title: Control, 0 h, RNA-seq, r2

description: Library name: CTRL_0h_r2


title: Control, 72 h, r3

status: Public on Jul 09 2026

type: SRA

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Library name: CTRL_72h_r3

library_source: transcriptomic

data_processing:
Reads were aligned using STAR, default mode for paired-end data
Aligned reads were quantified using featureCounts
Differential expression analysis was performed using the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided as .txt file

molecule: total RNA

organism: Homo sapiens

source_name: B-ALL cell line

growth_protocol: BlaER cells and subclones were grown in suspension in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin, 1X L-glutamine and 0,1X β-mercaptoethanol.

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

treatment_protocol: To induce transdifferentiation, the BlaER cells with shAGO2.1, shAGO2.2 and shCTRL were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Cells were collected at 0, 72 and 144 hours post induction.

tag: tissue

value: B-ALL cell line

tag: cell line

value: B-ALL cell line with shCTRL

tag: cell type

value: B cell intermediate to iMac


title: Control, 144 h, r1

description: Library name: CTRL_144h_r1

value: iMac


title: Control, 72 h, r1

description: Library name: CTRL_72h_r1


title: Control, 0 h, r3

description: Library name: CTRL_0h_r3

value: B cell


title: Control, 0 h, r1

description: Library name: CTRL_0h_r1


title: AGO2 KD, Region 2, 144 h, r3

description: Library name: AGO2_KD2_144h_r3

value: B-ALL cell line with shAGO2-KD2


title: AGO2 KD, Region 2, 144 h, r1

description: Library name: AGO2_KD2_144h_r1


title: AGO2 KD, Region 2, 72 h, r3

description: Library name: AGO2_KD2_72h_r3


title: AGO2 KD, Region 2, 72 h, r2

description: Library name: AGO2_KD2_72h_r2


title: 2693269_JW_012

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

country: USA

institute: St Jude Children's Research Hospital

description: Library name: 2693269_JW_012

library_source: transcriptomic single cell

data_processing:
Single-cell RNA libraries, sequenced by 10x Genomics, were processed using CellRanger software (v7.0.0) with default parameters. The count function mapped the raw reads to the human reference genome GRCh38 and generated a gene expression count matrix. The filtered_feature_bc_matrix were used for downstream analysis in Seurat (V. 5.3.0) using R (V. 4.2.3). Seurat tutorial(https://satijalab.org/seurat/articles/seurat5_integration) was followed for downstream analysis, where batch effects were corrected using harmony integration method.
Assembly: hg38
Supplementary files format and content: filterd_featured_bc_matrix.h5

molecule: polyA RNA

source_name: hCD34 cells

growth_protocol: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) mobilized with G-CSF from healthy donors were expanded 7 days in StemSpan™ SFEM II with CD34⁺ Expansion Supplement, human LDL, and Penicillin-Streptomycin. Cells were then cultured with thrombopoietin (50 ng/mL, increased to 100 ng/mL after 3 days) to induce megakaryocyte differentiation. On day 14, cells were harvested.

extract_protocol:
Cells were processed for single cell RNA-seq via the 10X Genomics 3' v3.1 kit
Libraries were constructed via the 10X Genomics 3' v3.1 kit

treatment_protocol: For each experimental condition (DMSO vs. treatment; non-targeting vs. sgRNA), equal number of cells were allocated per group when thrombopoietin was added to the cells. The cells were cultured with thrombopoietin for 7 days and at the end of the 7 days, the cells were harvested.

value: hCD34 cells

tag: genotype

value: Wild type

tag: treatment

value: Revumenib

tag: batch


title: CnT_H3K27me3_K27MKO_Wk10_Rep2

status: Public on Jul 10 2026

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

library_source: genomic

data_processing:
*library strategy: CUT&TAG-Direct
Reads were aligned to the human hg38 (target genome) and E. coli K-12 MG1655 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, E. coli K-12 (MG1655)
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: DIPG-XIII

growth_protocol: DIPG-XIII cells were maintained in tumor stem medium as gliomaspheres in low attachment culture flasks in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&TAG-Direct was performed with anti-H3K27me3 (CST 9733). Tagmented genomic DNA was extracted using 1%SDS/Proteinase K
Released, tagmented DNA from ~50,000 starting cells was amplified using non-hot-start polymerase (NEB M0541S) using the following program: 58oC, 5 mins; 72oC, 5mins; 98oC 30s; (98oC 10s, 63oC 30s) x 12 cycles total, 72oC, 1min.

treatment_protocol: Differentiation was induced by treatment with DMEM/F-12 medium containing 10% FBS

value: DIPG-XIII

value: Glioma

value: Serum differentiation

tag: time

tag: cut&tag antibody


title: Single cell mRNA sequenicing of A549 perturbed cells, channel 1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

address: 600 16th street

institute: UCSF

description:
Library name: A549_ch1_WTS
mRNA library of single cell perturb seq experiment

data_processing:
STAR version 2.7.11b
Assembly: hg38
Supplementary files format and content: .H5AD files contain raw single cell mRNA counts, with cell filtering and guide calling
Supplementary files format and content: .MTX files countain cellXfeature (gene or guide depending on library) for each channel

source_name: Lung

extract_protocol:
10x 5'
Chromium Next GEM Single Cell 5' HT Kit v2

value: Lung

value: Basal

value: Single-cell perturb seq


title: HEK293T_siMTA3_sRNA_1

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: siMTA3_sRNA_1

data_processing:
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

extract_protocol:
small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of HEK293T cells treated with siRNA using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment . The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform


title: LN-229 cells, CP3 1000 nM, 24 h, biol rep 1

city: Chicago

first: Jingxin

last: Wang

address: Abbott Memorial Hall 210A, 947 E 58th St.

department: Section of Genetic Medicine

institute: University of Chicago

description:
Library name: Exp1_LN229_polyA_CP3_1000_1
Column 'Exp1_LN229_polyA_CP3_1000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

data_processing:
Reads were aligned to the human reference genome GRCh38 with STAR using two-pass mode per sample, using the Gencode v44 comprehensive gene annotation.
Gene-level read counts were generated with featureCounts (Subread) against Gencode v44 comprehensive gene models, in unstranded mode.
Intron-junction-level counts were generated with leafcutter (extract junctions from STAR-aligned BAMs; leafcutter_cluster.py to define junction clusters); the per-cluster numerator count matrix (`*_perind_numers.counts.gz`) is provided as a processed data file.
Assembly: GRCh38 (Gencode Release 44 comprehensive annotation)
Supplementary files format and content: Two file types are provided. (1) Gzipped tab-separated featureCounts gene-by-sample raw read-count tables (`Exp1_GeneCounts.tsv.gz`, `Exp2_GeneCounts.tsv.gz`): first 6 columns are Geneid/Chr/Start/End/Strand/Length followed by one column of integer counts per sample. (2) Gzipped space-separated leafcutter junction-cluster-by-sample numerator count tables (`Exp1_leafcutter_perind_numers.counts.gz`, `Exp2_leafcutter_perind_numers.counts.gz`): header row lists sample names; each data row has `chrom:start:end:cluster_id` followed by one integer per sample (junction-supporting reads).

growth_protocol: LN-229 glioblastoma cells were cultured in DMEM supplemented with 5% FBS, 1x ThermoFisher anti(biotic)-anti(mycotic), at 37 °C, 5% CO2. GM12878 lymphoblastoid cells were cultured in RPMI 1640 supplemented with 15% FBS, 1x ThermoFisher anti-anti, at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy column-based purification kit following the manufacturer's protocol.
Strand-specific polyA-enriched RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer's protocol.

treatment_protocol: Cells were treated with the indicated splicing-modulator compound (or DMSO vehicle) at the specified dose for 24 hours prior to harvest.

value: glioblastoma


title: AGO2 KD, Region 2, 0 h, r3

description: Library name: AGO2_KD2_0h_r3


title: AGO2 KD, Region 2, 0 h, r1

description: Library name: AGO2_KD2_0h_r1


title: AGO2 KD, Region 1, 144 h, r3

description: Library name: AGO2_KD1_144h_r3

value: B-ALL cell line with shAGO2-KD1


title: AGO2 KD, Region 2, 0 h, r2

description: Library name: AGO2_KD2_0h_r2

value: B-ALL cell line


title: LN-229 cells, CP3 1000 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 2

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_1000_2
Column 'Exp1_LN229_polyA_CP3PlusBPN_1000_2' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: CP3 at 1000 nM + constant 25 µM BPN15477 co-treatment (24 h)


title: AGO2 KD, Region 1, 144 h, r2

description: Library name: AGO2_KD1_144h_r2


title: AGO2 KD, Region 1, 144 h, r1

description: Library name: AGO2_KD1_144h_r1


title: AGO2 KD, Region 1, 72 h, r3

description: Library name: AGO2_KD1_72h_r3

value: B cell intermediate to iMac


title: AGO2 KD, Region 1, 72 h, r2

description: Library name: AGO2_KD1_72h_r2


title: AGO2 KD, Region 1, 72 h, r1

description: Library name: AGO2_KD1_72h_r1


title: TET2 KD, 0 h, RNA-seq, r2

description: Library name: TET2_KD_0h_r2

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using the RNase H to remove ribosomal RNA. The enriched mRNA was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE100 (read length).

