title: SL, LbNOX, rep1

description:
Library name: LBNOX_1
LbNOX_RNA-seq_raw_counts.csv


title: 5'-NRXN1-973-iGLUT-Best-BiolRep-2

status: Public on Mar 05 2025

type: SRA

city: New York

first: GANG

last: FANG

state: NY

address: 1425 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 973-DIV21-iGLUT-Best-R2

library_source: transcriptomic

data_processing:
Reads were first mapped by STAR v2.7.2a to a hg38/mm10 hybrid reference.
All reads unique mapped to hg38 were exracted.
Read counts of each gene were counted by featureCounts v2.0.3.
Assembly: hg38
Supplementary files format and content: CSV file of raw read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: For iGLUT neurons, at day -1 hiPSCs expanded in 10cm dishes were dissociated with accutase (StemCell Technologies, #07920), washed and pelleted with a 1:4 ratio of accutase to DMEM for 5 min at 1000 rcf, and re-suspended with StemFlex media containing ROCK inhibitor, THX (10µM/mL; Sigma Aldrich, SML1045). The hiPSCs are then co-transduced with TetO-Ngn2-Puro (Addgene #79049) or TetO-Ngn2-Neo (Addgene# 99378) and UCb-rtTA (legacy vector from the lab of Fred Gage) and seeded at 1.0-1.5x106 cells in 1.5mL per well on 6-well plates were coated with 2x Matrigel for at least one hour at 37°C. The hiPSC-viral mixture was then incubated overnight. The following morning (day 0), a full media change with iGLUT induction media was performed with the following recipe: Neurobasal Media: 1x N2 (Life technologies #17502-048), 1x B-27 minus Vitamin A (Life technologies #12587-010), 1x Antibiotic-Antimycotic, 1x Sodium Pyruvate, 1x GlutaMax (Life technologies #35050), 500µg/mL cyclic-AMP (Sigma #D0627), 200µM L-ascorbic acid (Sigma #A0278), 20ng/ml BDNF (Peprotech #450-02), 20ng/ml GDNF (Peprotech #450-10), 1µg/ml natural mouse laminin (Life technologies #23017015). On days 1-2, iGLUT cells were treated with respective antibiotic concentrations at 1µg/mL puromycin (Sigma# P7255) or 0.5µg/mL neomycin (Life technologies #11811-031). On day 3, antibiotic medium was withdrawn and iGLUT cells were treated with 4µM Ara-C. On Day 4, iGLUT cells were dissociated with accutase for 15 min, washed and pelleted with a 1:4 ratio of accutase to DMEM for 5 min at 800 rcf, and re-suspended with iGLUT media containing ROCK inhibitor, Ara-C and 2% low-hemoglobin FBS (R&D systems #S11510). iGLUT neurons were distributed among wells (500-750k cells per 24wp or 0.75-1.5E6 cell per 12wp) pre-seeded with confluent mouse glia. The following day, iGLUT neurons received a full media change with Brainphys maturation media (Brainphys, 1x N2, 1x B-27 minus Vitamin A, 1x Antibiotic-Antimycotic, 500µg/mL cyclic-AMP, 200µM Ascorbic Acid, 20ng/ml BDNF, 20ng/ml GDNF, 2% low-hemoglobin FBS, 1µg/ml Mouse Laminin) supplemented with Ara-C and were subsequently monitored for growth of non-neuronal/glial cells. Ara-C treatment was tittered down with half-media changes (without Ara-C) every 3-4 days until used for experiments.  iGABA production paralleled the methods aforementioned. hiPSCs were instead co-transduced with TetO-Ascl1-puro (Addgene #97330) or TetO-Ascl1-neo, TetO-Dlx2-hygro (Addgene #97329) and UCb-rtTA and seeded at 0.8-1.2x106 cells in 1.5mL per well on 6-well plates similarly prepared. The following morning (day 0), a full media change with iGABA induction media (DMEM/F-12 + Glutamax, 1x N2, 1x B-27 minus Vitamin A, 1x Antibiotic-Antimycotic) was performed. On days 1-2 iGABA cells were selected with respective antibiotic concentrations at 1µg/mL puromycin or 0.5µg/mL neomycin and 0.25µg/mL hygromycin (Life Technologies #10687010), followed by antibiotic withdrawal and Ara-C treatment on day 3. iGABA neurons were re-seeded identically to iGLUT cells, at 150-250k cells per 24wp well. iGABA cultures were morphologically QC’ed prior to all experiments, with uncharacteristic batches being discarded.

extract_protocol:
For the isolation of RNA, 2D cells were lysed using TRIzol (Life Technologies #15596026) and purified using the Qiagen miRNeasy Kit (Qiagen Cat# 74106) according to the manufacturer’s instructions.
Libraries were prepared via the Kapa Hyper library prep with ribo-erase (Roche #KK8541), according to the manufacturer's instructions.

treatment_protocol: beta-estradiol was reconstituted in DMSO and subsequently diluted in Brainphys maturation media for a final concentration of 30nM. Neurons were treated daily (in half media changes). iGLUT and iGABA neurons were treated starting from ~DIV14-18. Chronic treatments for functional experiments extended daily beta-estradiol replenishments for ~14 days and harvested on DIV21 ~4 hours post final dosage. ASOs were delivered using Lipofectamine RNAiMAX Transfection Reagent (Thermo, #13778075). The Lipofectamine RNAiMAX was diluted in Opti-MEM Medium (Thermo, #31985070). ASO was then diluted in Opti-MEM Medium at 1µM. The diluted ASO was added in a 1:1 ratio to the diluted Lipofectamine RNAiMAX and incubated at room temperature for 5 minutes. The ASO-lipid complex was added to cells, and incubated for 72 hours post-transfection, until RNA harvest. ASO samples for RNA-Seq were harvested on DIV17.

tag: cell line

tag: cell type

value: hiPSC-derived-GLUT

tag: genotype

tag: treatment

value: Beta-estradiol

tag: time

tag: experimental batch


title: Gr2-35_ZT13_20-2

city: St. Paul

first: kathleen

last: Greenham

state: MN

address: 1445 Gortner Avenue

institute: University of Minnesota

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.

organism: Brassica napus

source_name: leaf

growth_protocol: Seeds were inbibed on wet whatman paper for five days before sowing into 4inch wide pots filled with MetroMix360. Growth conditions were 28C/22C day/night temperatures, 14 hour day lengths with 400 umol/m2/s light intensity and 40% relative humidity for the duration of the four week experiment.

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT

treatment_protocol: Plants were equally separated into two treatments for the duration of the experiment: 100% watering (well-watered) and 20% watering (water limited). The target watering weights were determined as described in Fahlgren et al. (Fahlgren et al., 2015). All pots were watered once to 100% capacity on the first day of the experiment, and then weighed twice per day to maintain a target water weight through day seven on the Bellwether phenotyping platform. Starting on day eight, water limited plants were allowed to dry down to 20% capacity and maintained at 20% capacity until day 14 (seven days after water limitation treatment began). At this point all watering amounts were increased by 10% for the rest of the experiment.

tag: tissue

value: leaf

tag: temperature

tag: photoperiod

tag: timepoint (zt_=_hours_after_dawn)

value: Gruener Schnittrohl_BnASSYST-219

value: Water limited, 20% full capacity


title: SL_vector, rep3

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: PB_3
LbNOX_RNA-seq_raw_counts.csv

data_processing:
FASTQ files were aligned to the reference genome using DRAGEN v3.10 (Illumina) to generate BAM files.
Raw counts matrix was generated using featureCounts/subread.
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse ESC

growth_protocol: Mouse ESC lines were maintained in Knockout DMEM with 10% fetal bovine serum. Cells were mainted either with leukemia ininhibitory factor (LIF) or LIF + inhibitors against GSK3B and MEK (2i).

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 9.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: For experiments, medium was switched to a mixture of DMEM and NB with 10% dialyzed fetal bovine serum and 0.2 mM sodium pyruvate.

value: mouse ESC


title: 5'-NRXN1-973-iGLUT-Best-BiolRep-1

description: Library name: 973-DIV21-iGLUT-Best-R1


title: SL_vector, rep2

description:
Library name: PB_2
LbNOX_RNA-seq_raw_counts.csv


title: 5'-NRXN1-972-iGLUT-Vehicle-BiolRep-3

description: Library name: 972-DIV21-iGLUT-Veh-R3

value: Vehicle


title: Gr2-35_ZT19_20-1


title: Gr2-35_ZT19_100-3

value: Well watered, 100% full capacity


title: 5'-NRXN1-972-iGLUT-Vehicle-BiolRep-2

description: Library name: 972-DIV21-iGLUT-Veh-R2


title: 194 st

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

description:
Library name: 194st
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw Illumina base call files were demultiplexed and converted into FASTQ files using CellRanger mkfastq v5.0.0. The resulting FASTQ files were loaded into STARsolo v2.7.9a for alignment to the 10x reference GRCh38-2020-A53. Count matrices generated with the –soloFeatures GeneFull argument were used for downstream analyses.
For Sample A211, CellRanger v5.0.0 was used to align and process reads
Assembly: GRCh38-2020-A53
Supplementary files format and content: *barcodes.tsv: 10X cell barcodes
Supplementary files format and content: *features.tsv: Tab-separated list of features (genes or clone) and identifiers for type of feature.
Supplementary files format and content: *matrix.mtx: Sparse count matrix

source_name: Stomach

extract_protocol:
Fresh pinch biopsies were washed twice in DPBS before being coarsely chopped with a scalpel and transferred into 0.5 mL DPBS solution containing 0.1 WU ml-1 Liberase TH (Roche, 5401151001) and 0.5 U ml-1 RQ1 DNase I (Promega, M6101). The samples were incubated at 37 °C in successive 10-minute rounds with gentle vortexing every 2 minutes and trituration every 5 minutes. At the end of each round of incubation, large tissue pieces were spun down in a microcentrifuge and the supernatant containing single cells was passed through a 70-um cell strainer fitted onto a 50-mL conical tube containing 8 mL DPBS + 1% bovine serum albumin (BSA; Sigma-Aldrich, A7906) in DPBS on ice. 0.5 mL fresh dissociation solution was added to the tissue at the beginning of each incubation step. The samples were further filtered through the 0.35 um cell-strainer cap of a FACS tube and single cells were pelleted by centrifugation at 400g for 4 minutes at 4 °C. Samples were washed twice in 1 mL DPBS + 0.04% BSA and finally resuspended in 50 uL DPBS + 0.04% BSA, at which point they were counted in 0.2% trypan blue (Gibco, 15250061) in preparation for 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 library preparation. For the frozen BE biopsy from Patient 2, the tissue was quickly thawed at 37 °C and rinsed three times in DPBS + 10% fetal bovine serum (GE, SH30396.03) before being dissociated and filtered as described above. After the final filtering step, dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) following the manufacturer’s protocol.
Single-cell suspensions were loaded onto a 10x Chromium Controller for GEM generation of approximately 5,000-10,000 cells for each sample. 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 Dual Index library preparation was performed following the manufacturer’s protocol. Library quality was confirmed on an Agilent 2100 Bioanalyzer Instrument using the High Sensitivity DNA Kit (Agilent). Libraries were paired-end sequenced on an Illumina NextSeq 550 with 28 cycles for Read 1 and 43 cycles for Read 2, as well as 10 cycles for both indices.

