title: BMC02428-001 MM End Induction 1st Draw

description:
Library name: BMC02428-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Caucasian


title: BMC02427-003 MM Pre-Treatment

status: Public on Jul 15 2026

type: SRA

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
Library name: BMC02427-003
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

library_source: transcriptomic

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Library strategy: CITE-seq

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
BMMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca automatic cell counter.  Individual samples are hashtagged with unique oligo barcodes and stained with an antibody dependent tag (ADT) panel and pooled. Pools are stained with a viability dye (FSV510) and sorted for live cells using BD Aria Cell Sorter. Live cells are then collected and diluted to appropriate concentrations for 3' CITEseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

tag: tissue

value: Bone Marrow

tag: cell type

value: BMMC

tag: subject id

tag: birth year

tag: Sex

value: Female

tag: race

tag: days since_first_visit

tag: visit

value: MM Pre-Treatment

tag: batch id

tag: sample bridging_control

value: FALSE


title: BMC02426-002 MM Post Transplant 90 Days

description:
Library name: BMC02426-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Male

value: MM Post Transplant 90 Days


title: SNI,DAY14,SAMPLE2

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Nanshitou Street, Haizhu District

department: Department of Anesthesiology

country: China

institute: Zhujiang hospital, Southern Medical University

description: Library name: SNI,DAY14,SAMPLE2

library_source: transcriptomic single cell

data_processing:
Raw gene expression matrices generated per sample using CellRanger were imported into R (version 4.0.0) and converted to a Seurat object using the Seurat R package (version 4.1.0)41. Dead cells and doublets were removed. The first, the total number of UMIs and genes, and percentage of UMIs derived from mitochondrial genome for each cell were counted. Then, Cells which had over 15% UMIs derived from mitochondrial genome were discarded. Next, the upper bound was calculated as mean plus two standard deviation (SD) and the lower bound as mean minus two SD for both the total UMIs and genes, respectively. Finally, Cells with total UMIs or genes outside of the upper and lower bounds were removed.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix fles

organism: Mus musculus

source_name: hippocampus

extract_protocol:
After successful establishment of the SNI model, mice were randomly selected for tissue sampling. The whole fresh hippocampus tissues were placed in sterile petri dishes and rinsed with 10 mL of 4 °C pre-chilled DPBS, repeated 1-2 times to remove residual tissue protection solution. The rinsed tissues were placed in a new petri dish. After adding type II collagenase working solution, the tissues were cut into small pieces of about 1-2 mm3. The cut tissues were transferred to a 50 mL centrifuge tube containing 5 mL of digestion solution and placed in a 37 °C water bath for shaking and digestion. After digestion, the digest was filtered through a pre-wetted 70 μm cell sieve. Thereafter, the filtrate was collected into a new 50 mL centrifuge tube. After washing with 10 mL of DPBS containing 2% FBS, the filtrate was collected into the same centrifuge tube. Following centrifugation at 900 g for 30 min at room temperature, the supernatant was discarded. The pellet was added to 5 mL of DPBS containing 2% FBS, and the cells were resuspended by gentle pipetting and mixing. After centrifugation and the supernatant discarded, 3 mL of pre-chilled red blood cell lysate was added to the cell pellet and incubated at room temperature for 3 min. After discarding the supernatant, the pellet was added to 5 mL of pre-chilled DPBS containing 2% FBS. The cell suspension was stained by trypan blue and was counted using Countess® II Cell Counting. If the cell viability was more than 80%, 10× Genomics sample processing was carried out.
The prepared cell suspension, 10× barcode gel magnetic beads and oil were added to different chambers of Chromium Chip B respectively, and Gel Beads-Emulsion (GEM) was formed through the microfluidic cross system. The GEM was transferred to the PCR machine for reverse transcription, with 30 nt oligo-dT reverse transcription primers on the gel magnetic beads. The poly-A RNA in cells was reverse transcribed into first strand cDNA with barcode and unique molecular identifiers (UMI) information. After magnetic bead purification of first-strand cDNA, the cDNA was amplified by RT-PCR. Afterwards, amplified cDNA was digested and fragmented, and the optimal fragment was screened with magnetic beads. The cDNA library containing P5 and P7 adapters was prepared by end-repairing, adding A, and connecting Read 2 sequencing primers with adapters. Following purification, the concentration of cDNA was measured using Qubit and fragment size was measured using Agilent 2100.The libraries were sequenced on Novaseq 6000.

value: hippocampus

value: ALL CELL

tag: treatment

value: SNI


title: SNI,DAY21,SAMPLE1

description: Library name: SNI,DAY21,SAMPLE1


title: BMC02425-001 MM End Induction 1st Draw

description:
Library name: BMC02425-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: MM End Induction 1st Draw


title: SNI,DAY14,SAMPLE1

description: Library name: SNI,DAY14,SAMPLE1


title: BMC02424-001 MM Pre-Treatment

description:
Library name: BMC02424-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SNI,DAY7,SAMPLE2

description: Library name: SNI,DAY7,SAMPLE2


title: BMC02422-002 MM End Induction 1st Draw

description:
Library name: BMC02422-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: BMC02423-001 MM Post Transplant 90 Days

description:
Library name: BMC02423-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SNI,DAY7,SAMPLE1

description: Library name: SNI,DAY7,SAMPLE1


title: SNI,DAY3,SAMPLE3

description: Library name: SNI,DAY3,SAMPLE3


title: BMC02421-002 MM Pre-Treatment

description:
Library name: BMC02421-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: SNI,DAY3,SAMPLE2

description: Library name: SNI,DAY3,SAMPLE2


title: BMC02420-002 MM Pre-Treatment

description:
Library name: BMC02420-002
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: scRNA-seq of UniCVac tumor

city: Shanghai

first: wang

last: wanting

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: scRNA_UniCVac

data_processing:
Raw sequencing data (FASTQ files) were processed, aligned to the mm10 mouse (or hg38 homo sapiens) reference genome, and quantified using the official 10x Genomics Cell Ranger pipeline.
Assembly: mm10; hg38
Supplementary files format and content: MTX and TSV files containing raw UMI counts per cell

molecule: polyA RNA

source_name: tumor

extract_protocol:
Freshly excised tumors were mechanically minced and enzymatically digested using a tumor dissociation kit containing Collagenase IV and DNase I at 37°C. The digested cell suspensions were passed through a 70um cell strainer. Red blood cells were lysed, and dead cells were removed to ensure high cell viability (>80%) prior to sequencing.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller to generate single-cell gel beads-in-emulsion (GEMs). Single-cell RNA-seq libraries were constructed using the Chromium Single Cell 3' Reagent Kits (10x Genomics) according to the manufacturer's official protocol.

value: tumor


title: scRNA-seq of control tumor

description: Library name: scRNA_control


title: OE_ola-24_rep2

city: Macau

first: Cuiting

last: Zhang

address: Taipa

institute: University of Macau

description: Library name: OE_ola-24_rep2

data_processing:
The reads were aligned against GRCh38 (hg38) via HISAT2. FeatureCounts was used to quantification of reads that mapping to each gene and differential expression analysis was conducted by DESeq2.
Assembly: hg38
Supplementary files format and content: csv files include raw counts of each sample.

source_name: Cell line

extract_protocol:
TRIzol reagent was applied to extract total RNA. After RNA extraction, assess the concentration and integrity of the product by Agilent 2100 Bioanalyzer.
NEBNext Ultra™ II RNA Library Prep Kit for Illumina was used for library construction as per the manufacturer’s instructions.

value: Cell line

tag: cell line

value: Breast cancer cells

tag: genotype

value: BRCA1 overexpression

value: Olaparib


title: OE_ola-24_rep3

description: Library name: OE_ola-24_rep3


title: OE_ola-24_rep1

description: Library name: OE_ola-24_rep1


title: Hippocampus, KA, H3K18la,ChIP, rep3

city: chongqing

first: yuan

last: meng

address: No. 1 Youyi Road, Yuzhong District

department: Department of Neurology

institute: The First Affiliated Hospital  of Chongqing Medical University

description:
Library name: Hippo_KA_H3K18la_ChIP_rep3
H3K18la ChIP-seq in mouse hippocampus

library_source: genomic

data_processing:
Raw sequencing reads in FASTQ format were processed using fastp (v0.20.0) for quality control. Adapter sequences, low-quality reads, poly-G sequences, and reads containing more than 5 ambiguous bases (N) were removed. Reads shorter than 15 bp after filtering were discarded.
Clean reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.2.0) with default parameters.
Only uniquely mapped reads were retained, and PCR duplicates were removed.
Peak calling was performed using MACS2 (v2.2.8) with input samples as control, and peaks with q-value < 0.05 were retained.
Peak annotation was performed using ChIPseeker (v1.34.1).
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: Hippocampus tissue

