
Supplementary files format and content: .txt files with isoforms counts from RSEM (human)

growth_protocol: 77-5 cells (T-Rex-293) were maintained in DMEM medium supplemented with 10% FBS  and 1% P/S

extract_protocol:
Qiagen RNeasy Mini kit
Illumina® Stranded mRNA Prep


title: T387, onBME, rep1

description: Library name: T387-BME-1


title: Dorsal skin_Midnight_Female4

description: Library name: 56DA

data_processing:
Raw fastq files were processed by trimming using trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) with the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; SLIDINGWINDOW:10:30; LEADING:28; TRAILING:28; MINLEN:75. After trimming the quality of the reads was checked using FASTQC
Reads were aligned using STAR aligner version 2.7.11a (https://github.com/alexdobin/STAR), with the ENSEMBL green anole (Anolis carolinensis) genome and gtf (AnoCar2.0v2, Anolis_carolinensis.AnoCar2.0v2.112.gtf) as references. BAM files were counted using featurecounts (https://subread.sourceforge.net/).
Assembly: AnoCar2.0v2
Supplementary files format and content: csv files contain ether raw counts for each sample

extract_protocol:
RNAeasy kit
Library construction performed by BGI Genomics

value: Dorsal skin


title: T387, 2D, rep3

description: Library name: T387-2D-3


title: Dorsal skin_Midnight_Female3

description: Library name: 55DA

value: Female


title: 77-5_Dox_2 (RNA-seq)


title: blood_25w_history-only_ID_1024

value: blood


title: blood_25w_history-only_ID_1026

value: 25 gestational week


title: blood_25w_history-only_ID_1028


title: blood_25w_history-only_ID_1013


title: 77-5_Dox_1 (RNA-seq)

value: BAC clone RP23-424E11


title: T387, 2D, rep2

description: Library name: T387-2D-2


title: Dorsal skin_Midnight_Female2

description: Library name: 54DA


title: T387, 2D, rep1

description: Library name: T387-2D-1


title: 77-5_3 (RNA-seq)

value: control


title: blood_25w_history-only_ID_1011


title: ALKappacardiac3

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Library name: AL1313

data_processing:
Reads were mapped to GRCh38
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: Tab separated file having raw read count for each sample in singular file

source_name: cardiac

growth_protocol: hiPSCs were plated at 2 x 106 viable cells per well on Matrigel-coated 6-well plates with 2mL of mTESR and incubated at 37 °C under normoxic, 5% carbon dioxide conditions. mTESR was replaced every 24 hours for two days. After two days, cardiomyocyte differentiation was induced using STEMdiffTM Cardiomyocyte differentiation media (StemCell Technologies; #05010) upon >95% confluence of hiPSCs per manufacturer’s instructions. Day 4, 8, 11, and 15 iPSC-derived cardiomyocytes were used for characterization assays by RT-qPCR and directly visualized via live cell imaging on the Keyence BZ-X710 All-in-one Fluorescence Microscope. Day 15 iPSC-derived cardiomyocytes, which demonstrated spontaneous beating, were used for dosing experiments

extract_protocol:
RNA was extracted from iPSC-derived cardiomyocytes by RNeasy mini extraction kit (Qiagen, Hilden, Germany, Cat. No. 74104), purified using a genomic DNA removal kit (ThermoFisher, Waltham, MA, Cat. no. AM1906)
mRNA library preparation (poly A enrichment)

treatment_protocol: Spontaneously beating day 15 iPSC-derived cardiomyocytes were dosed with 0.02 mg/mL of cardiomyopathy and non-cardiomyopathy associated LCs. Undosed iPSC-derived cardiomyocytes, cardiomyocytes dosed with non-cardiomyopathy associated AL LCs, and cardiomyocytes dosed with non-amyloid LCs were used as negative controls. Dosed and naïve cells were incubated at 37ºC (normoxic and 5% carbon dioxide conditions).

value: cardiac

value: iPSC

value: cardiomyocyte


title: Dorsal skin_Midnight_Female1

description: Library name: 53DA


title: 77-5_2 (RNA-seq)


title: Dorsal skin_Midnight_Male4

description: Library name: 52DA

value: male


title: 77-5_1 (RNA-seq)


title: blood_25w_history-only_ID_1005

value: female


title: ALKappacardiac1

description: Library name: AL1311


title: Dorsal skin_Midnight_Male3

description: Library name: 51DA

value: WT


title: blood_25w_control_ID_1058

description: Gene expression data from 25th gestational week pregnant control woman

source_name: pregnant control woman, transcript from blood at 25 gestational week