value: Stomach


title: 195 be

description:
Library name: 195be
10X Genomics

source_name: Barrett's Esophagus

value: Barrett's Esophagus


title: 195 scj2

description:
Library name: 195scj2
10X Genomics

source_name: Squamocolumnar Junction

value: Squamocolumnar Junction


title: SL, LbNOX, rep3

description:
Library name: LBNOX_3
LbNOX_RNA-seq_raw_counts.csv


title: 194 scj

description:
Library name: 194scj
10X Genomics


title: 5'-NRXN1-972-iGLUT-Vehicle-BiolRep-1

description: Library name: 972-DIV21-iGLUT-Veh-R1


title: 195 scj1

description:
Library name: 195scj1
10X Genomics


title: SL, vector, rep1

description:
Library name: PB_1
LbNOX_RNA-seq_raw_counts.csv


title: Gr2-35_ZT13_20-1


title: 194 es

description:
Library name: 194es
10X Genomics

source_name: Esophagus

value: Esophagus


title: 5'-NRXN1-972-iGLUT-Best-BiolRep-3

description: Library name: 972-DIV21-iGLUT-Best-R3


title: Pooled_cells_HTO

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

description: Library name: WP-A-C-hashtag_NGS24-H281_AHL3HJDSXC

library_source: other

data_processing:
The Cellranger (v8.0) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment, filtering, UMI counting and to separate two samples by barcode (cellranger multi).
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.18) and Seurat (5.1.0).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 10% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge datasets from two samples, clusters were identified based on PCA using FindClusters function. Differentially expressed genes were calculated using FindAllMarkers function (Seurat package).
Assembly: GRCm38
Supplementary files format and content: Text counts table: counts of genes for all cells (no-filtered)
Supplementary files format and content: Text counts table: call of hashtags for all cells (no filtered)
Library strategy: CITE-seq

molecule: protein

source_name: lung

extract_protocol:
After hashtag labelling, cells were pooled and approximately 10 000 cells suspended in PBS with 0.04% BSA were loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.

treatment_protocol: Chimeric mice (transferred with either Tgfbr2 fl/fl or LyzM-Cre Tgfbr2 fl/fl bone marrow) were treated with 50 ng diphtheria toxin treatment 10 days before sacrifice. CD45.1-CD45.2+Ly6G-SiglecF-CD11b+SSCloCD64+ cells from each group were FACS-sorted and barcoded with different Biolegend anti-mouse Hastags before being pooled:   ACCCACCAGTAAGAC  TotalSeq-B0301 for group Control CTTGCCGCATGTCAT TotalSeq-B0303 for group Tgfbr2-KO

value: lung

value: FACS-sorted CD45.1-CD45.2+Ly6G-SiglecF-CD11b+SSCloCD64+ cells from lung single-cell suspension

value: Pooled Tgfbr2 fl/fl and LyzM-Cre Tgfbr2 fl/fl


title: Gr2-35_ZT13_100-1


title: Gr2-35_ZT19_20-3


title: Pooled_cells_chromium

description: Library name: WP-A-C-cDNA_NGS24-H283_AHL3HJDSXC

data_processing:
The Cellranger (v8.0) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment, filtering, UMI counting and to separate two samples by barcode (cellranger multi).
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.18) and Seurat (5.1.0).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 10% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge datasets from two samples, clusters were identified based on PCA using FindClusters function. Differentially expressed genes were calculated using FindAllMarkers function (Seurat package).
Assembly: GRCm38
Supplementary files format and content: Text counts table: counts of genes for all cells (no-filtered)
Supplementary files format and content: Text counts table: call of hashtags for all cells (no filtered)

value: Chimeric mice (transferred with either Tgfbr2 fl/fl or LyzM-Cre Tgfbr2 fl/fl bone marrow) were treated with 50 ng diphtheria toxin treatment 10 days before sacrifice.


title: 5'-NRXN1-972-iGLUT-Best-BiolRep-2

description: Library name: 972-DIV21-iGLUT-Best-R2


title: 193 st

description:
Library name: 193st
10X Genomics


title: Gr2-35_ZT1_100-2


title: H3-Arc

city: NanJing

first: Xu

last: Feng

state: Jiangsu

address: 101 Long Mian avenue

country: China

institute: Nanjing Medical University

description: Library name: smaple6

data_processing:
The cDNA library was sequenced using Illumina Novaseq6000
Assembly: mm10
Supplementary files format and content: NCD-Arc-vs-HFD-Arc.all.xls
Supplementary files format and content: NCD-Arc-vs-HFD-Arc.all.xls:gene expression FPKM data

source_name: Brian

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: Brian

tag: Sex

value: male


title: 5'-NRXN1-972-iGLUT-Best-BiolRep-1

description: Library name: 972-DIV21-iGLUT-Best-R1

value: hiPSC-derived-GLUT

value: Beta-estradiol


title: 193 es

description:
Library name: 193es
10X Genomics


title: DH20_ZT7_20-3

value: leaf


title: H2-Arc

description: Library name: smaple5


title: 193 be1

description:
Library name: 193be1
10X Genomics


title: DH20_ZT1_20-2

value: Water limited, 20% full capacity


title: H1-Arc

description: Library name: smaple4


title: DH20_ZT1_100-1


title: 193 be2

description:
Library name: 193be2
10X Genomics


title: Control-690-iGLUT-shWT-BiolRep-3

description: Library name: 690-DIV21-iGLUT-shWT-R3

value: Control

value: WT targeting shRNA

value: Control-shRNA-WT-iGLUT


title: C3-Arc

description: Library name: smaple3


title: C2-Arc

description: Library name: smaple2


title: Control-690-iGLUT-shNEG-BiolRep-3

description: Library name: 690-DIV21-iGLUT-shNEG-R3

value: Non-targeting shRNA


title: DH20_ZT1_20-3


title: 192 be2

description:
Library name: 192be2
10X Genomics

value: Barrett's Esophagus


title: 192 be1

description:
Library name: 192be1
10X Genomics


title: C1-Arc

description: Library name: smaple1


title: DH20_ZT13_20-2


title: whole-cell RNA, endoplasmic reticulum, biol rep 3

city: Palo Alto

first: Maria

last: Barna

state: CA

address: 240 Pasteur Dr, BMI 4500

department: Genetics

institute: Stanford University

description: Library name: ALIBi_ER_vs_cyto_E_LY_3

data_processing:
For all RNA-seq analysis, the reference genome was generated using STAR/2.7.9a on the Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27 and --sjdbOverhang 149. Alignment was performed with adapter sequences AGATCGGAAGAGCACA CGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG ATCTCGGTGGTCGCCGTATCATT, and --clip3pAdapterMMp 0.1 0.1. Read counting was performed with htseq-count from htseq/0.11.2 -m intersection-nonempty -s reverse -i gene_id with annotations from GENCODE vM27. Genes were included in downstream analysis if the mean raw count across all samples was at least 5.  For RNA-seq analysis comparing cytosolic and ER ALIBi, differential abundance of read counts was performed using DESeq2 with a design matrix of “~ organelle + fraction + replicate + organelle:fraction” where “organelle” has values of “cytoplasm” or “endoplasmic reticulum” and “fraction” has values of “lysate” (whole-cell RNA fraction) or “eluate” (ribosome-bound RNA fraction). GO-Slim Cellular Component gene ontology terms were mapped using the PANTHER database. For comparison to existing ER transcriptome and translatome datasets from HEK293 cells, mouse gene IDs were converted based on the corresponding ENSEMBL gene ID or UCSC ID in each species, and mouse genes with no human homologs were excluded.  For RNA-seq analysis of ER ALIBi with Lsg1, Nmd3, or Gnl3 siRNA knockdown, differential abundance of read counts was analyzed separately for the whole-cell RNA fractions and for the ER ribosome-bound RNA fractions from cells transfected with ER-ALIBi using DESeq2 with a design matrix of “~replicate + sirna” where “sirna” has values representing either the siRNA-targeted gene or “scramble” (non-targeting control siRNA). For the Nmd3 and Gnl3 whole-cell RNA fractions, one out of three replicates for each condition was excluded from analysis because it appeared as an outlier in principle component analysis (PCA). Uniprot subcellular location codes were used to identify genes encoding membrane proteins or secreted/lumenal proteins.  For all RNA-seq analysis, adjusted p-values reflect multiple comparison correction using the Benjamini-Hochberg method, as implemented in DESeq2.
Assembly: Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27
Supplementary files format and content: Tab-delimited HTSeq output files containing raw counts

source_name: Rpl31-FTA E14Tg2a.4 mESCs

growth_protocol: E14Tg2a.4 mESCs were a gift from Thom Saunder’s lab (University of Michigan). Cell line identity was verified via short tandem repeat profiling performed by the American Type Culture Collection (ATCC, 137-XV, Manassas, VA). Cells were cultured in Knockout DMEM (ThermoFisher 10829-018) supplemented to a final concentration of 15% ES-qualified fetal bovine serum (MilliporeSigma ES-009-B), 1% non-essential amino acids (MilliporeSigma TMS-001-C), 2 mM L-glutamine (MilliporeSigma TMS-002-C), 1% penicillin/streptomycin (ThermoFisher 15140-122), 55 μM beta-mercaptoethanol (ThermoFisher 21985-023), and 1000 U/mL mouse leukemia inhibitory factor (mLIF, Gemini 400-495 10^7). Media was changed daily and cells were passaged every two days. Mycoplasma testing was performed according to the manufacturer’s instructions using the PromoKine PCR Mycoplasma Test Kit (PK-CA91-1096, Heidelberg, Germany).

extract_protocol:
Prior to affinity purification, an aliquot of cell lysate was reserved and mixed at a volume ratio of 1:9 with TRIzol (Thermo 15596-018) in an RNA non-stick tube. After affinity purification, eluate was mixed at a volume of 1:3 with TRIzol LS (Thermo 10296010) in an RNA non-stick tube. RNA was extracted using the DirectZol kit (R2060), following the manufacturer protocol without the on-column DNAse treatment. Extracted RNA was treated with Turbo DNAse (AM2239) per the manufacturer protocol and re-purified with an RNA Clean & Concentrator-5 column (R1016) per the manufacturer protocol. RNA concentration was estimated by Nanodrop 2000 (Thermo), and RNA integrity number (RIN) was assessed on an Agilent 2100 Bioanalyzer (total RNA pico) at the Stanford Protein and Nucleic Acid Facility.
For each sample, 750 ng of RNA was used as input for the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490) and indices from the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (New England Biolabs E7335S, E7500S), per the manufacturer protocol with 9 cycles of PCR amplification. Libraries were assessed on an Agilent 2100 Bioanalyzer (DNA 1000) to have an amplicon size of ~300 bp. Libraries were sequenced by Novogene on a Novaseq X or X Plus with paired-end 150 bp reads to a total target depth of 20 - 26 million read pairs per sample.

