title: 7day sham

value: 7-day neonatal mice were underwent sham operation on the left hindlimbs. RNA was collected from uninjured Achilles tendons 5 days postoperatively.


title: CTRL_01_BM

status: Public on Mar 15 2025

type: SRA

city: Shanghai

first: LU

last: MENG

address: No.320 Yue Yang Road

department: Immunology

country: China

institute: Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: bone marrow b cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BM-B cells were obtained using the EasySep™ Mouse B Cell Isolation Kit

tag: tissue

value: bone marrow

tag: strain

tag: genotype


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 0:15 rep1

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
Library name: splitPE26-E1
molar ratio 0:15 rep1
sPE_sep_processed_date.xls

library_source: genomic

data_processing:
*library strategy: Amplicon Sequencing
Traget site and protential off-target sites were amplified by PCR using the primer sequences, then sequenced on an Illumina NovaSeq system. Deep sequencing data analysis was processed using CRISPResso2 and untreated cells were used as negative controls to exclude PCR amplification and sequencing errors. Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
On-target editing efficiencies, which are greater than 0.1%, were quantified as a percentage of (number of on-target reads) / (number of total reads).
Assembly: sequence.txt
Supplementary files format and content: xlsx files, percentage of total sequencing reads with on-target editing or off-target editing for all libraries, percentage of total sequencing reads with indels.

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cell

growth_protocol: HEK293T cell and Hepa1-6 cell were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% GlutaMAX (Thermo #35050061). Cells were passaged every 2-3 days. After one day post-transduction, the medium was changed. Cells were harvested at 72 hours post-transduction.

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA Kit (TIANGEN #DP304) according to the manufacturer’s protocol.
The region that integrated with genomic DNA including RT template was PCR amplified from genomic DNA for HTS. For the first round of PCR, genomic sites of interest were amplified from 150 ng of genomic DNA using Q5 PCR Master Mix (New England Biolabs #M0544S) with the primers containing Illumina forward and reverse adapters. 50 uL of PCR 1 reaction was performed with forward and reverse primers each at 0.25 uM, ~1 uL of genomic DNA extract, and 25 uL of Q5 PCR Master Mix. To add a unique sequencing index, 50 uL of a given PCR 2 contained 2.5 uL of previous step unpurified PCR product; a unique forward or reverse primer pair, each at 0.25 uM; and 25 uL of Q5 PCR Master Mix. Primers are listed in Table S1. PCR 2 products were purified by DNA AMPure XP beads (Beckman Coulter #A63882) and eluted with 25 uL of water. DNA concentration was quantified by Nanodrop One (Thermo Fisher Scientific).

treatment_protocol: Cells were transfected at 60%-70% confluency using 3 uL of Lipofectamine 3000 (Thermo Fisher) with 1500 ng each half of the Split-PE. Three days post transfection, cells were collected. All animal experiments were conducted under the protocol approved by Institutional Animal Care and Use Committee (IACUC) of the Westlake University. C57BL/6 male mice were purchased and housed in the Laboratory Animal Resource Center (LARC) at the Westlake University. The LARC is a certified pathogen-free and environmental-control facility (21 ± 2°C, 55 ± 15% humidity and 12:12-h light: dark cycle). AAV were injected into the tail vein of six-week-old male C57BL/6 mice.

tag: cell line

value: HEK293T cell

tag: cell type

value: human embryonic kidney cells

value: WT

tag: treatment


title: CTRL_02_BM


title: LN018

status: Public on Mar 14 2025

city: Hohhot

first: lin

last: zhu

state: Antioxidants

address: The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock Co-built by the School of Life Sciences of Inner Mongolia University and the Ministry of Agriculture

institute: Inner Mongolia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: muscle

extract_protocol:
Freeze muscle tissue in liquid nitrogen and harvest RNA using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: muscle

tag: age


title: L7A5KO_01_BM

description: SLC7A5 knockout (KO) mice by breeding SLC7A5fl/fl mice with CD19-Cre mice


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 0:15 rep2

description:
Library name: splitPE26-E2
molar ratio 0:15 rep2
sPE_sep_processed_date.xls


title: v3em PE3 plasmids lipo 3000 transfection at Dnmt1 site rep1

description:
Library name: splitPE28-1
rep1
sPE_sep_processed_date.xls

source_name: Hepa1-6 cell

value: Hepa1-6 cell

value: mouse hepatocellular carcinoma cells


title: LN015

value: MSTN+/-


title: LN013


title: LN012


title: LN020


title: LN019


title: LN011


title: 6month cut

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: RNA was pooled from 9 independent mice.

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Assembly: mm10

source_name: Achilles tendon

growth_protocol: Achilles tendons were harvested from 7-day and 6-mouth-old male Scx-EGFP mice treated with tenotomy or sham operations using surgical microscope. In tenotomy group, distal stumps of the Achilles tendons without surrounding connective tissue were selectively collected.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen).The integrity of the isolated RNA was verified using the Bioanalyzer RNA6000 pico kit (Agilent Technologies).
Due to an RNA integrity value of the samples were less than 8, RNA-Seq libraries were prepared from 10ng of RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Multiplex Oligos for Illumina. Each library was sequenced on MiSeq (Illumina) with MiSeq Reagent kit V3 150 cycle (Illumina) by 75 base pair-end reads. Differentially expressed genes were determined by an exact test after normalization.

value: Scx-EGFP homo (C57BL/6 background)

tag: Sex

value: Male

value: 6-month adult mice were underwent Achilles tenotomy on the right hindlimbs. RNA was collected from uninjured Achilles tendons 5 days postoperatively.

value: Achilles tendon


title: LN014


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 5:15 rep1

description:
Library name: splitPE26-E4
molar ratio 5:15 rep1
sPE_sep_processed_date.xls


title: LN010


title: Naphthalene treated, rep1

city: Seoul

first: Bogun

last: Kim

address: 145, Anam-ro

department: Department of Biotechnology

country: South Korea

institute: Korea University

description: Library name: NPT1

data_processing:
Sequenced reads were trimmed for adaptor or low-quality sequence using TrimGalore v0.6.7 in --paired mode.
Trimmed reads were mapped to the mouse reference genome mm39 using HISAT2 v2.2.1 with --max-intronlen 150000 parameter.
Read counting was performed using featureCounts v2.0.6 using -p --countReadPairs -B -C parameters. Differentially expressed gene (DEG) analysis was performed using edgeR v4.2.1.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: lung

extract_protocol:
Total RNA was isolated from adult lungs (right cranial lobes) of four control and four naphthalene-injected mice using Trizol reagent (Life Technologies) combined with on-column DNase digestion (TURBO DNAse, Ambion) to avoid contamination by genomic DNA.
DNA Library preparation was performed at Macrogen (South Korea) using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit protocol

value: lung

value: naphthalene


title: Naphthalene treated, rep4

description: Library name: NPT4


title: Naphthalene treated, rep3

description: Library name: NPT3


title: Naphthalene treated, rep2

description: Library name: NPT2


title: Control, rep1

description: Library name: CON1

value: no treatment


title: 2dA1

city: Sendai

first: Yunyu

last: Fu

address: 4-1, Seiryouchou, Aoba-ku

institute: Tohoku University

description: Library name: Sample1

data_processing:
mRNA sequencing was performed on an Illumina 6000 platform (Macrogen, Japan) with a 101 bp read length. All adapters and low-quality reads were removed using FastQC. The R package ‘DESeq2’ was used for analysis, with a threshold of P value < 0.05 and fold change > ±1.2 for differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: iPSCs

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq standed mRNA Library Prep Kit

treatment_protocol: For the shaking culture, cells were cultured in low-attachment culture flasks (Thermo Fisher Scientific) containing an osteogenic induction medium. The flasks were then placed on a seesaw shaker with a constant frequency of 0.3 Hz

value: iPSCs

value: Aherent culture


title: 2dF1

description: Library name: Sample3

value: Shaking culture


title: Control, rep4

description: Library name: CON4


title: 2dF2

description: Library name: Sample4


title: Pol II 500k 1%, 10 min Rep2

city: Baltimore

first: Patricia

middle: J

last: Gearhart

state: Maryland

address: 251 Bayview Blvd, Rm 06009C

department: Laboratory of Molecular Biology and Immunology

country: USA

institute: NIH/NIA

description: Library name: 591

data_processing:
Demultiplexing using bcl2convert
Adapter trimming using trimgalore
Alignment using bowtie2
Duplicate marking and removal using SAMtools
Peak calling using MACS2
IDR analysis using idr
Assembly: GRCm39 (mm39)
Supplementary files format and content: BED files containing all mapped and QC'd reads are provided
Supplementary files format and content: Bedgraph files containing peak data are provided for non-IgG samples (IgG used as control for peak calling within experiments)
Library strategy: CUT&Run

source_name: Splenic

growth_protocol: Primary B cells purified from mouse spleens were stimulated in RPMI 1640 supplemented with 10% FBS, 1% GlutaMAX, 1% Pen/Strep, 50 micromolar 2-me. Cells were cultured at 37C 5% CO2 for 48 hours

extract_protocol:
Cells were fixed with 0.1-1% formaldehyde for 1-10 minutes and quenched with glycine. Nuclei were isolated and used for CUT&RUN modified for primary B cells
EpiCypher Library Prep Kit