value: controls


title: ALKappacardiac2

description: Library name: AL1312


title: Dorsal skin_ALAN_Male4

description: Library name: 92DA

value: ALAN


title: ML364-3, replicate 3, scRNAseq

first: panpan

last: Dai

address: 115 Donghu Road, Wuhan, China

data_processing:
Sequencing was performed on the NovaSeq 6000 System (Illumina). scRNA-seq raw data were generated through 10 x platform and mapping using CellRanger (6.1.2) on the mouse reference refdata-gex-mm10-2020-A.
Assembly: mmu10(NCBI release 100)
Supplementary files format and content: MTX fle and TSV fle contain counts for each barcodes and genes

source_name: Mouse subcutaneous tumor

extract_protocol:
Place the extracted tumor tissue in a sterile culture dish on ice, wash it with phosphate-buffered saline (PBS), then cut it into small pieces (approximately 1mm³) on ice, and enzymatically digest it with collagenase Ⅱ (Worthington) at 37°C for 60 minutes, gently blowing and mixing throughout the process. Following enzymatic digestion, filter the cell suspension first through a 70 μm mesh, and then through a 30 μm mesh to eliminate cell clumps in the suspension. Subsequently, the sample undergoes red blood cell lysis, followed by washing with a calcium and magnesium ion-free phosphate-buffered saline solution, and then with PBS containing 10% bovine serum albumin to further eliminate debris. Trypan blue staining is employed for assessing cell viability. Add an appropriate volume of pre-cooled washing buffer, gently blow and mix until the final cell concentration reaches 700-1200 cells/μL.
Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size.TruSeq Read 1 (Re ad 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (Read 2 primer sequence) are added via End Repair, A tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primer s used in Illumina bridge amplification. Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 450bp.

value: Mouse subcutaneous tumor

value: LLC

value: Tumor cell and others


title: 77-5_Dox_1 (eCLIP)

value: Rbfox1 expression

value: Doxycycline


title: ML364-2, replicate 2, scRNAseq


title: ALLambdacardiac3

description: Library name: AL10213


title: Dorsal skin_Midnight_Male1

description: Library name: 49DA

value: Dorsal skin

value: Midnight


title: ALLambdacardiac2

description: Library name: AL10212


title: ML364-1, replicate 1, scRNAseq


title: DMSO-2, replicate 2, scRNAseq


title: blood_25w_control_ID_1057

value: blood

value: 25 gestational week


title: Brain _Midnight_Female4

description: Library name: 48BA

value: Brain

value: Female


title: blood_25w_control_ID_1053


title: Brain _Midnight_Female3

description: Library name: 47BA


title: MMKappanoncardiac3

description: Library name: MM71543

value: cardiac

value: iPSC

value: cardiomyocyte


title: Brain _Midnight_Female2

description: Library name: 46BA

value: WT


title: DMSO-1, replicate 1, scRNAseq


title: MMKappanoncardiac2

description: Library name: MM71542


title: blood_25w_control_ID_1051

value: controls

value: female


title: MMKappanoncardiac1

description: Library name: MM71541


title: cKO biol rep 2

description: Sex was not determined

data_processing:
Barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Limb buds

extract_protocol:
Total RNA was prepared with a Quick RNA Microprep (Zymo Research, R1051).
Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Chromium, PN-1000268) was used.