treatment_protocol: Lysis buffer: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 2% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide, 1X Halt EDTA-Free Protease Inhibitor (ThermoFisher 78425), 0.1 U/µL Superase RNAse Inhibitor (ThermoFisher AM2696), 0.014 U/µL Turbo DNAse (ThermoFisher AM2239), 1 U/mL apyrase (New England Biolabs M0398L) in Ultrapure distilled water (ThermoFisher 10977-015).  RNAse removal buffer: 100 mM NaOH (MilliporeSigma 72068), 50 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Salt wash: 100 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Wash I: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Wash II: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 300 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Elution buffer (ThermoFisher 12575015): 1X AcTEV buffer, 1 mM DTT, 1% v/v AcTEV protease in Ultrapure distilled water (ThermoFisher 10977-015).  General precautions: once cells were transfected, exposure to ambient light and temperatures below 37 °C was minimized. Lysis, centrifugation, pulldown, and wash steps were carried out in a dark room with samples and buffers chilled to 4 C. Protein low-binding microcentrifuge tubes were used unless otherwise specified.  For samples not treated with siRNA, Rpl31-FTA mESCs were transfected with plasmids encoding the appropriate N- and C-terminal ALIBi fragments. 1.5 µg of each ALIBi plasmid was diluted in 100 µL Opti-MEM. In parallel, 7.5 µL of Lipofectamine 2000 was diluted in 100 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 3 million trypsinized cells were resuspended in 300 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 2 minutes at room temperature, and plated into one well of a 6-well plate containing 1.5 mL warmed media. Plates were incubated at 37 °C for 4 hours to allow reattachment before changing to fresh media. Media was changed 24 hours after transfection. At 48 hours after transfection, cells were changed to media containing 100 µg/mL cycloheximide and 50 uM biotin. Plates were immediately placed on a blue light transilluminator inside a 37 °C incubator for 15 minutes. Plates were washed once with ice-cold DPBS containing 100 µg/mL CHX, before adding 500 µL ice-cold lysis buffer per well. After incubating plates with lysis buffer on ice for 5 minutes, lysate was pipetted up and down six times in the plate with a P1000 pipet to fully dislodge cells and transferred to a 1.5 mL microcentrifuge tube. The lysate was further incubated for 15 minutes on ice, then clarified by centrifuging at 17,000 g for 3 minutes at 4 C. A 300 µL aliquot of the clarified lysate was added to pre-washed beads for affinity purification. For each sample, a 150 µL aliquot of beads was pre-washed as follows: the storage buffer was removed and the beads were washed twice with 500 µL of RNAse removal buffer, once with 500 µL of salt wash, and twice with 500 µL of Wash I. After adding clarified lysate, beads were rotated at 4 °C for 1 h, then washed once with a double bead volume of Wash I and twice with a double bead volume of Wash II. The beads were then incubated in one bead volume of elution buffer at room temperature for 1 h on a thermomixer at 800 rpm.  For samples with Lsg1, Nmd3, or Gnl3 siRNA knockdown and subsequent RNA-seq, a modified transfection was performed: 0.625 µg of each ALIBi plasmid and 26.7 pmol of Lsg1 siRNA (Horizon Discovery M-057491-01-0005), Nmd3 siRNA (Horizon Discovery M-051297-01-0005), Gnl3 siRNA (Horizon Discovery M-051664-01-0005), or control siRNA (Horizon Discovery D-001206-14-05) were diluted in 41.7 µL Opti-MEM. In parallel, 3.13 µL of Lipofectamine 2000 was diluted in 41.7 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 1.25 million trypsinized cells were resuspended in 125 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 10 minutes at room temperature, and plated into one well of a 6-well plate containing 2 mL warmed media. The remaining steps were performed as described above, with the modification that ALIBi activation, cell lysis, and affinity purification were performed 24 h after transfection.

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells

tag: organelle

value: endoplasmic reticulum

tag: fraction

value: whole-cell

tag: replicate

value: biol rep 3


title: 189 st

description:
Library name: 189st
10X Genomics

value: Stomach


title: Control-690-iGLUT-shWT-BiolRep-1

description: Library name: 690-DIV21-iGLUT-shWT-R1


title: 191 be

description:
Library name: 191be
10X Genomics


title: DH20_ZT7_100-2

value: Well watered, 100% full capacity


title: Control-690-iGLUT-shNEG-BiolRep-1

description: Library name: 690-DIV21-iGLUT-shNEG-R1


title: Control-690-iGLUT-shWT-BiolRep-2

description: Library name: 690-DIV21-iGLUT-shWT-R2


title: 3'-NRXN1-641-iGLUT-shNEG-BiolRep-2

description: Library name: 641-DIV24-iGLUT-shNEG-R2


title: whole-cell RNA, endoplasmic reticulum, biol rep 2

description: Library name: ALIBi_ER_vs_cyto_E_LY_2

value: biol rep 2


title: 189 es2

description:
Library name: 189es2
10X Genomics

value: Esophagus


title: DH20_ZT13_20-3


title: 3'-NRXN1-641-iGLUT-shNEG-BiolRep-1

description: Library name: 641-DIV24-iGLUT-shNEG-R1

value: hiPSC-derived-GLUT


title: whole-cell RNA, endoplasmic reticulum, biol rep 1

description: Library name: ALIBi_ER_vs_cyto_E_LY_1

value: biol rep 1


title: Control-690-iGLUT-shNEG-BiolRep-2

description: Library name: 690-DIV21-iGLUT-shNEG-R2


title: DH20_ZT7_20-1

value: leaf

value: Water limited, 20% full capacity


title: DH20_ZT7_20-2


title: ribosome-bound RNA, endoplasmic reticulum, biol rep 3

description: Library name: ALIBi_ER_vs_cyto_E_IP_3

value: ribosome-bound


title: 188 es

description:
Library name: 188es
10X Genomics


title: 3'-NRXN1-641-iGLUT-shMT-BiolRep-2

description: Library name: 641-DIV24-iGLUT-shMT2-R2

value: MT Targeting shRNA


title: 3'-NRXN1-641-iGLUT-shMT-BiolRep-3

description: Library name: 641-DIV24-iGLUT-shMT2-R3


title: ribosome-bound RNA, endoplasmic reticulum, biol rep 2

description: Library name: ALIBi_ER_vs_cyto_E_IP_2


title: 188 be

description:
Library name: 188be
10X Genomics


title: DH20_ZT13_100-3


title: ribosome-bound RNA, endoplasmic reticulum, biol rep 1

description: Library name: ALIBi_ER_vs_cyto_E_IP_1


title: DH20_ZT7_100-3


title: whole-cell RNA, cytosol, biol rep 3

description: Library name: ALIBi_ER_vs_cyto_C_LY_3

value: cytosol


title: 3'-NRXN1-641-iGLUT-ASO-MT-BiolRep-2

description: Library name: 641-DIV17-iGLUT-ASONRXN-R2

value: MT Targeting ASO


title: 187 st

description:
Library name: 187st
10X Genomics


title: 3'-NRXN1-641-iGLUT-shMT-BiolRep-1

description: Library name: 641-DIV24-iGLUT-shMT2-R1


title: 187 es

description:
Library name: 187es
10X Genomics


title: 3'-NRXN1-641-iGLUT-ASO-MT-BiolRep-1

description: Library name: 641-DIV17-iGLUT-ASONRXN-R1


title: 189 es1

description:
Library name: 189es1
10X Genomics


title: DH20_ZT19_100-3


title: Gr2-35_ZT1_20-3

value: Gruener Schnittrohl_BnASSYST-219


title: DH20_ZT19_20-3


title: 3'-NRXN1-641-iGLUT-ASO-NEG-BiolRep-2

description: Library name: 641-DIV17-iGLUT-ASONEG-R12

value: Non-targeting ASO


title: whole-cell RNA, cytosol, biol rep 1

description: Library name: ALIBi_ER_vs_cyto_C_LY_1

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells


title: 188 st

description:
Library name: 188st
10X Genomics


title: ribosome-bound RNA, cytosol, biol rep 3

description: Library name: ALIBi_ER_vs_cyto_C_IP_3

value: biol rep 3


title: 3'-NRXN1-641-iGLUT-ASO-NEG-BiolRep-1

description: Library name: 641-DIV17-iGLUT-ASONEG-R1


title: DH20_ZT1_100-2


title: DH20_ZT19_20-2


title: DH20_ZT19_100-2


title: 3'-NRXN1-581-iGABA-shNEG-BiolRep-2

description: Library name: 581-DIV49-iGABA-shNEG-R1

value: hiPSC-derived-iGABA

value: Non-targeting shRNA


title: 186 be

description:
Library name: 186be
10X Genomics

value: Barrett's Esophagus


title: 185 be

description:
Library name: 185be
10X Genomics


title: ribosome-bound RNA, cytosol, biol rep 1

description: Library name: ALIBi_ER_vs_cyto_C_IP_1


title: DH20_ZT19_20-1


title: DH20_ZT19_100-1

value: Well watered, 100% full capacity


title: ribosome-bound RNA, cytosol, biol rep 2

description: Library name: ALIBi_ER_vs_cyto_C_IP_2

value: biol rep 2


title: 3'-NRXN1-581-iGABA-shMT-BiolRep-2

description: Library name: 581-DIV49-iGABA-shMT2-R1


title: DH20_ZT1_20-1


title: skin wound, DM+IL37tg-4

city: Shanghai

first: xiaoming

last: zhu

state: --- Select One ---

address: 12 wulumuqi road,shanghai

department: Department of Endocrinology and Metabolism,

institute: Huashan Hospital,Fudan University

description:
Library name: Sample13
Column name in raw_counts_All_Samples.csv: a_85_D10

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.. The clean reads were mapped to the reference genome using HISAT2.
Assembly: After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: skin wound

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: skin wound

value: STZ


title: Brain, metastasis, rep6 (miRNA-Seq)

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

description:
Library name: Sample_12
T_rep6

data_processing:
Normalized expression value of miRNAs were analyzed using the iDEP 1.1 tool (http://bioinformatics.sdstate.edu/idep11). Within iDEP, hierarchical clustering was conducted with a Z score cutoff of 3, followed by k-Means clustering of the 100 most variable miRNAs and principal component analysis (PCA). Differential gene expression was assessed using the DESeq2 software package, the DEG1 analysis was performed with a false discovery rate (FDR) cutoff of 0.1 and a minimum fold change (FC) of 2. Significantly upregulated miRNAs were defined with FC ≥ 2 and FDR ≤ 0.05, while miRNAs with FC ≤ -2 and FDR ≤ 0.05 were classified as downregulated.
Raw sequencing data (fastq) was aligned to human reference genome version GRCh38 using Novoalign algorithm and BAM files were generated.
Assembly: GRCh38
Supplementary files format and content: Processed data files are txt files, containing information of 6 replicates of glioblastoma samples and brain metastases samples of lung adenocarcinoma origin

source_name: Brain

extract_protocol:
For total RNA purification, 30 mg/sample of flash-frozen tissue samples were dissected on ice. The tissue samples were disrupted and homogenized with a MagNa Lyser device (Roche Ltd., Switzerland). MiRNA-enriched total RNA isolation was performed according to the manufacturer's instructions using the miRNeasy Mini Kit (Qiagen, Hilden, Germany). The quantity and quality of the isolated RNA were determined using a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA).
The NEBNext Multiplex Small RNA Perp Set for Illumina (1-48) 96 rxn kit (New England BioLabs, Ipswich, MA, USA) was used for library preparation, for which the quality of the RNA samples was examined with the Eukaryotic Total RNA Nano Assay on the Agilent Bio Analyzer (Agilent Technologies, Santa Clara, CA, USA). For small RNA-seq library, 1 µg of total RNA with an RNA integrity number (RIN) score >7 was used. Fragment size distribution and molarity of libraries were also checked on Agilent BioAnalyzer DNA1000 chip (Agilent Technologies, Santa Clara, CA, USA). Finally, the libraries were sequenced on an Illumina NextSeq 500 Sequencing System (Illumina, San Diego, CA, USA) with read lengths of 50 base pairs (single reads). Fastq files were aligned to the human reference genome (GRCh38) using the Novoalign algorithm.