value: Splenic

value: Follicular B cell

tag: antibody

value: RNA Polymerase II

value: 48 hour stim w anti-CD40 and IL-4


title: Control, rep3

description: Library name: CON3


title: 2dA2

description: Library name: Sample2


title: IgG 500k 1%, 10 min Rep2

description: Library name: 590

value: IgG


title: Pol II 500k 1%, 1 min Rep2

description: Library name: 588


title: LN016

value: muscle


title: IgG 500k 0.1%, 10 min Rep1

description: Library name: 584


title: IgG 500k 1%, 1 min Rep2

description: Library name: 587


title: H3K4me3 500k 1%, 10 min Rep2

description: Library name: 589


title: Pol II 500k 0.1%, 10 min Rep1

description: Library name: 585


title: H3K4me3 500k 0.1%, 10 min Rep1

description: Library name: 583


title: Pol II 500k 1%, 10 min Rep1

description: Library name: 582


title: H3K4me3 500k 1%, 1 min Rep2

description: Library name: 586


title: IgG 500k 1%, 10 min Rep1

description: Library name: 581


title: H3K4me3 500k 1%, 10 min Rep1

description: Library name: 580


title: Pol II 100k 1%, 10 min Rep1

description: Library name: 576


title: IgG 100k 1%, 10 min Rep1

description: Library name: 575


title: Pol II 250k 1%, 10 min Rep1

description: Library name: 579


title: Control, rep2

description: Library name: CON2


title: IgG 250k 1%, 10 min Rep1

description: Library name: 578


title: H3K4me3 250k 1%, 10 min Rep1

description: Library name: 577


title: Pol II 500k 0.1%, 1 min Rep1

description: Library name: 573


title: H3K4me3 100k 1%, 10 min Rep1

description: Library name: 574


title: H3K4me3 500k 0.1%, 1 min Rep1

description: Library name: 571


title: Pol II 250k 0.1%, 1 min Rep1

description: Library name: 570


title: IgG 250k 0.1%, 1 min Rep1

description: Library name: 569


title: H3K4me3 250k 0.1%, 1 min Rep1

description: Library name: 568


title: Pol II 100k 0.1%, 1 min Rep1

description: Library name: 567


title: Pol II 500k 1%, 1 min Rep1

description: Library name: 564


title: H3K4me3 100k 0.1%, 1 min Rep1

description: Library name: 565


title: IgG 500k 1%, 1 min Rep1

description: Library name: 563


title: H3K4me3 500k 1%, 1 min Rep1

description: Library name: 562


title: PDAC, TMAB3/siRNA, 7 days post-3rd treatment, rep2

city: New Haven

first: Haoting

last: Chen

state: CT

address: 333 Cedar St

institute: Yale University

description:
Library name: TMAB3/siRNA
10x Chromium system

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data (FASTQ files, 10X Genomics) were aligned to mm10 mouse reference genome using the Cell Ranger Single Cell software (10x Genomics). R package Seurat version 4.1.1 (51) was used to analyze the output data under RStudio version 4.2.0.
Assembly: Mouse mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx, h5 archives)

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
Pancreatic tumors were collected after 7 days post-treatment. To dissociate, tumors were minced and washed in Hank’s Balanced Salt Solution (Corning) and incubated with collagenase (Collagenase type V 0.012% (w/v) (Sigma), Soy Trypsin Inhibitor 0.012% (w/v) (Gibco) and DNase (Sigma) and incubated with heating for 40 minutes at 37° C on the gentleMACS Octo Dissociator (Miltenyi Biotechnology) program (37_m_TDK_1). Cells were filtered using a 70 μm nylon mesh (Fisher Scientific). Ebioscience 1X RBC Lysis Buffer (Thermo Fisher) was added to lyse red blood cells. Single-cell suspensions were prepared, and dead cells were excluded using the EasyStep Dead Cell Removal (Annexin V) Kit (STEM Cell Technologies).
For each group, 5,000 cells were used for the 10x Genomics 3’ v2 single-cell assay. Reverse transcription, cDNA amplification, and library preparation were performed according to the manufacturer's protocol at the Yale Center for Genome Analysis.

value: Pancreas

value: KPC

value: Pancreatic ductal adenocarcinoma cell


title: PDAC, TMAB3, 7 days post-3rd treatment, rep 2

description:
Library name: TMAB3
10x Chromium system


title: Liver, Control, 4 hours, Rep 4

city: Manchester

first: Giuseppe

last: D’Agostino

address: Rumford Street off Dover Street

department: Division of Diabetes, Endocrinology & Gastroenterology

country: United Kingdom

institute: The University of Manchester

description: Library name: Sample 8

data_processing:
Evaluate sequency quality; trim reads; map reads to genome; generated hit counts for genes; compare gene hit counts; analyze gene ontology
Assembly: Mus musculus GRCm38
Supplementary files format and content: CSV; log2FoldChange; pvalue; padj; samples; gene name

source_name: Liver

extract_protocol:
Trizol + column
PolyA

value: Liver

value: CNO 1mg kg-1


title: Liver, AgRP activated, 4 hours, Rep 4

description: Library name: Sample 4


title: PDAC, PBS, 7 days post-3rd treatment, rep2

description:
Library name: PBS
10x Chromium system

value: PBS


title: Liver, Control, 4 hours, Rep 3

description: Library name: Sample 7


title: Liver, AgRP activated, 4 hours, Rep 2

description: Library name: Sample 2


title: IgG 500k 0.1%, 1 min Rep1

description: Library name: 572


title: Liver, Control, 4 hours, Rep 2

description: Library name: Sample 6


title: Liver, Control, 4 hours, Rep 1

description: Library name: Sample 5


title: MC38_H_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description:
Library name: Sample 5
MC38_raw_counts.txt

data_processing:
FASTQ files were preprocessed with trim-galore for adapter trimming and low quality filtering of the reads.
Filtered sequence reads were aligned to reference GRCm39 mouse transcriptome  with salmon aligner (v.1.10.0) using a decoy-aware transcriptome index with k-mers of length 31. GENCODE Gene Set version M35 was used for gene annotation.
Transcripts were merged to genes using Bioconductor R (v.4.3.1) package tximport (v1.28.0). Gene-level normalization and differential expression analysis were performed with R package DESeq2 v.1.40.2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw count values for each Sample

source_name: liver

extract_protocol:
RNA was extracted with Norgen Single Cell RNA Purification Kit and RNA integrity and concentration was assessed with Nanodrop
Library preparation was performed with Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Poly(A) Beads 2.0 and sequencing was performed with Illumina Novaseq 6000 platform. The resulting raw reads were assessed for quality by FastQC. The mean per-base quality score (Phred-score) was consistently above 35 for all samples.

value: liver

value: lin- CD45+CD11b+F4/80high

value: Macrophages

value: female

tag: disease state

value: liver metastasis


title: MC38_L_rep1

description:
Library name: Sample 2
MC38_raw_counts.txt

value: lin- CD45+CD11b+F4/80low


title: MC38_H_rep2

description:
Library name: Sample 3
MC38_raw_counts.txt


title: MC38_L_rep3

description:
Library name: Sample 6
MC38_raw_counts.txt

value: in- CD45+CD11b+F4/80low


title: MC38_L_rep2

description:
Library name: Sample 4
MC38_raw_counts.txt


title: Liver, AgRP activated, 4 hours, Rep 1

description: Library name: Sample 1


title: IgG 100k 0.1%, 1 min Rep1

description: Library name: 566

value: Splenic

value: Follicular B cell


title: MC38_H_rep1

description:
Library name: Sample 1
MC38_raw_counts.txt


title: 4_CHIR, replicate 1, scRNAseq

city: BARCELONA

first: Patryk

last: Polinski

state: BARCELONA

address: C/ del Dr. Aiguader, 88

country: Spain

institute: EMBL Barcelona

description: 10x Genomics

data_processing:
Alignment, filtering, barcode, and unique molecular identifier (UMI) counting were conducted with cellranger-8.0.1 count pipeline using the mouse reference assembly (mm10) and annotation available on 10x genomics website with default settings (https://www.10xgenomics.com)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastruloid

growth_protocol: Gastruloids were generated as previously described Beccari et al., 2018 (https://www.nature.com/articles/s41586-018-0578-0) with following modifications: In none of the experiments, we have treated gastruloids with CHIR between 48-72hpa as indicated in the original protocol

extract_protocol:
Respective number of gastruloids of the four different conditions at 96hpa were collected from 96-well plates and transferred to a 15ml falcon (control: n=50; 2-DG, 2-DG+ActA, 2-DG+CHIR: n=75). Medium was removed and gastruloids were washed with prewarmed PBS -/- (Sigma, D8537). PBS-/- was removed and 1ml TrypLE (Thermo Fisher Scientific, 12604) was added. Samples were incubated for 5min at 37°C with repeated flicking. Cell suspension was then gently pipetted up and down to ensure a single-cell suspension. Subsequently, 4ml of ice-cold 0.1% RNAse-free BSA in PBS-/- (BPBS) was added and cell suspension was centrifuged at 170g for 3min at 4°C. All following steps were performed on ice/at 4°C. Cells were washed 2 times in BPBS, before they were resuspended in 300µl BPBS using a wide bore P1000 tip. Cell suspension was then passed through a cell strainer (Corning, 352235), counted and diluted to a target concentration of 1.0-1.5x106 cells/ml.
Library preparation and sequencing was performed by the CRG Genomics Unit. Cells were barcoded using a Chromium GEM-X Single Cell 3' Reagent Kits v4 (10x Genomics) according to manufacturer’s instructions. Libraries were sequenced with a NovaSeq 6000 system (Illumina).