value: Limb buds

value: Limb bud cells

value: Mettl14 flox/flox

value: Mettl14 knockout


title: Dorsal skin_Midnight_Male2

description: Library name: 50DA

value: male


title: Brain _Midnight_Female1

description: Library name: 45BA


title: Brain _Midnight_Male4

description: Library name: 44BA


title: blood_25w_control_ID_1044


title: cHet biol rep 2

description: Sex was not determined

value: Mettl14 wt/flox

value: Mettl14 hetero as control


title: cKO biol rep 1

description: Sex was not determined


title: blood_25w_control_ID_1045

value: blood


title: blood_25w_control_ID_1039

value: 25 gestational week


title: Brain _Midnight_Male3

description: Library name: 43BA

value: Brain

value: Midnight


title: cHet biol rep 1

description: Sex was not determined


title: Brain _Midnight_Male2

description: Library name: 42BA


title: ALLambdanoncardiac3

description: Library name: AL51263

value: cardiac


title: ALLambdacardiac1

description: Library name: AL10211

value: iPSC


title: blood_25w_control_ID_1037


title: blood_25w_control_ID_1043


title: ALLambdanoncardiac2

description: Library name: AL51262

value: cardiomyocyte


title: Brain _Midnight_Male1

description: Library name: 41BA

value: WT


title: blood_25w_control_ID_1046

value: controls


title: ALLambdanoncardiac1

description: Library name: AL51261


title: FS6KD, 17 weeks, scRNAseq

city: Osaka

first: Yasunori

last: Shintani

address: 6-1, Kishibe-shinmachi, Suita

department: Molecular Pharmacology

country: Japan

institute: National Cerebral and Cardiovascular Center

description: 10X Genomics

data_processing:
Demultiplexing of cell barcodes, read mapping and alignment was performed by Cell Ranger pipeline provided by 10X Genomics.
Assembly: mm10 (mouse), GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Nuclei isolation from mouse heart tissues: Nuclei were isolated according to Frankenstein protocol with minor modifications. Heart tissue was homogenized by using glass douncer in EZ PREP lysis buffer. Homogenate was filtered through a 70 μm followed by 20 μm and centrifuged at 500 x g for 5 min at 4°C to remove cell debris and aggregates. Nuclei pellet was suspended in ice-cold EZ PREP lysis buffer and incubated on ice for 3 min. After centrifugation at 500 x g for 5 min at 4°C, nuclei pellet was incubated with nuclei washing and resuspension buffer consisting of 1X PBS, 1% BSA, 0.1% Tween-20 and 0.2 U/μl RNase inhibitor (TAKARA Bio) for 5 min before an additional resuspension. Nuclei were centrifuged at 500 x g for 5 min at 4°C and the nuclei pellet was resuspended with nuclei washing and resuspension buffer then sorted by FACS.  Nuclei isolation from human heart tissues: Nuclei were isolated using Singulator 100 system (S2 Genomics, Inc) according to manufacturer’s recommendations. Collected nuclei were centrifuged at 500 x g for 10 min at 4°C and pellets were resuspended with 4 ml nuclei washing and resuspension buffer containing 1X PBS, 1% BSA, and 0.2 U/μl RNase inhibitor. Additional centrifugation at 500 x g for 5 min at 4°C was performed and the nuclei pellet was resuspended with another washing and resuspension buffer.
Droplets capturing single nucleus from whole heart nuclei suspension were used for library generation in the 10X Genomics Chromium controller according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagent Kit v.3 User Guide.

value: Heart

value: Female

value: Cardiac cell populations

value: Ndufs6 knockdown

value: CI-deficiency mitochondrial cardiomyopathy model

tag: age

value: 17 weeks


title: Media3

description: Library name: Media3

tag: cell type


title: blood_25w_control_ID_1033

value: female


title: FS6KD, 12 weeks, scRNAseq

description: 10X Genomics

tag: disease state

value: 12 weeks


title: Ovary_Midday_Female3

description: Library name: 39OA

source_name: Ovary

value: Ovary

value: Midday


title: Media2

description: Library name: Media2


title: Media1

description: Library name: Media1


title: Ovary_Midday_Female2

description: Library name: 38OA


title: FS6KD, 8 weeks, scRNAseq

description: 10X Genomics

value: 8 weeks


title: blood_25w_control_ID_1036

value: blood

value: 25 gestational week


title: blood_25w_control_ID_1032


title: Atf3-/-FS6KD, replicate4, RNA-seq

description:
Atf3KO_5
Atf3KO_raw_count.tsv

data_processing:
Sequenced reads were mapped to the mouse reference genome sequence (GRCm38_p6). BAM files were then each converted into one integrated count file using FeatureCounts (ver 2.0.0).
Assembly: GRCm38_P6
Supplementary files format and content: Tab-delimited text file including raw_counts

extract_protocol:
RNA was isolated from mice hearts using RNeasy fibrous kit (QIAGEN)
Libraries were prepared for sequencing using a TruSeq Stranded mRNA sample prep kit (Illumina) according to the manufacturer's instructions.

value: Atf3 knockout, Ndufs6 knockdown


title: blood_25w_control_ID_1030


title: Naive3

description: Library name: Naive3

value: cardiac

value: iPSC

value: cardiomyocyte


title: Testes_Midday_Male4

description: Library name: 36TA

value: Testes

value: male

value: WT


title: Ovary_Midday_Female1

description: Library name: 37OA

value: Female


title: blood_25w_control_ID_1027

value: controls


title: Atf3-/-FS6KD, replicate3, RNA-seq

description:
Atf3KO_4
Atf3KO_raw_count.tsv

value: Heart


title: Atf3-/-FS6KD, replicate2, RNA-seq

description:
Atf3KO_3
Atf3KO_raw_count.tsv


title: Ovary_Midday_Female4

description: Library name: 40OA


title: HREC24T cells Confluent-3

city: Grand Forks

first: Sonalika

last: Singhal

state: NS

address: 1301 N Columbia Rd

department: Pathology

institute: University of North Dakota

description:
Sample9-SS09
Illumina TruSeq Total RNA kit

data_processing:
High-quality reads were aligned to the human reference genome (GRCh38) using HISAT2, and transcript abundance was quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab Separated Values: tab formats for gene expression matrices, with rows as genes and columns as samples.