value: Brain


title: whole-cell RNA, cytosol, biol rep 2

description: Library name: ALIBi_ER_vs_cyto_C_LY_2

value: whole-cell


title: 185 es

description:
Library name: 185es
10X Genomics

value: Esophagus


title: skin wound, DM+IL37tg-3

description:
Library name: Sample12
Column name in raw_counts_All_Samples.csv: a_84_D10


title: Brain, metastasis, rep5 (miRNA-Seq)

description:
Library name: Sample_11
T_rep5


title: 3'-NRXN1-581-iGABA-shNEG-BiolRep-1

description: Library name: 581-DIV46-iGABA-shNEG-R1


title: 187 be

description:
Library name: 187be
10X Genomics


title: 3'-NRXN1-581-iGABA-shMT-BiolRep-1

description: Library name: 581-DIV46-iGABA-shMT2-R1

value: MT Targeting shRNA


title: DH20_ZT13_20-1

value: leaf

value: Water limited, 20% full capacity


title: Brain, metastasis, rep4 (miRNA-Seq)

description:
Library name: Sample_10
T_rep4


title: 3'-NRXN1-581-iGLUT-shNEG-BiolRep-2

description: Library name: 581-DIV23-iGLUT-shNEG-R2

value: hiPSC-derived-GLUT


title: skin wound, DM+IL37tg-1

description:
Library name: Sample10
Column name in raw_counts_All_Samples.csv: a_82_D10


title: DH20_ZT7_100-1


title: Brain, metastasis, rep3 (miRNA-Seq)

description:
Library name: Sample_9
T_rep3


title: 3'-NRXN1-581-iGLUT-shNEG-BiolRep-1

description: Library name: 581-DIV23-iGLUT-shNEG-R1


title: Brain, metastasis, rep2 (miRNA-Seq)

description:
Library name: Sample_8
T_rep2


title: skin wound, DM-3

description:
Library name: Sample9
Column name in raw_counts_All_Samples.csv: a_21_D10

value: WT


title: DH20_ZT13_100-2


title: Brain, metastasis, rep1 (miRNA-Seq)

description:
Library name: Sample_7
T_rep1


title: 3'-NRXN1-581-iGLUT-shMT-BiolRep-1

description: Library name: 581-DIV23-iGLUT-shMT-R1


title: 3'-NRXN1-581-iGLUT-shMT-BiolRep-2

description: Library name: 581-DIV23-iGLUT-shMT-R2


title: skin wound, DM-2

description:
Library name: Sample8
Column name in raw_counts_All_Samples.csv: a_18_D10


title: skin wound, DM-1

description:
Library name: Sample7
Column name in raw_counts_All_Samples.csv: a_12_D10


title: Brain, glioblastoma, rep6 (miRNA-Seq)

description:
Library name: Sample_6
G_rep6


title: DH12.6-33_ZT13_20-1


title: skin wound, non-DM-5

description:
Library name: Sample5
Column name in raw_counts_All_Samples.csv: a_7_D10

value: PBS


title: DH12.6-33_ZT7_100-3


title: Brain, glioblastoma, rep4 (miRNA-Seq)

description:
Library name: Sample_4
G_rep4


title: 3'-NRXN1-581-iGLUT-ASO-MT-BiolRep-2

description: Library name: 581-DIV17-iGLUT-ASONRXN-R2

value: MT Targeting ASO


title: Brain, glioblastoma, rep5 (miRNA-Seq)

description:
Library name: Sample_5
G_rep5


title: DH12.6-33_ZT13_100-3


title: skin wound, DM+IL37tg-2

description:
Library name: Sample11
Column name in raw_counts_All_Samples.csv: a_83_D10


title: 3'-NRXN1-581-iGLUT-ASO-NEG-BiolRep-2

description: Library name: 581-DIV17-iGLUT-ASONeg-R2

value: Non-targeting ASO


title: 3'-NRXN1-581-iGLUT-ASO-MT-BiolRep-1

description: Library name: 581-DIV17-iGLUT-ASONRXN-R1


title: DH12.6-33_ZT7_20-3


title: Brain, glioblastoma, rep3 (miRNA-Seq)

description:
Library name: Sample_3
G_rep3


title: skin wound, non-DM-6

description:
Library name: Sample6
Column name in raw_counts_All_Samples.csv: a_8_D10


title: DH12.6-33_ZT19_20-2


title: skin wound, non-DM-4

description:
Library name: Sample4
Column name in raw_counts_All_Samples.csv: a_6_D10


title: skin wound, non-DM-3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.csv: a_5_D10


title: 3'-NRXN1-581-iGLUT-ASO-NEG-BiolRep-1

description: Library name: 581-DIV17-iGLUT-ASONeg-R1


title: Brain, glioblastoma, rep2 (miRNA-Seq)

description:
Library name: Sample_2
G_rep2


title: DH20_ZT1_100-3


title: skin wound, non-DM-2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.csv: a_3_D10


title: Brain, glioblastoma, rep1 (miRNA-Seq)

description:
Library name: Sample_1
G_rep1


title: DH12.6-33_ZT1_100-3


title: Control-553-iGLUT-shWT-BiolRep-1

description: Library name: 553-DIV21-iGLUT-shWT1-R2

value: Control

value: WT targeting shRNA

value: Control-shRNA-WT-iGLUT


title: Control-553-iGLUT-shWT-BiolRep-2

description: Library name: 553-DIV21-iGLUT-shWT1-R3


title: DH12.6-33_ZT1_20-2


title: skin wound, non-DM-1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.csv: a_2_D10


title: DH12.6-33_ZT7_100-1

value: Well watered, 100% full capacity


title: DH12.6-33_ZT7_100-2


title: A196V-A196L_patient_11_repl2

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.3.8) using the parameters --species Hsap --cluster-id 0.95 --min-cov 0.0005 --max-mismatches 0.075 --control-condition WT --deconv-cov-ratio 0.4 --remap-mismatches 0.05. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters, and on read counts summed by isotype.
Assembly: hg38
Supplementary files format and content: csv; mim-tRNAseq generated tRNA transcript read counts
Library strategy: mim-tRNAseq

source_name: patient derived human lymphoblastoid cell line

extract_protocol:
Cells were lysed in LiDS/LET buffer (5% LiDS in 20 mM Tris, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH7.4, 100 μg/ml Proteinase K). Lysates were incubated at 60°C for 10 minutes, pushed 10 times through a 1-ml syringe with a 26G needle, and mixed by vortexing. Two volumes of cold acid phenol (pH 4.3), 1/10 volume 1-Bromo-3-chloropropane and 50 µg glycogen were added. Samples were mixed vigorously by vortexing, followed by centrifuging at 10,000 g, 4°C. The aqueous phase was transferred to a new tube and the phenol/BCP extraction was repeated. RNA was precipitated by the addition of 3 volumes of 100% ethanol and incubation at -20°C for 30 min. Pellets were washed with 80% ethanol, air-dried, and resuspended in RNase-free water.
Libraries were prepared using the mim-tRNAseq workflow (Behrens 2021, 2022) and sequenced on an Illumina NextSeq 500 platform. For V144M/V144M and control samples (experiment 1), libraries were purified by gel size selection prior to sequencing. For A196V/A196L (Patient 10), A196V/A196L (Patient 11) and control samples (experiment 2), the library gel size selection step was omitted.

value: Human lymphoblastoid

value: A196V/A196L (Patient 11)


title: Raver1-/- BMDMs, TNF/TAK1-i, bio rep 1

city: WORCESTER

first: Egil

last: Lien

state: MA

address: 364 plantation st

institute: University of Massachusetts Chan Medical School

data_processing:
DolphinNext Platform
Samples were  quality-controlled using FragmentAnalysis
high-throughput sequencing reads were mapped with STAR v2.7.0 (39) (default parameters) to the GRCm38.p6 (mm10) reference genome (mouse_mm10_refseq ) and quantified using Kallisto.
Differential expression analysis was performed using DESeq2
Alternative splicing was quantified with rMATS v4.1.0 (40), scaffolded on the RefSeq mm10 annotations (downloaded from UCSG Genome Browser), with parameters “—libType fr-firststrand -- readLength 151 -variable-read-length.”
Assembly: mm10
Supplementary files format and content: comma-separated values files include normalized read counts for each sample
Supplementary files format and content: tab-delimited text files include alternative splicing events for each sample

source_name: BMDMs

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow harvested from femurs and tibia of 6–20-week-old mice, in DMEM supplemented with 10% fetal calf serum (FCS), 25 mM HEPES, and 10% L929 conditioned medium containing M-CSF for 6 days, then seeded in 6-well plates at 2 million cells per well.

extract_protocol:
RNA was extracted using the RNeasy RNA extraction kit (Qiagen).
A pair-end RNA-seq library was generated using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina).

treatment_protocol: BMDMs were untreated (NT), or stimulated with TNF (10 ng/ml) or TNF+TAK1-inhibitor (0.4 µM) for 1 hour.

value: BMDMs


title: Control_repl1_exp2

value: patient derived human lymphoblastoid cell line

value: Control (Experiment 2)


title: A196V-A196L_patient_11_repl3


title: DH12.6-33_ZT1_100-1


title: Control-3182-iGABA-shWT-BiolRep-3

description: Library name: 3182-DIV35-iGABA-shWT1-R3

value: hiPSC-derived-iGABA

value: Control-shRNA-WT-iGABA


title: Raver1-/- BMDMs, TNF/TAK1-i, bio rep 2


title: Control-553-iGLUT-shNEG-BiolRep-1

description: Library name: 553-DIV21-iGLUT-shNEG-R2

value: Non-targeting shRNA


title: DH12.6-33_ZT13_100-1

value: leaf


title: Control_repl2_exp2


title: DH12.6-33_ZT1_20-3

value: Water limited, 20% full capacity


title: A196V-A196L_patient_11_repl1


title: Control-3182-iGABA-shWT-BiolRep-2

description: Library name: 3182-DIV35-iGABA-shWT1-R2


title: Control-3182-iGABA-shWT-BiolRep-1

description: Library name: 3182-DIV35-iGABA-shWT1-R1


title: A196V-A196L_patient_10_repl3

value: A196V/A196L (Patient 10)


title: Control-553-iGLUT-shNEG-BiolRep-2

description: Library name: 553-DIV21-iGLUT-shNEG-R3

value: hiPSC-derived-GLUT


title: Control-3182-iGABA-shNEG-BiolRep-3

description: Library name: 3182-DIV35-iGABA-shNEG-R3


title: DH12.6-33_ZT19_100-3


title: Raver1-/- BMDMs, TNF, bio rep 1

value: TNF


title: A196V-A196L_patient_10_repl2


title: Raver1-/- BMDMs, TNF/TAK1-i, bio rep 3


title: DH12.6-33_ZT19_20-3


title: A196V-A196L_patient_10_repl1


title: Raver1-/- BMDMs, NT, bio rep 3

value: NT


title: Control-3182-iGABA-shNEG-BiolRep-2

description: Library name: 3182-DIV35-iGABA-shNEG-R2

value: Control


title: Control-3182-iGABA-shNEG-BiolRep-1

description: Library name: 3182-DIV35-iGABA-shNEG-R1


title: Raver1-/- BMDMs, TNF, bio rep 3


title: V144M-V144M_repl1


title: DH12.6-33_ZT19_20-1


title: V144M-V144M_repl2


title: Control-2607-iGABA-shWT-BiolRep-3

description: Library name: 2607-DIV35-iGABA-shWT-R3

value: WT targeting shRNA


title: DH12.6-33_ZT19_100-1

value: Well watered, 100% full capacity


title: Control-2607-iGABA-shWT-BiolRep-2

description: Library name: 2607-DIV35-iGABA-shWT-R2


title: WT BMDMs, TNF/TAK1-i, bio rep 3

value: WT


title: Raver1-/- BMDMs, TNF, bio rep 2


title: WT BMDMs, TNF/TAK1-i, bio rep 2


title: Control_repl1_exp1

value: Human lymphoblastoid

value: Control (Experiment 1)


title: Control_repl2_exp1

value: patient derived human lymphoblastoid cell line


title: Control-2607-iGABA-shWT-BiolRep-1

description: Library name: 2607-DIV35-iGABA-shWT-R1


title: DH12.6-33_ZT7_20-2


title: SN biological replicate donor C

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 110) and quantified at the transcript level using salmon
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM
Assembly: hg38
Supplementary files format and content: Expression_FPKM