value: gastruloid

value: 96h post aggregation

value: 5mM 2-DG (Sigma, D8375) and 3microM CHIR (Tocris, #4423)


title: Young males control replicate 3 gastrocnemius

city: Boston

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description:
Illumina NovaSeq X Plus
GP124_3G

data_processing:
Fastq files were mapped to the genome using STAR v.2.7.2b
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: excel file containing raw counts for each sample

source_name: gastrocnemius

extract_protocol:
Total RNA was purified from mouse heart and gastrocnemius tissues using the AllPrep DNA/RNA/Protein Mini Kit according to the manufacturer's protocol (Qiagen)
mRNA-seq (polyA-enrichment); Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

value: gastrocnemius

value: young (5-month-old)

value: male

value: control


title: Young males control replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP125_2G


title: Young males control replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP124_5G


title: Young females control replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP123_3G


title: Young males control replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP124_1G


title: Young males control replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP124_2G


title: Young females control replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP122_4G


title: Old males control replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP113_5G

value: old (24-month-old)


title: Old males control replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP112_5G


title: Young females control replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP123_2G


title: Liver, AgRP activated, 4 hours, Rep 3

description: Library name: Sample 3

value: Liver

value: CNO 1mg kg-1


title: Old males control replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP112_4G


title: Young females control replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP122_1G


title: Old males control replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP117_2G


title: 3_ACT, replicate 1, scRNAseq

description: 10x Genomics

value: 5mM 2-DG (Sigma, D8375) and 50ng/ml Act-A (R&D Systems, #AFL338)


title: Old females control replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP110_1G

value: female


title: 2_2DG, replicate 1, scRNAseq

description: 10x Genomics

value: 5mM 2-DG (Sigma, D8375)


title: 1_CTRL, replicate 1, scRNAseq

description: 10x Genomics


title: Old males control replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP113_1G


title: PDAC, TMAB3/3p-hpRNA, 7 days post-3rd treatment, rep 2

description:
Library name: TMAB3/3p-hpRNA
10x Chromium system

value: Pancreas

value: KPC

value: Pancreatic ductal adenocarcinoma cell


title: Old females control replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP110_3G


title: Old females control replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP111_3G


title: Young males ELAM replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP125_5G

value: ELAM


title: Young males ELAM replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP125_1G


title: Young males ELAM replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP125_4G


title: Young females ELAM replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP123_4G


title: Young males ELAM replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP125_3G


title: Young females ELAM replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP123_1G


title: Young females ELAM replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP122_5G


title: Young females ELAM replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP122_2G


title: Young males ELAM replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP124_4G


title: Old males ELAM replicate 3 gastrocnemius

description:
Illumina NovaSeq X Plus
GP113_3G


title: Old females control replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP114_3G


title: Old females ELAM replicate 2  gastrocnemius

description:
Illumina NovaSeq X Plus
GP111_1G


title: Old females ELAM replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP110_5G


title: Old females ELAM replicate 3  gastrocnemius

description:
Illumina NovaSeq X Plus
GP111_2G


title: Young males control replicate 4 heart

description:
Illumina NovaSeq X Plus
GP124_5H

source_name: heart

value: heart


title: Old males ELAM replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP117_1G


title: Young females ELAM replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP122_3G


title: Young females control replicate 4 heart

description:
Illumina NovaSeq X Plus
GP123_3H


title: Old males ELAM replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP113_4G


title: Young females control replicate 2 heart

description:
Illumina NovaSeq X Plus
GP122_4H


title: Old males ELAM replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP112_2G


title: Old males control replicate 2 heart

description:
Illumina NovaSeq X Plus
GP112_5H


title: Old females control replicate 5 heart

description:
Illumina NovaSeq X Plus
GP114_3H


title: Old males control replicate 1 heart

description:
Illumina NovaSeq X Plus
GP112_4H


title: Old males ELAM replicate 1 gastrocnemius

description:
Illumina NovaSeq X Plus
GP112_1G


title: Old females ELAM replicate 5 gastrocnemius

description:
Illumina NovaSeq X Plus
GP115_5G


title: Old females control replicate 2 gastrocnemius

description:
Illumina NovaSeq X Plus
GP110_2G


title: Old females ELAM replicate 4 gastrocnemius

description:
Illumina NovaSeq X Plus
GP114_5G


title: Old females control replicate 1 heart

description:
Illumina NovaSeq X Plus
GP110_1H


title: Young males control replicate 5 heart

description:
Illumina NovaSeq X Plus
GP125_2H


title: Young males ELAM replicate 5 heart

description:
Illumina NovaSeq X Plus
GP125_5H


title: Young males ELAM replicate 4 heart

description:
Illumina NovaSeq X Plus
GP125_4H


title: Young males control replicate 3 heart

description:
Illumina NovaSeq X Plus
GP124_3H


title: Young males ELAM replicate 3 heart

description:
Illumina NovaSeq X Plus
GP125_3H


title: Young males ELAM replicate 2 heart

description:
Illumina NovaSeq X Plus
GP125_1H


title: Young females ELAM replicate 5 heart

description:
Illumina NovaSeq X Plus
GP123_4H


title: Young males control replicate 2 heart

description:
Illumina NovaSeq X Plus
GP124_2H


title: D37, K562-expanded, pre-activated

type: genomic

city: Hamburg

first: Michael

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

country: Germany

institute: UKE Hamburg

hyb_protocol: DNA was bisulfite-treated and converted with the NucleoSpin Tissue kit according to manufacturer’s instructions

scan_protocol: Using illumina iScan according to recommended scanner setting

data_processing:
Methylation data were processed using minfi and noob normalization. SNP containing, cross-hybridising and sex chromosome probes were removed by DMRcate (v2.8.5).
Tab-separated values of average raw beta

label: Cy3 and Cy5

label_protocol: Standard illumina protocol

extract_protocol: DNA was extracted from the sorted NK cells using a NucleoSpin kit


title: D37, K562-expanded, control


title: Young males control replicate 1 heart

description:
Illumina NovaSeq X Plus
GP124_1H


title: Young females control replicate 3 heart

description:
Illumina NovaSeq X Plus
GP123_2H


title: Old males control replicate 4 heart

description:
Illumina NovaSeq X Plus
GP113_5H


title: Young females control replicate 1 heart

description:
Illumina NovaSeq X Plus
GP122_1H


title: Old males control replicate 5 heart

description:
Illumina NovaSeq X Plus
GP117_2H


title: Old females control replicate 3 heart

description:
Illumina NovaSeq X Plus
GP110_3H


title: Old males control replicate 3 heart

description:
Illumina NovaSeq X Plus
GP113_1H


title: Old females control replicate 2 heart

description:
Illumina NovaSeq X Plus
GP110_2H


title: Young females ELAM replicate 1 heart

description:
Illumina NovaSeq X Plus
GP122_2H


title: Young males ELAM replicate 1 heart

description:
Illumina NovaSeq X Plus
GP124_4H


title: Old females control replicate 4 heart

description:
Illumina NovaSeq X Plus
GP111_3H


title: D25, K562-expanded, control


title: Old males ELAM replicate 5 heart

description:
Illumina NovaSeq X Plus
GP117_1H


title: Young females ELAM replicate 3 heart

description:
Illumina NovaSeq X Plus
GP122_5H


title: Young females ELAM replicate 4 heart

description:
Illumina NovaSeq X Plus
GP123_1H


title: D03, mag-iso, pre-activated


title: Young females ELAM replicate 2 heart

description:
Illumina NovaSeq X Plus
GP122_3H


title: D34, K562-expanded, pre-activated


title: Old males ELAM replicate 4 heart

description:
Illumina NovaSeq X Plus
GP113_4H


title: Old males ELAM replicate 2 heart

description:
Illumina NovaSeq X Plus
GP112_2H


title: D25, K562-expanded, pre-activated


title: D20, K562-expanded, pre-activated


title: Old males ELAM replicate 3 heart

description:
Illumina NovaSeq X Plus
GP113_3H


title: D03, mag-iso, control


title: Old males ELAM replicate 1 heart

description:
Illumina NovaSeq X Plus
GP112_1H


title: D02, mag-iso, pre-activated


title: D01, mag-iso, pre-activated


title: D02, mag-iso, control


title: Old females ELAM replicate 5 heart

description:
Illumina NovaSeq X Plus
GP115_5H


title: Old females ELAM replicate 4 heart

description:
Illumina NovaSeq X Plus
GP114_5H


title: D34, K562-expanded, control


title: Old females ELAM replicate 3  heart

description:
Illumina NovaSeq X Plus
GP111_2H


title: Old females ELAM replicate 2  heart

description:
Illumina NovaSeq X Plus
GP111_1H


title: B6-Rag1-KO mutant mice implanted with pooled MC38

city: Guangzhou

first: ZHE

state: Guangdong

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description:
Rag1
result.count.txt

data_processing:
Fastq files were checked with Fastqc (v. 0.11.9) for quality control. The adapters were removed from the raw reads with Cutadapt (v. 1.18) and mapped to human reference genome (hg38) with STAR (v. 2.7.1a). SAM files were converted to Bam format using Samtools (v. 1.3.1). Gene expression levels and differences were calculated using Cufflinks (v. 0.17.3) and HTseq-count (v. 0.13.5).
Assembly: mm 10
Supplementary files format and content: tab-delimited file includes raw counts for each sample

extract_protocol:
Total RNAs were extracted from the cells with Trizol. The mRNA was isolated and fragmented using mRNA Capture Beads (VAHTS mRNA Capture Beads, N401).
The resultant RNAs samples were reverse-transcribed for library construction with NEB Next® VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina, NR604. The libraries were purified by DNA clean beads (VAHTS DNA Clean Beads, N411) for size selection for 200-300 bp fragments, and analyzed on Agilent 2100 Bioanalyzer (Agilent) for measuring fragment size distribution.