source_name: Kidney

growth_protocol: DMEM:F12 serum free media

extract_protocol:
Total RNA Qiagene columns
RNA samples were assessed for quality using a bioanalyzer, and libraries were prepared using a strand-specific RNA sequencing protocol to capture both coding and non-coding RNAs. Sequencing was performed on an Illumina platform using the Illumina TruSeq Total RNA kit and modified Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step to fit the Aviti workflow. Libraries were sequenced to ~40M 75bp paired-end reads on the Element Aviti, generating paired-end reads. The raw reads were quality-checked and trimmed to remove adapters and low-quality bases.

treatment_protocol: No Treatment

value: Kidney

value: Epitheial Cells


title: Testes_Midday_Male2

description: Library name: 34TA

source_name: Testes


title: Naive1

description: Library name: Naive1


title: Testes_Midday_Male3

description: Library name: 35TA


title: Atf3-/-FS6KD, replicate1, RNA-seq

description:
Atf3KO_1
Atf3KO_raw_count.tsv


title: HREC24T cells Confluent-2

description:
Sample8-SS08
Illumina TruSeq Total RNA kit


title: FS6WT, 8 weeks, scRNAseq

description: 10X Genomics

value: Cardiac cell populations

value: control


title: Testes_Midday_Male1

description: Library name: 33TA

value: Midday


title: HREC24T cells Confluent-1

description:
Sample7-SS07
Illumina TruSeq Total RNA kit


title: Naive2

description: Library name: Naive2


title: Atf3+/+FS6KD, replicate3, RNA-seq

description:
Atf3WT_4
Atf3KO_raw_count.tsv

value: Atf3 WT, Ndufs6 knockdown


title: Liver_Midday_Female4

description: Library name: 32LA

value: Liver


title: HRTPTR3 Cells Confluent-3

description:
Sample6-SS06
Illumina TruSeq Total RNA kit

value: HRTPT


title: Atf3+/+FS6KD, replicate2, RNA-seq

description:
Atf3WT_2
Atf3KO_raw_count.tsv


title: blood_25w_control_ID_1020

value: blood

value: 25 gestational week

value: female


title: blood_25w_control_ID_1029


title: Liver_Midday_Female3

description: Library name: 31LA


title: Atf3+/+FS6KD, replicate1, RNA-seq

description:
Atf3WT_1
Atf3KO_raw_count.tsv


title: blood_25w_control_ID_1023


title: HRTPTR2 Cells Confluent-2

description:
Sample5-SS05
Illumina TruSeq Total RNA kit


title: Liver_Midday_Female2

description: Library name: 30LA


title: HRTPTR1 Cells Confluent-1

description:
Sample4-SS04
Illumina TruSeq Total RNA kit


title: Liver_Midday_Female1

description: Library name: 29LA


title: MyoAAV2-shAtf3, replicate2, RNA-seq

description:
Cont_2
AAV_raw_count.tsv

value: Atf3 knockdown


title: RPTEC-TERT1 cells confluent-3

description:
Sample3-SS03
Illumina TruSeq Total RNA kit


title: blood_25w_control_ID_1022


title: Atf3+/+FS6KD, replicate4, RNA-seq

description:
Atf3WT_5
Atf3KO_raw_count.tsv


title: blood_25w_control_ID_1019


title: Liver_Midday_Male4

description: Library name: 28LA

value: male


title: MyoAAV2-shAtf3, replicate3, RNA-seq

description:
Cont_3
AAV_raw_count.tsv


title: blood_25w_control_ID_1017


title: RPTEC-TERT1 cells confluent-2

description:
Sample2-SS02
Illumina TruSeq Total RNA kit

value: WT


title: MyoAAV2-shAtf3, replicate1, RNA-seq

description:
Cont_1
AAV_raw_count.tsv

value: Female


title: Liver_Midday_Male3

description: Library name: 27LA


title: RPTEC-TERT1 cells confluent-1

description:
Sample1-SS01
Illumina TruSeq Total RNA kit


title: MyoAAV2-shCtrl, replicate3, RNA-seq

description:
Atf3_3
AAV_raw_count.tsv


title: blood_25w_control_ID_1014

value: controls


title: TRT7 (L14)

city: Nakhon Ratchasima

first: Chao

last: Ban

address: 111 University Avenue Muang,

country: Thailand

institute: Suranaree University of Technology

description: Library name: L14

data_processing:
Gene expression levels were quantified with RSEM (version 1.3.1) (Li and Dewey, 2011). Differential gene expression analysis between the two groups was performed using DESeq2 (version 1.4.5) (Love et al., 2014). The transcripts were filtered for sufficient normalized read depth, requiring transcripts per million greater than 0 (TPM > 0) in at least 5 samples per group.
Assembly: GCA_002263795.2
Supplementary files format and content: Column 1, RNA_id; Column 2, gene_id; Column 3, gene_symbol; Column 4 - 17,   Sample_TPM: TPM of each gene; Column 18-31, Sample: read_count, count of each gene.