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation
Libraries for transcriptome analysis were prepared using Smart-seq 2 protocol (PMID: 24056875)

value: Bone Marrow

value: segmented neutrophils


title: DH12.6-33_ZT19_100-2


title: Control-2607-iGABA-shNEG-BiolRep-2

description: Library name: 2607-DIV35-iGABA-shNEG-R3

value: hiPSC-derived-iGABA

value: Control-shRNA-WT-iGABA


title: DH12.6-33_ZT1_100-2

value: leaf


title: Control-2607-iGABA-shNEG-BiolRep-1

description: Library name: 2607-DIV35-iGABA-shNEG-R1

value: Non-targeting shRNA


title: SN biological replicate donor B


title: WT BMDMs, TNF/TAK1-i, bio rep 1

value: BMDMs


title: WT BMDMs, TNF, bio rep 3


title: DH12.6-33_ZT13_100-2


title: 973-5-iGLUT-DIV21-BiolRep-2

description: Library name: 973-5-iGLUT-DIV21-R2

data_processing:
Reads were first mapped by STAR v2.7.2a to a hg38/mm10 hybrid reference.
All reads unique mapped to hg38 were exracted.
Read counts of each gene were counted by featureCounts v2.0.3.
Assembly: hg38
Supplementary files format and content: Tab-delimite txt file of raw read counts

value: hiPSC-derived-GLUT

value: Case-vs-Control


title: DH12.6-33_ZT13_20-3

value: Water limited, 20% full capacity


title: Raver1-/- BMDMs, NT, bio rep 2

value: NT


title: WT BMDMs, TNF, bio rep 2

value: TNF


title: BC biological replicate donor C

value: band cells


title: Raver1-/- BMDMs, NT, bio rep 1


title: DH12.6-33_ZT1_20-1


title: WT BMDMs, TNF, bio rep 1

value: WT


title: MM biological replicate donor C

value: metamyelocytes


title: DH12.6-33_ZT7_20-1


title: 973-5-iGLUT-DIV21-BiolRep-1

description: Library name: 973-5-iGLUT-DIV21-R1


title: 973-5-iGABA-DIV35-BiolRep-3

description: Library name: 973-5-iGABA-DIV35-R3


title: WT BMDMs, NT, bio rep 3


title: Da2-44_ZT1_100-3

value: Darmor

value: Well watered, 100% full capacity


title: 973-5-iGABA-DIV35-BiolRep-2

description: Library name: 973-5-iGABA-DIV35-R2


title: MM biological replicate donor B

value: Bone Marrow


title: WT BMDMs, NT, bio rep 2


title: Da2-44_ZT13_100-2


title: WT BMDMs, NT, bio rep 1


title: MY biological replicate donor C

value: myelocytes


title: 973-5-iGLUT-DIV21-BiolRep-3

description: Library name: 973-5-iGLUT-DIV21-R3


title: MY biological replicate donor B


title: Cart_Repeated_24hr_rep2

city: Tokyo

first: Yusuke

last: Arino

address: 7-3-1 Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

data_processing:
After adapter sequences were removed using fastp(ver.0.23.4) , resulting RNA reads were mapped to the mouse reference genome using STAR(version 2.7.8a), with the reference index created from GRCm39.primaryassembly.genome.fa and gencode.vM33.annotation.gtf, both obtained from GENCODE. Expression levels were calculated using RSEM(ver.1.3.1).
Assembly: GENCODE(FASTA file:GRCm39.primaryassembly.genome.fa , GTF file:ncode.vM33.annotation.gtf)
Supplementary files format and content: tab-delimited text file includes gene count in each samples

source_name: Cartilage

extract_protocol:
Harvested tissues were homogenized, and total RNA was extracted using TRI Reagent (Molecular Research Center, Inc.). Total RNA was further purified with the Direct-zol RNA Kit (#R2062, Zymo Research, Irvine, CA) according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection) NEBNext® Ultra™ ll Directional RNA Library Prep Kit following manufacturer's protocols.

value: Cartilage


title: 973-5-iGABA-DIV14-BiolRep-3

description: Library name: 973-5-iGABA-DIV14-R3

value: hiPSC-derived-iGABA


title: 973-5-iGABA-DIV14-BiolRep-2

description: Library name: 973-5-iGABA-DIV14-R2


title: Da2-44_ZT13_100-3

value: leaf


title: BC biological replicate donor B


title: Cart_Single_24hr_rep2


title: Da2-44_ZT19_100-3


title: Cart_Repeated_24hr_rep1


title: NCP6 biological replicate donor C

value: neutrophil-committed progenitors 6


title: Da2-44_ZT7_20-3


title: Cart_Single_24hr_rep1


title: Cart_Single_4hr_rep2


title: NCP6 biological replicate donor B


title: 972-5-iGLUT-DIV21-BiolRep-3

description: Library name: 972-5-iGLUT-DIV21-R3


title: Da2-44_ZT1_100-1


title: 972-5-iGLUT-DIV21-BiolRep-2

description: Library name: 972-5-iGLUT-DIV21-R2


title: Da2-44_ZT13_20-3


title: Cart_Single_4hr_rep1


title: NCP5 biological replicate donor C

value: neutrophil-committed progenitors 5


title: Da2-44_ZT13_100-1


title: 972-5-iGLUT-DIV21-BiolRep-1

description: Library name: 972-5-iGLUT-DIV21-R1

value: hiPSC-derived-GLUT


title: Da2-44_ZT7_20-2


title: 972-5-iGABA-DIV35-BiolRep-3

description: Library name: 972-5-iGABA-DIV35-R3

value: Case-vs-Control


title: Cart_Single_1hr_rep2


title: PM biological replicate donor A

value: promyelocites


title: 973-5-iGABA-DIV35-BiolRep-1

description: Library name: 973-5-iGABA-DIV35-R1


title: Cart_Single_1hr_rep1


title: 973-5-iGABA-DIV14-BiolRep-1

description: Library name: 973-5-iGABA-DIV14-R1


title: Da2-44_ZT7_100-1


title: NCP5 biological replicate donor A


title: Da2-44_ZT7_100-2


title: Cart_Control_rep3


title: NCP4 biological replicate donor C

value: neutrophil-committed progenitors 4


title: 972-5-iGABA-DIV35-BiolRep-R1

description: Library name: 972-5-iGABA-DIV35-R1


title: NCP4 biological replicate donor B


title: Cart_Control_rep2


title: NCP6 biological replicate donor A


title: 972-5-iGABA-DIV14-BiolRep-3

description: Library name: 972-5-iGABA-DIV14-R3


title: 972-5-iGABA-DIV14-BiolRep-2

description: Library name: 972-5-iGABA-DIV14-R2


title: Cart_Control_rep1


title: NCP5 biological replicate donor B


title: Da2-44_ZT19_100-2


title: Syn_Repeated_24hr_rep3

source_name: Synovium

value: Synovium


title: NCP4 biological replicate donor A


title: Da2-44_ZT19_20-3

value: Water limited, 20% full capacity


title: 641-6-iGLUT-DIV21-BiolRep-3

description: Library name: 641-6-iGLUT-DIV21-R3


title: NCP3 biological replicate donor C

value: neutrophil-committed progenitors 3


title: Syn_Repeated_24hr_rep2


title: Da2-44_ZT19_20-2


title: 972-5-iGABA-DIV14-BiolRep-1

description: Library name: 972-5-iGABA-DIV14-R1


title: NCP3 biological replicate donor B


title: Syn_Repeated_24hr_rep1


title: NCP3 biological replicate donor A


title: 972-5-iGABA-DIV35-BiolRep-2

description: Library name: 972-5-iGABA-DIV35-R2


title: 641-6-iGLUT-DIV21-BiolRep-2

description: Library name: 641-6-iGLUT-DIV21-R2


title: NCP2 biological replicate donor C

value: neutrophil-committed progenitors 2


title: Da2-44_ZT19_100-1

value: Darmor


title: Syn_Single_24hr_rep3


title: 641-6-iGLUT-DIV21-BiolRep-1

description: Library name: 641-6-iGLUT-DIV21-R1


title: Da2-44_ZT1_20-2


title: Syn_Single_24hr_rep2


title: Da2-44_ZT19_20-1


title: NCP2 biological replicate donor B


title: 641-6-iGABA-DIV35-BiolRep-3

description: Library name: 641-6-iGABA-DIV35-R3


title: Da2-44_ZT1_100-2

value: Well watered, 100% full capacity


title: Syn_Single_24hr_rep1


title: Da2-44_ZT7_100-3


title: NCP2 biological replicate donor A

value: Bone Marrow


title: Syn_Single_4hr_rep3


title: 641-6-iGABA-DIV35-BiolRep-2

description: Library name: 641-6-iGABA-DIV35-R2


title: 641-6-iGABA-DIV35-BiolRep-1

description: Library name: 641-6-iGABA-DIV35-R1


title: Syn_Single_4hr_rep2


title: NCP1 biological replicate donor B

value: neutrophil-committed progenitors 1


title: NCP1 biological replicate donor A


title: NCP1 biological replicate donor C


title: Ca4-32_ZT13_100-1


title: 641-6-iGABA-DIV14-BiolRep-2

description: Library name: 641-6-iGABA-DIV14-R2


title: Syn_Single_4hr_rep1


title: 641-6-iGABA-DIV14-BiolRep-3

description: Library name: 641-6-iGABA-DIV14-R3


title: Syn_Single_1hr_rep3


title: H1, Lateral mesoderm differentiation protocol Rep3

city: Toronto

first: Rony

last: Chidiac

state: Ontario

address: 160 College St

department: CCBR

country: Canada

institute: University of Toronto

data_processing:
The transcript reads from FASTQ files were aligned to the Homo Sapiens transcriptome and quantified using Kallisto (Bray et al. 2016), following default parameters. Differential expression analysis was performed using the R Bioconductor DESEq2 package (Bray et al. 2016; Love, Huber, and Anders 2014) using default parameters with the independent filtering option disabled, with thresholds of raw fold change > 1.5 and adjusted P-value < 0.1
Assembly: hg19
Supplementary files format and content: normalized count matrix (meta data is provided as supplemental file)
Supplementary files format and content: DESEQ2_F2L6vsF7L6

extract_protocol:
H1 Cells were harvested with TrypLE Select enzyme (Gibco, 12-604-021) and neutralized using 10% FBS (Gibco, 12483020) in DMEM/F12. Then, RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
RNA-seq libraries were generated using TruSeq Stranded Total Library Preparation kit following manufacturer's protocol. Library quality was assessed with the 5200 Agilent Fragment Analyzer (ThermoFisher)

value: Human Embryonic stem cells

value: parental

value: Standard lateral mesoderm differentiation protocol (Adapted from Loh K. Cell 2016)


title: Ca4-32_ZT7_20-3

value: leaf


title: 641-6-iGABA-DIV14-BiolRep-1

description: Library name: 641-6-iGABA-DIV14-R1

value: hiPSC-derived-iGABA


title: H1, Lateral mesoderm differentiation protocol Rep2


title: Ca4-32_ZT19_100-3


title: Syn_Single_1hr_rep2


title: Syn_Single_1hr_rep1


title: 581-5-iGLUT-DIV21-BiolRep-3

description: Library name: 581-5-iGLUT-DIV21-R3

value: hiPSC-derived-GLUT


title: H1, Lateral mesoderm differentiation protocol Rep1


title: 581-5-iGLUT-DIV21-BiolRep-2

description: Library name: 581-5-iGLUT-DIV21-R2

value: Case-vs-Control


title: Syn_Control_rep3


title: Ca4-32_ZT19_100-1


title: H1, Paraxial mesoderm differentiation protocol Rep3

value: Standard paraxial mesoderm differentiation protocol (Adapted from Loh K. Cell 2016)


title: Da2-44_ZT13_20-2


title: Ca4-32_ZT13_100-3


title: Da2-44_ZT13_20-1


title: Syn_Control_rep2


title: 581-5-iGLUT-DIV21-BiolRep-1

description: Library name: 581-5-iGLUT-DIV21-R1


title: Da2-44_ZT1_20-1


title: 581-5-iGABA-DIV35-BiolRep-3

description: Library name: 581-5-iGABA-DIV35-R3


title: Syn_Control_rep1


title: H1, Paraxial mesoderm differentiation protocol Rep2


title: Ca4-32_ZT19_20-2


title: H1, Paraxial mesoderm differentiation protocol Rep1


title: Ca4-32_ZT1_20-1


title: H1, F7L6.13 Day4 Rep3

value: F7L6.13 (FZD7/LRP6) agonist


title: 581-5-iGABA-DIV35-BiolRep-1

description: Library name: 581-5-iGABA-DIV35-R1


title: Ca4-32_ZT1_20-2


title: DC_SSOP_6h_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38) reference genome using HISAT2 v.2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: lymph node

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq mRNA HT LP Kit (Takara Bio, Japan).

value: lymph node

value: dendritic cell

tag: strain

value: vaccination with SSOP


title: 581-5-iGABA-DIV14-BiolRep-3

description: Library name: 581-5-iGABA-DIV14-R3


title: DC_SSOP_6h_2


title: H1, F7L6.13 Day4 Rep2


title: Ca4-32_ZT1_100-3

source_name: leaf


title: DC_SSOP_6h_1


title: Ca4-32_ZT13_100-2


title: H1, F7L6.13 Day4 Rep1


title: 581-5-iGABA-DIV14-BiolRep-2

description: Library name: 581-5-iGABA-DIV14-R2


title: H1, F2L6.13 Day4 Rep3

value: F2L6.13 (FZD2/LRP6) agonist


title: 581-5-iGABA-DIV14-BiolRep-1

description: Library name: 581-5-iGABA-DIV14-R1


title: DC_SM102_ 6h_3

value: vaccination with SM102


title: Ca4-32_ZT7_100-3

value: Well watered, 100% full capacity


title: H1, F2L6.13 Day4 Rep2


title: DC_SM102_ 6h_2


title: Ca4-32_ZT7_20-1

value: Water limited, 20% full capacity


title: 553-3-iGLUT-DIV21-BiolRep-3

description: Library name: 553-3-iGLUT-DIV21-R3

value: Control


title: H1, F2L6.13 Day4 Rep1

value: Human Embryonic stem cells


title: DC_SM102_ 6h_1


title: Ca4-32_ZT1_100-2


title: DC_PBS_3

value: vaccination with PBS


title: H1, Day0 Rep3

value: parental


title: 553-3-iGLUT-DIV21-BiolRep-1

description: Library name: 553-3-iGLUT-DIV21-R1


title: Ca4-32_ZT13_20-1

value: leaf


title: 553-3-iGLUT-DIV21-BiolRep-2

description: Library name: 553-3-iGLUT-DIV21-R2


title: DC_PBS_2


title: 553-3-iGABA-DIV35-BiolRep-3

description: Library name: 553-3-iGABA-DIV35-R3

value: hiPSC-derived-iGABA


title: DC_PBS_1


title: Ca4-32_ZT19_20-1


title: Ca4-32_ZT19_20-3


title: 581-5-iGABA-DIV35-BiolRep-2

description: Library name: 581-5-iGABA-DIV35-R2


title: Lymph Node, SSOP_6h_3

source_name: Lymph Node

extract_protocol:
Total RNA was extracted from mouse lymph node tissue with RNA cultured cell Kit and TissueLyser II (Qiagen) following the manufacturer’s instruction.
Illumina library was prepared using TruSeq stranded mRNA Kit (Illumina).

value: Lymph Node


title: 553-3-iGABA-DIV35-BiolRep-2

description: Library name: 553-3-iGABA-DIV35-R2

value: Case-vs-Control


title: Ca4-32_ZT1_20-3


title: Lymph Node, SSOP_6h_2


title: 553-3-iGABA-DIV35-BiolRep-1

description: Library name: 553-3-iGABA-DIV35-R1


title: blood, cognitively normal control, 89y.o., female [DK22119_63]

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

institute: Ehime University

data_processing: The sequencing was done using the NextSeq 500/550 High Output Kit v2.5 (75 cycles) (Illumina, Sun Diego, CA, USA) on a NextSeq500 (Illumina) according to the manufacturer’s instructions. A p-value of 0.05 was set as the threshold for significantly differentially expressed genes (DEGs). Data analysis was conducted using CLC Genomics Workbench (QIAGEN, Germantown, MD, USA).

source_name: blood

extract_protocol:
Blood was collected into PaxGene Blood RNA Systems tubes (BD, Tokyo, Japan), and RNA was isolated according to the manufacturer’s protocol.
RNA-seq library preparation was performed using 145 ng total RNA from each sample. An RNA-seq library of each sample was prepared with the QuantiSeq 3’mRNA-Seq Library Prep Kit for Illumina (LEXOGEN, Greenland, NH, USA), and globin mRNA was removed using the Globin Block Modules for QuantSeq (LEXOGEN) according to the manufacturer’s protocol.

value: blood

tag: disease state

value: cognitively normal control

tag: age

value: female


title: 553-3-iGABA-DIV14-BiolRep-3

description: Library name: 553-3-iGABA-DIV14-R3

extract_protocol:
For the isolation of RNA, 2D cells were lysed using TRIzol (Life Technologies #15596026) and purified using the Qiagen miRNeasy Kit (Qiagen Cat# 74106) according to the manufacturer’s instructions.
Libraries were prepared via the Kapa Hyper library prep with ribo-erase (Roche #KK8541), according to the manufacturer's instructions.

tag: cell line


title: Lymph Node, SSOP_6h_1


title: Ca4-32_ZT7_100-2

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT


title: blood, cognitively normal control, 87y.o., female [DK22119_62]


title: 553-3-iGABA-DIV14-BiolRep-2

description: Library name: 553-3-iGABA-DIV14-R2

tag: cell type


title: blood, cognitively normal control, 92y.o., male [DK22119_61]

value: male


title: Ca4-32_ZT19_100-2

tag: genotype


title: blood, cognitively normal control, 85y.o., female [DK22119_60]


title: Lymph Node, SM102_6h_3

tag: treatment


title: Ca4-32_ZT7_100-1


title: Lymph Node, SM102_6h_2


title: H1, Day0 Rep2


title: 553-3-iGABA-DIV14-BiolRep-1

description: Library name: 553-3-iGABA-DIV14-R1

tag: time


title: H1, Day0 Rep1


title: 2607-4-iGLUT-DIV21-BiolRep-3

description: Library name: 2607-4-iGLUT-DIV21-R3

value: hiPSC-derived-GLUT

tag: experimental batch


title: blood, cognitively normal control, 76y.o., male [DK22119_59]

tag: tissue


title: 2607-4-iGLUT-DIV21-BiolRep-2

description: Library name: 2607-4-iGLUT-DIV21-R2


title: Lymph Node, PBS_3


title: Ca4-32_ZT1_100-1

tag: temperature


title: blood, cognitively normal control, 84y.o., male [DK22119_57]


title: Ca4-32_ZT7_20-2

tag: photoperiod


title: blood, cognitively normal control, 86y.o., male [DK22119_58]


title: Lymph Node, SM102_6h_1


title: 2607-4-iGLUT-DIV21-BiolRep-1

description: Library name: 2607-4-iGLUT-DIV21-R1


title: Lymph Node, PBS_2


title: Br2-31_ZT13_100-1

tag: timepoint (zt_=_hours_after_dawn)


title: blood, cognitively normal control, 76y.o., male [DK22119_56]

tag: Sex


title: Lymph Node, PBS_1


title: 2607-4-iGABA-DIV35-BiolRep-1

description: Library name: 2607-4-iGABA-DIV35-R1


title: 2607-4-iGABA-DIV35-BiolRep-2

description: Library name: 2607-4-iGABA-DIV35-R2


title: Br2-31_ZT13_20-3


title: blood, cognitively normal control, 88y.o., female [DK22119_54]


title: 2607-4-iGABA-DIV14-BiolRep-3

description: Library name: 2607-4-iGABA-DIV14-R3


title: Br2-31_ZT19_20-2


title: Brain, wildtype, 7month, 4 [Methyl-Seq]

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

library_source: genomic

data_processing:
Basecalling was done with RTA3 implementation software in the NovaSeq 6000 system.
Sequenced reads were trimmed using TrimGalore (v0.6.7) to remove adapters, low quality  reads, and reads <40 bp in length.
Cleaned reads were mapped to the mm10 mouse reference genome using Bismark (v0.23.1) and bowtie2 (2.2.5).
Mapped reads were assessed for changes in methylation between WT and HEM mice using methylKit (v1.22.0) using a 1000 bp sliding window.
Assembly: mm10
Supplementary files format and content: tab delimited text files containing DMR percent methylation information.
Library strategy: Enzymatic Methyl-Seq

molecule: genomic DNA

source_name: Brain homogenate

growth_protocol: Mice were provided with food and water ad libitum and housed in a 12-hour light/dark cycle.

extract_protocol:
The AllPrep DNA/RNA MiniKit (Qiagen; Germantown, MD; Product ID: 80204) was used to individually extract RNA and DNA from each flash-frozen lysate sample. All RNA and DNA samples were stored at -80°C for later use.
Enzymatic Methyl-seq samples were prepared  using NEBNext enzymatic methyl-seq kit by Yale University's Genomics Core facility

treatment_protocol: Microglia extraction was performed on brains dissected from the mice involved in this study. Microglia were selected for using IBA1 magnetic beat isolation. The protocol employed is thoroughly described in PMID: 34940397.

value: Brain homogenate

value: IBA1 selected microglia

value: 7 months

value: WT


title: Brain, wildtype, 7month, 3 [Methyl-Seq]


title: 2607-4-iGABA-DIV14-BiolRep-2

first: GANG

last: FANG

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 2607-4-iGABA-DIV14-R2

value: Control


title: Br2-31_ZT7_20-1

first: kathleen

last: Greenham

address: 1445 Gortner Avenue

institute: University of Minnesota

value: Water limited, 20% full capacity


title: blood, cognitively normal control, 87y.o., female [DK22119_52]


title: 2607-4-iGABA-DIV14-BiolRep-1

description: Library name: 2607-4-iGABA-DIV14-R1


title: blood, cognitively normal control, 89y.o., female [DK22119_53]


title: Brain, wildtype, 7month, 2 [Methyl-Seq]


title: Brain, mThy1-Asyn, 7month, 6 [Methyl-Seq]

value: HEM


title: iPSC-EC + Wnt, low shear, 2

city: Morgantown

first: Moriah

last: Katt

state: WV

address: 1306 Evansdale Dr

institute: West Virginia University

data_processing:
STAR
featurecounts
Assembly: hg38
Supplementary files format and content: csv, counts

extract_protocol:
Qiagen Miniprep RNA Kit
polyA enrichment

value: EC + Wnt

value: low shear


title: blood, cognitively normal control, 83y.o., female [DK22119_50]


title: iPSC-EC + Wnt, low shear, 3


title: Br2-31_ZT13_20-2

value: leaf


title: Br2-31_ZT7_100-2

value: Well watered, 100% full capacity


title: Brain, mThy1-Asyn, 7month, 5 [Methyl-Seq]


title: blood, cognitively normal control, 78y.o., male [DK22119_49]


title: iPSC-EC + Wnt, low shear, 1


title: Br2-31_ZT1_20-1


title: blood, cognitively normal control, 85y.o., female [DK22119_55]


title: Brain, mThy1-Asyn, 7month, 4 [Methyl-Seq]


title: iPSC-EC + Wnt, high shear, 3

value: high shear


title: blood, cognitively normal control, 90y.o., male [DK22119_48]

value: blood


title: Br2-31_ZT13_100-3


title: Brain, mThy1-Asyn, 7month, 3 [Methyl-Seq]


title: blood, cognitively normal control, 83y.o., female [DK22119_47]

value: cognitively normal control


title: iPSC-EC + Wnt, high shear, 2


title: Br2-31_ZT1_20-3


title: Brain, mThy1-Asyn, 7month, 2 [Methyl-Seq]


title: Br2-31_ZT19_100-1


title: Brain, wildtype, 7month, 1 [Methyl-Seq]


title: blood, cognitively normal control, 79y.o., female [DK22119_46]

value: female


title: blood, cognitively normal control, 80y.o., male [DK22119_51]

value: male


title: iPSC-EC + Wnt, high shear, 1


title: Br2-31_ZT1_100-1


title: Br2-31_ZT13_20-1


title: iPSC-EC, low shear, 3

value: EC


title: Brain, mThy1-Asyn, 7month, 1 [Methyl-Seq]

value: Brain homogenate


title: Br2-31_ZT1_100-3


title: blood, cognitively normal control, 81y.o., female [DK22119_44]


title: Brain, wildtype, 10month, 5 [Methyl-Seq]

value: IBA1 selected microglia

value: 10 months


title: iPSC-EC, low shear, 2


title: Br2-31_ZT7_100-1


title: Brain, wildtype, 10month, 4 [Methyl-Seq]

value: WT


title: iPSC-EC, low shear, 1


title: blood, cognitively normal control, 80y.o., male [DK22119_43]


title: Br2-31_ZT7_20-2


title: Brain, wildtype, 10month, 2 [Methyl-Seq]


title: iPSC-EC, high shear, 3


title: Brain, wildtype, 10month, 3 [Methyl-Seq]


title: Br2-31_ZT1_100-2


title: blood, mild cognitive impairment due to Alzheimer's disease, 83y.o., male [DK22119_40]


title: iPSC-EC, high shear, 2


title: blood, mild cognitive impairment due to Alzheimer's disease, 79y.o., female [DK22119_41]


title: blood, mild cognitive impairment due to Alzheimer's disease, 90y.o., male [DK22119_42]


title: Brain, wildtype, 10month, 1 [Methyl-Seq]


title: iPSC-EC, high shear, 1


title: Br2-31_ZT19_20-1


title: blood, mild cognitive impairment due to Alzheimer's disease, 89y.o., female [DK22119_38]


title: Brain, mThy1-Asyn, 10month, 5 [Methyl-Seq]


title: iPSC-"BMEC-like", low shear, 3

value: BMEC-like


title: Br2-31_ZT19_100-3


title: iPSC-"BMEC-like", low shear, 2


title: Br2-31_ZT13_100-2


title: blood, mild cognitive impairment due to Alzheimer's disease, 80y.o., male [DK22119_37]


title: Brain, mThy1-Asyn, 10month, 4 [Methyl-Seq]


title: blood, mild cognitive impairment due to Alzheimer's disease, 87y.o., female [DK22119_36]


title: iPSC-"BMEC-like", low shear, 1


title: Br2-31_ZT1_20-2

value: Water limited, 20% full capacity


title: Br2-31_ZT19_20-3


title: Brain, mThy1-Asyn, 10month, 2 [Methyl-Seq]

value: HEM


title: iPSC-"BMEC-like", high shear, 3


title: blood, mild cognitive impairment due to Alzheimer's disease, 77y.o., male [DK22119_35]


title: Br2-31_ZT7_100-3


title: Brain, mThy1-Asyn, 10month, 1 [Methyl-Seq]


title: blood, mild cognitive impairment due to Alzheimer's disease, 73y.o., male [DK22119_34]


title: iPSC-"BMEC-like", high shear, 2


title: Br2-31_ZT7_20-3


title: Brain, wildtype, 7month, 4

data_processing:
Basecalling was done with RTA3 implementation software in the NovaSeq 6000 system.
Sequenced reads were trimmed for adapter sequence and low-quality sequence using TrimGalore (v0.6.7)
Reads were mapped to the mm10 reference genome using Hisat2 (v2.2.1) sequence analysis program to identify transcripts.
Count values were calculated using featureCounts in Rsubread (v2.18.0)
Counts were normalized by DESeq2 (v1.44.0) and rlogTransformed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rlog transformed values for each sample in the matrix

extract_protocol:
The AllPrep DNA/RNA MiniKit (Qiagen; Germantown, MD; Product ID: 80204) was used to individually extract RNA and DNA from each flash-frozen lysate sample. All RNA and DNA samples were stored at -80°C for later use.
Total RNA was extracted from each sample with Qiagen RNeasyplus mini kitfollowing manufacturer's recommendations. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 7 months


title: iPSC-"BMEC-like", high shear, 1


title: Av1-30_ZT19_100-1

value: Aviso


title: blood, mild cognitive impairment due to Alzheimer's disease, 82y.o., male [DK22119_32]


title: Brain, wildtype, 7month, 3


title: BM MNCs, CCUS, CUS-0

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description:
scRNA-seq
bm_scrna_expr.rds

data_processing:
Sequencing analysis was performed using 10x Genomics’ CellRanger software (version 7.2.0). Fastq files were generated using the CellRanger MkFastq pipeline (version 7.2.0). Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger Count pipeline. The digital expression matrix was analyzed with the R package Seurat (version 5.1.0)
Assembly: hg38
Supplementary files format and content: raw count expression matrix

extract_protocol:
FACS-purified live BM MNCs or NK/T cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: Bone Marrow Mononuclear cells


title: Av1-30_ZT7_20-3

city: St. Paul

value: leaf


title: Brain, wildtype, 7month, 2


title: blood, cognitively normal control, 82y.o., male [DK22119_45]

value: blood


title: blood, mild cognitive impairment due to Alzheimer's disease, 86y.o., female [DK22119_31]


title: PDX tumor, palbociclib + NBI-961, replicate 4

city: Cleveland

first: Jessica

middle: Rose

last: Bobbitt

state: Ohio

address: 9620 Carnegie Ave N Bldg

department: Pathology

institute: Case Western Reserve University

data_processing:
Library preparations were sequenced on Illumina platform and paired-end reads were generated.
Paired end reads were analyzed with Partek Flow Software. STAR was used to align reads to Hg38 and DESeq2 was used to assess differentially expressed genes with a false discovery rate (FDR) of <0.5.
Assembly: hg38
Supplementary files format and content: read counts, txt

source_name: breast cancer

growth_protocol: Tumor pieces from TM00098 (The Jackson Laboratory, Bar Harbor, ME, USA), were orthotopically implanted into both inguinal mammary fat pads of adult female NOD/scid/γ (NSG) mice.

extract_protocol:
RNA was isolated from the TM00098 PDX tumors according to the manufacturer’s protocol (RNeasy Plus Mini Kit, Qiagen, Hilden, Germany).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Mice with palpable tumors (~300 mm3) were randomized into four treatment groups: vehicle (DMSO), palbociclib alone (50mg/kg), NBI-961 alone (10mg/kg), or the combination of palbociclib and NBI-961. Mice were treated 5 days a week for 22 days.

value: breast cancer

value: patient derived xenograft

value: triple negative breast cancer

value: Palbociclib + NBI-961


title: blood, mild cognitive impairment due to Alzheimer's disease, 76y.o., female [DK22119_33]

value: female


title: Av1-30_ZT19_20-2


title: PDX tumor, palbociclib + NBI-961, replicate 3


title: blood, mild cognitive impairment due to Alzheimer's disease, 80y.o., female [DK22119_30]


title: Brain, mThy1-Asyn, 10month, 3 [Methyl-Seq]

value: Brain homogenate

value: IBA1 selected microglia


title: Brain, wildtype, 7month, 1

value: WT


title: Av1-30_ZT13_100-3

value: Well watered, 100% full capacity


title: PDX tumor, palbociclib + NBI-961, replicate 2


title: Av1-30_ZT19_20-1

value: Water limited, 20% full capacity


title: blood, mild cognitive impairment due to Alzheimer's disease, 83y.o., female [DK22119_29]


title: Brain, mThy1-Asyn, 7month, 5

value: HEM


title: PDX tumor, palbociclib + NBI-961, replicate 1


title: blood, mild cognitive impairment due to Alzheimer's disease, 82y.o., male [DK22119_28]

value: male


title: Av1-30_ZT7_100-2

value: Aviso


title: PDX tumor, NBI-961, replicate 3


title: PDX tumor, Palbociclib, replicate 4

value: Palbociclib


title: Brain, mThy1-Asyn, 7month, 3

value: 7 months


title: PDX tumor, NBI-961, replicate 2


title: Av1-30_ZT1_20-1

value: leaf


title: Brain, mThy1-Asyn, 7month, 2


title: PDX tumor, NBI-961, replicate 1


title: blood, mild cognitive impairment due to Alzheimer's disease, 90y.o., female [DK22119_23]

value: blood


title: blood, mild cognitive impairment due to Alzheimer's disease, 85y.o., female [DK22119_26]


title: Av1-30_ZT7_100-3


title: Brain, wildtype, 10month, 4

value: 10 months


title: blood, mild cognitive impairment due to Alzheimer's disease, 82y.o., female [DK22119_24]


title: PDX tumor, Palbociclib, replicate 3

value: breast cancer

value: patient derived xenograft


title: Av1-30_ZT19_100-2


title: PDX tumor, Palbociclib, replicate 2

value: triple negative breast cancer


title: blood, mild cognitive impairment due to Alzheimer's disease, 85y.o., female [DK22119_25]

value: female


title: Av1-30_ZT1_20-3


title: Av1-30_ZT13_100-2


title: Av1-30_ZT1_100-2


title: blood, mild cognitive impairment due to Alzheimer's disease, 75y.o., male [DK22119_22]


title: Brain, mThy1-Asyn, 7month, 1

value: Brain homogenate


title: Brain, wildtype, 10month, 2

value: IBA1 selected microglia


title: Brain, mThy1-Asyn, 7month, 6


title: blood, Alzheimer's disease, 80y.o., male [DK22119_21]

value: Alzheimer's disease


title: blood, Alzheimer's disease, 80y.o., male [DK22119_20]


title: Brain, wildtype, 10month, 3

value: WT


title: Brain, mThy1-Asyn, 7month, 4


title: blood, mild cognitive impairment due to Alzheimer's disease, 87y.o., female [DK22119_27]


title: Brain, wildtype, 10month, 5


title: PDX tumor, Palbociclib, replicate 1


title: Av1-30_ZT7_100-1

value: Well watered, 100% full capacity


title: PDX tumor, vehicle, replicate 4

value: Vehicle


title: Av1-30_ZT13_20-3

value: Water limited, 20% full capacity


title: blood, Alzheimer's disease, 85y.o., female [DK22119_19]


title: blood, Alzheimer's disease, 93y.o., female [DK22119_17]


title: Brain, mThy1-Asyn, 10month, 3

value: HEM


title: Av1-30_ZT13_100-1

value: Aviso


title: oeIGF2BP3-3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit. . The short reads less than 16nt were also dropped.
clean reads were aligned to the GRCh38 genome by HISAT2 allowing 1 mismatch.
Uniquely mapped reads were used for gene reads number and fragments per kilobase of transcript per million fragments mapped (FPKM) calculation.
The R Bioconductor package DESeq2 was utilized to screen out the differentially expressed genes (DEGs). The P-value < 0.05 and fold change > 1.5 or < 0.67 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as described previously. In brief, ABLas detection of ten types of ASEs was based on the splice junction reads, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES and A5SS&ES. To assess RBP regulated ASE, Student’s t-test was performed to evaluate the significance of the ratio alteration of AS events. Those events which were significant at P-value cutoff corresponding to a false discovery rate cutoff of 5% were considered RBP regulated ASEs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: AGS cell

growth_protocol: To overexpress IGF2BP3, the pcDNA3.1-3xFlag-IGF2BP3 (NM_006547.3) was purchased from Youbio Biotech (Changsha PRC).