value: crispr library


title: D20, K562-expanded, control


title: strain LP307R biol rep 3

city: Greenville

first: Brett

middle: D

last: Keiper

state: NC

address: 600 Moye Blvd

department: Biochem and Mol Biol

institute: Brody School of Med at ECU

description:
Library name: S12
column name in counts-tpm.csv: S12

data_processing:
The sequencing core compiled read counts and stats for all 3 replicates of both bead-captured RNA and total RNA. Sequence reads were pseudo-aligned to C. elegans Ensemble reference transcriptome (WBcel235) and the gene transcript abundance was quantified by using Kallisto (v.0.48.0).
Differential expression of genes and transcripts were achieved by using DESeq2 (v.1.34.0) in RStudio (Build 386 with R v.4.4.1) with a significance set at adjusted p-value<0.05 and log2FoldChange (fc) larger than 1. In all cases except direct IFE-1 to IFE-3 comparison, fold enrichment is calculated relative to reads from total RNA extracted from the KX155 total lysate.
Functional analyses were conducted using ClusterProfiler (v4.2.2) and a gene-set enrichment assay. Note that IFE-3 mRNPs retained more mRNAs than IFE-1 mRNPs, but were greater than mKate2:PH or GFP::PH, which gave little useful information (data not used for publication). Precipitated RNA-Seq was sampled based on mass (ng RNA) and thereby normalized between IFE-1, IFE-3 and total RNA. Therefore, all enrichments are indicative of preferential binding of the IFE to an mRNA over its representation in the initial population. Enrichment as calculated by “Log2 Fold Change” and filters of p value stringency were used to generate the distinct mRNA lists described for IFE-1 and IFE-3 in the Gajjar, et al. manuscript to Genetics (2025).
At least 21,600 entries were returned in all three analyses to effectively cover 46,934 WormBase gene designations from the C elegans transcriptome.
Assembly: C. elegans Ensemble reference transcriptome WBcel235
Supplementary files format and content: tpm file includes abundance in csv format

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown 3 days on 10 cm OP50 and chicken egg plates at 20°C.

extract_protocol:
Worm pellets were subsequently crushed in a mortar and pestle under liquid N2 with an equal volume of mRNP immunoprecipitation buffer (50 mM Tris-HCl [pH 8.0], 300 mM NaCl, 10 mM MgCl2, 1 mM EGTA, 2 mM dithiothreitol (DTT), 800 U of RNAsin/ml (Promega), 4 mM Vanadyl-ribonucleoside complex, 2X HALT complete protease inhibitor (ThermoFisher), 14 mM E64 protease inhibitor (SigmaAldrich), then centrifuged at 14,000 × g at 4°C for 15 min. The resultant supernatant was subjected to 20-50 μL of packed equilibrated GFP or RFP-targeted Nano-Trap agarose beads (Chromotek) and bound for 1.5 hrs. at 4°C while rotating. All immunoprecipitations were done on 6-10 mg of total C. elegans protein. After binding, beads were washed 4X in medium salt high detergent buffer (50 mM Tris-HCl [pH 7.8], 300 mM NaCl, 0.5% NP-40, 0.5% deoxycholic acid). The Trap beads (or an aliquot of the initial homogenate for unenriched control) were extracted with Trizol. Total RNA was also isolated from the same frozen worm samples by standard methods using Trizol. Resuspended precipitate was further extracted with phenol:chloroform:isoamyl alcohol (25:24:1), and twice with chloroform:isoamyl alcohol (24:1), then ethanol precipitated. GlycoBlue (Invitrogen) was used as a co-precipitant. RNA quality and quantity was determined using NanoDrop® ND-1000 spectrophotometer.
RNA sequencing services were outsourced to Admera Health, LLC. RNA (>1 ug) from three replicates were sent. Library type: RNA (rRNA depleted), NEBNext Ultra II non-directional with Qiaseq Fast Select HMR.

treatment_protocol: Worms were washed off plates using physiological buffer M9 and allowed to purge gut contents for 30 min at room temperature. Worms were then floated over 35% sucrose at 4°C to remove debris and bacteria, washed with 0.1 M NaCl, then flash frozen by drops in liquid nitrogen in the presence of 14 mM E64 protease inhibitor (Sigma-Aldrich), 4 mM Vanadyl-ribonucleoside RNase inhibitor (Sigma-Aldrich), and 0.2% Tween 20 detergent.

value: whole worm

value: mKate::PH Chr II insertion

value: mKate::Ctl RIP

tag: batch

value: RFP pulldown


title: strain LP306G biol rep 3

description:
Library name: S14
column name in counts-tpm.csv: S14

value: GFP::PH Chr II insertion

value: GFP::Ctl RIP

value: GFP pulldown


title: strain KX155G biol rep 3

description:
Library name: S13
column name in counts-tpm.csv: S13

value: mKate::ife-1 III, GFP::ife-3 V CRISPR

value: GFP::IFE-3 RIP


title: strain KX155C biol rep 2

description:
Library name: S10
column name in counts-tpm.csv: S10

value: mKate::IFE-1 GFP::IFE-3 total RNA

value: lysate


title: Tum_ILC1_R3

data_processing:
FASTQ files were preprocessed with trim-galore for adapter trimming and low quality filtering of the reads.
Filtered sequence reads were aligned to reference GRCm39 mouse transcriptome  with salmon aligner (v.1.5.0) using a decoy-aware transcriptome index with k-mers of length 31. GENCODE Gene Set version M27 was used for gene annotation.
Transcripts were merged to genes using Bioconductor R (v.4.3.1) package tximport (v1.28.0). Gene-level normalization and differential expression analysis were performed with R package DESeq2 v.1.40.24
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw count values for each Sample

extract_protocol:
RNA was extracted with Norgen Single Cell RNA Purification Kit and RNA integrity and concentration was assessed with Nanopore
Library preparation was performed with SMARTer Stranded Total RNA-Seq kit v2-Pico Input and sequencing was performed with Illumina Novaseq 6000 platform. The resulting raw reads were assessed for quality by FastQC. The mean per-base quality score (Phred-score) was consistently above 35 for all samples. FASTQ files were preprocessed with trim-galore.

value: liver

tag: cell population

value: lin- CD45+ NKp46+ CD49a+ CD49b+

value: CD49a+ NK cells

value: female

value: liver metastasis


title: C57BL/6 wild-type mice implanted with pooled MC38

description:
C57
result.count.txt

value: crispr library


title: strain KX155R biol rep 3

description:
Library name: S11
column name in counts-tpm.csv: S11

value: whole worm

value: mKate::IFE-1 RIP


title: strain LP306G biol rep 2

description:
Library name: S09
column name in counts-tpm.csv: S09


title: Tum_NK_R3

value: lin- CD45+ NKp46+ CD49a- CD49b+

value: NK cells


title: strain KX155G biol rep 2

description:
Library name: S08
column name in counts-tpm.csv: S08


title: Par_NK_R3

value: metastasis-free liver


title: strain LP307R biol rep 2

description:
Library name: S07
column name in counts-tpm.csv: S07

value: mKate::PH Chr II insertion

value: mKate::Ctl RIP

value: RFP pulldown


title: Par_ILC1_R2

value: lin- CD45+ NKp46+ CD49a+ CD49b-


title: Tum_NK_R2


title: Tum_ILC1_R1


title: strain KX155C biol rep 1

description:
Library name: S05
column name in counts-tpm.csv: S05

value: mKate::ife-1 III, GFP::ife-3 V CRISPR

value: mKate::IFE-1 GFP::IFE-3 total RNA


title: Par_NK_R2

value: liver


title: D01, mag-iso, control


title: strain KX155R biol rep 2

description:
Library name: S06
column name in counts-tpm.csv: S06


title: strain KX155G biol rep 1

description:
Library name: S03
column name in counts-tpm.csv: S03

value: GFP::IFE-3 RIP

value: GFP pulldown


title: strain KX155C biol rep 3

description:
Library name: S15
column name in counts-tpm.csv: S15

value: lysate


title: strain LP306G biol rep 1

description:
Library name: S04
column name in counts-tpm.csv: S04

value: GFP::PH Chr II insertion

value: GFP::Ctl RIP


title: Old females ELAM replicate 1 heart

description:
Illumina NovaSeq X Plus
GP110_5H

value: heart

value: old (24-month-old)