organism: Bos taurus

extract_protocol:
According to the manufacturer`s instructions, total RNA was obtained from liver tissue using TRIzol reagent (Molecular Research Center, Cincinnati, Ohio, USA)
RNA reverse transcription, library preparation, and RNA sequencing (RNA-seq) were carried out at BGI Co., Ltd. (Shenzhen, China). Briefly, total RNA was enriched for mRNA by poly(A) selection using oligo(dT) magnetic beads, followed by reverse transcription and cDNA synthesis. The resulting double-stranded cDNA underwent end repair, 5'-phosphorylation, and 3'-adenylation to prepare for adapter ligation. The adapter-ligated products were then PCR amplified, denatured, and circularized using bridging primers to create single-stranded circular DNA libraries. Sequencing was performed on the DNBSEQ platform with PE500 (BGI Co., Ltd., Shenzhen, China). The raw sequencing data were processed using SOAPnuke (v1.5.6, RRID:SCR_015025) to eliminate low-quality and adapter-contaminated reads. The filtering criteria were as follows: 1) removal of reads containing adapter sequences, 2) exclusion of reads with more than 5% unknown bases (N), and 3) discarding low-quality reads, defined as those in which more than 20% of the bases had a quality score below 15.

tag: breed

value: Holstein


title: Liver_Midday_Male1

description: Library name: 25LA


title: MyoAAV2-shCtrl, replicate2, RNA-seq

description:
Atf3_2
AAV_raw_count.tsv

value: Heart


title: TRT6 (L13)

description: Library name: L13


title: Ventral skin_Midday_Female4

description: Library name: 24VA

value: Ventral skin


title: E2_20mol

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

description:
Library name: E2_20mol
Isolated transgenes from Round 2 of eGFP-LUC VLVs cultured in 20 uM molnupiravir for Round 1 and Round 2, to identify transgene substitutions.

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTCAGGATCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGGCCCATGGAAGATGCCAAAAACATTAAGAAGGGCCCAGCGCCATTCTACCCACTCGAAGACGGGACCGCCGGCGAGCAGCTGCACAAAGCCATGAAGCGCTACGCCCTGGTGCCCGGCACCATCGCCTTTACCGACGCACATATCGAGGTGGACATTACCTACGCCGAGTACTTCGAGATGAGCGTTCGGCTGGCAGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATCGGATCGTGGTGTGCAGCGAGAATAGCTTGCAGTTCTTCATGCCCGTGTTGGGTGCCCTGTTCATCGGTGTGGCTGTGGCCCCAGCTAACGACATCTACAACGAGCGCGAGCTGCTGAACAGCATGGGCATCAGCCAGCCCACCGTCGTATTCGTGAGCAAGAAAGGGCTGCAAAAGATCCTCAACGTGCAAAAGAAGCTACCGATCATACAAAAGATCATCATCATGGATAGCAAGACCGACTACCAGGGCTTCCAAAGCATGTACACCTTCGTGACTTCCCATTTGCCACCCGGCTTCAACGAGTACGACTTCGTGCCCGAGAGCTTCGACCGGGACAAAACCATCGCCCTGATCATGAACAGTAGTGGCAGTACCGGATTGCCCAAGGGCGTAGCCCTACCGCACCGCACCGCTTGTGTCCGATTCAGTCATGCCCGCGACCCCATCTTCGGCAACCAGATCATCCCCGACACCGCTATCCTCAGCGTGGTGCCATTTCACCACGGCTTCGGCATGTTCACCACGCTGGGCTACTTGATCTGCGGCTTTCGGGTCGTGCTCATGTACCGCTTCGAGGAGGAGCTATTCTTGCGCAGCTTGCAAGACTATAAGATTCAATCTGCCCTGCTGGTGCCCACACTATTTAGCTTCTTCGCTAAGAGCACTCTCATCGACAAGTACGACCTAAGCAACTTGCACGAGATCGCCAGCGGCGGGGCGCCGCTCAGCAAGGAGGTAGGTGAGGCCGTGGCCAAACGCTTCCACCTACCAGGCATCCGCCAGGGCTACGGCCTGACAGAAACAACCAGCGCCATTCTGATCACCCCCGAAGGGGACGACAAGCCTGGCGCAGTAGGCAAGGTGGTGCCCTTCTTCGAGGCTAAGGTGGTGGACTTGGACACCGGTAAGACACTGGGTGTGAACCAGCGCGGCGAGCTGTGCGTCCGTGGCCCCATGATCATGAGCGGCTACGTTAACAACCCCGAGGCTACAAACGCTCTCATCGACAAGGACGGCTGGCTGCACAGCGGCGACATCGCCTACTGGGACGAGGACGAGCACTTCTTCATCGTGGACCGGCTGAAGAGCCTGATCAAATACAAGGGCTACCAGGTAGCCCCAGCCGAACTGGAGAGCATCCTGCTGCAACACCCCAACATCTTCGACGCCGGGGTCGCCGGCCTGCCCGACGACGATGCCGGCGAGCTGCCCGCCGCAGTCGTCGTGCTGGAACACGGTAAAACCATGACCGAGAAGGAGATCGTGGACTATGTGGCCAGCCAGGTTACAACCGCCAAGAAGCTGCGCGGTGGTGTTGTGTTCGTGGACGAGGTGCCTAAAGGACTGACCGGCAAGTTGGACGCCCGCAAGATCCGCGAGATTCTCATTAAGGCCAAGAAGGGCGGCAAGATCGCCGTGTCGACTGTTTAA
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.