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads（Vazyme, N401）. The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605). Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Adaptor (N323). After purification of ligation product and size fractioning to 300-500bps, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: The AGS cell line (CL-0022, Procell Life Science & Technology Co., Ltd., China) were cultured at 37 ℃ with 5% CO2 in Ham's F-12 (PM150810, Procell, Wuhan, China) with 10% fetal bovine serum (FBS) (1009-141, Gibco, China), 100 μg/mL streptomycin, 100 U/mL penicillin. Plasmid transfection of AGS cells was performed using Lipofectamine 3000 (L3000015, Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for following experiments.

value: AGS cell

value: GF2BP3 overexpression in  AGS cells


title: blood, Alzheimer's disease, 83y.o., male [DK22119_15]

value: blood

value: male


title: PDX tumor, vehicle, replicate 3

value: breast cancer


title: Brain, mThy1-Asyn, 10month, 2

value: 10 months


title: PDX tumor, vehicle, replicate 1

value: patient derived xenograft

value: triple negative breast cancer


title: blood, Alzheimer's disease, 81y.o., male [DK22119_18]


title: Av1-30_ZT19_20-3

value: leaf


title: oeIGF2BP3-2


title: Brain, mThy1-Asyn, 10month, 1

value: Brain homogenate

value: IBA1 selected microglia


title: PDX tumor, vehicle, replicate 2

value: WT


title: Brain, mThy1-Asyn, 10month, 4


title: Brain, mThy1-Asyn, 10month, 5


title: Av1-30_ZT1_20-2


title: Av1-30_ZT13_20-2


title: Av1-30_ZT7_20-1


title: Sample_WT-3

city: Hangzhou

first: Yirong

last: Wu

state: 浙江省

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital

data_processing:
After passing the library inspection, the library preparations were sequenced on a NovaSeq 6000 platform (Chi-Biotech, Guangzhou, China) and 150 bp stand-specific paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: csv format file includes TPM values for each samples

source_name: Myocardium

extract_protocol:
ThemRNA-seq Library Prep kit (Vazyme, Nanjing, China, cat#NR612-02)wasusedtoprepareatranscriptomelibrarywith at least 1.5 μg total RNA.
The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used.A total of 1 µg total RNA per sample was used as input material for the mRNA library preparation. Most of Eukaryote 'mRNA have polyA tails, which are enriched by Oligo (dT) magnetic beads. Then, the obtained mRNA was randomly interrupted by bivalent cations, and the first strand of cDNA was synthesized in the 1st Strand Enzymes Reverse transcriptase system using the segmented mRNA as the template and the random oligonucleotide as the primer, and the second strand of cDNA was synthesized using the 2nd Strand Enzymes and dNTPs. The purified double stranded cDNA undergoes end repair, A-tailed addition, and sequencing connections to screen for cDNA of around 200-300bp. PCR amplification is performed and the PCR product is purified again, ultimately obtaining a library.And then, library quality was assessed on the Agilent 4200 TapeStation.

value: Myocardium

value: wild type

value: Ligation of left anterior descending branch


title: blood, Alzheimer's disease, 83y.o., female [DK22119_14]

value: Alzheimer's disease

value: female


title: blood, Alzheimer's disease, 88y.o., female [DK22119_13]


title: NC-3

value: AGS cell

value: AGS cell (control plasmid)


title: Brain, wildtype, 10month, 1


title: Av1-30_ZT13_20-1

value: Aviso

value: Water limited, 20% full capacity


title: blood, Alzheimer's disease, 87y.o., male [DK22119_12]

value: blood

value: male


title: blood, Alzheimer's disease, 90y.o., female [DK22119_16]


title: Av1-30_ZT1_100-1

value: Well watered, 100% full capacity


title: Sample_WT-2


title: Av1-30_ZT7_20-2


title: NC-2


title: Sample_ITIH5KD-3

value: ITIH5 knockdown


title: Sample_WT-1


title: blood, Alzheimer's disease, 83y.o., male [DK22119_10]


title: Av1-30_ZT1_100-3

value: leaf


title: blood, Alzheimer's disease, 82y.o., male [DK22119_11]


title: blood, Alzheimer's disease, 79y.o., female [DK22119_09]


title: CB3 TET2 KO

description:
Sample8
bulk RNA-seq
bulk_expr.csv

source_name: Cord Blood

value: Cord Blood

value: NK cells


title: CB3 DNMT3A KO

description:
Sample9
bulk RNA-seq
bulk_expr.csv


title: Sample_ITIH5KD-1


title: oeIGF2BP3-1

value: GF2BP3 overexpression in  AGS cells


title: Al1-29_ZT7_100-2


title: CB3 Cas9

description:
Sample7
bulk RNA-seq
bulk_expr.csv


title: Sample_ITIH5KD-2

value: Myocardium


title: blood, Alzheimer's disease, 91y.o., female [DK22119_07]


title: 5XFAD without the MR1/MAIT cell axis Both Male and Female

city: Indianapolis

first: Season

last: Johnson

state: Indiana

address: 950 W Walnut ST, R2 359 Research II

department: Microbiology and Immunology

institute: IU School of Medicine

data_processing:
CellRanger 7.0.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat was used for integrative analysis of the samples.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain Hippocampus

extract_protocol:
Brains were removed and hippocampi were sub-dissected and flash-frozen in dry ice, then stored at -80°C until the experiment. The 10x Genomics Chromium Nuclei Isolation Kit (PN-1000494, 10X Genomics, Pleasanton, CA) with 20mg of hippocampus.
The single nuclei analysis was performed using the 10X Chromium single cell system (10X Genomics) and the NovaSeq 6000 sequencer (Illumina, San Diego, CA). The final nuclei concentration of 700-1200/µL was chosen for targeted nuclei recovery of 10,000. Following the CG000204_ChromiumNextGEMSingleCell3'v3.1_Rev D (10X Genomics), nuclei suspension along with RT reagents, and the single-cell multiome gel beads and partition oil, was transferred onto a Next GEM Chip G in separate wells and the chip was loaded to the Chromium X Controller for GEM generation and barcoded, followed by RT reaction then cDNA synthesis and cDNA library preparation. The resulting cDNA libraries were sequenced separately, cDNA library for 28bp and 91bp paired end was sequenced on Illumina NovaSeq 6000.

value: Brain Hippocampus

value: pooled male and female

value: Brain Cells

value: 5XFAD x MR1 KO


title: Al1-29_ZT1_20-1


title: 5XFAD Mice Both Male and Female


title: blood, Alzheimer's disease, 90y.o., male [DK22119_06]

value: Alzheimer's disease


title: CB2 Cas9

description:
Sample4
bulk RNA-seq
bulk_expr.csv


title: blood, Alzheimer's disease, 83y.o., female [DK22119_05]

value: female


title: Al1-29_ZT1_100-3


title: CB2 TET2 KO

description:
Sample5
bulk RNA-seq
bulk_expr.csv


title: Cultured SVF cells, iWAT, scRNA seq

city: Beijing

first: Meng

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: 10x Genomics

data_processing:
Raw fastq sequencing data were processed using Cell Ranger 7.0.0 with the "--include-introns" option enabled to include reads mapping to the introns annotated in Ensembl, and the mm10 mouse reference genome was utilized to quantify gene expression levels.
Assembly: mm10
Supplementary files format and content: *barcodes.tsv.gz: gzipped tab-separated values (TSV) file containing unique cell barcodes. *DFAT_features.tsv.gz: gzipped tab-separated values (TSV) file containing feature (gene) information, including gene names and identifiers. *DFAT_matrix.mtx.gz: gzipped Matrix Market (MTX) file containing the sparse expression matrix with gene counts per cell, indexed by cell barcodes and features.

source_name: Adipose tissue

extract_protocol:
Adherent cells were gently washed 3 times with PBSto remove residual culture medium and debris. An appropriate amount of 0.25% Trypsin-EDTA(Gibco, Cat#25200-056) was added to ensure complete coverage of the cells, which were then incubated at 37°C for 3-5 minutes. Cell morphology changes were observed under a microscope, and when the cells became round and began to detach from the culture plate, the plate was gently shaken to facilitate cell detachment. Complete culture medium containing serum was added to terminate the dissociation process. Complete culture medium containing serum was added to terminate the dissociation process. The cell suspension was centrifuged at 450g for 10 minutes to obtain a cell pellet, which was then resuspended in sorting buffer supplemented with 2% FBS.
Isolated cells were stained with 7-AAD at a concentration of 5 μg/mL and subjected to FACS sorting. Number of cells were quantified with a Countstar Rigel S5 Automated Cell Counter. Approximately 20,000 cells were applied to the Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10x Chromium Controller using the Single-Cell 3′ Reagent Kit v3.1 (10x Genomics). The following program was used for GEM-Reverse Transcription: 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. The resulting emulsions were lysed for cDNA isolation and purification with the Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Scientific) and amplified with PCR. cDNA quality was assessed with an Agilent 2100 Bioanalyzer. cDNA amplicon size was optimized by enzymatic fragmentation and size selection. P5, P7, i7, and i5 sample indexes and TruSeq Read 2 (read 2 primer sequence) were added by end repair, A-tailing, adaptor ligation, and PCR, respectively. Final libraries containing the P5 and P7 primers were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads, aiming for a coverage of approximately 50,000 raw reads per cell.

value: Adipose tissue

value: Primary cultured cells

value: SVF cells


title: NC-1

value: AGS cell

value: AGS cell (control plasmid)


title: Al1-29_ZT19_100-3

value: Well watered, 100% full capacity


title: blood, Alzheimer's disease, 80y.o., male [DK22119_04]

value: blood

value: male


title: Cultured DFAT cells, iWAT, scRNA seq

description: 10x Genomics

value: DFAT cells


title: blood, Alzheimer's disease, 80y.o., male [DK22119_02]


title: blood, Alzheimer's disease, 91y.o., female [DK22119_08]