value: female

value: ELAM


title: Par_ILC1_R1

value: metastasis-free liver


title: Tum_NK_R1

value: lin- CD45+ NKp46+ CD49a- CD49b+

value: NK cells

value: liver metastasis


title: strain LP307R biol rep 1

description:
Library name: S02
column name in counts-tpm.csv: S02

value: whole worm

value: mKate::PH Chr II insertion

value: mKate::Ctl RIP

value: RFP pulldown


title: Par_ILC1_R3

value: liver

value: lin- CD45+ NKp46+ CD49a+ CD49b-


title: strain KX155R biol rep 1

description:
Library name: S01
column name in counts-tpm.csv: S01

value: mKate::ife-1 III, GFP::ife-3 V CRISPR

value: mKate::IFE-1 RIP


title: Par_NK_R1


title: Tum_ILC1_R2

value: lin- CD45+ NKp46+ CD49a+ CD49b+

value: CD49a+ NK cells


title: Primary_4 scRNAsq

city: Toronto

last: Taylor

state: ON

address: 686 Bay St.

country: Canada

institute: Hospital for Sick Children

description: 10x Genomics

data_processing:
Cell Ranger software v.3.0.2 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebellar tumour

extract_protocol:
Primary tumours and spinal leptomeninges were dissected from mice, dissociated into a single cell suspension using Liberase and ran on the 10x instrument using 10x Genomics Chromium Single Cell 3' Solution V2/V3 protocol
10x Genomics Chromium Single Cell 3' Solution V2/V3 protocol

value: Cerebellar tumour

tag: developmental stage

value: Adult 20.9 weeks

tag: metastatic burden

value: High

value: SB11/SB76/patched1heterozygous mutant


title: LPT_MET_4 scRNAsq

description: 10x Genomics

source_name: Spinal leptomeninges

value: Spinal leptomeninges

value: female


title: LPT_WT_3 scRNAsq

description: 10x Genomics

value: Control

value: Math1-GFP/SB76/patched1 wild-type


title: Primary_3 scRNAsq

description: 10x Genomics

value: Adult 27.3 weeks

value: Low


title: LPT_MET_3 scRNAsq

description: 10x Genomics


title: LPT_WT_2 scRNAsq

description: 10x Genomics

value: Adult 23.0 weeks


title: Alu swap, in vitro SHAPE experiment, untreated, replicate 1

city: Chapel Hill

first: Justin

last: Waldern

address: 250 Bell Tower Dr

department: Biology

institute: The University of North Carolina at Chapel Hill

description:
Library name: SW_SHAPE_untreated_rep1
MaP_profiles_SW_RC.tar.gz

library_source: other

data_processing:
Shapemapper2 v2.1.5
ShapeJumper  v1.0
JuMP filtering: SHAPE-JuMP frequencies were calculated with using the data from normalizeDeletionRates.py in the ShapeJumper package, with low count (<20) JuMP events omitted. Low count JuMP events were omitted because they can be artificially high in this system due to both a low JuMP count and a low read depth (i.e., 1 event in 1 read is a 100% frequency), where the low read depth occurs on JuMPs deep into the read from the poor processivity of the reverse transcriptase. Differences are taken as the AMT-treated minus the untreated values.
Assembly: GRCh38/hg38
Supplementary files format and content: MaP_profiles.tar.gz contains files of the format _profile.txt from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: JuMP_data.tar.gz contain csv files of processed -JuMP data. These files contain position information for each deletion recorded (nucleotide_position_i, and nucleotide_position_j), as well as information on the counts and read-depth normalized frequencies of deletions in AMT-treated and untreated conditions

molecule: other

source_name: in vitro SHAPE experiment

growth_protocol: For in-cell probing (library names include "DMSic") HeLa cells (ATCC number CCL 2) were cultured in high glucose DMEM (Gibco) supplemented with10% fetal bovine serum (Sigma) and 0.5 % pen/strep (Gibco). Cells were maintained at 37° C and 5% CO2. Plasmid constructs were transfected into cells, and cells were later DMS probed

extract_protocol:
For in-cell probing, RNA was isolated with Trizol reagent. For in vitro probing, RNA was generated by in vitro transcription with NEB HiScribe T7 High Yield RNA Synthesis kit
For MaP RT, superscript II was used to generate cDNA. For JuMP, C8 enzyme was used to perform RT. In-cell and SHAPE-JuMP libraries were constructed with two rounds of PCR to add Illumina adaptor sequences and barcodes. In vitro MaP libraries were prepared using the NEBNext Ultra II FS DNA Library Prep kit for Illumina

value: in vitro SHAPE experiment

value: Swapped Alus

value: untreated


title: Alu swap, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: SW_SHAPE_untreated_rep2
MaP_profiles_SW_RC.tar.gz


title: Reverse complement, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: RC_SHAPE_5NIA_rep2
MaP_profiles_SW_RC.tar.gz

value: Reverse complemented Alus

value: SHAPE (5NIA)


title: Alu swap, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: SW_SHAPE_5NIA_rep1
MaP_profiles_SW_RC.tar.gz


title: Reverse complement, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: RC_SHAPE_5NIA_rep1
MaP_profiles_SW_RC.tar.gz


title: Primary_2 scRNAsq

description: 10x Genomics

source_name: Cerebellar  tumour

value: Cerebellar  tumour

value: Adult 15.3 weeks


title: LPT_WT_1 scRNAsq

description: 10x Genomics

value: Adult 12.1 weeks

value: male


title: LPT_MET_2 scRNAsq

description: 10x Genomics

value: High

value: SB11/SB76/patched1heterozygous mutant


title: Primary_1  scRNAsq

description: 10x Genomics

value: Cerebellar tumour

value: Adult 20.0 weeks

value: female


title: MC38 tumor, SHM

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters.
Assembly: mm 10
Supplementary files format and content: Cell Ranger output files (barcodes, features, matrix)

source_name: MC38 tumors

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacturer’ s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: MC38 tumors

value: Mbtps1 KD


title: MC38 tumor, WT

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters.
Assembly: mm 10
Cell Ranger output files (barcodes, features, matrix)

value: Mbtps1 WT


title: GSC MES20, stiff, radiation-2

city: Pittsburgh

first: Po

last: Zhang

state: Pennsylvania

address: 5115 Centre Ave

institute: University of Pittsburgh,

description:
Library name: Trad2
soft-stiff-rad.xls

data_processing:
Raw FASTQ reads were processed using Trim Galore for quality trimming. Transcript mapping was performed with HISAT2 against the human reference genome (hg38). SAMtools was utilized for sorting, indexing, and format conversion from SAM files. Quantification and differential expression analysis were conducted using featureCounts and DESeq2.
Assembly: hg38
Supplementary files format and content: xlsx

source_name: glioblastoma

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Life Technologies, 15596018) and the Direct-zol RNA Miniprep Kit (Zymo Research, R2052).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: GSC MES20

value: Human glioma stem cells

value: stiff, radiation


title: GSC MES20, stiff, radiation-1

description:
Library name: Trad1
soft-stiff-rad.xls


title: GSC MES20, soft, radiation-2

description:
Library name: Srad2
soft-stiff-rad.xls

value: soft, radiation


title: GSC MES20, soft, radiation-3

description:
Library name: Srad3
soft-stiff-rad.xls


title: GSC MES20, stiff, radiation-3

description:
Library name: Trad3
soft-stiff-rad.xls


title: GSC MES20, soft, radiation-1

description:
Library name: Srad1
soft-stiff-rad.xls


title: MC38 cells, KD-3


title: GSC MES20, stiff-3

description:
Library name: stiff3
soft-stiff.xls

value: stiff


title: Alu swap, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: SW_SHAPE_5NIA_rep2
MaP_profiles_SW_RC.tar.gz

value: in vitro SHAPE experiment

value: Swapped Alus

value: SHAPE (5NIA)


title: Reverse complement, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: RC_SHAPE_untreated_rep2
MaP_profiles_SW_RC.tar.gz

value: Reverse complemented Alus

value: untreated


title: MC38 cells, KD-2


title: Reverse complement, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: RC_SHAPE_untreated_rep1
MaP_profiles_SW_RC.tar.gz