organism: Semliki Forest virus

extract_protocol:
Total RNA from VLV supernatant extracted. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Samples were sequenced with Novogene using their ‘Microbial PCR Product Whole Genome Sequencing’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.


title: blood_25w_control_ID_1001

data_processing: The Affymetrix CEL file were imported into the Partek Genomic Suite software and the analysis followed a specific pipeline. After importing the samples and giving attributes, the quality assessment and control were performed (QA/QC analysis). The data were firstly explored with the Principal Components Analysis (PCA) to find similarities and differences between the samples. Background correction was conducted using Robust Multi-strip Average (RMA) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm to integrate probe intensities to compute the expression levels for each gene transcript.

extract_protocol: Isolation of total RNA from blood PAXgene tubes was performed using the PAXgene blood miRNA kit according to the manufacturer’s protocol (PreAnalytiX, Hombrechtikon, CHE).


title: blood_25w_control_ID_1003


title: MyoAAV2-shCtrl, replicate1, RNA-seq

description:
Atf3_1
AAV_raw_count.tsv


title: E2_DMSO

description:
Library name: E2_DMSO
Isolated transgenes from Round 2 of eGFP-LUC VLVs cultured in DMSO for Round 1 and Round 2, to identify transgene substitutions.


title: blood_25w_control_ID_1006


title: Atf3_low, replicate 3, PIC

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). 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.
Assembly: GRCm38
Supplementary files format and content: comma-delimited file including UMI_raw_counts

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℃. cDNA;mRNA hybrids were purified with a Qiagen MinElute PCR Purification kit.
All subsequent steps are according to the CEL-seq2 method as follows: Second strand DNA is synthesized by nick translation method using RNase H, DNA polymerase I, and DNA ligase mix, by which only the cDNAs derived from the photo-irradiated region are filled-in to the 5' end of T7 promoter, thereby allowing the cDNAs to be linearly amplified as RNAs (aRNAs) by IVT reaction. The libraries are further reverse-transcribed, followed by paired-end sequencing on the Illumina platform.

value: Cardiomyocytes

value: Ndufs6 knockdown

tag: atf3 expression


title: TRT5 (L12)

description: Library name: L12


title: Ventral skin_Midday_Female3

first: Violeta

last: Trejo-Reveles

address: Old College, South Bridge, Edinburgh

description: Library name: 23VA

value: Midday


title: AC_270_R30

description: Isolated transgenes from Round 30 (E30) of Nb139-VP64 VLPs, to identify transgene substitutions.

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGCAAGTGCAGCTTCAAGAATCCGGGGGCGGATTGGTTCAAGCCGGTGGTAGCCTCAGGCTTTCTTGTGCTGCATCCGAACGCACCTTCTCAACCTATGCTATGGGGTGGTTTCGGCAGGCCCCTGGTAGAGAGAGGGAGTTCCTTGCACAAATTAATTGGTCAGGGACAACTACATATTATGCCGAGTCTGTCAAGGATAGAACAACTATTTCTAGGGACAACGCCAAGAATACAGTTTATTTGGAAATGAATAACCTGAATGCTGACGATACAGGAATTTACTTTTGTGCAGCCCATCCACAGCGCGGCTGGGGTTCTACTTTGGGTTGGACCTACTGGGGGCAGGGAACTCAAGTAAGCTCCGTAAGTTCCGGTGGTGGGGGTTCAGGAGGGGGAAAGCCTATACCAAATCCACTGTTGGGCCTGGACTCAACTCGTACCGGACATCATCATCATCACCACTCAGGAAGTGGGAAGCGTCCTGCTGCTACAAAAAAAGCTGGACAGGCTAAGAAAAAAAAAGGCTCTGATGCACTGGATGATTTTGATCTCGATATGCTGGGAAGCGATGCCCTTGATGACTTTGATCTGGACATGCTGGGATCCGATGCTCTTGACGACTTCGACTTGGATATGTTGGGGTCCGATGCACTTGATGATTTTGACCTTGACATGCTGTAA
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing

extract_protocol:
Total RNA from VLP supernatant extracted. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Samples were sequenced with Novogene using their ‘Microbial PCR Product Whole Genome Sequencing’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.