extract_protocol:
Tissue samples (sectioned into ~1 mm slices) were fixed in fixation buffer (PBS supplemented with 1% formaldehyde) for 10 min at room temperature with gentle agitation. Glycine was then added directly to a final concentration of 125 mM to quench the fixation. Samples were centrifuged, the supernatant was removed, and the tissue was washed twice with PBS.The tissue was subsequently resuspended in lysis buffer (25 mM Tris-HCl, 0.5% SDS, 5 mM EDTA, and protease inhibitors) and homogenized, followed by lysis on ice for 10 min. Genomic DNA was then fragmented to 100–500 bp using a Covaris E220 ultrasonicator.
Genomic DNA was transferred to a new pre-chilled microcentrifuge tube, and an equal volume of IP dilution buffer was added. A 20 μL aliquot was reserved for input control and Western blot analysis. The remaining lysate supernatant was divided into two portions and incubated with antibody- or IgG-conjugated magnetic beads overnight at 4°C with rotation. The beads were sequentially washed once with low-salt wash buffer, once with high-salt wash buffer, and once with LiCl wash buffer. After each wash, samples were centrifuged at 2,000 × g for 1 min, and the supernatant was removed. DNA was eluted by adding 120 μL elution buffer and incubating at 30°C with gentle vortexing for 15 min. Samples were briefly centrifuged, placed on a magnetic rack, and the supernatant was transferred to a new 1.5 mL tube. Proteinase K (2 μL, 20 mg/mL) was added, followed by incubation at 60°C with shaking for 1 h. DNA was purified using a DNA purification kit. The recovered DNA was used for library construction with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA; Cat. No. E7645L). End repair was performed by adding End Repair Reaction Buffer (10×) and End Prep Enzyme Mix, with incubation at 20°C for 30 min and 65°C for 30 min. Adaptor ligation was carried out by adding NEBNext Adaptor and Blunt/TA Ligase Master Mix, followed by incubation at 20°C for 15 min. USER Enzyme was then added to remove uracil bases from the adaptor, with incubation at 37°C for 15 min. A 1× volume of magnetic beads was directly added for purification, followed by 10 cycles of PCR amplification using Universal PCR Primer and Index (X) Primer. PCR conditions were as follows: initial denaturation at 98°C for 10 s; denaturation at 98°C for 10 s, annealing at 65°C for 30 s, and extension at 72°C for 30 s. The amplified libraries were size-selected and purified using AMPure XP Beads to obtain sequencing-ready libraries. Library quality was assessed by Qubit quantification and High Sensitivity DNA chip analysis. Finally, paired-end sequencing (PE150) was performed on an Illumina NovaSeq™ 6000 or NovaSeq X Plus platform.

treatment_protocol: Mice received stereotaxic injection of either saline or kainic acid into the hippocampus to establish a temporal lobe epilepsy model. Hippocampal tissues were collected 7 days after injection.

value: Hippocampus tissue

value: kainic acid

tag: chip antibody

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1432RM)


title: Hippocampus, KA, H3K18la,ChIP, rep2

description:
Library name: Hippo_KA_H3K18la_ChIP_rep2
H3K18la ChIP-seq in mouse hippocampus

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1431RM)


title: OE_ola-12_rep3

description: Library name: OE_ola-12_rep3


title: OE_ola-12_rep2

description: Library name: OE_ola-12_rep2


title: Hippocampus, Ctrl, H3K18la,ChIP, rep3

description:
Library name: Hippo_Ctrl_H3K18la_ChIP_rep3
H3K18la ChIP-seq in mouse hippocampus

value: saline

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1429RM)


title: Hippocampus, KA, H3K18la,ChIP, rep1

description:
Library name: Hippo_KA_H3K18la_ChIP_rep1
H3K18la ChIP-seq in mouse hippocampus

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1430RM)


title: OE_ola-12_rep1

description: Library name: OE_ola-12_rep1


title: OE_0_rep3

description: Library name: OE_0_rep3


title: Hippocampus, Ctrl, H3K18la,ChIP, rep2

description:
Library name: Hippo_Ctrl_H3K18la_ChIP_rep2
H3K18la ChIP-seq in mouse hippocampus

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1428RM)


title: OE_0_rep2

description: Library name: OE_0_rep2


title: Hippocampus, Ctrl, H3K18la,ChIP, rep1

description:
Library name: Hippo_Ctrl_H3K18la_ChIP_rep1
H3K18la ChIP-seq in mouse hippocampus

value: Anti-L-Lactyl-Histone H3 (Lys18) Rabbit mAb-ChIP Grade(PTM BIO, #PTM-1427RM)


title: Hippocampus, KA, input, rep3

description:
Library name: Hippo_KA_input_rep3
Input DNA from mouse hippocampus


title: OE_0_rep1

description: Library name: OE_0_rep1


title: Hippocampus, KA, input, rep2

description:
Library name: Hippo_KA_input_rep2
Input DNA from mouse hippocampus


title: EV_ola-24_rep3

description: Library name: EV_ola-24_rep3

value: WT


title: Hippocampus, KA, input, rep1

description:
Library name: Hippo_KA_input_rep1
Input DNA from mouse hippocampus


title: EV_ola-24_rep2

description: Library name: EV_ola-24_rep2


title: EV_ola-24_rep1

description: Library name: EV_ola-24_rep1


title: EV_ola-12_rep3

description: Library name: EV_ola-12_rep3


title: Hippocampus, Ctrl, input, rep3

description:
Library name: Hippo_Ctrl_input_rep3
Input DNA from mouse hippocampus


title: Hippocampus, Ctrl, input, rep2

description:
Library name: Hippo_Ctrl_input_rep2
Input DNA from mouse hippocampus


title: Hippocampus, Ctrl, input, rep1

description:
Library name: Hippo_Ctrl_input_rep1
Input DNA from mouse hippocampus


title: EV_ola-12_rep2

description: Library name: EV_ola-12_rep2


title: RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE3

city: New Haven

first: Saejeong

last: Park

state: Connecticut

address: 100 College St

institute: Yale University

description:
Library name: MP0PFE3
RNA-seq of mouse P0 mPFC samples

data_processing:
Single-nucleus multiomic data were processed using Cell Ranger ARC (v2.0.1, 10x Genomics) with default parameters. Reads were aligned to the reference genome, and gene expression matrices and chromatin accessibility fragment files were generated. CUT&Tag sequencing reads were processed using standard pipelines, including read alignment to the reference genome and identification of enriched regions. Bulk RNA-seq data were processed using standard pipelines, including read alignment to the reference genome and quantification of gene expression levels to generate gene-level count matrices.
Assembly: Human: hg38 Mouse: mm10
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for each sample. For single-nucleus multiomic data, processed files include gene expression matrices and chromatin accessibility fragment files. For CUT&Tag data, processed files include BigWig files, peak files, and signal tracks representing enriched genomic regions. For bulk RNA-seq, processed files include gene-level count matrices for each sample as well as differential gene expression analysis results.

source_name: mPFC

extract_protocol:
For human samples, nuclei were isolated from mid-fetal dorsolateral prefrontal cortex (dlPFC) tissue using a Dounce homogenization-based protocol in ice-cold lysis buffer, followed by filtration and iodixanol gradient centrifugation. The resulting nuclear pellets were resuspended in nuclei buffer supplemented with RNase inhibitor and DTT. For mouse samples, nuclei were isolated from medial prefrontal cortex (mPFC) and motor cortex (MC) tissues at postnatal day 1 (P1) using a similar homogenization-based protocol followed by filtration and centrifugation. For CUT&Tag experiments, nuclei were isolated from fresh frozen human cortical tissue using a commercial nuclei isolation kit according to the manufacturer’s instructions. For bulk RNA-seq, total RNA was extracted from dissociated mouse mPFC cells following enzymatic digestion and cell dissociation.
Single-nucleus multiomic libraries for gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. CUT&Tag libraries were prepared using a Hyperactive Universal CUT&Tag Assay Kit (Vazyme) following standard protocols. Briefly, isolated nuclei were incubated with primary antibodies targeting transcription factors (RARA, RARB, RXRG, MEIS2) or histone modifications (H3K27ac, H3K4me3), followed by secondary antibody incubation, Tn5 transposase binding, tagmentation, and PCR amplification. Bulk RNA-seq libraries were prepared from mouse mPFC cells using the VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s protocol.

value: mPFC


title: EV_ola-12_rep1

description: Library name: EV_ola-12_rep1


title: RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE2

description:
Library name: MP0PFE2
RNA-seq of mouse P0 mPFC samples


title: EV_0_rep3

description: Library name: EV_0_rep3


title: RNA-seq of Meis2-cKO mouse P0 mPFC sample MP0PFE1

description:
Library name: MP0PFE1
RNA-seq of mouse P0 mPFC samples


title: EV_0_rep2

description: Library name: EV_0_rep2


title: RNA-seq of CTR mouse P0 mPFC sample MP0PFC3

description:
Library name: MP0PFC3
RNA-seq of mouse P0 mPFC samples


title: EV_0_rep1

description: Library name: EV_0_rep1


title: RNA-seq of CTR mouse P0 mPFC sample MP0PFC2

description:
Library name: MP0PFC2
RNA-seq of mouse P0 mPFC samples


title: K562-RaPID, sgHBB, 18h, rep4, 25kbps

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description:
Library name: RaPIDseq_sgHBB_18h_rep4-25kbps_C3R5X95
X95_gCY201_12A3_Dox100_binned-25kbps.bw
X95_gCY201_12A3_Dox100_binned-5kbps.bw

data_processing:
Illumina NGS adapter trimming (cutadapt)
DamID PCR adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
alignment to Lambda phage genome (bowtie2)
count reads into GATC tiles of human genome (htseq-count)
spike-in correction, coverage-normalization (FPKM), background subtraction, and binning (analyzeRaPID)
Assembly: hg38
Supplementary files format and content: bigWig with RaPID-FPKM normalization at 5kbps and/or 25kbps binning
Library strategy: DamID-Seq

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum (tetracycline-screened), GlutaMAX, 1X PenStrep, 1ug/mL puromycin. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
genomic DNA
RaPID-labelled fragments were enriched per the DamID PCR protocol with methylated Lambda gDNA spike-in.
Enriched DNA fragments (200-2000bps) were then sheared to 300-600bps.
NGS libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: pre-treatment with doxycycline (20-24h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with Shield1 treatment  wherein siRNA is used, pretreated at -2d prior to CRISPR/Cas9 Nucleofection and again simultaneously with CRISPR/Cas9 Nucleofection.

value: blood

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB

tag: batch


title: RNA-seq of CTR mouse P0 mPFC sample MP0PFC1

description:
Library name: MP0PFC1
RNA-seq of mouse P0 mPFC samples


title: K562-RaPID, sgBFP, 18h, rep4, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep4-25kbps_C3R5X95
X95_gCY201_12A3_Dox100_binned-25kbps.bw
X95_gCY201_12A3_Dox100_binned-5kbps.bw

value: CRISPR/Cas9, sgBFP


title: snMultiome(snRNA-seq) of WT mouse P1 mPFC sample MmP1PFm

description:
Library name: MmP1PFm_GEX
snMultiome(snRNA-seq) of WT mouse P1 mPFC samples


title: K562-RaPID, sgMulti1, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgMulti1_18h_rep2-25kbps_C3R5X48
X48_gCY540_12A3_Dox100_noDrug_binned-25kbps.bw

value: CRISPR/Cas9, sgMulti1


title: K562-RaPID, sgOR7E39P, 18h, rep3, 25kbps

description:
Library name: RaPIDseq_sgOR7E39P_18h_rep3-25kbps_C3R5X48
X48_gCY530_12A3_Dox100_noDrug_binned-25kbps.bw

value: CRISPR/Cas9, sgOR7E39P


title: snMultiome(snRNA-seq) of WT mouse P1 motor cortex sample MmP1MCm

description:
Library name: MmP1MCm_GEX
snMultiome(snRNA-seq) of WT mouse P1 motor cortex samples


title: snMultiome(snATAC-seq) of WT mouse P1 mPFC sample MmP1PFm

description:
Library name: MmP1PFm_ATAC
snMultiome(snATAC-seq) of WT mouse P1 mPFC samples


title: K562-RaPID, sgOR7E89P, 18h, rep3, 25kbps

description:
Library name: RaPIDseq_sgOR7E89P_18h_rep3-25kbps_C3R5X48
X48_gCY538_12A3_Dox100_noDrug_binned-25kbps.bw

value: CRISPR/Cas9, sgOR7E89P


title: snMultiome(snATAC-seq) of WT mouse P1 motor cortex sample MmP1MCm

description:
Library name: MmP1MCm_ATAC
snMultiome(snATAC-seq) of WT mouse P1 motor cortex samples


title: K562-RaPID, sgHBB, 18h, rep3, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep3-25kbps_C3R5X48
X48_gCY201_12A3_Dox100_noDrug_binned-25kbps.bw
X48_gCY201_12A3_Dox100_noDrug_binned-5kbps.bw


title: snMultiome(snRNA-seq) of WT mouse P1 mPFC sample MfP1PFm

description:
Library name: MfP1PFm_GEX
snMultiome(snRNA-seq) of WT mouse P1 mPFC samples


title: K562-RaPID, sgBFP, 18h, rep3, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep3-25kbps_C3R5X48
X48_gCY201_12A3_Dox100_noDrug_binned-25kbps.bw
X48_gCY201_12A3_Dox100_noDrug_binned-5kbps.bw
X48_gCY530_12A3_Dox100_noDrug_binned-25kbps.bw
X48_gCY538_12A3_Dox100_noDrug_binned-25kbps.bw
X48_gCY540_12A3_Dox100_noDrug_binned-25kbps.bw


title: K562-RaPID, sgOR7E89P, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgOR7E89P_18h_rep2-25kbps_C3R5X47
X47_gCY538_12A3_Dox100_noDrug_binned-25kbps.bw


title: snMultiome(snRNA-seq) of WT mouse P1 motor cortex sample MfP1MCm

description:
Library name: MfP1MCm_GEX
snMultiome(snRNA-seq) of WT mouse P1 motor cortex samples


title: K562-RaPID, sgOR7E39P, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgOR7E39P_18h_rep2-25kbps_C3R5X47
X47_gCY530_12A3_Dox100_noDrug_binned-25kbps.bw


title: snMultiome(snATAC-seq) of WT mouse P1 mPFC sample MfP1PFm

description:
Library name: MfP1PFm_ATAC
snMultiome(snATAC-seq) of WT mouse P1 mPFC samples


title: K562-RaPID, sgBFP, 18h, rep9, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep9-25kbps_C3R5X47
X47_gCY530_12A3_Dox100_noDrug_binned-25kbps.bw
X47_gCY538_12A3_Dox100_noDrug_binned-25kbps.bw


city: Houston

first: Dongjoo

last: Choi

state: TX

address: 1 baylor plaza

institute: BCM

description:
Library name: Glo1OV_lib
Glo1 overexpression GBM single cell RNA sequencing

data_processing:
For single cell RNA sequencing, raw sequencing reads were processed using Cell Ranger with the mouse genome mm10 reference. Downstream analysis including quality filtering, removal of mitochondrial genes, doublet detection, variable gene selection, dimensionality reduction, and clustering was performed using Seurat and DoubletFinder. Cell type annotation was performed using SingleR with reference mouse cortical cell datasets.
Raw sequencing reads were processed using Cell Ranger (v3.0.2) with the mouse genome mm10 reference. Downstream analysis including quality filtering, removal of mitochondrial genes, doublet detection, variable gene selection, dimensionality reduction, and clustering was performed using Seurat (v4.1.0) and DoubletFinder. Cell type annotation was performed using SingleR with reference mouse cortical cell datasets.
Assembly: mm10
Supplementary files format and content: Processed data files include  filtered gene cell expression matrices for single cell RNA sequencing. Data are provided as tab delimited text matrices containing gene identifiers and normalized expression values for each sample or cell.

source_name: Brain

extract_protocol:
For single cell RNA sequencing, glioma regions were dissected from GFP positive tumor areas. Tissues were enzymatically dissociated using papain and DNase I in EBSS at 37°C. Cell suspensions were filtered, centrifuged, and subjected to red blood cell and debris removal. Cell viability was assessed by Trypan Blue exclusion and dead cells were removed when necessary.
For single cell RNA sequencing, viable single cells were processed using the 10x Genomics Chromium Single Cell 3′ v4 platform to generate GEMs and construct sequencing libraries. Libraries were sequenced on an Illumina NovaSeq 6000 instrument.

value: Brain

value: Glo1 Ov


title: K562-Dam, sgHBB, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep2-25kbps_C3R5X47
X47_gCY201_13C1_Dox100_noDrug_binned-25kbps.bw


title: snMultiome(snATAC-seq) of WT mouse P1 motor cortex sample MfP1MCm

description:
Library name: MfP1MCm_ATAC
snMultiome(snATAC-seq) of WT mouse P1 motor cortex samples


title: Glo1 knockdown GBM single cell RNA seq

description:
Library name: Glo1KD_lib
Glo1 knockdown GBM single cell RNA sequencing

value: Glo1 KD


title: K562-Dam, sgBFP, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep2-25kbps_C3R5X47
X47_gCY201_13C1_Dox100_noDrug_binned-25kbps.bw


title: Control GBM single cell RNA seq

description:
Library name: conGBM_lib
Control GBM single cell RNA sequencing

value: control


title: K562-RaPID, sgOR7E39P, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgOR7E39P_18h_rep1-25kbps_C3R5X45
X45_gCY530_12A3_Dox080_harv-18h_binned-25kbps.bw


title: K562-RaPID, sgMulti1, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgMulti1_18h_rep1-25kbps_C3R5X45
X45_gCY540_12A3_Dox080_harv-18h_binned-25kbps.bw


title: input Hippocampi, PTZ, rep 1

city: Zürich

first: Ana

last: Stankovic

address: Winterthurerstrasse 190

department: Brain research institute

institute: University of Zurich

description:
Library name: input_PTZ_1
input

data_processing:
ChIP-seq reads were processed with snakePipes (10). In short, paired-end raw sequencing reads were trimmed with trim_galore v0.6.5 and aligned to the mouse reference genome GRCm38 using bowtie2 v2.3.5.1. To quantify chromatin binding, alignments were deduplicated using Sambamba v0.7.1 and with sequencing coverages calculated via deepTools v3.3.2 over 100 nucleotide windows.
Assembly: GRCm38
Supplementary files format and content: bigwigs, sequence depth normalized coverages
Supplementary files format and content: raw (R1,R2) fastq files

source_name: Hippocampi

growth_protocol: Standard housing conditions

extract_protocol:
Cold hippocampi dissection followed by nuclei isolation, micrococal DNA digestion and immunoprecipitation.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: PTZ injected at 45mg/kg or equal volume of Saline for control samples.