title: MC38 cells, WT-3


title: GSC MES20, soft-3

description:
Library name: soft3
soft-stiff.xls

value: soft


title: GSC MES20, stiff-1

description:
Library name: stiff1
soft-stiff.xls


title: GSC MES20, stiff-2

description:
Library name: stiff2
soft-stiff.xls


title: MC38 cells, WT-2


title: MC38 cells, WT-1


title: GSC MES20, shCONT-2

description:
Library name: gscMES20nt2
GSCMES20shIQGAP3.xlsx

value: shCONT


title: MC38 tumor, KD-4


title: GSC MES20, soft-2

description:
Library name: soft2
soft-stiff.xls


title: MC38 tumor, KD-3


title: GSC MES20, shCONT-1

description:
Library name: gscMES20nt1
GSCMES20shIQGAP3.xlsx


title: GSC MES20, soft-1

description:
Library name: soft1
soft-stiff.xls


title: MC38 tumor, KD-5


title: LPT_MET_1 scRNAsq

description: 10x Genomics

value: Spinal leptomeninges

value: Adult 20.0 weeks

value: female

value: Low

value: SB11/SB76/patched1heterozygous mutant


title: MC38 tumor, KD-2

value: Mbtps1 KD


title: GSC MES20, shIQGAP3-2

description:
Library name: GSCMES20KD2
GSCMES20shIQGAP3.xlsx

value: glioblastoma

value: GSC MES20

value: Human glioma stem cells


title: GSC MES20, shIQGAP3-1

description:
Library name: GSCMES20KD1
GSCMES20shIQGAP3.xlsx


title: MC38 tumor, KD-1


title: MC38 tumor, WT-5

value: Mbtps1 WT


title: MC38 tumor, WT-2


title: MC38 tumor, WT-4


title: MC38 tumor, WT-1


title: BMDM_PT_rep1

city: Los Angeles

first: Aleksandr

last: Gorin

state: CA

address: 570 Boyer Hall

department: Medicine

institute: UCLA

data_processing:
ATAC-seq reads were aligned to the mm10 genome using bowtie2 version 2.2.5 with default parameters except –very-sensitive and –non-deterministic options and were filtered based on mapping score (MAPQ >30) by Samtools version 1.9
Duplicated reads were removed using Picard MarkDuplicates version 2.18.29.
MACS3 version 3.0.0b1 was used to identify peaks for each sample individually with default settings except FDR of 0.01, -f BAMPE, -g mm, and –nomodel.
Peaks from all samples were merged into a single file and raw peaks quantified using featureCounts.
Assembly: GRCm38
Supplementary files format and content: csv (table of merged peaks and log2 cpm counts for each peak)

source_name: BMDM

growth_protocol: Bone-marrow derived macrophages (BMDMs) were prepared by culturing bone marrow cells isolated from the femurs and tibias of 6-12 week old mice in complete media supplemented with 20 ng/mL m-CSF and fed on 2, 4, and 6 with additional complete media supplemented with m-CSF as described above. On day 7, adherent BMDMs were washed with PBS and lifted from culture dish with 10 mM EDTA (Fisher) in PBS (Gibco) and replated at 7.5X10^5 cells per well in 6-well plates.

extract_protocol:
Cells were lifted in with Accutase (ThermoFisher) and gentle cell scraping. 5x10^4 cells were utilized to prepare nuclei. Cell membranes were lysed using cold lysis buffer (10mM Tris-HCL pH 7.5, 3mM MgCl2, 10mM NaCl, and 0.1% IGEPAL CA-630). Nuclei were pelleted by centrifugation for 10 minutes at 500 × g, and suspended in the transposase reaction mixture (25 µl of 2X TD Buffer (Illumina), 2.5 µl of TD Enzyme 1 (Illumina), and 22.5 µl of nuclease-free water). The transposase reaction was performed for 30 minutes at 37 °C in a thermomixer shaker at 800RPM.  Then, fragmented DNA in the reaction was purified using MinElute PCR purification kit (QIAGEN).
Purified DNA fragments were amplified by PCR to obtain ATAC-seq libraries with Illumina Nextera sequencing primers.

treatment_protocol: BMDMs were stimulated with LPS (1ng/mL), CpG (100nM), polyI:C (1µg/mL), or TNF (10ng/mL) as indicated

value: BMDM

value: wildtype

value: 4 hours PolyI:C followed by 4 hours TNF


title: BMDM_PT_rep2


title: P3_H06_Participant_182_week_7

city: Adelaide

first: Feargal

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description:
Library name: P3_H06_S144
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.

value: Peripheral blood

value: male

tag: timepoint


title: P3_H03_Participant_149_week_7

description:
Library name: P3_H03_S120
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_H05_Participant_220_week_7

description:
Library name: P3_H05_S136
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_H01_Participant_187_week_6

description:
Library name: P3_H01_S104
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_H02_Participant_162_week_6

description:
Library name: P3_H02_S112
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_G05_Participant_161_week_7

description:
Library name: P3_G05_S135
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_H04_Participant_164_week_7

description:
Library name: P3_H04_S128
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_G02_Participant_105_week_6

description:
Library name: P3_G02_S111
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_PL_rep1

value: 4 hours PolyI:C followed by 4 hours LPS


title: P3_G04_Participant_217_week_7

description:
Library name: P3_G04_S127
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_PL_rep2


title: P3_F05_Participant_154_week_7

description:
Library name: P3_F05_S134
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_MT_rep1

value: 4 hours media followed by 4 hours TNF


title: BMDM_MP_rep1

value: 4 hours media followed by 4 hours PolyI:C


title: BMDM_MT_rep2


title: P3_G03_Participant_160_week_7

description:
Library name: P3_G03_S119
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: MC38 tumor, WT-3


title: P3_G01_Participant_039_week_6

description:
Library name: P3_G01_S103
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_F02_Participant_149_week_6

description:
Library name: P3_F02_S110
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_F03_Participant_223_week_7

description:
Library name: P3_F03_S118
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_MM_rep2

value: 4 hours media followed by 4 hours media


title: BMDM_MM_rep1


title: P3_F06_Participant_190_week_7

description:
Library name: P3_F06_S142
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_F01_Participant_221_week_6

description:
Library name: P3_F01_S102
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: female


title: MC38 cells, KD-1


title: P3_F04_Participant_044_week_7

description:
Library name: P3_F04_S126
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_MC_rep1

value: 4 hours media followed by 4 hours CpG


title: P3_E06_Participant_177_week_7

description:
Library name: P3_E06_S141
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_E04_Participant_162_week_7

description:
Library name: P3_E04_S125
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_CT_rep2

value: 4 hours CpG followed by 4 hours TNF


title: BMDM_MP_rep2


title: P3_E02_Participant_182_week_6

description:
Library name: P3_E02_S109
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_E03_Participant_040_week_7

description:
Library name: P3_E03_S117
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_CL_rep1

value: 4 hours CpG followed by 4 hours LPS


title: BMDM_MC_rep2


title: P3_E05_Participant_214_week_7

description:
Library name: P3_E05_S133
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_D06_Participant_246_week_6

description:
Library name: P3_D06_S140
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: BMDM_ML_rep1

value: 4 hours media followed by 4 hours LPS


title: BMDM_CT_rep1


title: P3_E01_Participant_254_week_6

description:
Library name: P3_E01_S101
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: CORT-2

city: Hangzhou

first: zhengrong

last: yao

address: Zijinhua road

institute: zhejiang university

data_processing:
Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2(v2.2.1)
Stringtie (v2.2.1) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab file includes raw counts for each sample
Supplementary files format and content: csv file includes raw counts for all samples

source_name: Small intestine

extract_protocol:
RNA was harvested using RNeasy micro kit(Qiagen 74004). 200 ng of total RNA was used for the construction of sequencing libraries.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X)，First strand cDNA was synthesized using random hexamer primer and M- MLV Reverse Transcriptase, then use RNase H to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Then PCR amplification, the PCR product was purified by AM Pure XP beads, and the library was finally obtained.

value: Small intestine

value: intestinal stem cells

value: i.p CORT


title: CORT-4


title: Vehicle-6

value: i.p Vehicle


title: Vehicle-5


title: CORT-5


title: BMDM_ML_rep2

value: BMDM

value: wildtype


title: P3_D04_Participant_251_week_7

description:
Library name: P3_D04_S124
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: Peripheral blood


title: P3_D05_Participant_234_week_7

description:
Library name: P3_D05_S132
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: CRS-3

value: Restraint stress


title: P3_D03_Participant_090_week_7

description:
Library name: P3_D03_S116
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: male


title: Vehicle-3


title: CRS-1+2


title: P3_D01_Participant_188_week_6

description:
Library name: P3_D01_S100
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_C03_Participant_207_week_6

description:
Library name: P3_C03_S115
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: Ctrl-3

value: Control


title: P3_C01_Participant_217_week_6

description:
Library name: P3_C01_S99
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: Ctrl-2


title: Ctrl-1


title: P3_C02_Participant_133_week_6

description:
Library name: P3_C02_S107
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: B3AR-Tg 9 weeks post TAC surgery biol rep 7 [K1588TG]