title: TRT4 (L11)

description: Library name: L11


title: Atf3_low, replicate 2, PIC


title: blood_25w_control_ID_1004


title: blood_25w_control_ID_1016


title: AC_270_R26

description: Isolated transgenes from Round 26 (E26) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: Ventral skin_Midday_Female1

description: Library name: 21VA


title: AC_270_R34

description: Isolated transgenes from Round 34 (E34) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: blood_25w_control_ID_1002


title: Atf3_low, replicate 1, PIC


title: TRT3 (L10)

description: Library name: L10


title: Ventral skin_Midday_Male4

description: Library name: 20VA


title: TRT2 (L9)

description: Library name: L9


title: Liver_Midday_Male2

description: Library name: 26LA


title: AC_270_R20

description: Isolated transgenes from Round 20 (E20) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: Ventral skin_Midday_Male3

description: Library name: 19VA


title: Atf3_high, replicate 3, PIC


title: TRT1 (L8)

description: Library name: L8


title: AC_270_R15

description: Isolated transgenes from Round 15 (E15) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: Atf3_high, replicate 2, PIC


title: Ventral skin_Midday_Male2

description: Library name: 18VA


title: Atf3_high, replicate 1, PIC


title: AC_270_R10

description: Isolated transgenes from Round 10 (E10) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: CON6 (L6)

description: Library name: L6


title: Ventral skin_Midday_Male1

description: Library name: 17VA


title: AC_270_R5

description: Isolated transgenes from Round 5 (E5) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: CON5 (L5)

description: Library name: L5


title: AC_213_R8_3

description: Isolated transgenes from Round 8 (E8) of tTA VLPs, to identify transgene substitutions. [Campaign 2]

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGCTAGATTAGATAAAAGTAAAGTGATTAACagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgcgtacagccgcgcgcgtacgaaaaacaattacgggtctaccatcgagggcctgctcgatctcccggacgacgacgcccccgaagaggcggggctggcggctccgcgcctgtcctttctccccgcgggacacacgcgcagactgtcgacggcccccccgaccgatgtcagcctgggggacgagctccacttagacggcgaggacgtggcgatggcgcatgccgacgcgctagacgatttcgatctggacatgttgggggacggggattccccgggtccgggatttaccccccacgactccgccccctacggcgctctggatatggccgacttcgagtttgagcagatgtttaccgatgcccttggaattgacgagtacggtgggtag
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing


title: AC_270_RA

description: Isolated transgenes from Round A (amplification) of Nb139-VP64 VLPs, to identify transgene substitutions.


title: CON3 (L3)

description: Library name: L3


title: CON4 (L4)

description: Library name: L4


title: Unchallenged

city: tianjin

first: wu

last: peng

address: 288 Nanjing Road

institute: Peking Union Medical College,

data_processing:
sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell ranger v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMIs for each Sample

source_name: bone marrow neutrophil

extract_protocol: 10x Genomics Single Cell 3’ Library Kit V2

tag: strain

value: bone marrow

tag: cell enrichment

value: enrich by cKit+

value: steady state


title: Challenged twice

value: E.coli challenge twice(48h)


title: Dorsal skin_Midday_Female3

city: Edinburgh

institute: The University of Edinburgh

description: Library name: 15DA

value: Dorsal skin


title: Dorsal skin_Midday_Female1

description: Library name: 13DA


title: Dorsal skin_Midday_Female2

description: Library name: 14DA


title: AC_213_R6_3

description: Isolated transgenes from Round 6 (E6) of tTA VLPs, to identify transgene substitutions. [Campaign 2]


title: Dorsal skin_Midday_Female4

description: Library name: 16DA


title: CON2 (L2)

description: Library name: L2

value: Liver


title: Host_Y_F5

city: Lund

first: Anna

last: Konturek-Ciesla

state: Skane

address: Klinikgatan 26, BMC B12

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Artificially single-ended: sequenced as paired-end, the sample barcode was sequenced in R1 and this information was moved to the headers/file names of the R2 sequences. Only these complete R2 files are included. The data originates from a forward-stranded library.

data_processing:
The cDNA library was paired-end sequenced on an Illumina NovaSeq X Plus, using a 10B Illumina kit (100 cycles), with a sequencing depth of 10 million reads per sample and the following read configuration: R1=26 cycles; i7=6 cycles and R2=60 cycles.
Read 1 was used to identify the sample barcode, and this information was moved to the headers of the R2 sequences. Read 2 was mapped to the Mouse GRCm38 reference genome using the STARsolo v.2.7.10b package.
Reads that mapped to multiple locations on the reference genome were discarded.
Generation of the count table was carried out using the STARsolo v.2.7.10b package.
Downstream analyses were performed using R v.4.2.1, including normalization and differential gene expression using DESeq2 v.1.36.0 package. Differentially expressed genes were identified based on adjusted p-value <0.1.
Assembly: mouse GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts of all samples

source_name: Bone marrow

extract_protocol:
Donor and host MPP Ly cells (Lineage-cKIT+SCA-1+IL7Ra-FLT3+CD150-) were isolated from the BM of each recipient by fluorescence-activated cell sorting (FACS) 16 weeks after CD45.2-saporin treatment. Two hundred MPP Ly cells were directly sorted into TRIzol reagent.
mRNA was reverse transcribed, barcoded with CEL-seq2 primers, pooled, and amplified with in vitro transcription. The resulting amplified RNA was fragmented and used to generate cDNA sequencing libraries with Truseq Small RNA adapters (Illumina).