value: Hippocampi


title: input Hippocampi, Saline, rep 1

description:
Library name: input_Saline_1
input


title: K562-RaPID, sgOR7E89P, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgOR7E89P_18h_rep1-25kbps_C3R5X45
X45_gCY538_12A3_Dox080_harv-18h_binned-25kbps.bw


title: K562-RaPID, sgBFP, 18h, rep8, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep8-25kbps_C3R5X45
X45_gCY538_12A3_Dox080_harv-18h_binned-25kbps.bw
X45_gCY540_12A3_Dox080_harv-18h_binned-25kbps.bw
X45_gCY530_12A3_Dox080_harv-18h_binned-25kbps.bw


title: Hippocampi, PTZ, rep 3

description:
Library name: PTZ_3
PTZ treated


title: Hippocampi, PTZ, rep 2

description:
Library name: PTZ_2
PTZ treated


title: Hippocampi, PTZ, rep 1

description:
Library name: PTZ_1
PTZ treated


title: K562-Dam, sgHBB, 24h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_24h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_24h_binned-25kbps.bw


title: K562-Dam, sgHBB, 21h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_21h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_21h_binned-25kbps.bw


title: Hippocampi, Saline, rep 3

description:
Library name: Saline_3
Saline


title: K562-Dam, sgHBB, 18h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_18h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_18h_binned-25kbps.bw


title: PB02710-003 MM CD38 Pre-treatment

description:
Library name: PB02710-003
H5 file contains RNA expression matrix

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Blood

value: PBMC

value: Female

value: Other

value: MM CD38 Pre-treatment

value: FALSE


title: Multiome, retina, GEX

city: South San Francisco

first: Oriol

last: Fornes

state: CA

address: 1 DNA Way

institute: Genentech

description:
Library name: LIB6223752
GEX component of joint single-nucleus multiome profiling

data_processing:
Joint alignment of single-nucleus RNA-seq and single-nucleus ATAC-seq reads was performed using Cell Ranger ARC (version 2.0.0).
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: retina

extract_protocol:
Eight retinas from 11- and 93-week-old C57BL/6 mice (4 per age group) were rapidly dissected from enucleated eyes in cold PBS, immediately snap-frozen on dry ice, and stored at -80°C. Snap-frozen retinal tissue was transferred into a glass Dounce homogenizer containing 500 µL chilled 0.1× lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.01% Tween-20, 0.01% Nonidet P40 Substitute, 0.001% digitonin, 1% BSA, 1 mM DTT, 1× RNase inhibitor in nuclease-free water) and immediately homogenized. Homogenates were incubated on ice for 5 minutes, gently triturated using a wide-bore pipette tip, and incubated on ice for an additional 10 minutes. Following lysis, 500 µL of chilled wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 1% BSA, 1 mM DTT, 1× RNase inhibitor in nuclease-free water) was added, and the samples were mixed gently. Nuclei suspensions were sequentially filtered through 70 µm and 40 µm Flowmi cell strainers to remove debris and aggregates, centrifuged at 500 × g for 5 minutes at 4°C, washed twice with chilled wash buffer, and resuspended in chilled diluted nuclei buffer (1× Nuclei Buffer with 1 mM DTT and 1× RNase inhibitor).
Single-nucleus ATAC and gene expression libraries were constructed jointly using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocols. Ten thousand nuclei were targeted for library preparation. Nuclei suspensions were loaded using the Chromium Next GEM Chip J Single Cell Kit (10X Genomics). The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform targeting a depth of 25,000 read pairs per nucleus.

value: retina

tag: library type

value: mRNA


title: Hippocampi, Saline, rep 2

description:
Library name: Saline_2
Saline


title: K562-Dam, sgHBB, 15h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_15h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_15h_binned-25kbps.bw

value: blood

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB


title: Hippocampi, Saline, rep 1

description:
Library name: Saline_1
Saline


title: K562-Dam, sgHBB, 12h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_12h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_12h_binned-25kbps.bw


title: C9_HFD6

city: Nanjing

first: Shuangya

last: Fan

address: 22 Hankou Road, Gulou District, Nanjing, Jiangsu Province, China

department: Medical school

institute: Nanjing University

description: Library name: Sample12

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: liver

value: HFD


title: K562-Dam, sgHBB, 9h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_9h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_09h_binned-25kbps.bw


title: C9_HFD5

description: Library name: Sample11


title: K562-Dam, sgHBB, 6h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_6h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_06h_binned-25kbps.bw


title: K562-Dam, sgHBB, 3h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_3h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_03h_binned-25kbps.bw


title: C9_HFD3

description: Library name: Sample9


title: K562-RaPID, sgHBB, 24h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_24h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_24h_binned-25kbps.bw


title: C9_HFD2

description: Library name: Sample8


title: K562-Dam, sgHBB, 0h, rep1, 25kbps

description:
Library name: DamNULLseq_sgHBB_0h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_00h_binned-25kbps.bw


title: C9_HFD4

description: Library name: Sample10


title: C9_HFD1

description: Library name: Sample7


title: K562-RaPID, sgHBB, 21h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_21h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_21h_binned-25kbps.bw


title: K562-RaPID, sgHBB, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_18h_binned-25kbps.bw
X43_gCY201_12A3_Dox080_18h_binned-5kbps.bw


title: K562-RaPID, sgHBB, 15h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_15h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_15h_binned-25kbps.bw


title: WT_HFD5

description: Library name: Sample5

value: WT


title: WT_HFD4

description: Library name: Sample4


title: K562-RaPID, sgHBB, 12h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_12h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_12h_binned-25kbps.bw


title: K562-RaPID, sgHBB, 9h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_9h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_09h_binned-25kbps.bw


title: K562-RaPID, sgHBB, 6h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_6h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_06h_binned-25kbps.bw


title: WT_HFD2

description: Library name: Sample2


title: WT_HFD3

description: Library name: Sample3


title: K562-RaPID, sgHBB, 3h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_3h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_03h_binned-25kbps.bw


title: WT_HFD1

description: Library name: Sample1


title: K562-RaPID, sgHBB, 0h, rep1, 25kbps

description:
Library name: RaPIDseq_sgHBB_0h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_00h_binned-25kbps.bw


title: HC_ELA_SAFit2_SocialInteraction_55

city: Solna

first: Juan Pablo

last: Lopez

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Library name: 22L006432

data_processing:
Sequence reads were processed using the nf-core RNA-seq pipeline (nf-core/rnaseq v3.6). Adapter trimming and quality control were performed using the default parameters.
Trimmed reads were aligned to the reference genome using STAR within the nf-core/rnaseq workflow, with Gencode M30 gene annotaion.
Gene-level read counts were generated based on Gencode M30 annotation. Strand-specific information was specified as reverse-stranded.
VST was performed using DESeq2 for downstream analysis. Duplicate read analysis (DupRadar) and library complexity estimation (Preseq) were skipped as specified in the pipleline options.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts for 246 RNA-seq samples

source_name: ventral hippocampus

extract_protocol:
Total RNA was isolated from punches using the miRNeasy Mini Kit (QIAGEN, Venlo, NL; cat. No. 1038703) according to the manufacturer's instructions, using Rnase-free technique throughout. After RNA isolation, RNA integrity number (RIN) was measured using the Agilent 2100 Bioanalyzer system and quantified by Qubit (Thermo Fisher Scientific). RNAs with a RIN value >7 were selected for mRNA sequencing (poly-A selected).
The libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (Illumina), following the kit's instructions.

value: ventral hippocampus


title: HC_ELA_SAFit2_NoInteraction_15

description: Library name: 22L006431


title: K562-Dam, sgBFP, 24h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_24h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_24h_binned-25kbps.bw

value: CRISPR/Cas9, sgBFP


title: K562-Dam, sgBFP, 21h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_21h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_21h_binned-25kbps.bw


title: HC_ELA_Vehicle_NoInteraction_43

description: Library name: 22L006429


title: PB02684-002 MM CD38 2 weeks

description:
Library name: PB02684-002
H5 file contains RNA expression matrix

value: Male

value: Caucasian

value: MM CD38 2 weeks


title: HC_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L006430


title: K562-Dam, sgBFP, 18h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_18h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_18h_binned-25kbps.bw


title: HC_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L006427


title: K562-Dam, sgBFP, 12h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_12h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_12h_binned-25kbps.bw


title: HC_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L006426


title: K562-Dam, sgBFP, 15h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_15h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_15h_binned-25kbps.bw


title: HC_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L006428


title: HC_ELA_Vehicle_NoInteraction_99

description: Library name: 22L006424


title: K562-Dam, sgBFP, 6h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_6h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_06h_binned-25kbps.bw


title: HC_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L006423


title: WT_HFD6

description: Library name: Sample6


title: K562-RaPID, sgBFP, 24h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_24h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_24h_binned-25kbps.bw


title: HC_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L006421


title: K562-Dam, sgBFP, 9h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_9h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_09h_binned-25kbps.bw


title: HC_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L006425


title: HC_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L006420


title: HC_ELA_Vehicle_NoInteraction_101

description: Library name: 22L006419


title: HC_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L006418


title: K562-RaPID, sgBFP, 9h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_9h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_09h_binned-25kbps.bw


title: HC_ELA_SAFit2_NoInteraction_71

description: Library name: 22L006416


title: HC_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L006415


title: K562-RaPID, sgBFP, 6h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_6h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_06h_binned-25kbps.bw


title: K562-RaPID, sgBFP, 3h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_3h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_03h_binned-25kbps.bw


title: HC_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L006412


title: K562-RaPID, sgBFP, 21h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_21h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_21h_binned-25kbps.bw


title: HC_ELA_SAFit2_NoInteraction_47

description: Library name: 22L006422


title: K562-Dam, sgBFP, 0h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_0h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_00h_binned-25kbps.bw


title: K562-Dam, sgBFP, 3h, rep1, 25kbps

description:
Library name: DamNULLseq_sgBFP_3h_rep1-25kbps_C3R5X43
X43_gCY201_13C1_Dox080_03h_binned-25kbps.bw


title: HC_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L006417


title: K562-RaPID, sgBFP, 12h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_12h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_12h_binned-25kbps.bw


title: K562-RaPID, sgBFP, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_18h_binned-25kbps.bw
X43_gCY201_12A3_Dox080_18h_binned-5kbps.bw


title: K562-RaPID, sgBFP, 15h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_15h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_15h_binned-25kbps.bw


title: HC_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L006411


title: K562-RaPID, sgHBB, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep2-25kbps_C3R5X42
12A3_gCY201_dox-80nM_binned-25kbps.bw
12A3_gCY201_dox-80nM_binned-5kbps.bw


title: HC_ELA_SAFit2_NoInteraction_87

description: Library name: 22L006413


title: HC_ELA_Vehicle_NoInteraction_13

description: Library name: 22L006414


title: K562-RaPID, sgVEGFA, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgVEGFA_18h_rep1-25kbps_C3R5X42
12A3_gCY323_dox-80nM_binned-25kbps.bw

value: CRISPR/Cas9, sgVEGFA


title: K562-RaPID, sgBFP, 0h, rep1, 25kbps

description:
Library name: RaPIDseq_sgBFP_0h_rep1-25kbps_C3R5X43
X43_gCY201_12A3_Dox080_00h_binned-25kbps.bw


title: HC_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L006410


title: K562-RaPID, sgBFP, 18h, rep2, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep2-25kbps_C3R5X42
12A3_gCY201_dox-80nM_binned-25kbps.bw
12A3_gCY201_dox-80nM_binned-5kbps.bw
12A3_gCY323_dox-80nM_binned-25kbps.bw


title: K562-RaPID, sgNTC, V5-tag_ChIPseq, rep1

description: Library name: C3R5X71_ChIPseq_V5_sgNTC

library_source: other

data_processing:
Illumina NGS adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
conversion to coverage (deepTools bamCoverage), separated by first-of-read-pair maaping strand.  Parameters: (--binSize 250 --normalizeUsing CPM --minMappingQuality 10 --extendReads) with either (--samFlagInclude 99) or (--samFlagInclude 83)
Assembly: hg38
Supplementary files format and content: bigWig with CPM normalization

molecule: protein

extract_protocol:
chromatin immunoprecipitation
xGen ssDNA & Low-Input DNA Library Prep Kit

treatment_protocol: pre-treatment with 100nM doxycycline (20h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with 1uM Shield1 treatment

value: K-562, RaPID, clone 12A3

value: CRISPR/Cas9, sgNTC


title: HC_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L006409


title: HC_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L006408


title: K562-RaPID, sgHBB, V5-tag_ChIPseq rep1

description: Library name: C3R5X71_ChIPseq_V5_sgHBB


title: K562-RaPID, sgNTC, RAD51-ChIPseq, rep1

description: Library name: C3R5X71_ChIPseq_RAD51_sgNTC


title: HC_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L006406


title: 6094_cl_22_N_2

city: Toronto

first: Cathy

middle: L

last: Barr

state: ON

address: 399 Bathurst St

country: Canada

institute: UHN

description: Library name: SB48

data_processing:
The design used three independent iPSC clones from each individual with replicates for each clone (24 sequencing reactions each for NPCs and for neurons). Fastq files were preprocessed with fastp version 0.23.1. RNA-Seq raw reads were aligned to the GRCh37 genome using STAR version 2.7.9a and transcription levels counted based on hg19 annotations using HTseq-count (HTSeq/0.11.0). Ambiguous reads were not counted.  Differentially expressed genes were called using DESeq2.
Assembly: GRCh37
Supplementary files format and content: fastq, raw count matrix

source_name: iPSC derived Neurons

growth_protocol: Peripheral blood mononuclear cells collected from human donors were reprogrammed to iPSCs, which were then differentiated into neural precursor cells and neurons following established protocols.

extract_protocol:
Total RNA extracted (from iPSC-derived NPCs and neurons)
RNA-seq libraries prepared according to standard Illumina protocols

value: iPSC derived Neurons

tag: age(y)

value: F

value: Strong Reader Sibling


title: HC_ELA_SAFit2_NoInteraction_7

description: Library name: 22L006407

tag: tissue


title: K562-RaPID, sgHBB, RAD51-ChIPseq, rep1

description: Library name: C3R5X71_ChIPseq_RAD51_sgHBB

value: blood

tag: cell type


title: HC_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L006405


title: 6094_cl_16_N_2

description: Library name: SB46

value: mRNA


title: 6094_cl_16_N_1

description: Library name: SB45


title: HC_ELA_Vehicle_NoInteraction_37

description: Library name: 22L006404


title: HC_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L006403


title: 6094_cl_9_N_2

description: Library name: SB44


title: 6094_cl_22_N_1

description: Library name: SB47


title: HC_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L006402


title: HC_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L006401


title: 6094_cl_9_N_1

description: Library name: SB43


title: 6093_cl_19_N_2

description: Library name: SB42

value: Reading Disability


title: HC_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L006400


title: HC_ELA_SAFit2_NoInteraction_39

description: Library name: 22L006399


title: HC_ELA_Vehicle_NoInteraction_69

description: Library name: 22L006398


title: 6093_cl_19_N_1

description: Library name: SB41


title: HC_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L006397


title: 6093_cl_16_N_2

description: Library name: SB40


title: 6093_cl_16_N_1

description: Library name: SB39


title: HC_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L006396


title: HC_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L006395


title: 6093_cl_8_N_1

description: Library name: SB37


title: 6093_cl_8_N_2

description: Library name: SB38


title: HC_ELA_SAFit2_NoInteraction_103

description: Library name: 22L006394


title: 5594_cl_24_N_2

description: Library name: SB36

value: M


title: HC_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L006393


title: 5594_cl_24_N_1

description: Library name: SB35


title: HC_ELA_Vehicle_NoInteraction_5

description: Library name: 22L006392


title: DMT_ELA_SAFit2_SocialInteraction_55

description: Library name: 22L006391

source_name: dorsomedial thalamus

value: dorsomedial thalamus


title: 5594_cl_10_N_2

description: Library name: SB34


title: 5594_cl_10_N_1

description: Library name: SB33


title: 5594_cl_2_N_2

description: Library name: SB32


title: 5594_cl_2_N_1

description: Library name: SB31


title: DMT_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L006389


title: DMT_ELA_SAFit2_NoInteraction_15

description: Library name: 22L006390


title: DMT_ELA_Vehicle_NoInteraction_43

description: Library name: 22L006388


title: 5593_cl_18_N_2

description: Library name: SB30


title: 5593_cl_18_N_1

description: Library name: SB29


title: 5593_cl_11_N_2

description: Library name: SB28


title: DMT_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L006385


title: DMT_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L006387


title: DMT_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L006386


title: 5593_cl_11_N_1

description: Library name: SB27


title: DMT_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L006384


title: 5593_cl_7_N_2

description: Library name: SB26


title: DMT_ELA_Vehicle_NoInteraction_99

description: Library name: 22L006383


title: 5593_cl_7_N_1

description: Library name: SB25


title: DMT_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L006382


title: 6094_cl_22_NPC_2

description: Library name: SB24

source_name: iPSC derived Neural Precursor Cells

value: iPSC derived Neural Precursor Cells


title: DMT_ELA_SAFit2_NoInteraction_47

description: Library name: 22L006381


title: DMT_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L006380


title: DMT_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L006379


title: 6094_cl_16_NPC_2

description: Library name: SB22


title: 6094_cl_16_NPC_1

description: Library name: SB21


title: 6094_cl_22_NPC_1

description: Library name: SB23


title: 6094_cl_9_NPC_2

description: Library name: SB20


title: 6094_cl_9_NPC_1

description: Library name: SB19


title: DMT_ELA_Vehicle_NoInteraction_101

description: Library name: 22L006378


title: DMT_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L006377


title: DMT_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L006376


title: 6093_cl_19_NPC_2

description: Library name: SB18


title: DMT_ELA_SAFit2_NoInteraction_71

description: Library name: 22L006375


title: 6093_cl_19_NPC_1

description: Library name: SB17


title: DMT_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L006374


title: 6093_cl_16_NPC_2

description: Library name: SB16


title: 6093_cl_16_NPC_1

description: Library name: SB15


title: DMT_ELA_Vehicle_NoInteraction_13

description: Library name: 22L006373


title: 6093_cl_8_NPC_2

description: Library name: SB14


title: DMT_ELA_SAFit2_NoInteraction_87

description: Library name: 22L006372


title: DMT_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L006371


title: DMT_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L006369


title: DMT_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L006370


title: 5594_cl_24_NPC_2

description: Library name: SB12


title: 6093_cl_8_NPC_1

description: Library name: SB13


title: DMT_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L006368


title: 5594_cl_24_NPC_1

description: Library name: SB11


title: 5594_cl_10_NPC_2

description: Library name: SB10


title: 5594_cl_10_NPC_1

description: Library name: SB9


title: DMT_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L006367


title: DMT_ELA_SAFit2_NoInteraction_7

description: Library name: 22L006366


title: 5594_cl_2_NPC_2

description: Library name: SB8


title: DMT_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L006365


title: 5594_cl_2_NPC_1

description: Library name: SB7


title: 5593_cl18_NPC_2

description: Library name: SB6


title: DMT_ELA_Vehicle_NoInteraction_37

description: Library name: 22L006363


title: 5593_cl18_NPC_1

description: Library name: SB5


title: DMT_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L006364


title: DMT_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L006362


title: 5593_cl11_NPC_2

description: Library name: SB4


title: 5593_cl11_NPC_1

description: Library name: SB3


title: DMT_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L006361


title: DMT_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L006360


title: DMT_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L006359


title: 5593_cl7_NPC_2

description: Library name: SB2


title: DMT_ELA_SAFit2_NoInteraction_39

description: Library name: 22L006358


title: 5593_cl7_NPC_1

description: Library name: SB1


title: HepG2_cells_CUT&Tag-H3K18Dla_20mM

city: tianjin

first: yong

last: zang

address: Heping District qixiangtailu22hao

institute: Tianjin Medical University

description: Library name: sample 8

data_processing:
FastQC tool was used to examine metrics, such as sequencing error rate, sequencing depth, and fragment length distribution
Aligned the preprocessed reads to a reference genome using alignment tool (Bowtie2)
Peak calling was performed using the model-based analysis of ChIP–seq (MACS2)
BigWig files were generated through Deeptools
Assembly: hg38
Supplementary files format and content: bigWig narrowPeak
Library strategy: CUT&Tag

source_name: HepG 2 cells

extract_protocol:
HepG2 cells treated with 0 or 20mM D-lactate for 48 hours were collected, quantified, and bound to Concanavalin A (ConA)-coated magnetic beads. The cells were resuspended in antibody buffer and incubated overnight at 4°C with a primary antibody targeting H3K18-Dla. After washing, secondary antibodies diluted in blocking buffer were applied at room temperature for 1 hour. Subsequently, Protein A/G-Tn5 transposase complexes were added and incubated with rotation for 1 hour to fragment and tag genomic DNA associated with the target protein.
DNA library was constructed with TruePreP Index Kit V2 for Illumina (TD202, Vazyme Biotech). The library was purified by VAHTS DNA Clean Beads (N411, Vazyme Biotech)

value: HepG 2 cells

value: Human liver cancer cells

value: WT

value: 20 mM D-lactate, 48h


title: DMT_ELA_Vehicle_NoInteraction_69

description: Library name: 22L006357


title: HepG2_cells_CUT&Tag-H3K18Dla_0mM

description: Library name: sample 7

value: 0 mM D-lactate, 48h


title: DMT_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L006356


title: DMT_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L006355


title: HepG2_cells_D_lactate_3

description: Library name: sample 6

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . p<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: xls files include Counts  for each Sample

extract_protocol:
RNA was harvested using Trizol.800ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by 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, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. 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 amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.


title: HepG2_cells_D_lactate_2

description: Library name: sample 5


title: DMT_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L006354


title: DMT_ELA_SAFit2_NoInteraction_103

description: Library name: 22L006353


title: HepG2_cells_D_lactate_1

description: Library name: sample 4


title: DMT_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L006352


title: HepG2_cells_control_3

description: Library name: sample 3


title: HepG2_cells_control_2

description: Library name: sample 2


title: DMT_ELA_Vehicle_NoInteraction_5

description: Library name: 22L006351


title: HepG2_cells_control_1

description: Library name: sample 1


title: BLA_ELA_SAFit2_SocialInteraction_55

description: Library name: 22L006350

source_name: basolateral amygdala

value: basolateral amygdala


title: Donor 2, non-invaded, Decidua parietalis

city: Graz

first: Julia

last: Feichtinger

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical University of Graz

description:
Library name: 148074
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline
The raw sequencing data was analyzed using the 10x Genomics Space Ranger (v1.2.2). The data was aligned to the human reference genome (GRCh38-2020-A) and quantified.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv:  list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Decidua

extract_protocol:
Fresh frozen tissue was OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Decidua


title: BLA_ELA_SAFit2_NoInteraction_15

description: Library name: 22L006349


title: Donor 2, invaded, Decidua basalis

description:
Library name: 148073
Fresh frozen Spatial transcriptome sequencing


title: BLA_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L006348


title: Donor 1, non-invaded, Decidua parietalis

description:
Library name: 148072
Fresh frozen Spatial transcriptome sequencing


title: BLA_ELA_Vehicle_NoInteraction_43

description: Library name: 22L006347


title: BLA_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L006346


title: Donor 1, invaded, Decidua basalis

description:
Library name: 148071
Fresh frozen Spatial transcriptome sequencing


title: BLA_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L006345


title: BLA_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L006344


title: BLA_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L006343


title: PBMCESO

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description:
Library name: Sample_04
10x Genomics

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: In vitro

extract_protocol:
Lung (the tumor site) and periphery blood cells harvested from experimental animals at Day 21 were subjected to FACS sorting for isolating Allo15ESO-T cells (hCD45+TCRVB13.1+hCD3+; Sample_02, Sample_03), and PBMCESO-T cells (hCD45+TCRVB13.1+hCD3+; Sample_05, Sample_06). Cells isolated from 6 experimental mice were combined for each group. Preinfusion sampling of therapeutical cells (Sample_01: Allo15ESO-T, Sample_04: PBMCESO-T) were also sorted and subjected to scRNA-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: In vitro

tag: time

value: T cells


title: BLA_ELA_Vehicle_NoInteraction_99

description: Library name: 22L006342


title: PBMCESO_PB

description:
Library name: Sample_06
10x Genomics

value: Blood


title: AlloESO_LN

description:
Library name: Sample_02
10x Genomics

source_name: Lung

value: Lung


title: BLA_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L006341


title: AlloESO

description:
Library name: Sample_01
10x Genomics


title: BLA_ELA_SAFit2_NoInteraction_47

description: Library name: 22L006340


title: 48S Footprints of HEK293T RPS26del replicate 2

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
Library name: RPS26del_2
counts.txt column RPS26del_2

data_processing:
Trimming with cutadapt (CTGTAGGCACCATCAAT -m 16) and QC with TRIMMOMATIC (MINLEN:16 TRAILING:15 SLIDINGWINDOW:5:15).
Successive mapping to rRNAs, tRNAs with bowtie and lncRNAs (hg38) with HISAT2. Final mapping to transcriptome hg38, MANE Ensemble DB v108  with HISAT2.
Counted with FeatureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts values for each sample

growth_protocol: 5% CO2, 37°C, humdifed athmosphere

extract_protocol:
HEK293T RPS26 p.R100_M115del homozygous cells were generated by CRISPR/CAS9. Translation initiation of HEK293T WT and RPS26del was analysed by 48S footprinting (TCP-seq). Cells were crosslinked by HCHO 0.3% for 5 min on ice. Reaction was stopped by 0.125 M Glycine pH 2. Cells were lysed in polysome lysis buffer (20 mM TRIS pH 7, 1.5 mM MgCl2, 100 mM KCl, 1.5% NP40). The lysate was digested by RNase I and loaded onto a sucrose gradient. The fractions containing the 40S were extracted and footprints were isolated by TRIzol.
Extracted RNA were processed through library preparation according to the Ribo-seq protocol (Ingolia et al, 2012)

value: RPS26 p.R100_M115 homozygous


title: BLA_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L006339


title: 48S Footprints of HEK293T RPS26del replicate 1

description:
Library name: RPS26del_1
counts.txt column RPS26del_1


title: BLA_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L006338


title: 48S Footprints of HEK293T WT replicate 2

description:
Library name: WT_2
counts.txt column WT_2


title: BLA_ELA_Vehicle_NoInteraction_101

description: Library name: 22L006337


title: 48S Footprints of HEK293T WT replicate 1

description:
Library name: WT_1
counts.txt column WT_1


title: BLA_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L006336


title: CO-F3

city: Oxford

first: HungJu

last: Chueh

address: Dorothy Crowfoot Hodgkin Building

department: Nuffield Department of Clinical Neuroscience

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 6
10X Genomics

data_processing:
Fastq files were aligned to Homo sapiens GRCh38, in Cellranger (v7.1.0). Single cell 3' v3. Intron included.
PercellQCmetrics to decide outliers based on 3 MADS (scuttle)
Evaluate doublets using scdblfinder
Assembly: GRCh38-2020-A
Supplementary files format and content: *.h5 file type

source_name: hiPSC

growth_protocol: iPSC differentiation into dopaminergic neurons cocultured with iPSC-drived microglia from DIV59  onwards to DIV 73

extract_protocol:
Cells were first dissociated in Accutase for 30 minutes at 37 C to generate a single cell suspension. Cells were fixed in 100% methanol following the 10X Genomics established protocol.
Library preparation and mRNA barcoding was performed using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), following the manufacturer’s instructions. 10,000-cell recovery was the targeted for each sample. One library was prepared for each condition with microglia (OX3-9) and dopaminergic neuron (SFC831-03-05) . Libraries were sequenced with NovaSeq 6000 (Illumina).

treatment_protocol: Non-seeded control (NSC) and fibril treated (F)

value: hiPSC

value: Induced pluripotent stem cell derived dopaminergic neurons

value: healthy control microglia (OX3-9) and patient derived dopaminergic neuron (SFC831-03-05)

value: Fib treated (F)


title: CO-F2

description:
Library name: Sample 5
10X Genomics

value: control microglia (OX3-9) and patient derived dopaminergic neuron (SFC831-03-05)


title: BLA_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L006335


title: CO-F1

description:
Library name: Sample 4
10X Genomics


title: BLA_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L006333


title: CO-NSC3

description:
Library name: Sample 3
10X Genomics

value: Non-seeded control (NSC)


title: BLA_ELA_Vehicle_NoInteraction_13

description: Library name: 22L006332


title: CO-NSC2

description:
Library name: Sample 2
10X Genomics


title: BLA_ELA_SAFit2_NoInteraction_87

description: Library name: 22L006331


title: CO-NSC1

description:
Library name: Sample 1
10X Genomics


title: RNA_3D-iMac-Ecoli-Rep2

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

data_processing:
For RNA-seq, reads were trimmed using TrimGalore software (version 0.4.4) with default settings. Subsequently, the adaptor-trimmed paired-end RNA-Seq reads were aligned to the hg38 whole genome employing hisat2 with the -p16 parameter. Read counts were determined by utilizing htseq-count (version 0.11.1) and specifying the following parameters: -r pos -a 10 -t exon -s no -i gene_id -m union. Normalization of raw data counts and identification of differentially expressed genes were carried out with the aid of DESeq2 software, adhering to specific criteria (|log2fc| ≥ 1 and false discovery rate [FDR] ≤ 0.05). For ATAC-seq, all paired-end raw reads underwent processing with TrimGalore (version 0.4.4) to eliminate adapters and low-quality sequences. The adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq data were then aligned to the hg38 genome using bowtie2 (version 2.3.5) 52, employing the following parameters: --t --q --N 1 --L 25. PCR duplicates and multiply mapped reads were subsequently removed by utilizing Picard tools MarkDuplicates (available at https://broadinstitute.github.io/picard/). Following this, replicate BAM files for each time point were consolidated, and reads aligning to blacklisted genomic regions were discarded prior to peak calling with MACS253 (version 2.2.6). The enriched transcription factor motifs were analyzed using Homer (version 4.10.4, findMotifsGenome). Additionally, signal tracks for each sample were created with the bamCoverage function from deeptools and normalized to Reads Per Kilobase Million (RPKM) for ease of visualization.
Assembly: GRCh38
Supplementary files format and content: For single-cell datasets, processed data are UMI matrix and cell barcodes produced by Cellranger pipeline.
Supplementary files format and content: bw

extract_protocol:
Total RNA were extracted by TRIZol.
RNA-seq library were prepared according to SMART-seq2 protocol. ATAC-seq library were prepared according to the omni-ATAC-seq protocol.  CHIP-seq library were prepared according an ultra-low-input native ChIP-seq protocol.Single-cell libraries were prepared according to 10X genomics' manual.

value: macrophage

tag: protocol


title: BLA_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L006329


title: RNA_3D-iMac-Ecoli-Rep1


title: BLA_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L006330


title: RNA_3D-iMac_SP14_Rep2

tag: time point


title: BLA_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L006327


title: RNA_3D-iMac_SP6A_Rep2


title: BLA_ELA_SAFit2_NoInteraction_7

description: Library name: 22L006325


title: BLA_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L006324


title: RNA_3D-iMac_SP6A_Rep1


title: RNA_3D-iMac_day23_FBS_Rep3


title: BLA_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L006323


title: RNA_3D-iMac_day23_FBS_Rep2


title: BLA_ELA_Vehicle_NoInteraction_37

description: Library name: 22L006322


title: BLA_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L006321


title: RNA_3D-iMac_day19_FBS_Rep3


title: BLA_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L006320


title: t=24h, rep1

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

institute: Israel Institute For Biological Research

description: Library name: sample 16

data_processing:
Sequenced reads were trimmed using FastQC for data filtering, and trimmed reads were mapped via HISAT2 for read alignment, followed by featureCounts quantification and differential expression analysis using DESeq
Assembly: GRCm39
Supplementary files format and content: raw_counts.csv

growth_protocol: RAW264.7 cells were mainained in DMEM supplemented with 10% Fetal bovine aserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Jak1 KO cells were maintained in the sasme medium supplemented with 5ug/ml puromycin

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TrueSeq mRNA Prep kit (Illumina), following manufacturer’s protocols

treatment_protocol: Cells were seeded 24h post infection. 90% confluent cells were infected with LVS-GFP strain at MOI=2500 for 3h. Following 1h of 50ug/ml gentamicin to kill extracellular bacteria.after which  cells were maintaind with 2ug/ml gentamicin. cells were harvested for RNA extraction at 0,0.5,1.5,4,8,24,48h post infection

value: Macrophage

value: WT

value: F. tularensis infection


title: BLA_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L006319

value: basolateral amygdala


title: RNA_3D-iMac_day19_FBS_Rep1


title: RNA_3D-iMac_day19_FBS_Rep2


title: RNA_3D-iMac_day16_FBS_Rep2


title: RNA_3D-iMac_day16_FBS_Rep3


title: BLA_ELA_Vehicle_NoInteraction_69

description: Library name: 22L006316


title: RNA_3D-iMac_day16_FBS_Rep1


title: BLA_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L006315


title: PBMCESO_LN

description:
Library name: Sample_05
10x Genomics


title: RNA_3D-iMac_day23_Rep2


title: BLA_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L006313


title: BLA_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L006314


title: RNA_3D-iMac_day23_Rep1


title: BLA_ELA_SAFit2_NoInteraction_103

description: Library name: 22L006312


title: BLA_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L006311


title: AlloESO_PB

description:
Library name: Sample_03
10x Genomics


title: RNA_3D-iMac_day19_Rep2


title: BLA_ELA_Vehicle_NoInteraction_5

description: Library name: 22L006310


title: RNA_3D-iMac_day19_Rep1


title: Nacc_ELA_SAFit2_SocialInteraction_55

description: Library name: 22L006309

source_name: nucleus accumbens shell

value: nucleus accumbens shell


title: PB02689-001 Flu Year 1 Day 90

city: Seattle

first: Allen Institute

last: For Immunology

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: PB02689-001
H5 file contains RNA expression matrix

value: PBMC

tag: subject id

tag: birth year

tag: Sex

value: Male

tag: race

value: Other

value: Flu Year 1 Day 90

value: FALSE


title: PB02688-001 MM Post Induction 2-Cycles

description:
Library name: PB02688-001
H5 file contains RNA expression matrix

value: Blood

value: Female

value: Caucasian

tag: days since_first_visit

tag: visit

value: MM Post Induction 2-Cycles

tag: batch id

tag: sample bridging_control


title: Nacc_ELA_SAFit2_NoInteraction_15

description: Library name: 22L006308

tag: treatment


title: t=4h, rep2

description: Library name: sample 11

tag: cell line

tag: genotype


title: RNA_3D-iMac_day16_Rep2


title: t=4h, rep3

description: Library name: sample 12


title: Nacc_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L006307


title: RNA_3D-iMac_day16_Rep1


title: BLA_ELA_SAFit2_NoInteraction_71

description: Library name: 22L006334


title: Nacc_ELA_Vehicle_NoInteraction_43

description: Library name: 22L006306


title: RNA_3D-iMac_day12_Rep3


title: RNA_3D-iMac_day12_Rep4


title: Nacc_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L006305


title: Nacc_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L006304


title: RNA_3D-iMac_day12_Rep1


title: Nacc_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L006303


title: RNA_3D-iMac_day12_Rep2


title: Nacc_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L006302


title: RNA_2D-iMac_day12_Rep4


title: BLA_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L006326


title: RNA_3D-iMac_SP14_Rep1


title: BLA_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L006328


title: Nacc_ELA_Vehicle_NoInteraction_99

description: Library name: 22L006301


title: RNA_2D-iMac_day12_Rep3


title: Nacc_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L006300


title: RNA_2D-iMac_day12_Rep2


title: Nacc_ELA_SAFit2_NoInteraction_47

description: Library name: 22L006299


title: RNA_2D-iMac_day12_Rep1


title: ChIP_3D-iMac_day12_K27me3_Rep3

tag: antibody


title: ChIP_3D-iMac_day12_K27me3_Rep2


title: Nacc_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L006297

tag: tissue


title: Nacc_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L006298


title: RNA_3D-iMac_day23_FBS_Rep1

tag: cell type


title: Nacc_ELA_Vehicle_NoInteraction_101

description: Library name: 22L006296


title: Nacc_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L006295


title: Nacc_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L006294


title: ChIP_3D-iMac_day12_K4me3_Rep3


title: ChIP_3D-iMac_day12_K27me3_Rep1


title: ChIP_3D-iMac_day12_K4me3_Rep2


title: Nacc_ELA_SAFit2_NoInteraction_71

description: Library name: 22L006293


title: Nacc_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L006292


title: ChIP_2D-iMac_day12_K27me3_Rep2


title: Nacc_ELA_Vehicle_NoInteraction_13

description: Library name: 22L006291


title: Nacc_ELA_SAFit2_NoInteraction_87

description: Library name: 22L006290


title: Nacc_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L006289


title: Nacc_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L006288


title: DSP-1001660019865-E-A03

city: Dallas

first: Chengsong

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: Library name: Sample 242

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: IA

tag: scan name

tag: roi

tag: segment


title: DSP-1001660019865-E-A02

description: Library name: Sample 241


title: Nacc_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L006287


title: DSP-1001660019865-E-A05

description: Library name: Sample 244

value: Desmin


title: DSP-1001660014867-C-H12

description: Library name: Sample 240

value: PF


title: DSP-1001660014867-C-H11

description: Library name: Sample 239


title: Nacc_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L006285


title: Nacc_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L006286


title: DSP-1001660014867-C-H10

description: Library name: Sample 238


title: Nacc_ELA_SAFit2_NoInteraction_7

description: Library name: 22L006284


title: DSP-1001660014867-C-H09

description: Library name: Sample 237


title: DSP-1001660019865-E-A04

description: Library name: Sample 243


title: DSP-1001660014867-C-H08

description: Library name: Sample 236


title: Nacc_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L006282


title: DSP-1001660014867-C-H06

description: Library name: Sample 234


title: DSP-1001660014867-C-H05

description: Library name: Sample 233


title: DSP-1001660014867-C-H07

description: Library name: Sample 235


title: Nacc_ELA_Vehicle_NoInteraction_37

description: Library name: 22L006281


title: Nacc_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L006279


title: DSP-1001660014867-C-H04

description: Library name: Sample 232


title: Nacc_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L006278


title: DSP-1001660014867-C-H03

description: Library name: Sample 231


title: DSP-1001660014867-C-H02

description: Library name: Sample 230


title: Nacc_ELA_SAFit2_NoInteraction_39

description: Library name: 22L006276


title: DSP-1001660014867-C-H01

description: Library name: Sample 229


title: Nacc_ELA_Vehicle_NoInteraction_69

description: Library name: 22L006275


title: DSP-1001660014867-C-G12

description: Library name: Sample 228


title: DSP-1001660014867-C-G10

description: Library name: Sample 226


title: Nacc_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L006274


title: Nacc_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L006273


title: Nacc_ELA_SAFit2_NoInteraction_103

description: Library name: 22L006271


title: Nacc_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L006272


title: Nacc_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L006270


title: DSP-1001660014867-C-G07

description: Library name: Sample 223


title: DSP-1001660014867-C-G06

description: Library name: Sample 222


title: Nacc_ELA_Vehicle_NoInteraction_5

description: Library name: 22L006269


title: DSP-1001660014867-C-G05

description: Library name: Sample 221

value: CF


title: ACC_ELA_SAFit2_NoInteraction_15

description: Library name: 22L006267

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: DSP-1001660014867-C-G04

description: Library name: Sample 220


title: ACC_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L006266


title: DSP-1001660014867-C-G03

description: Library name: Sample 219


title: ACC_ELA_Vehicle_NoInteraction_43

description: Library name: 22L006265


title: DSP-1001660014867-C-G02

description: Library name: Sample 218


title: ACC_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L006264


title: DSP-1001660014867-C-G01

description: Library name: Sample 217


title: DSP-1001660014867-C-F12

description: Library name: Sample 216


title: ACC_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L006263


title: ACC_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L006261


title: DSP-1001660014867-C-F11

description: Library name: Sample 215


title: DSP-1001660014867-C-F10

description: Library name: Sample 214


title: ACC_ELA_Vehicle_NoInteraction_99

description: Library name: 22L006260


title: DSP-1001660014867-C-F09

description: Library name: Sample 213


title: ACC_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L006259


title: ACC_ELA_SAFit2_NoInteraction_47

description: Library name: 22L006258


title: DSP-1001660014867-C-F08

description: Library name: Sample 212


title: ACC_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L006257


title: DSP-1001660014867-C-F07

description: Library name: Sample 211


title: DSP-1001660014867-C-F06

description: Library name: Sample 210


title: ACC_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L006256


title: Nacc_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L006283


title: DSP-1001660014867-C-F05

description: Library name: Sample 209


title: ACC_ELA_Vehicle_NoInteraction_101

description: Library name: 22L006255


title: Nacc_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L006280


title: ACC_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L006253


title: ACC_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L006254


title: DSP-1001660014867-C-F04

description: Library name: Sample 208


title: DSP-1001660014867-C-F03

description: Library name: Sample 207


title: Nacc_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L006277


title: DSP-1001660014867-C-F02

description: Library name: Sample 206


title: ACC_ELA_SAFit2_NoInteraction_71

description: Library name: 22L006252


title: DSP-1001660014867-C-F01

description: Library name: Sample 205


title: ACC_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L006251


title: DSP-1001660014867-C-G11

description: Library name: Sample 227


title: DSP-1001660014867-C-E12

description: Library name: Sample 204


title: DSP-1001660014867-C-G09

description: Library name: Sample 225


title: ACC_ELA_Vehicle_NoInteraction_13

description: Library name: 22L006250


title: DSP-1001660014867-C-E10

description: Library name: Sample 202


title: ACC_ELA_SAFit2_NoInteraction_87

description: Library name: 22L006249


title: ACC_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L006248


title: DSP-1001660014867-C-G08

description: Library name: Sample 224


title: DSP-1001660014867-C-E09

description: Library name: Sample 201


title: DSP-1001660014867-C-E11

description: Library name: Sample 203


title: DSP-1001660014867-C-E08

description: Library name: Sample 200


title: ACC_ELA_SAFit2_SocialInteraction_55

description: Library name: 22L006268


title: ACC_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L006244


title: DSP-1001660014867-C-E07

description: Library name: Sample 199


title: ACC_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L006246


title: DSP-1001660014867-C-E06

description: Library name: Sample 198


title: ACC_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L006245


title: DSP-1001660014867-C-E05

description: Library name: Sample 197


title: ACC_ELA_SAFit2_NoInteraction_7

description: Library name: 22L006243


title: DSP-1001660014867-C-E04

description: Library name: Sample 196


title: ACC_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L006241


title: DSP-1001660014867-C-E03

description: Library name: Sample 195


title: DSP-1001660014867-C-E02

description: Library name: Sample 194


title: ACC_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L006242


title: ACC_ELA_Vehicle_NoInteraction_37

description: Library name: 22L006240


title: ACC_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L006247


title: ACC_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L006262


title: DSP-1001660014867-C-E01

description: Library name: Sample 193


title: ACC_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L006238


title: ACC_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L006239


title: DSP-1001660014867-C-D11

description: Library name: Sample 191


title: DSP-1001660014867-C-D12

description: Library name: Sample 192


title: ACC_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L006237


title: DSP-1001660014867-C-D10

description: Library name: Sample 190


title: ACC_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L006236


title: BLA_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L006318

value: basolateral amygdala


title: ACC_ELA_SAFit2_NoInteraction_39

description: Library name: 22L006235


title: DSP-1001660014867-C-D08

description: Library name: Sample 188


title: DSP-1001660014867-C-D09

description: Library name: Sample 189


title: ACC_ELA_Vehicle_NoInteraction_69

description: Library name: 22L006234


title: DSP-1001660014867-C-D07

description: Library name: Sample 187


title: BLA_ELA_SAFit2_NoInteraction_39

description: Library name: 22L006317


title: ACC_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L006233


title: RNA_3D-iMac_day23_Rep3

value: macrophage

tag: time point

tag: protocol


title: ACC_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L006231


title: DSP-1001660014867-C-D05

description: Library name: Sample 185


title: ACC_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L006232


title: DSP-1001660014867-C-D04

description: Library name: Sample 184