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analysed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline.
In this pipeline, reads were mapped using Salmon  to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm39.cdna.all.fa file.
Then, estimated transcript abundances from Salmon were imported into R using the tximeta package
Assembly: Mus_musculus.GRCm39.cdna.all.fa
Supplementary files format and content: Matrix of reads counts

source_name: adult ventricular myocytes (AVM)

extract_protocol:
AVM from B3AR-Tg and WT mice were isolated 9 weeks post-TAC by cardiac Langendorff perfusion. Thereafter, AVM were plated for an hour before being processed for RNA extraction using Purelink RNA micro kit.
500ng were processed for library preparation  after ribodepletion (TruSeq Stranded Total RNA LT Sample Prep Kit)
RNAseq sequencing was performed on Illumina NovaSeq 6000 - Paired end >60 millions read

value: adult ventricular myocytes (AVM)

value: 9 weeks post TAC surgery


title: P3_D02_Participant_229_week_6

description:
Library name: P3_D02_S108
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: female


title: BMDM_CL_rep2


title: CRS-4+5+6


title: P3_C06_Participant_236_week_7

description:
Library name: P3_C06_S139
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_B04_Participant_232_week_7

description:
Library name: P3_B04_S122
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_B03_Participant_168_week_6

description:
Library name: P3_B03_S114
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_C05_Participant_189_week_7

description:
Library name: P3_C05_S131
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: B3AR-Tg 9 weeks post TAC surgery biol rep 4 [K1376TG]


title: P3_B06_Participant_187_week_7

description:
Library name: P3_B06_S138
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_B05_Participant_244_week_7

description:
Library name: P3_B05_S130
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_B01_Participant_185_week_6

description:
Library name: P3_B01_S98
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: B3AR-Tg 9 weeks post TAC surgery biol rep 5 [K1493TG]


title: B3AR-Tg 9 weeks post TAC surgery biol rep 3 [K1850TG]


title: B3AR-Tg 9 weeks post TAC surgery biol rep 8 [K1590TG]


title: B3AR-Tg 9 weeks post TAC surgery biol rep 2 [K1816TG]


title: B3AR-Tg 9 weeks post TAC surgery biol rep 6 [K1582TG]


title: P3_A06_Participant_233_week_7

description:
Library name: P3_A06_S137
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT  9 weeks post TAC surgery biol rep 8 [K1876WT]

value: WT


title: P3_A05_Participant_082_week_7

description:
Library name: P3_A05_S129
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_A04_Participant_208_week_7

description:
Library name: P3_A04_S121
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_B02_Participant_160_week_6

description:
Library name: P3_B02_S106
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_C04_Participant_179_week_7

description:
Library name: P3_C04_S123
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT  9 weeks post TAC surgery biol rep 5 [K1646WT]


title: P3_A07_Participant_074_week_7

description:
Library name: P3_A07_S145
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: B3AR-Tg 9 weeks post TAC surgery biol rep 1 [K1695TG]


title: WT  9 weeks post TAC surgery biol rep 7 [K1669WT]


title: P3_A03_Participant_215_week_6

description:
Library name: P3_A03_S113
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P3_A02_Participant_159_week_6

description:
Library name: P3_A02_S105
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT  9 weeks post TAC surgery biol rep 3 [K1464WT]


title: WT  9 weeks post TAC surgery biol rep 4 [K1509WT]


title: P3_A01_Participant_238_week_6

description:
Library name: P3_A01_S97
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_H06_Participant_254_week_7

description:
Library name: P2_H06_S96
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_H05_Participant_166_week_7

description:
Library name: P2_H05_S88
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT  9 weeks post TAC surgery biol rep 1 [K1283WT]


title: P2_H04_Participant_168_week_7

description:
Library name: P2_H04_S80
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_H02_Participant_161_week_6

description:
Library name: P2_H02_S64
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_6 at ZT10 in short day entrained 12-day seedlings

city: York

first: Daphne

last: Ezer

address: Wentworth Way

institute: University of York

description:
Library name: WT_6_C
Column name in TPM_ril_all: WT_6_C

data_processing:
Illumina adapters were trimmed using CutAdapt v3.4(Martin 2011).
Reads were quantified using Salmon v1.6.0 (Patro et al. 2017) and the TAIR10 transcriptome (Berardini et al. 2015).
Variant calling was done using GATK workflow described on the GATK website (Caetano-Anolles, 2023).
Assembly: TAIR10
Supplementary files format and content: TPM_ril_all.csv is a csv table containing gene expression data (TPM).  Every row is a gene name and each column is a different sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seeds were surface-sterilized and plated onto MS medium with 3% sucrose in clusters of ~50 seeds, and then stratified for 4 days. After stratification, seedlings were entrained in two cabinets under  8/16 light dark cycle with a constant temperature of 22° for 12 days.

extract_protocol:
Total RNA was isolated from whole plant tissue using the Qiagen RNeasy Plant Mini Kit. Residual genomic DNA was removed using the Invitrogen Turbo DNA-free kit, according to the manufacturer’s protocol.
Libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina, using the NEBNext poly(A) magnetic isolation module.

treatment_protocol: On day 12, individuals in treatment cabinet left in the light at ZT8. On day 12 at ZT10 all plants were harvested and snap-frozen in liquid nitrogen.

value: whole seedling

value: ZT10, control (dark)


title: WT_9 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_9_T
Column name in TPM_ril_all: WT_9_T

value: ZT10, 2 hours extended light


title: WT_9 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_9_C
Column name in TPM_ril_all: WT_9_C


title: WT_6 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_6_T
Column name in TPM_ril_all: WT_6_T


title: P2_H01_Participant_216_week_6

description:
Library name: P2_H01_S56
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_G03_Participant_220_week_6

description:
Library name: P2_G03_S71
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_G06_Participant_228_week_7

description:
Library name: P2_G06_S95
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_G05_Participant_201_week_7

description:
Library name: P2_G05_S87
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_5 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_5_T
Column name in TPM_ril_all: WT_5_T


title: P2_G04_Participant_203_week_7

description:
Library name: P2_G04_S79
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_F06_Participant_180_week_7

description:
Library name: P2_F06_S94
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT  9 weeks post TAC surgery biol rep 2 [K1393-2WT]


title: WT_5 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_5_C
Column name in TPM_ril_all: WT_5_C


title: WT  9 weeks post TAC surgery biol rep 6 [K1658WT]


title: WT_2 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_2_C
Column name in TPM_ril_all: WT_2_C


title: P2_F03_Participant_069_week_6

description:
Library name: P2_F03_S70
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_2 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_2_T
Column name in TPM_ril_all: WT_2_T


title: P2_G01_Participant_181_week_6

description:
Library name: P2_G01_S55
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_F01_Participant_214_week_6

description:
Library name: P2_F01_S54
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_3 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_3_T
Column name in TPM_ril_all: WT_3_T


title: P2_H03_Participant_232_week_6

description:
Library name: P2_H03_S72
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_3 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_3_C
Column name in TPM_ril_all: WT_3_C


title: P2_F05_Participant_056_week_7

description:
Library name: P2_F05_S86
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_F04_Participant_059_week_7

description:
Library name: P2_F04_S78
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_4 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_4_T
Column name in TPM_ril_all: WT_4_T


title: P2_F02_Participant_189_week_6

description:
Library name: P2_F02_S62
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_76 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_76_T
Column name in TPM_ril_all: WT_76_T


title: WT_4 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_4_C
Column name in TPM_ril_all: WT_4_C


title: P2_E04_Participant_231_week_7

description:
Library name: P2_E04_S77
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_73 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_73_T
Column name in TPM_ril_all: WT_73_T


title: WT_76 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_76_C
Column name in TPM_ril_all: WT_76_C


title: P2_E02_Participant_135_week_6

description:
Library name: P2_E02_S61
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_E06_Participant_212_week_7

description:
Library name: P2_E06_S93
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_73 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_73_C
Column name in TPM_ril_all: WT_73_C


title: P2_E05_Participant_213_week_7

description:
Library name: P2_E05_S85
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_74 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_74_C
Column name in TPM_ril_all: WT_74_C


title: WT_74 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_74_T
Column name in TPM_ril_all: WT_74_T


title: WT_71 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_71_C
Column name in TPM_ril_all: WT_71_C


title: P2_D05_Participant_230_week_7

description:
Library name: P2_D05_S84
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_77 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_77_T
Column name in TPM_ril_all: WT_77_T


title: P2_D03_Participant_186_week_6

description:
Library name: P2_D03_S68
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_E03_Participant_166_week_6

description:
Library name: P2_E03_S69
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_71 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_71_T
Column name in TPM_ril_all: WT_71_T


title: WT_78 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_78_T
Column name in TPM_ril_all: WT_78_T


title: P2_D04_Participant_207_week_7

description:
Library name: P2_D04_S76
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_D06_Participant_199_week_7

description:
Library name: P2_D06_S92
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_77 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_77_C
Column name in TPM_ril_all: WT_77_C


title: WT_65 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_65_C
Column name in TPM_ril_all: WT_65_C


title: P2_D02_Participant_201_week_6

description:
Library name: P2_D02_S60
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_C06_Participant_239_week_7

description:
Library name: P2_C06_S91
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_64 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_64_T
Column name in TPM_ril_all: WT_64_T


title: WT_78 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_78_C
Column name in TPM_ril_all: WT_78_C


title: WT_64 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_64_C
Column name in TPM_ril_all: WT_64_C


title: WT_65 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_65_T
Column name in TPM_ril_all: WT_65_T


title: P2_C04_Participant_148_week_7

description:
Library name: P2_C04_S75
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_C02_Participant_236_week_6

description:
Library name: P2_C02_S59
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_E01_Participant_213_week_6

description:
Library name: P2_E01_S53
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_62 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_62_T
Column name in TPM_ril_all: WT_62_T


title: P2_C01_Participant_208_week_6

description:
Library name: P2_C01_S51
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_C03_Participant_252_week_6