treatment_protocol: Young ex vivo expanded HSCs were transplanted into young (3 months) and aged (16 months) mice treated with G-CSF/AMD3100. 20 weeks after transplantation, mice were treated with CD45.2-saporin to deplete host BM cells.

value: Bone marrow

value: MPP Ly

tag: cell origin

value: host

tag: recipient

value: young


title: Dorsal skin_Midday_Male4

description: Library name: 12DA

value: male

value: WT


title: CON1 (L1)

description: Library name: L1

source_name: Liver

value: Holstein


title: Host_Y_F3


title: Challenged once

value: E.coli challenge once(24h)


title: Dorsal skin_Midday_Male3

description: Library name: 11DA


title: Host_Y_F1


title: Dorsal skin_Midday_Male2

description: Library name: 10DA


title: AC_213_R2_3

description: Isolated transgenes from Round 2 (E2) of tTA VLPs, to identify transgene substitutions. [Campaign 2]


title: HCT116-TSA1

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

description: FPKM_ HCT-TSA1

data_processing:
The raw reads were filtered by removing reads containing adapter, poly-N and low quality reads for subsequent analysis. The steps of sequencing data filtering:
1) removing reads containing adapter;
2) removing reads containing poly-N (i.e., unrecognized bases), reads with a ratio greater than 5%;
3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read).
All the downstream analyses were based on clean data with high quality.
Assembly: hg38
Supplementary files format and content: Excel file includes FPKM values for each Sample.

growth_protocol: HCT116 colon cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol (Takara). A total amount of 1μg qualified RNA per sample was used as input material for the library preparation.
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s recommendations. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations under elevated temperature in Vazyme Frag/Prime Buffer. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. Then, the cDNA fragments were end repaired with the addition of a single ‘A’ base at the 3'-end of each strand, ligated with the special sequencing adapters (Vazyme, N803) subsequently. The products were purified and size selected with VAHTS TM DNA Clean Beads (Vazyme, N411) in order to get appropriate size for sequencing. PCR was performed and aimed products were purified.

treatment_protocol: HCT116 were treated with DMSO (0.1%), SAHA (1μM) and TSA (0.1μM) for 24 h.

value: colon cancer

value: TSA


title: CON7(L7)

description: Library name: L7


title: AC_213_R10_2

description: Isolated transgenes from Round 10 (E10) of tTA VLPs, to identify transgene substitutions. [Campaign 1]


title: HCT116-TSA2

description: FPKM_ HCT-TSA2


title: Host_Y_F9


title: AC_213_R10_3

description: Isolated transgenes from Round 10 (E10) of tTA VLPs, to identify transgene substitutions. [Campaign 2]


title: Brain _Midday_Female4

description: Library name: 8BA

value: Brain

value: Female

value: Midday


title: Dorsal skin_Midday_Male1

description: Library name: 9DA


title: HCT116-SAHA1

description: FPKM_ HCT-SAHA1

value: SAHA


title: Host_A_F6

value: aged


title: Host_A_F7


title: HCT116-SAHA2

description: FPKM_ HCT-SAHA2


title: Host_A_F9


title: HCT116-Blank2

description: FPKM_ HCT-Blank2

value: DMSO


title: AC_213_R6_2

description: Isolated transgenes from Round 6 (E6) of tTA VLPs, to identify transgene substitutions. [Campaign 1]


title: Brain _Midday_Female2

description: Library name: 6BA


title: Host_A_F10


title: Brain _Midday_Female3

description: Library name: 7BA


title: AC_213_R4_3

description: Isolated transgenes from Round 4 (E4) of tTA VLPs, to identify transgene substitutions. [Campaign 2]


title: AC_213_R2_2

description: Isolated transgenes from Round 2 (E2) of tTA VLPs, to identify transgene substitutions. [Campaign 1]


title: HCT116-Blank1

description: FPKM_ HCT-Blank1


title: Donor_Y_F9

value: donor


title: AC_213_RA

description: Isolated transgenes from Round A (amplification) of tTA VLPs, to identify transgene substitutions.


title: Donor_Y_F5

value: Bone marrow


title: Brain _Midday_Male4

description: Library name: 4BA