treatment_protocol: BlaER cells with shTET2 and shCTRL were first pre-treated with doxycycline (1 µg/ml) for 48 hours. Next, to induce transdifferentiation cells were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Doxycycline (1 µg/ml) was re-added every 48 hours during the process. Cells were collected at 0, 72 and 144 hours post induction.

value: B-ALL cell line with shTET2

value: Doxycycline (1 µg/ml)


title: AGO2 KD, Region 1, 0 h, r3

description: Library name: AGO2_KD1_0h_r3

value: B cell


title: AGO2 KD, Region 1, 0 h, r2

description: Library name: AGO2_KD1_0h_r2


title: Control, 144 h, RNA-seq, r2

description: Library name: CTRL_144h_r2

value: B-ALL cell line with shCTRL

value: iMac


title: AGO2 KD, Region 1, 0 h, r1

description: Library name: AGO2_KD1_0h_r1


title: TET2_ChIP_FLAG_r2

description: Library name: TET2_FLAG_r2

data_processing:
Quality control of sequenced reads was assesed by FastQC
TrimGalore was used to remove adapter sequences. Trimmed reads were aligned using Bowtie2 and filtered with samtools
Duplicates reads were removed using picard and peak calling was performed using MACS2
bigwig tracks were generated using DeepTools bamCoverage (-normalizeUsing RPKM  -binSize 10)
Assembly: GRCh38
Supplementary files format and content: bigWig files used for browser exploration data
Supplementary files format and content: Annotated Excel files from the narrowPeak calling

extract_protocol:
ChIP experiments were performed with a modified protocol (from Sardina et al. Cell Stem Cell. 2018) for dual crosslinking.  Briefly, 50 million cells were first cross-linked with 2 mM DSG (Fisher Scientific) followed by 1% formaldehyde (Sigma) second crosslinking.  Chromatin was sheared to 100-300bp fragments and conjugated with 5 µg of anti-FLAG M2 antibody (Sigma) rotating ON at 4ºC.Finally, DNA was purified by phenol: chloroform:isoamyl alcohol (25:24:1) extraction and ethanol precipitated.
ChIP-seq libraries were prepared by an external sequencing service provider. In brief, the following steps were followed: (1) Take IPed-DNA and Input DNA for sample qualification. (2) DNA-end repair, 3'-dA overhang and adaptor ligation. (3) PCR amplification and size selection. (4) Library quality control; (5) Library circularization; (6) The library was amplified to make DNA nanoball (DNB); (7) Sequencing on DNBSEQ (DNBSEQ Technology) platform. Sequencing read Length: SE50

value: BLaER subclone harboring TET2-FLAG


title: TET2_ChIP_FLAG_r1

description: Library name: TET2_FLAG_r1


title: 4 WT_ip M1

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Peking University People’s Hospital

country: China

institute: Peking University People’s Hospital

description: Library name: WT_ip M1

data_processing:
Clean reads were mapped to the GRCm38 genome by Bowtie2. Samtools rmdup was used to remove potential PCR duplicates. The results were visualized using IGV_Win_2.3.92.
Assembly: GRCm38/mm10
Supplementary files format and content: xls

organism: Mus musculus

source_name: bone marrow

extract_protocol:
BMDMs from WT or ELF-1 KO mice were induced by LPS for 6 hours to obtain M1 macrophages for ChIP-seq assay. Samples were lysed with 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS, 1× protease inhibitor cocktail, and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200-500 bp). 20 uL chromatin was saved at −20 °C for input DNA, and 100ul chromatin was used for immunoprecipitation by anti-mouse ELF-1 antibodies (sc-133096 X, Santa Cruz).
The ChIP-seq assay was performed by Wuhan Igenebook Biotechnology Co. Ltd (China). Trimmomatic (version 0.36) was used to filter out low-quality reads.

value: bone marrow


title: 3 WT_input M1

description: Library name: WT_input M1


title: 2 Elf1_KO_ip M1

description: Library name: Elf1_KO_ip M1


title: TET2_ChIP_CTRL_r2

description: Library name: CTRL_r2


title: TET2_ChIP_CTRL_r1

description: Library name: CTRL_r1


title: GA80B4B8-02

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (TFS) by automatic loading of the cards using an Orbitor R2 robot to increase throughput.

data_processing:
For each RT-qPCR well, we examined a variety of quality control (QC) metrics exported by ExpressionSuite software. Cq values for miRNA amplifications were included in statistical analysis if they had an AmpScore ≥1.0 with CqConf ≥0.8. MiRNA amplifications (e.g., let-7b-5p) that showed performance slightly below those thresholds (either AmpScore ≥0.9 with CqConf ≥0.8, or CqConf ≥0.75 with AmpScore ≥1.0) had Cq values accepted for statistical analysis conditional on meeting other criteria for good amplification (strong consistency of Cq values across triplicate wells). For accepted amplifications we examined the appropriateness of the baseline separation from the recorded Cq value and compared our QC assessments with other quality flags exported by QuantStudio, finding nothing unusual. Amplifications with acceptable QC but Cq >35 were considered censored values and given special handling using censoring-aware methods in the analysis. Amplifications that did not meet the QC standards for accepted or censored amplifications were considered missing measurements, regardless of Cq value. Amplifications labeled "Undetermined" by QuantStudio were also considered missing measurements. As a final fidelity check we 1) examined the amplifications for the two negative control miRNAs (miR-1293 and miR-647) to verify that no sample had a Cq value recorded for either of those with acceptable QC, and 2) verified that the spike-in positive control (cel-miR-39-3p) and primary endogenous normalization control (miR-16-5p) were both completely observed with acceptable QC in all replicates for all samples. The other endogenous normalizer control miRNAs (miR-24-3p, miR-92a-3p, miR-204-5p) showed good performance, with expression of miR-24-3p and miR-92a-3p in 100% of samples and miR-204-5p in 77% of samples. Given our built-in redundancy of normalizer control miRNAs and model-based methods of normalization that can handle noninformative missing data, we considered this amount of normalizer measurement dropout acceptable.
For technical calibration, all raw Cq values were adjusted for RNA isolation differences via median-alignment of the cel‑miR‑39‑3p spike‑in control reactions as an exogenous calibration factor. This adjustment represented the largest contribution to the overall normalization, with 57% of the technical variance explained by differences in spike-in control values (Note that we define technical variance as the variance in average Cq values across samples.) After technical calibration, all Cq values for the cel‑miR‑39‑3p spike-in (being exactly aligned by median) were removed from the dataset and did not contribute to later normalization steps. Next, these technical calibrated Cq values were batch calibrated to remove residual artifacts attributed to processing order. We fit a linear mixed-effects regression model including the same 5-knot restricted cubic spline of the RT-qPCR run order as above, plus indicators for known abnormal sample or processing events (e.g., visible hemolysis), with PCR run batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Batch calibration adjustments were relatively minor for our dataset, accounting for 10% of the technical variance.
Calibrated Cq values were normalized using a mixed-effects model on the endogenous miRNA normalizer Cq values only. The model included quadratic effects of age (interaction effect of age with itself, to model the effect of age at differing ages rather than assuming the effect is linear for all ages), fully-interacted indicators for sex and diagnosis group to adjust out study factors (because we wish to retain these factors for analysis), and crossed random effects of miRNA and sample to model the miRNA-sample interaction. We used this model to estimate the residual differences between samples as BLUPs (best linear unbiased predictions). The BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples. The resulting normalized Cq values were recentered to the global median of the input Cq value distribution. This final normalization step accounted for 26% of the technical variance in the data. The remaining 7% of technical variance was unexplained. After normalization, 83% of the total Cq variance (expected between-miRNA variance plus signal and residual technical and noise variance) was attributable to differences in mean expression across miRNAs (expected variance), 9% was attributable to sample-miRNA interactions (the biological signal), and <1% to differences in mean expression across samples (the residual technical variance, meaning the normalization was highly successful); the remainder of ~7% is residual variance (the measurement noise). We verified that the normalized Cq values of the normalizer miRNAs themselves had essentially flat profiles and noted that the normalization achieved substantial variance reduction.
Censored Cq values are quantitatively unreliable because their measurement falls outside the linear range of the assay. These were treated as interval observations, defined as an unobserved value falling between an upper and a lower limit. For the purposes of regression on the Cq values as an outcome predicted by diagnosis status these can be handled as interval observations directly via modeling. However, when the Cq values are used as predictors of diagnosis status the interval observation must be collapsed to a single most-likely value falling within the interval. To accomplish this, we used a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA. For the Bayesian prior distribution on the mean level for the miRNA, we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a censored observation was taken as the posterior grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.98, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. (The mean overestimate was 0.95 Cq.)
Prior to imputation the normalized Cq values, both censored and uncensored, are converted to an expression scale using inverted Cq units so that positive values mark higher expression. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the censoring threshold of 35 (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Missing Cq values were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements for most purposes, but in this context the recorded Cq (with all normalization adjustments) was used as the lower bound and the maximum cycle number (40) as the upper bound. Finally, all the interval bounds were subtracted from the maximum cycle number of 40 to invert the scale.

label: FAM

source_name: total cell-free biofluid RNA

label_protocol: MiRNA was converted to cDNA as previously described using the TaqMan Advanced miRNA cDNA Synthesis kit (TFS). Briefly, 3 μL of total RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription. The resulting cDNA (5 μL) was added to a 14-cycle universal miR-amplification step. The miR-amplification reaction was diluted 1:10 with nuclease free water, 220 µL of the diluted cDNA was mixed with 220 µL of nuclease free water and 440 µL of TaqMan Fast Advanced master mix (TFS). The RT-qPCR mix (100 µL) was loaded into custom TaqMan Advanced Human miRNA Custom Cards.

extract_protocol: Total RNA was isolated from 100 μL of plasma using the MagMax Mirvana Total RNA Isolation Kit (Thermo Fisher Scientific, TFS) using a KingFisher Apex System (TFS) automated purification instrument following the manufacturer’s protocol. For the RNA isolation, the 289 plasma samples were processed in a total of 4 batches (3 plates x 80 samples = 240, 1 plate x 49 samples). On the first day, plasma samples were mixed with 5 µL of proteinase K and 45 µL of digestion buffer and incubated for 30 minutes at 65°C. 100 µL of lysis buffer containing 1% β-mercaptoethanol was added to each well, mixed and stored at -20°C overnight. The following day, the plate was thawed to room temperature and an exogenous cel-miR-39-3p spike-in control (TFS) was added at a final concentration of 3 pM, followed by the addition of 20 µL of magnetic isolation beads. Samples were mixed for 5 minutes using a plate shaker followed by the addition of 270 µL of isopropanol and brief mix. The sample plate as well as 4 wash plates (each containing 150 µL of wash buffer), a DNase plate containing 45 µL of Turbo DNase buffer and 2 µL of DNase, and an elution plate containing 50 µL of nuclease free water were all processed using the KingFisher Apex instrument. Following the DNase step, 50 µL re-binding buffer and 100 µL of isopropanol was added to each well and automation was resumed for the washing and elution steps. All isolations were completed within two consecutive days. Following the elution step, the miRNA concentration of a subset of samples from each batch (minimum of 30% of samples per batch across each plate) was measured using the Qubit miRNA Assay kit (TFS) and read using a Qubit 4.0 fluorometer (TFS) to ensure the isolation was consistent across the batch. Prior to the eluted RNA being frozen at -80°C until RT-qPCR, each plate of 80 RNA samples was divided into 2 plates of 40 RNA samples, as 40 is the maximum number of miRNA RT-qPCR assays that can be processed in a day, and the plate with 49 RNA samples was divided into 1 plate of 40 samples and 1 plate of 9 samples. Thus, the RT-qPCR was performed with the 289 eluted RNA samples in a total of 8 batches (7 x 40 RNA = 280, 1 x 9 RNA), with one batch being completed per day in unbroken succession to mitigate time drift in measurements.

tag: donor id

value: Plasma

tag: disease

value: AD

tag: Sex

value: Male

tag: age

tag: mmse

tag: anatomical location

value: Circulating blood

tag: sample collection method

value: Venous

tag: starting amount

tag: holding temperature


title: LG107_191

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

institute: Weill Cornell Medicine

description:
Library name: Sample27
mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: GRCm38 (mm10) for mouse tissue and GRCh38 (hg38) for human tissue
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

tag: tissue

value: hippocampus


title: FA80805Z-06

value: NC

value: Female


title: AA809W8M-02


title: LG107_168

description:
Library name: Sample25
mRNA expression in mouse hippocampus


title: EA80JJRL-01


title: Whole blood DNA methylation, NHW CONTROL, 70yo F, 207215830104_R01C01

type: genomic

first: Sebastián

last: Cruz-González

state: California

hyb_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip (EPIC v1.0, ~850K CpG sites) according to the manufacturer's standard Infinium HD Assay protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system to generate raw IDAT files.

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

source_name: whole blood

label_protocol: Bisulfite conversion of genomic DNA was performed prior to hybridization following standard protocols for the Illumina Infinium MethylationEPIC BeadChip array. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch.

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

tag: disease state

value: Healthy control

value: whole blood

tag: ethnicity

value: NHW

tag: cohort


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207215820046_R08C01


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I172

city: Tel Aviv

first: Lubna

last: Khair

address: Weizmann 6

country: Israel

institute: Sourasky medical center

description:
Library name: I172_S40
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.567delG, p.Gln189Hisfs*16; Age: 15; Sex: male; Sample ID: I172; Mutation group: 11; Family: v; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

data_processing:
Raw sequencing reads were quality-checked, adapter-trimmed, and aligned to the human reference genome (GRCh38) using Bismark in non-directional mode. CpG methylation calls were extracted using the Bismark methylation extractor. Methylation percentages were calculated as the number of methylated reads divided by the total reads covering each CpG site. Differentially methylated regions (DMRs) and differentially methylated CpGs (DMCs) were identified using the methylKit package in R after standard coverage filtering, removal of extreme coverage outliers, and false discovery rate (FDR) correction (FDR < 0.05).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include CpG methylation calls, methylation percentages, differentially methylated CpGs (DMCs), differentially methylated regions (DMRs), and methylKit output files generated from RRBS analysis.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from peripheral blood leukocytes using the Gentra Puregene Blood Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. For samples collected as saliva, genomic DNA was isolated using standard laboratory procedures. DNA concentration and purity were assessed prior to library preparation.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were prepared using the Zymo-Seq RRBS Library Prep Kit (Zymo Research, Irvine, CA, USA). Genomic DNA was quantified using a Qubit 4 fluorometer, digested with MspI, end-repaired, A-tailed, ligated to methylated adapters, and subjected to bisulfite conversion followed by PCR amplification. Library quality and fragment size distribution were assessed using an Agilent TapeStation 4200. Libraries were pooled equimolarly and sequenced on an Illumina NextSeq 2000 platform using paired-end 2 × 51 bp reads.

value: peripheral blood

tag: cell type

value: leukocytes

tag: genotype

value: COL7A1 c.567delG, p.Gln189Hisfs*16


title: sorted splenocytes, A20 CD11c-ko, HTO, 3 biological replicates

city: Zwijnaarde

first: Bart

last: Lambrecht

address: Technologiepark

department: IRC

country: Belgium

institute: VIB

description: Library name: KVD002_HTO

data_processing:
The Cell Ranger pipeline (10× Genomics, version 6.1.2) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2, and the i7 sample index for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, unique molecular identifiers filtering, and gene counting was performed using the Cell Ranger suite version 6.1.2 (10× Genomics) and Seurat. For further analysis, we used the filtered featurebarcode matrix generated by CellRanger (v6.1.2 10× Genomics).
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values and matrix files
Supplementary files format and content: Seurat Objects

source_name: Spleen

extract_protocol:
3 A20CD11c-ko mice and 3 littermate Tnfaip3fl/fl Itgax-Cre- mice were included for single cell sequencing, all female and 12 weeks old. Mice were injected IV with pentobarbital containing fluorescently labeled anti-CD45 antibodies to exclude circulating cells. To facilitate cell sorting, we carried out magnetic-activaded cell sorting (MACS) on enzymatically digested splenocytes to remove neutrophils, B and T cells from a portion of the splenocytes. Briefly, 80x106 splenocytes were stained with FITC-labeled CD3, CD19 and Ly-6G antibodies and Fc block for 30’. Following washing, 160 µL anti-FITC beads (Miltenyi Biotec; 130-048-701) were added for 15’ at 4°C. The resuspended cells were then passed through a LS column (Miltenyi Biotec; 130-042-401) in a magnetic field and the effluent was collected. All samples were manually counted and 4x106 cells were isolated and spun down. The cell pellet was resuspended and incubated for 30’ on ice with 50 µL of staining mix in PBS containing 0.04% BSA, fluorescently labeled antibodies, Fc block, TruStain FcX Block (BioLegend; 101320), the mouse cell surface protein antibody panel containing 160 oligo-conjugated antibodies and 9 TotalSeq-A isotype controls (TotalSeq-A, BioLegend) and TotalSeq-A cell hashing antibodies (BioLegend) diluted 1:1000. 35000 viable cells (a fixed number of CD45-, CD19+, CD3+, Ly6G+, CD11c or 120G8+ and residual CD45+ cells) were sorted per organ in BSA-coated tubes on FACSAria II and III (BD Biosciences). Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). Biological replicates were multiplexed per lane.
The DNA libraries were prepared using the GemCode Single Cell 3′ Gel Bead and Library kit, version NextGEM 3.1 (10× Genomics) according to the manufacturer's instructions with the addition of amplification primers (3 nM, 5′CCTTGGCACCCGAGAATT*C*C and 5′GTGACTGGAGTTCAGACGTGTGC*T*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein and/or hashtag oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 3′ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index Polymerase Chain Reaction (PCR) using Illumina's Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer's instructions.

value: Spleen

value: Splenocytes

value: A20fl/fl, CD11c Cre-Tg

tag: treatment

value: Spontaneous


title: EA808PNQ-11

value: Plasma


title: PWA19-0778

value: PD

value: Male


title: sorted splenocytes, A20 CD11c-ko, cDNA, 3 biological replicates

description: Library name: KVD002_cDNA


title: EA80B4DT-02

value: Circulating blood

value: Venous


title: sorted splenocytes, wild-type, HTO, 3 biological replicates

description: Library name: KVD001_HTO

value: A20fl/fl, CD11c Cre-neg


title: sorted splenocytes, wild-type, ADT, 3 biological replicates

description: Library name: KVD001_ADT


title: sorted splenocytes, wild-type, cDNA, 3 biological replicates

description: Library name: KVD001_cDNA


title: GA80743R-04

value: AD

value: Female


title: D2_Tc1_K4

city: wuhan

first: Jiayu

last: Song

address: wuhan

institute: WUHAN University

description: Library name: samples6

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstream analyses werebasedon the clean data with high quality.
Assembly: GRCm38
Supplementary files format and content: text files include raw read count

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted from Tc1 cells of indicated coditions cultured for 2 days using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen and lymph nodes

value: RASA3 KO


title: PWA10-0023


title: D2_Tc1_K3

description: Library name: samples5


title: BA80B8NT-04

value: NC


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2181

description:
Library name: I2181_S34
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: DDEB; Gene: COL7A1; Mutation: c.6100G>A, p.Gly2034Arg; Clinical severity: Severe; Age: 2; Sex: male; Sample ID: I2181; Mutation group: 9; Family: s; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes

value: COL7A1 c.6100G>A, p.Gly2034Arg

tag: batch


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB28

description:
Library name: EB28_S35
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: DDEB; Gene: COL7A1; Mutation: c.6100G>A, p.Gly2034Arg; Clinical severity: Mild; Age: 23; Sex: female; Sample ID: EB28; Mutation group: 9; Family: t; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_IgG_Control_TSM

data_processing:
Reads were aligned to the human hg38 (target genome) and Saccharomyces cerevisiae sacCer3 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, sacCer3
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN (Cleavage under targets and release using nuclease). Enriched genomic DNA fragments were extracted using Monarch PCR & DNA Cleanup columns (NEB T1030S).
3-15ng of genomic DNA was used for library construction. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

tag: cell line

value: DIPG-XIII

value: Glioma

value: WT

value: Serum differentiation

tag: time

tag: cut&run antibody


title: CnT_H3K27me3_ASCL1KO_Wk10_Rep1

tag: cut&tag antibody


title: D2_Tc1_K1

description: Library name: samples4


title: PWA13-0542

tag: donor id

value: Plasma

tag: disease

value: PD

tag: Sex

tag: age

tag: mmse


title: CA808WKC-04

tag: tissue

value: Male

tag: anatomical location

value: Circulating blood

tag: sample collection method

tag: starting amount

tag: holding temperature


title: D2_Tc1_W4

description: Library name: samples3

tag: genotype

value: wild type


title: D2_Tc1_W2

description: Library name: samples2


title: JA8083ZS-02

value: Venous


title: PWA11-0325


title: D2_Tc1_W1

description: Library name: samples1


title: JA80B4FK-02

value: AD


title: Chronic restraint stress mouse C8 dorsal striatum D1-enriched segment

city: Seoul

first: Jinhee

last: Bae

address: 5, Hwarang-ro 14-gil

country: South Korea

institute: KIST

description:
Library name: DS_D1_C8
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C8; paired with DS_D2_C8.

data_processing:
fastq.gz files were processed using the GeoMx NGS analysis pipeline, in which sequencing reads were aligned to the probe-specific GeoMx RTS_ID barcode whitelist and deduplicated using unique molecular identifiers to generate digital count conversion (DCC) files.
Deduplicated probe counts were imported into the GeoMx DSP Data Analysis Suite for segment-level quality control and downstream analysis.
Segment quality-control criteria included at least 1,000 raw reads, at least 80% stitched and trimmed reads, at least 50% alignment rate, at least 50% sequencing saturation, a geometric mean of negative probe counts of at least 1, no-template control counts below 2,000, tissue area of at least 1,000 square micrometers, and at least 200 nuclei per segment.
Underperforming probes were removed when their mean count was no greater than 10% of the total probe counts for the corresponding gene. Genes were excluded when their expression was below the limit of quantitation in more than 20% of segments. The limit of quantitation was calculated as the geometric mean of negative probes multiplied by the square of the geometric standard deviation of negative probes.
Filtered target-level count data were normalized using Q3 normalization.
Gene-level expression analyses were performed using log2-transformed Q3-normalized expression values.
Assembly: N/A; sequencing reads were aligned to GeoMx RTS_ID probe barcodes rather than to a reference genome. Probe-to-gene annotations are supplied in the accompanying PKC file.
Supplementary files format and content: DS_CRS_D1.D2_processed data.txt: tab-delimited Q3-normalized target-level expression values for all detected genes and all 38 D1- and D2-enriched segments; rows represent genes and columns represent unique library names.
Supplementary files format and content: Individual .dcc files contain deduplicated probe-level counts and RTS_ID barcodes for each GeoMx segment. The accompanying .pkc file contains the probe annotation and target information needed to interpret the RTS_IDs.
Library strategy: Spatial Transcriptomics

source_name: dorsal striatum

growth_protocol: Male heterozygous Drd2-Cre mice, B6.FVB(Cg)-Tg(Drd2-cre)ER44Gsat/Mmcd, were used at 11-13 weeks of age. Mice were singly housed under a 12-h reversed light/dark cycle, with lights off at 8:00 AM and lights on at 8:00 PM. Food and water were available ad libitum.

extract_protocol:
Mouse brains were fixed in 4% paraformaldehyde at 4°C for 24 h, sequentially dehydrated in ethanol, paraffin embedded, and sectioned at 5 μm thickness. RNAscope fluorescence labeling was performed using probes targeting Drd1 and Drd2 to define D1- and D2-enriched neuronal compartments. Sections were hybridized with the GeoMx Mouse Whole Transcriptome Atlas probe set. Photocleavable indexing oligonucleotides from each selected compartment were released by UV illumination and collected by microcapillary aspiration.
Photocleaved indexing oligonucleotides collected from each GeoMx segment were used for next-generation sequencing library preparation according to the GeoMx DSP workflow. Libraries were amplified, indexed, purified, pooled, and sequenced using an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice assigned to the chronic restraint stress group were restrained for 6 h per day for 21 consecutive days using a rectangular restraint device. Control mice were handled for approximately 3 min per day during the same period. Brains were collected 3 days after the final restraint session.

value: dorsal striatum

tag: cell type

value: Drd1-enriched neuronal compartment

value: male

tag: model

value: Chronic restraint stress mouse model

tag: treatment

value: Chronic restraint stress for 6 h/day for 21 consecutive days


title: BA807J7L-07

value: NC


title: Chronic restraint stress mouse C9 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C9
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C9; paired with DS_D2_C9.


title: Chronic restraint stress mouse C7 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C7
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C7; paired with DS_D2_C7.


title: PWA10-0038

value: Female


title: Chronic restraint stress mouse C6 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C6
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C6; paired with DS_D2_C6.


title: PWA19-0772


title: LG107_169

description:
Library name: Sample26
mRNA expression in mouse hippocampus

value: hippocampus


title: 1 Elf1_KO_input M1

description: Library name: Elf1_KO_input M1

value: bone marrow


title: Chronic restraint stress mouse C5 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C5
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C5; paired with DS_D2_C5.


title: AA807Z6F-09


title: PWA12-0444


title: Chronic restraint stress mouse C4 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C4
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C4; paired with DS_D2_C4.


title: Chronic restraint stress mouse C3 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C3
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C3; paired with DS_D2_C3.


title: Chronic restraint stress mouse C2 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C2
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C2; paired with DS_D2_C2.


title: GA808Q05-04


title: AGO2 KD, Region 2, 72 h, r1

description: Library name: AGO2_KD2_72h_r1

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

value: B-ALL cell line

tag: cell line

value: B-ALL cell line with shAGO2-KD2

value: B cell intermediate to iMac


title: Chronic restraint stress mouse C1 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_C1
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C1; paired with DS_D2_C1.


title: PWA10-0089

value: Plasma

value: PD


title: Control mouse N10 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N10
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N10; paired with DS_D2_N10.

value: Non-stressed control

value: Control handling for approximately 3 min/day for 21 consecutive days


title: CA809WBK-02

value: AD

value: Circulating blood

value: Venous


title: sorted splenocytes, A20 CD11c-ko, ADT, 3 biological replicates

description: Library name: KVD002_ADT

value: Spleen

value: Splenocytes

value: A20fl/fl, CD11c Cre-Tg

value: Spontaneous


title: HA80B4CX-02

value: NC

value: Female


title: Control mouse N9 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N9
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N9; paired with DS_D2_N9.

value: dorsal striatum

value: Drd1-enriched neuronal compartment

value: male


title: CA809FGN-03

value: Male


title: Control mouse N7 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N7
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N7; paired with DS_D2_N7.


title: Control mouse N8 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N8
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N8; paired with DS_D2_N8.


title: EA8091JC-02

value: Plasma


title: DLBC-03-016

value: DLB


title: Control mouse N6 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N6
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N6; paired with DS_D2_N6.

value: Non-stressed control


title: PWA10-0110

value: PD


title: Control mouse N5 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N5
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N5; paired with DS_D2_N5.

value: Control handling for approximately 3 min/day for 21 consecutive days


title: PWA18-0739

value: Circulating blood


title: JA808RKS-11

value: Venous


title: Control mouse N4 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N4
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N4; paired with DS_D2_N4.


title: Control mouse N3 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N3
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N3; paired with DS_D2_N3.


title: PWA11-0280


title: PWA10-0187


title: Control mouse N2 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N2
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N2; paired with DS_D2_N2.


title: PWA11-0238


title: KA807PQW-05


title: Control mouse N1 dorsal striatum D1-enriched segment

description:
Library name: DS_D1_N1
FFPE dorsal striatal Drd1-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N1; paired with DS_D2_N1.


title: Chronic restraint stress mouse C9 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C9
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C9; paired with DS_D1_C9.

value: Drd2-enriched neuronal compartment

value: Chronic restraint stress mouse model

value: Chronic restraint stress for 6 h/day for 21 consecutive days


title: Chronic restraint stress mouse C8 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C8
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C8; paired with DS_D1_C8.


title: HA808PZ0-04


title: MTA3,THP1,ML6, biol rep 2

description: Library name: MTA3_THP1_ML6_2

data_processing:
ATAC seq data are trimmed with Trim_Galore/0.6.5, aligned to genome GRCh38, sorted and indexed using Bowtie2/2.3.5.1 and SAMtools/1.9-IGB-gcc-4.9.4. Then unmapped reads, reads shorter than 20bp, and reads mapping to mitochondrial chromosomes are removed. Duplicated reads are removed using picard/2.9.4. Each replicate is downsampled to ~120 million reads to remove bias, using samtools view -s function. Reads counts at RNA central noncoding genes (gene body +-150bp) are extracted with bedtools coverage -counts BEDTools/2.26.0. Peaks are called with MACS2/2.2.5
ChIP-seq data were processed following a standardized pipeline. Raw paired-end reads were trimmed with Trim_Galore/0.6.5, and read quality was assessed using FastQC. Trimmed reads were aligned to the human reference genome GRCh38_noalt_as using Bowtie2/2.3.5.1, and resulting SAM files were converted to BAM, sorted, and indexed using SAMtools/1.9-IGB-gcc-4.9.4. Normalized signal tracks (20 bp bin size, smoothed over 60 bp) were generated with deepTools/3.2.1 using bamCoverage with RPGC normalization. Read coverage over RNA central noncoding genes (gene body +-150bp) s or custom-defined genomic windows was computed using BEDTools/2.26.0 with the coverage function. Peaks were identified using MACS2/2.2.5.
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

growth_protocol: THP−1 cells were obtained from ATCC (Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 106 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP−1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
ATAC seq samples of DMSO and 50nM Romidepsin treated THP1 cells  are prepared from 70k cells per sample using ATAC-Seq Kit (Cat #53156 Active Motif), following manufacturer's protocol for Cell Sample Preparation. Libraries are quantified using bioanalyzer and sequenced on a NovaSeq X Plus on a 25B lane with 2x150nt reads. for ChIP seq Equal numbers of THP-1 monocytes, THP-1 derived macrophages, and ML-60218 treated monocytes were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 × 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 min. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 min of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1× RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 s on, 60 s off; 20 additional cycles on a Bioruptor sonicator: 30 s on, 30 s off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled ChIP grade Protein G magnetic beads (Cell Signaling Technology). Antibody used in this study are: MTA3 (Proteintech, #14682-1-AP), MTA2 (Invitrogen, #PA1-41581), MTA1 (Proteintech, #30545-1-AP), MBD2 (Proteintech, #55200-1-AP), HDAC2 (ActiveMotif AbFlex, #91197), HDAC1 (Proteintech, #10197-1-AP), and CDK2AP1 (Proteintech, #13060-2-AP). 5 ug of antibody per ChIP was coupled to 60 uL of beads and rotated overnight with sheared chromatin at 4°C. Beads were then washed 5× in ChIP wash buffer (Santa Cruz), 1× in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65°C overnight, followed by digestion of RNA (30 min RNase (Cell Signaling Technology cat #7012), 1mg/exp incubation at 37°C) and digestion of protein (30 min, 30ug/1 exp proteinase K (Cell Signaling Technology cat #10012) incubation at 45°C). ChIP DNA was then purified on a minElute column (Qiagen), followed by DNA library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina) and size selection of 350-550 bp fragments via gel extraction (Qiagen). small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of THP-1 monocytes ± Romidepsin exposure using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment . The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform

treatment_protocol: THP-1 derived macrophages were collected after 72-h exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 min followed by cell wash in phosphate-buffered saline (PBS) buffer. THP-1 cells by treatment with RNA polymerase III inhibitor ML-60218 (Catalog# 557403-10MG, SigmaAldrich) at a final concentration of 25 μM or Romidepsin (FK 228)(Catalog# HY-15149, MedChemExpress) at a final concentration at 50 nM and cells collected at 2 h post-exposure followed by cell wash in PBS buffer.

tag: chip antibody


title: PWA11-0300


title: Chronic restraint stress mouse C7 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C7
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C7; paired with DS_D1_C7.


title: HA8095SB-03


title: Chronic restraint stress mouse C6 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C6
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C6; paired with DS_D1_C6.


title: PWA17-0673


title: FA80B8MN-04

value: AD


title: Chronic restraint stress mouse C4 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C4
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C4; paired with DS_D1_C4.


title: Chronic restraint stress mouse C5 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C5
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C5; paired with DS_D1_C5.


title: Chronic restraint stress mouse C3 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C3
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C3; paired with DS_D1_C3.


title: PWA11-0434


title: AD_Quinn_1


title: PWA11-0239


title: PWA19-0750


title: Chronic restraint stress mouse C1 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C1
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C1; paired with DS_D1_C1.


title: Control mouse N10 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N10
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N10; paired with DS_D1_N10.


title: Chronic restraint stress mouse C2 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_C2
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse C2; paired with DS_D1_C2.


title: GA80B8KK-02

value: NC


title: Control mouse N9 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N9
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N9; paired with DS_D1_N9.


title: Control mouse N8 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N8
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N8; paired with DS_D1_N8.


title: PWA11-0212


title: KA807X8D-03

value: Female


title: DA809PN9-02


title: Control mouse N4 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N4
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N4; paired with DS_D1_N4.

value: dorsal striatum


title: Control mouse N6 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N6
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N6; paired with DS_D1_N6.


title: PWA19-0764


title: Control mouse N3 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N3
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N3; paired with DS_D1_N3.


title: Control mouse N2 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N2
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N2; paired with DS_D1_N2.


title: Control mouse N1 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N1
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N1; paired with DS_D1_N1.


title: PWA11-0415


title: Paneth cells, P55WT, zinc deficient diet, rep 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

description:
Library name: WT_ZDD_9
none
WT_ZDD-9

data_processing:
checking read quality with fastqc v0.12.1 – no quality based preprocessing required
data were mapped with the STAR (2.7.10a) to the mouse reference genome/transcriptome (mm39/gencode v28) using default paremeters with following additions: --clip5pNbases 12 to remove a strong sequence bias at the 5’ end, --quantMode GeneCounts to obtain read counts per sample immediatly from STAR per sample read couns were merged into a count matrix and further processed in R using the DESeq2 libary
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%. Duo to the nature of the set up, conrol (PBS) samples that were also used in GSE237759 were merged into the dataset, as standard diet controls, to give a total n value of 6 (P55KO, normal food), 5 (P55WT, normal food) and 4 for the other groups. Batch correction was performed at the level of DESeq2 by adding a batch run parameter to the desig formula.
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: purified paneth cells

growth_protocol: mice were kept in an SPF animal house with ad libitum access to food and water

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
RNA was extracted using the RNeasy Plus Micro Kit according to the manufacturers instructions. RNA was shipped to VIB nucleomics core for library preparation and sequencing RNA-seq libraries were prepared using the illumina TruSeq Stranded mRNA kit using the manufacturers instructions

treatment_protocol: Mice were either given zinc deficient food for 7 eekd or kept on standard chow for the same period

value: purified paneth cells

tag: diet

value: Zinc deficient diet, 7 weeks


title: PWA11-0282

tag: donor id


title: PWA19-0749

tag: disease

value: Male


title: Paneth cells, P55WT, zinc deficient diet, rep 3

description:
Library name: WT_ZDD_8
none
WT_ZDD-8


title: PWA11-0227

value: Plasma

tag: Sex


title: PWA13-0546

tag: age


title: Paneth cells, P55WT, zinc deficient diet, rep 2

description:
Library name: WT_ZDD_11
none
WT_ZDD-11


title: PWA19-0753

tag: mmse


title: Paneth cells, P55WT, zinc deficient diet, rep 1

description:
Library name: WT_ZDD_10
none
WT_ZDD-10

tag: tissue


title: Paneth cells, P55WT, normal food, rep 1

description:
Library name: WT_ST_7
This sample was from the same group of mice used in GSE237759 (group Paneth cells, P55WT + PBS)
WT_ST-7

value: standard chow, 7 weeks


title: KA80B4JJ-02

tag: anatomical location


title: CA8099TM-03

tag: sample collection method


title: GA8082S2-07

tag: starting amount


title: Paneth cells, P55KO, zinc deficient diet, rep 4

description:
Library name: P55_ZDD_4
none
P55_ZDD-4


title: Control mouse N7 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N7
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N7; paired with DS_D1_N7.

value: male

value: Non-stressed control


title: PWA11-0228

value: PD

tag: holding temperature


title: DLBC-03-008

value: DLB

value: Circulating blood


title: AD_Quinn_5

value: Venous


title: Paneth cells, P55KO, zinc deficient diet, rep 1

description:
Library name: P55_ZDD_1
none
P55_ZDD-1

tag: genotype


title: Paneth cells, P55KO, normal food, rep 2

description:
Library name: P55_ST_6
This sample was from the same group of mice used in GSE237759 (group Paneth cells, P55KO + PBS)
P55_ST-6


title: Paneth cells, P55KO, zinc deficient diet, rep 2

description:
Library name: P55_ZDD_2
none
P55_ZDD-2


title: Paneth cells, P55KO, normal food, rep 1

description:
Library name: P55_ST_5
This sample was from the same group of mice used in GSE237759 (group Paneth cells, P55KO + PBS)
P55_ST-5


title: AA80865X-04


title: KA808S6T-02


title: Mouse cortex APOE3 astrocyte graft AD APP-80

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description:
Library name: AAM-03_L24
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)

data_processing:
Raw FASTQ files were quality-assessed with FastQC v0.11.9.
Reads were trimmed and filtered using Trimmomatic v0.39.
Ribosomal RNA reads were depleted using SortMeRNA v4.3.6.
After depletion of rRNA sequences, reads were aligned to the mouse reference genome (GENCODE M. musculus GRCm39 vM36) using HISAT2 v2.2.1.
Gene-level counts were quantified using Subread featureCounts v2.0.6. Only mouse-specific reads were retained (mean 25,973,659 mouse reads per sample). Differential expression analysis was performed with DESeq2 v1.44.0 in R v4.3.3, with RIN and total RNA input as covariates. Comparison: APOE4 AD mice vs APOE3 AD mice.
Assembly: GRCm39 (GENCODE vM36)
Supplementary files format and content: mouse_raw_counts_matrix.txt: gene-level raw read counts for mouse transcripts, one row per Ensembl gene ID, one column per sample.

source_name: cortex

extract_protocol:
Total RNA was extracted from 5 mg of cortical brain tissue using the NYZ Total RNA Isolation Kit (NZYTech, MB13402). RNA quantity was assessed using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32855) and RNA integrity was confirmed using the Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Chips (Agilent Technologies, 5067-1513). All samples exhibited RIN values ranging from 7.8 to 9.6 (one sample RIN N/A, DV200=69%).
Libraries were prepared using 10ng of total RNA input with the SMARTer Stranded Total RNA-seq Kit v3 - Pico Input Mammalian (Takara Bio, Cat. Nos. 634489-634492) and the SMARTer RNA Unique Dual Index Kit 24U (Takara Bio, Cat. No. 634451), following the manufacturer's user manual. Library quality and size distribution were verified on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626). Library average size: 380 bp.

value: cortex

value: mouse cortical tissue

tag: cell type

value: 7.5 months


title: HA80884K-03

value: NC


title: KA807L92-02


title: Mouse cortex APOE3 astrocyte graft AD APP-76

description:
Library name: AAM-03_L23
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)

value: AD


title: Mouse cortex APOE4 astrocyte graft AD APP-72

description:
Library name: AAM-03_L22
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: Mouse cortex APOE4 astrocyte graft AD APP-71

description:
Library name: AAM-03_L21
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: KA80896J-02

value: Female


title: HA80B8JT-02


title: BA809Q11-02


title: Mouse cortex APOE3 astrocyte graft AD APP-66

description:
Library name: AAM-03_L20
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: Mouse cortex APOE4 astrocyte graft AD APP-46

description:
Library name: AAM-03_L26
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)

value: 6 months


title: PWA19-0746


title: DLBC-03-024


title: Mouse cortex APOE3 astrocyte graft AD APP-78

description:
Library name: AAM-03_L12
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: Mouse cortex APOE4 astrocyte graft AD APP-73

description:
Library name: AAM-03_L11
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: PWA10-0011


title: Mouse cortex APOE4 astrocyte graft AD APP-70

description:
Library name: AAM-03_L10
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-70)


title: BA8076BX-02


title: PWA10-0157


title: HA8071LZ-02


title: Mouse cortex APOE4 astrocyte graft AD APP-69

description:
Library name: AAM-03_L09
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE4 astrocyte progenitors 6 months post-transplant (APP-69)


title: Mouse cortex APOE3 astrocyte graft AD APP-65

description:
Library name: AAM-03_L08
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE3 astrocyte progenitors 6 months post-transplant (APP-65)


title: Mouse cortex APOE3 astrocyte graft AD APP-64

description:
Library name: AAM-03_L07
Bulk RNA-seq of mouse cortical tissue from AD chimeric mouse engrafted with human iPSC-derived APOE3 astrocyte progenitors 6 months post-transplant (APP-64)


title: PWA12-0538


title: EA8077RX-04


title: Control mouse N5 dorsal striatum D2-enriched segment

description:
Library name: DS_D2_N5
FFPE dorsal striatal Drd2-enriched neuronal compartment isolated by RNAscope-guided GeoMx segmentation from mouse N5; paired with DS_D1_N5.

value: dorsal striatum

value: Drd2-enriched neuronal compartment

tag: model

value: Control handling for approximately 3 min/day for 21 consecutive days


title: AD_Quinn_2

value: Plasma


title: anti-PD1 treated day 8

city: Lund

first: Björn

last: Frendeus

state: Skane

address: Ideongatan 1

country: Sweden

institute: BioInvent International

description:
Library name: Sample10
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting anf aggregation were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes#v7-0-0)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Harvested tumors were cut into small (2-3 mm) pieces using scalpels. Tissue pieces were enzymatically digested using 0,5 mg/ml Liberase TM (Merck) and 200 kunitz/ml DNAse (Merck) for 2x5 min at 37 degrees with slight vortex in between. Digestion reaction was quenched with 5 mL of RPMI (containing 10% FCS) and cells were filtered through a 70 mm cell-strainer. Viable lymphocytes were isolated using Lympholyte-M Separation Media (Cedarlane) gradients. Lymphocytes were stained with viability dye and CD45 antibody and live CD45+ cells were sorted using a FACS AriaFusion (Becton Dickinson). Cells were counted (NucleoCounter NC-202, ChemoMetec) and fixed according to “10x sample fixation Protocol” from 10x Genomics and kept at -80 °C until analyzed using scRNA- seq.
The viable CD45+ cells were sorted using FACS and samples were fixed using 4% paraformaldehyde (PFA) for 20 hours at 4 °C, followed by long-term storage at –80 °C according to ‘10x Genomics’ flex fixation kit recommendations. In short, prior to library preparation, samples were thawed, washed, and hybridized with barcoded probe sets according to the Chromium Next-GEM Flex protocol (10x Genomics). Approximately 10k cells per sample were targeted for capture, and the pooled samples were loaded onto a Chromium X instrument using a Chip Q. The sequencing Libraries were sequenced on an Illumina NovaSeq 6000

value: Tumor

value: CD45 positive cells

value: 6-8 weeks old

tag: strain

value: BALB/c

tag: treatment

tag: time

value: day 8

tag: batch

value: batch 1


title: anti-CTLA4 treated day 8 rep

description:
Library name: Sample11
10x Genomics

value: anti-CTLA4 REP


title: PWA11-0374

tag: donor id

value: PD

value: Male

value: Circulating blood

value: Venous


title: anti-CTLA4 treated day 8

description:
Library name: Sample9
10x Genomics

value: Female


title: DLBC-03-017

tag: disease

value: DLB


title: TNFR2-5A05 treated day 8

description:
Library name: Sample8
10x Genomics

tag: Sex

value: TNFR2 5A05


title: PWA12-0520

tag: age


title: PWA11-0352

tag: mmse


title: TNFR2-3F10 treated day 8

description:
Library name: Sample7
10x Genomics

tag: tissue

value: TNFR2 3F10


title: PWA18-0738

tag: anatomical location


title: HA808T4F-08

value: NC

tag: sample collection method


title: LN-229 cells, DMSO vehicle, 24 h, biol rep 3

description:
Library name: Exp1_LN229_polyA_DMSO_NA_3
Column 'Exp1_LN229_polyA_DMSO_NA_3' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy column-based purification kit following the manufacturer's protocol.
Strand-specific polyA-enriched RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer's protocol.

tag: cell line

value: glioblastoma

value: DMSO vehicle (24 h)


title: DA80CH8J-02

value: Plasma

value: AD

tag: starting amount

tag: holding temperature


title: Isotype control day 8

description:
Library name: Sample6
10x Genomics

value: Tumor

tag: cell type

value: CD45 positive cells

value: 6-8 weeks old

value: BALB/c

value: Isotype Control


title: anti-PD1 treated day 2

description:
Library name: Sample5
10x Genomics

value: day 2

value: batch 1


title: PWA11-0210

value: PD

value: Male

value: Circulating blood

value: Venous


title: anti-CTLA4 treated day 2

description:
Library name: Sample4
10x Genomics

value: Female


title: DA8099RB-07

value: NC


title: GA807W5Q-07


title: TNFR2-5A05 treated day 2

description:
Library name: Sample3
10x Genomics

value: TNFR2 5A05


title: EA808SX3-08


title: TNFR2-3F10 treated day 2

description:
Library name: Sample2
10x Genomics

value: TNFR2 3F10


title: PWA10-0102

value: Plasma


title: Isotype control day 2

description:
Library name: Sample1
10x Genomics


title: D844

city: Bonn

first: Daniel Sebastian

last: Galvis Montes

address: Venusberg Campus 1

country: Germany

institute: Universitätsklinikum Bonn

description:
Library name: 542
Column name 542 in 2023-08-02-counts-ova-mch.txt

data_processing:
Fastp v0.23.2 was used for adapter trimming and removal of low-quality reads (parameters: --dont_overwrite --dup_calc_accuracy 6).
Salmon v1.8.0 was used for quantification with options: --validateMappings --gcBias.
Quantification data were imported with tximeta v1.14.1 and summarized to gene level.
Differential expression analysis was performed using DESeq2 v1.36.0 with surrogate variable adjustment by sva v3.44.0.
Assembly: GENCODE M29 (mouse) transcriptome and genome build was used.
Supplementary files format and content: tab-delimited text file includes gene-level raw counts for each sample

source_name: Hippocampus

extract_protocol:
Brains were quickly removed and the left hippocampus was dissected. Total RNA was isolated and purified using the RNeasy micro kit (Qiagen) according to the manufacturer’s protocol. The quality and integrity of total RNA was assessed using a Tapestation 2200 (Agilent Technologies). RNA was considered as intact with an RNA Integrity Number (RINe) > 7. High purity RNA was considered with a OD260/280=1.8-2.1 and OD260/230 > 1.5 values. After purification, . Sequencing was performed on a NovaSeq 6000 System (Illumina) using cycle paired-end sequencing.
mRNA was used for library preparation using the TruSeq RNA Library Prep (Illumina) according to the manufacturer’s protocol

value: Hippocampus

tag: time point

tag: genotype

value: OT-I/Rag-/-

value: rAAV-hSyn-OVA-mCherry


title: JA807NQL-10


title: FA809WTM-02

value: AD


title: D845

description:
Library name: 540
Column name 540 in 2023-08-02-counts-ova-mch.txt

tag: treatment


title: CA8098LK-02


title: D706

description:
Library name: 538
Column name 538 in 2023-08-02-counts-ova-mch.txt

value: rAAV-hSyn-mCherry


title: D705

description:
Library name: 536
Column name 536 in 2023-08-02-counts-ova-mch.txt


title: BA80C2MC-03


title: Paneth cells, P55KO, zinc deficient diet, rep 3

description:
Library name: P55_ZDD_3
none
P55_ZDD-3

value: purified paneth cells

tag: diet

value: Zinc deficient diet, 7 weeks


title: D851

description:
Library name: 534
Column name 534 in 2023-08-02-counts-ova-mch.txt

tag: batch


title: DLBC-03-009

tag: donor id

value: DLB


title: FA808RFZ-04

tag: disease


title: D843

description:
Library name: 532
Column name 532 in 2023-08-02-counts-ova-mch.txt


title: GA80BHF1-02

tag: Sex


title: AD_Quinn_4

tag: age


title: D667

description:
Library name: 530
Column name 530 in 2023-08-02-counts-ova-mch.txt


title: D661

description:
Library name: 528
Column name 528 in 2023-08-02-counts-ova-mch.txt


title: D722

description:
Library name: 526
Column name 526 in 2023-08-02-counts-ova-mch.txt


title: PWA11-0381

value: PD

tag: mmse


title: PWA10-0124

tag: tissue

value: Male


title: D720

description:
Library name: 524
Column name 524 in 2023-08-02-counts-ova-mch.txt


title: KA80CTX0-02

tag: anatomical location

value: Circulating blood


title: D696

description:
Library name: 520
Column name 520 in 2023-08-02-counts-ova-mch.txt


title: D703

description:
Library name: 518
Column name 518 in 2023-08-02-counts-ova-mch.txt


title: D702

description:
Library name: 516
Column name 516 in 2023-08-02-counts-ova-mch.txt


title: KA80C2DK-02

tag: sample collection method

value: Venous


title: D701

description:
Library name: 514
Column name 514 in 2023-08-02-counts-ova-mch.txt


title: PWA10-0147


title: D700

description:
Library name: 512
Column name 512 in 2023-08-02-counts-ova-mch.txt


title: PWA15-0620


title: EA8077CV-03


title: BEC-B544

description:
Library name: 492
Column name 492 in 2023-08-02-counts-ova-mch.txt


title: DA80BHJ6-02


title: D743

description:
Library name: 490
Column name 490 in 2023-08-02-counts-ova-mch.txt


title: BEC-B542

description:
Library name: 486
Column name 486 in 2023-08-02-counts-ova-mch.txt


title: D740

description:
Library name: 488
Column name 488 in 2023-08-02-counts-ova-mch.txt


title: BEC-B541

description:
Library name: 484
Column name 484 in 2023-08-02-counts-ova-mch.txt


title: DA807XHS-05

value: Female


title: AA807PY3-02


title: D684

description:
Library name: 482
Column name 482 in 2023-08-02-counts-ova-mch.txt


title: PWA10-0008


title: EA807Q06-03


title: WT_F9

description:
Library name: Sample24
mRNA expression in mouse hippocampus

value: hippocampus

value: Wild Type


title: PWA12-0473


title: WT_F5

description:
Library name: Sample23
mRNA expression in mouse hippocampus


title: WT_F4

description:
Library name: Sample22
mRNA expression in mouse hippocampus


title: PWA11-0217


title: Mouse_wt

description:
Library name: Sample21
mRNA expression in mouse hippocampus


title: PWA18-0740


title: Mouse_F3_146

description:
Library name: Sample20
mRNA expression in mouse hippocampus

value: G3 Terc -/-


title: Mouse_F1

description:
Library name: Sample19
mRNA expression in mouse hippocampus


title: GA8083DJ-13

value: Plasma

value: NC


title: LG145_136

description:
Library name: Sample17
mRNA expression in mouse hippocampus


title: Mouse-147

description:
Library name: Sample18
mRNA expression in mouse hippocampus


title: KA80CCDB-02


title: KA807K8L-03


title: LG145_134

description:
Library name: Sample16
mRNA expression in mouse hippocampus


title: AD_Quinn_10


title: LG145_132

description:
Library name: Sample15
mRNA expression in mouse hippocampus


title: LG180_864

description:
Library name: Sample8
mRNA expression in mouse hippocampus


title: FA809072-04


title: LG180_787

description:
Library name: Sample7
mRNA expression in mouse hippocampus

value: Ctrl


title: PWA11-0283


title: LG180_785

description:
Library name: Sample6
mRNA expression in mouse hippocampus


title: HA80BCPC-03


title: LG180_784

description:
Library name: Sample5
mRNA expression in mouse hippocampus


title: LG180_769

description:
Library name: Sample4
mRNA expression in mouse hippocampus


title: AA8086VQ-03


title: LG180_768

description:
Library name: Sample3
mRNA expression in mouse hippocampus


title: PWA12-0455


title: AA8088Z7-05


title: LG180_758

description:
Library name: Sample1
mRNA expression in mouse hippocampus


title: CA807CDR-03


title: Biol Rep 4 Tfr

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

institute: University Hospital Bonn

description:
Library name: 8983 Q3
Column name in Raw_counts_All_Samples.txt: DE68NGSUKBR147359

data_processing:
Raw sequencing reads in FASTQ format were subjected to quality control using FastQC (v0.12.1).
Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39).
Clean reads were aligned to the Mus musculus reference genome (GRCm39, Ensembl release 104) using HISAT2 (v2.2.1) with default parameters.
Read counts per gene were generated using featureCounts (v2.0.1) from the Subread package, based on Ensembl gene annotations.
Assembly: GRCm39 (Ensembl release 104)
Supplementary files format and content: Tab-delimited text file includes raw counts per gene for each sample.

source_name: CD4 T cells

growth_protocol: Treg, Tfr, and Tfh cell subsets were generated in vitro from naive CD4+ T cells obtained from GREAT.Smart-17A.FoxP3hCD2 triple-reporter donor mice.

extract_protocol:
After 3.5 days of cell culture, T cells were harvested, stained, and sorted on a BD FACSAriaFusion cell sorter for FoxP3+CXCR5– (Treg), FoxP3+CXCR5+ (Tfr), and Foxp3–CXCR5+(Tfh) cells among viable CD8–CD19–CD4+ lymphocytes using a 70-micron nozzle. RNA was isolated using TRIzol™ LS Reagent (Invitrogen, #10296028) according to the manufacturer’s instructions. RNA was cleaned up with a RNeasy Mini Kit (catalog #74104) according to the manufacturer’s instructions.
The sequencing library was prepared according to manufacturer´s guidelines with the QuantSeq FWD 3´-mRNA-Seq Kit from Lexogen using 50 ng total RNA as input. Libraries were single-end sequenced with 1x100 bp on a S1 flow cell of an Illumina NovaSeq 6000 instrument to a depth of 10 M raw reads on average at the NGS Core Facility of University Hospital Bonn

value: CD4 T cells

tag: culture condition

value: Tfr

value: GREAT (Ifngtm3.1Lky) Smart-17A (Il17atm1.1Lky) Foxp3hCD2 (Foxp3tm1(CD2/CD52)Shori)


title: HA808SG1-02

value: AD

tag: starting amount


title: Biol Rep 4 Tfh

description:
Library name: 8983 Tfh
Column name in Raw_counts_All_Samples.txt: DE25NGSUKBR147357

value: Tfh


title: DLBC-03-023

value: DLB

tag: holding temperature


title: Biol Rep 3 Treg

description:
Library name: 8982 Treg
Column name in Raw_counts_All_Samples.txt: DE63NGSUKBR147352

tag: cell type

value: Treg


title: Biol Rep 3 Tfr

description:
Library name: 8982 Q3
Column name in Raw_counts_All_Samples.txt: DE79NGSUKBR147355


title: KA80JJX3-03

value: Male


title: DLBC-03-011

value: Circulating blood


title: Biol Rep 3 Tfh

description:
Library name: 8982 Tfh
Column name in Raw_counts_All_Samples.txt: DE36NGSUKBR147353


title: PWA11-0202

value: PD

value: Venous


title: PWA13-0540

value: Female


title: Biol Rep 2 Tfr

description:
Library name: 8808 Q3
Column name in Raw_counts_All_Samples.txt: DE90NGSUKBR147351


title: AA807X29-07


title: GA809VMP-02


title: Biol Rep 2 Treg

description:
Library name: 8808 Treg
Column name in Raw_counts_All_Samples.txt: DE74NGSUKBR147348


title: PWA11-0440


title: KA808BG5-03


title: Biol Rep 1 Tfh

description:
Library name: 8807 Tfh
Column name in Raw_counts_All_Samples.txt: DE58NGSUKBR147345


title: PWA19-0774


title: D755

description:
Library name: 510
Column name 510 in 2023-08-02-counts-ova-mch-5d.txt

value: Hippocampus

tag: time point

value: OT-I/Rag-/-

value: rAAV-hSyn-mCherry


title: PWA11-0302

value: Plasma


title: D724

description:
Library name: 506
Column name 506 in 2023-08-02-counts-ova-mch-5d.txt

tag: genotype


title: BA8081QL-07

value: NC


title: Biol Rep 2 Tfh

description:
Library name: 8808 Tfh
Column name in Raw_counts_All_Samples.txt: DE47NGSUKBR147349

value: CD4 T cells


title: Biol Rep 1 Tfr

description:
Library name: 8807 Q3
Column name in Raw_counts_All_Samples.txt: DE04NGSUKBR147347

value: Tfr


title: D723

description:
Library name: 504
Column name 504 in 2023-08-02-counts-ova-mch-5d.txt

tag: treatment


title: PWA19-0776


title: Biol Rep 1 Treg

description:
Library name: 8807 Treg
Column name in Raw_counts_All_Samples.txt: DE85NGSUKBR147344

value: GREAT (Ifngtm3.1Lky) Smart-17A (Il17atm1.1Lky) Foxp3hCD2 (Foxp3tm1(CD2/CD52)Shori)


title: HA809886-02

value: AD


title: D787

description:
Library name: 502
Column name 502 in 2023-08-02-counts-ova-mch-5d.txt

value: rAAV-hSyn-OVA-mCherry


title: JA80C8G7-02


title: PWA11-0353


title: BA809C72-07


title: D745

description:
Library name: 508
Column name 508 in 2023-08-02-counts-ova-mch-5d.txt


title: D786

description:
Library name: 500
Column name 500 in 2023-08-02-counts-ova-mch-5d.txt


title: PWA10-0096


title: D726

description:
Library name: 498
Column name 498 in 2023-08-02-counts-ova-mch-5d.txt


title: D725

description:
Library name: 496
Column name 496 in 2023-08-02-counts-ova-mch-5d.txt


title: HA807L75-06


title: Wildtype-footshock replicate5 [Grin2b_KI_WT_S6]

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: All mice were housed and bred at the mouse facility of Korea Advanced Institute of Science and Technology (KAIST) and maintained according to the Animal Research Requirements of KAIST. All animals were fed ad libitum and housed under 12 h light/dark cycle. All procedures were approved by the Committee of Animal Research at KAIST (KAIST; KA2020-90).

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: strain

value: male

value: wildtype

value: Foot-shock


title: CA80B8LJ-02

extract_protocol: Total RNA was isolated from 100 μL of plasma using the MagMax Mirvana Total RNA Isolation Kit (Thermo Fisher Scientific, TFS) using a KingFisher Apex System (TFS) automated purification instrument following the manufacturer’s protocol. For the RNA isolation, the 289 plasma samples were processed in a total of 4 batches (3 plates x 80 samples = 240, 1 plate x 49 samples). On the first day, plasma samples were mixed with 5 µL of proteinase K and 45 µL of digestion buffer and incubated for 30 minutes at 65°C. 100 µL of lysis buffer containing 1% β-mercaptoethanol was added to each well, mixed and stored at -20°C overnight. The following day, the plate was thawed to room temperature and an exogenous cel-miR-39-3p spike-in control (TFS) was added at a final concentration of 3 pM, followed by the addition of 20 µL of magnetic isolation beads. Samples were mixed for 5 minutes using a plate shaker followed by the addition of 270 µL of isopropanol and brief mix. The sample plate as well as 4 wash plates (each containing 150 µL of wash buffer), a DNase plate containing 45 µL of Turbo DNase buffer and 2 µL of DNase, and an elution plate containing 50 µL of nuclease free water were all processed using the KingFisher Apex instrument. Following the DNase step, 50 µL re-binding buffer and 100 µL of isopropanol was added to each well and automation was resumed for the washing and elution steps. All isolations were completed within two consecutive days. Following the elution step, the miRNA concentration of a subset of samples from each batch (minimum of 30% of samples per batch across each plate) was measured using the Qubit miRNA Assay kit (TFS) and read using a Qubit 4.0 fluorometer (TFS) to ensure the isolation was consistent across the batch. Prior to the eluted RNA being frozen at -80°C until RT-qPCR, each plate of 80 RNA samples was divided into 2 plates of 40 RNA samples, as 40 is the maximum number of miRNA RT-qPCR assays that can be processed in a day, and the plate with 49 RNA samples was divided into 1 plate of 40 samples and 1 plate of 9 samples. Thus, the RT-qPCR was performed with the 289 eluted RNA samples in a total of 8 batches (7 x 40 RNA = 280, 1 x 9 RNA), with one batch being completed per day in unbroken succession to mitigate time drift in measurements.

value: Male

value: Circulating blood


title: Wildtype-footshock replicate4 [Grin2b_KI_WT_S5]


title: PWA18-0736

value: PD

value: Female

value: Venous


title: Wildtype-footshock replicate3 [Grin2b_KI_WT_S4]


title: DLBC-03-007

value: DLB


title: BEC-R385

description:
Library name: 494
Column name 494 in 2023-08-02-counts-ova-mch.txt

value: Hippocampus

value: OT-I/Rag-/-

value: rAAV-hSyn-mCherry

tag: batch


title: JA808VB8-05

tag: donor id

value: Plasma


title: EA807X3D-03

tag: disease


title: AA809LF3-03

tag: Sex


title: Wildtype-footshock replicate2 [Grin2b_KI_WT_S3]

tag: age


title: D683

description:
Library name: 479
Column name 479 in 2023-08-02-counts-ova-mch.txt


title: Wildtype-footshock replicate1 [Grin2b_KI_WT_S1]


title: Wildtype-control replicate6 [Grin2b_KI_WT_C6]

value: Control


title: KA808FWK-09

value: NC

tag: mmse


title: GA808G3D-03

tag: tissue


title: PWA10-0079

tag: anatomical location


title: Wildtype-control replicate5 [Grin2b_KI_WT_C5]


title: HA8098JD-02

value: AD

tag: sample collection method


title: Wildtype-control replicate4 [Grin2b_KI_WT_C4]

value: Brain


title: FA807N6L-03


title: CA808W2B-04


title: AA80B402-03


title: Wildtype-control replicate3 [Grin2b_KI_WT_C3]

value: male


title: DA808WLF-02


title: Wildtype-control replicate2 [Grin2b_KI_WT_C2]

value: wildtype


title: EA80C4M9-02


title: Wildtype-control replicate1 [Grin2b_KI_WT_C1]


title: EA8086SD-04


title: KA809DS9-02


title: Heterotype-footshock replicate6 [Grin2b_KI_HT_S6]

value: heterotype

value: Foot-shock


title: Heterotype-footshock replicate5 [Grin2b_KI_HT_S5]


title: JA8076MM-07

value: Male

value: Circulating blood


title: Heterotype-footshock replicate4 [Grin2b_KI_HT_S4]


title: DA809W9M-02


title: Heterotype-footshock replicate2 [Grin2b_KI_HT_S2]


title: Heterotype-footshock replicate3 [Grin2b_KI_HT_S3]


title: PWA13-0552

value: PD


title: PWA11-0380

value: Venous


title: Heterotype-footshock replicate1 [Grin2b_KI_HT_S1]


title: AA807GVW-03

value: Female


title: Heterotype-control replicate6 [Grin2b_KI_HT_C6]


title: Heterotype-control replicate5 [Grin2b_KI_HT_C5]


title: Heterotype-control replicate4 [Grin2b_KI_HT_C4]


title: HA80C6GF-02


title: AD_Quinn_6


title: FA80BN4V-02


title: Heterotype-control replicate3 [Grin2b_KI_HT_C3]


title: HA808GK1-08


title: KA8091CZ-02


title: PWA12-0533


title: Heterotype-control replicate2 [Grin2b_KI_HT_C2]


title: Heterotype-control replicate1 [Grin2b_KI_HT_C1]


title: FA8081SR-07


title: Wildtype-DCS-vehicle replicate6

value: vehicle


title: PWA18-0733


title: LG180_764

description:
Library name: Sample2
mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus


title: Wildtype-DCS-vehicle replicate5


title: CA80B8QV-07


title: PWA12-0531


title: Wildtype-DCS-vehicle replicate4


title: KA808P5Z-04


title: Wildtype-DCS-vehicle replicate3


title: DLBC-03-018

value: DLB


title: Wildtype-DCS-vehicle replicate2


title: Wildtype-DCS-vehicle replicate1


title: PWA10-0055

value: Plasma