description:
Library name: P2_C03_S67
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_B06_Participant_243_week_7

description:
Library name: P2_B06_S90
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_61 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_61_T
Column name in TPM_ril_all: WT_61_T


title: P2_B05_Participant_221_week_7

description:
Library name: P2_B05_S82
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_C05_Participant_155_week_7

description:
Library name: P2_C05_S83
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_B04_Participant_066_week_7

description:
Library name: P2_B04_S74
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_61 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_61_C
Column name in TPM_ril_all: WT_61_C


title: WT_63 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_63_T
Column name in TPM_ril_all: WT_63_T


title: P2_D01_Participant_178_week_6

description:
Library name: P2_D01_S52
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_69 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_69_T
Column name in TPM_ril_all: WT_69_T


title: P2_B03_Participant_200_week_6

description:
Library name: P2_B03_S66
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_62 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_62_C
Column name in TPM_ril_all: WT_62_C


title: WT_68 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_68_T
Column name in TPM_ril_all: WT_68_T


title: WT_68 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_68_C
Column name in TPM_ril_all: WT_68_C


title: P2_B01_Participant_097_week_6

description:
Library name: P2_B01_S50
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_A06_Participant_173_week_7

description:
Library name: P2_A06_S89
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_A05_Participant_151_week_7

description:
Library name: P2_A05_S81
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_B02_Participant_151_week_6

description:
Library name: P2_B02_S58
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_66 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_66_C
Column name in TPM_ril_all: WT_66_C


title: P2_A04_Participant_192_week_7

description:
Library name: P2_A04_S73
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_59 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_59_T
Column name in TPM_ril_all: WT_59_T


title: WT_63 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_63_C
Column name in TPM_ril_all: WT_63_C


title: P2_A03_Participant_212_week_6

description:
Library name: P2_A03_S65
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_59 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_59_C
Column name in TPM_ril_all: WT_59_C


title: P2_A02_Participant_251_week_6

description:
Library name: P2_A02_S57
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P2_A01_Participant_043_week_6

description:
Library name: P2_A01_S49
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_58 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_58_T
Column name in TPM_ril_all: WT_58_T


title: WT_58 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_58_C
Column name in TPM_ril_all: WT_58_C


title: P1_H06_Participant_171_week_7

description:
Library name: P1_H06_S48
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_57 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_57_T
Column name in TPM_ril_all: WT_57_T


title: P1_H05_Participant_159_week_7

description:
Library name: P1_H05_S40
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_57 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_57_C
Column name in TPM_ril_all: WT_57_C


title: WT_69 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_69_C
Column name in TPM_ril_all: WT_69_C


title: P1_H04_Participant_011_week_7

description:
Library name: P1_H04_S32
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_H03_Participant_165_week_6

description:
Library name: P1_H03_S24
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_H02_Participant_148_week_6

description:
Library name: P1_H02_S16
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_55 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_55_T
Column name in TPM_ril_all: WT_55_T


title: WT_66 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_66_T
Column name in TPM_ril_all: WT_66_T


title: P1_H01_Participant_209_week_6

description:
Library name: P1_H01_S8
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_55 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_55_C
Column name in TPM_ril_all: WT_55_C


title: WT_54 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_54_T
Column name in TPM_ril_all: WT_54_T


title: P1_G06_Participant_050_week_7

description:
Library name: P1_G06_S47
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_G05_Participant_126_week_7

description:
Library name: P1_G05_S39
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_54 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_54_C
Column name in TPM_ril_all: WT_54_C


title: WT_52 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_52_T
Column name in TPM_ril_all: WT_52_T


title: P1_G04_Participant_227_week_7

description:
Library name: P1_G04_S31
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_52 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_52_C
Column name in TPM_ril_all: WT_52_C


title: P1_G03_Participant_155_week_6

description:
Library name: P1_G03_S23
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_51 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_51_T
Column name in TPM_ril_all: WT_51_T


title: P1_G02_Participant_225_week_6

description:
Library name: P1_G02_S15
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_G01_Participant_239_week_6

description:
Library name: P1_G01_S7
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_51 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_51_C
Column name in TPM_ril_all: WT_51_C


title: P1_F06_Participant_229_week_7

description:
Library name: P1_F06_S46
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_F05_Participant_216_week_7

description:
Library name: P1_F05_S38
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_50 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_50_C
Column name in TPM_ril_all: WT_50_C


title: P1_F04_Participant_247_week_7

description:
Library name: P1_F04_S30
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_49 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_49_T
Column name in TPM_ril_all: WT_49_T


title: WT_56 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_56_C
Column name in TPM_ril_all: WT_56_C


title: P1_F03_Participant_230_week_6

description:
Library name: P1_F03_S22
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_56 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_56_T
Column name in TPM_ril_all: WT_56_T


title: P1_F02_Participant_228_week_6

description:
Library name: P1_F02_S14
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_48 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_48_T
Column name in TPM_ril_all: WT_48_T


title: P1_F01_Participant_227_week_6

description:
Library name: P1_F01_S6
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_E06_Participant_215_week_7

description:
Library name: P1_E06_S45
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_47 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_47_T
Column name in TPM_ril_all: WT_47_T


title: WT_48 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_48_C
Column name in TPM_ril_all: WT_48_C


title: WT_47 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_47_C
Column name in TPM_ril_all: WT_47_C


title: P1_E05_Participant_174_week_7

description:
Library name: P1_E05_S37
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_46 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_46_T
Column name in TPM_ril_all: WT_46_T


title: P1_E04_Participant_245_week_7

description:
Library name: P1_E04_S29
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_45 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_45_T
Column name in TPM_ril_all: WT_45_T


title: P1_E03_Participant_199_week_6

description:
Library name: P1_E03_S21
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_E02_Participant_032_week_6

description:
Library name: P1_E02_S13
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_45 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_45_C
Column name in TPM_ril_all: WT_45_C


title: P1_E01_Participant_197_week_6

description:
Library name: P1_E01_S5
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_D06_Participant_224_week_7

description:
Library name: P1_D06_S44
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_46 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_46_C
Column name in TPM_ril_all: WT_46_C


title: WT_44 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_44_T
Column name in TPM_ril_all: WT_44_T


title: WT_50 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_50_T
Column name in TPM_ril_all: WT_50_T


title: P1_D05_Participant_200_week_7

description:
Library name: P1_D05_S36
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_44 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_44_C
Column name in TPM_ril_all: WT_44_C


title: P1_D04_Participant_181_week_7

description:
Library name: P1_D04_S28
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_42 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_42_T
Column name in TPM_ril_all: WT_42_T


title: P1_D03_Participant_150_week_6

description:
Library name: P1_D03_S20
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_42 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_42_C
Column name in TPM_ril_all: WT_42_C


title: WT_49 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_49_C
Column name in TPM_ril_all: WT_49_C


title: P1_D02_Participant_171_week_6

description:
Library name: P1_D02_S12
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_41 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_41_C
Column name in TPM_ril_all: WT_41_C


title: WT_40 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_40_T
Column name in TPM_ril_all: WT_40_T


title: P1_C06_Participant_185_week_7

description:
Library name: P1_C06_S43
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_39 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_39_T
Column name in TPM_ril_all: WT_39_T


title: P1_C05_Participant_186_week_7

description:
Library name: P1_C05_S35
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_40 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_40_C
Column name in TPM_ril_all: WT_40_C


title: WT_39 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_39_C
Column name in TPM_ril_all: WT_39_C


title: P1_C04_Participant_204_week_7

description:
Library name: P1_C04_S27
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_38 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_38_T
Column name in TPM_ril_all: WT_38_T


title: P1_C02_Participant_234_week_6

description:
Library name: P1_C02_S11
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_41 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_41_T
Column name in TPM_ril_all: WT_41_T


title: WT_38 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_38_C
Column name in TPM_ril_all: WT_38_C


title: WT_36 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_36_T
Column name in TPM_ril_all: WT_36_T


title: P1_B06_Participant_176_week_7

description:
Library name: P1_B06_S42
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_B04_Participant_238_week_7

description:
Library name: P1_B04_S26
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_36 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_36_C
Column name in TPM_ril_all: WT_36_C


title: P1_B03_Participant_179_week_6

description:
Library name: P1_B03_S18
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_B02_Participant_164_week_6

description:
Library name: P1_B02_S10
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_34 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_34_T
Column name in TPM_ril_all: WT_34_T


title: P1_B01_Participant_203_week_6

description:
Library name: P1_B01_S2
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_34 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_34_C
Column name in TPM_ril_all: WT_34_C


title: WT_31 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_31_T
Column name in TPM_ril_all: WT_31_T


title: P1_D01_Participant_204_week_6

description:
Library name: P1_D01_S4
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_31 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_31_C
Column name in TPM_ril_all: WT_31_C


title: WT_30 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_30_T
Column name in TPM_ril_all: WT_30_T


title: P1_A04_Participant_145_week_7

description:
Library name: P1_A04_S25
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_A05_Participant_197_week_7

description:
Library name: P1_A05_S33
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_C03_Participant_154_week_6

description:
Library name: P1_C03_S19
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: P1_C01_Participant_083_week_6

description:
Library name: P1_C01_S3
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination