title: AB4475

description:
Library name: Sample673
MARS


title: CAR14_P

status: Public on Jul 21 2026

type: SRA

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

country: China

institute: Sichuan University

description:
Library name: sample17
processed Cell Ranger single-cell gene expression output archive

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files generated from the 10x Genomics platform were aligned to the human GRCh38 reference genome (reference version 6.1.2), and gene expression matrices were quantified with Cell Ranger v4.3.0 using default parameters.
For each sample, Cell Ranger output files containing filtered gene expression matrices and associated barcode and feature annotations were compressed as sample-specific .tar.gz archives. The per-sample processed outputs were also collected into a combined .tar.gz archive for convenient GEO submission.
Cell Ranger count matrices were imported into Seurat v4.0 for downstream quality control and analysis. Potential doublets were detected with Scrublet v0.2.3; low-quality cells and genes were filtered before normalization and integration.
For downstream analysis, counts were normalized and log-transformed, highly variable genes were selected, and batch effects across transplant samples were corrected using a mutual-nearest-neighbor/FastMNN-based workflow. Clustering was performed with graph-based methods and visualized by UMAP.
Major immune and blood cell populations and finer cell states were annotated by comparing cluster-specific differentially expressed genes with canonical markers and the relevant literature.
Assembly: Homo sapiens GRCh38 (10x Genomics/Cell Ranger human reference, version 6.1.2)
Supplementary files format and content: Sample-specific processed data files are .tar.gz archives of Cell Ranger outputs. Each archive contains analysis-ready 10x Genomics single-cell gene expression matrix files, including filtered matrix, barcode and feature/gene annotation files, and associated Cell Ranger summary or metadata files where available.
Supplementary files format and content: A combined .tar.gz archive contains all per-sample Cell Ranger processed outputs for kidney graft tissue and peripheral blood single-cell RNA-seq samples.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Fresh peripheral blood and kidney graft tissue samples were processed immediately after collection to generate single-cell suspensions for single-cell RNA sequencing. Peripheral blood mononuclear cells were isolated by density-gradient centrifugation, followed by red blood cell lysis with ammonium chloride-based lysis buffer on ice for 5-7 min. Cells were washed twice with pre-chilled PBS and resuspended in PBS containing 0.04% BSA. Kidney tissue was minced on ice, enzymatically dissociated according to the 10x Genomics tissue dissociation workflow, mechanically triturated, sequentially filtered through 70-um and 40-um strainers, centrifuged and resuspended in PBS containing 0.04% BSA. Cell viability was assessed by trypan blue exclusion, and debris removal was performed when necessary before single-cell capture.
Single-cell suspensions were loaded onto 10x Genomics Chromium microfluidic chips using 3' v3 chemistry and processed with the Chromium Controller to generate barcoded gel-bead emulsions. cDNA synthesis and gene expression library construction were performed with the Chromium Single Cell 3' v3 reagent kit according to the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

tag: tissue

value: peripheral blood

tag: subject status

value: CAMR

tag: cohort

value: Discovery

tag: Sex

value: M

tag: age（years）

tag: donor type

value: Deceased donor

tag: post-transplant time_(years)

tag: maintenance immunosuppressive_regimen

value: Tacrolimus + mycophenolate mofetil + corticosteroids

tag: clinical sample_id


title: AB4474

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample672
MARS

library_source: transcriptomic

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

molecule: polyA RNA

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM

tag: gate

value: PC

tag: batch


title: CAR13_P

description:
Library name: sample16
processed Cell Ranger single-cell gene expression output archive


title: CAR12_P

description:
Library name: sample15
processed Cell Ranger single-cell gene expression output archive


title: AB4472

description:
Library name: Sample671
MARS


title: AB4471

description:
Library name: Sample670
MARS


title: CAR04_P

description:
Library name: sample14
processed Cell Ranger single-cell gene expression output archive

value: Living donor


title: CAR02_P

description:
Library name: sample13
processed Cell Ranger single-cell gene expression output archive


title: AB4470

description:
Library name: Sample669
MARS


title: AB4469

description:
Library name: Sample668
MARS


title: AB4616

description:
Library name: Sample692
MARS


title: AB4468

description:
Library name: Sample667
MARS


title: CAR01_P

description:
Library name: sample12
processed Cell Ranger single-cell gene expression output archive


title: CAMRT2P_P

description:
Library name: sample11
processed Cell Ranger single-cell gene expression output archive

value: Validation

value: F


title: AB4467

description:
Library name: Sample666
MARS


title: CAMRT1P_P

description:
Library name: sample10
processed Cell Ranger single-cell gene expression output archive


title: CAMRC3P_P

description:
Library name: sample9
processed Cell Ranger single-cell gene expression output archive


title: AB4466

description:
Library name: Sample665
MARS


title: AB4464

description:
Library name: Sample664
MARS


title: CAMRC1P_P

description:
Library name: sample8
processed Cell Ranger single-cell gene expression output archive


title: AB4463

description:
Library name: Sample663
MARS


title: CAMR36_T

description:
Library name: sample7
processed Cell Ranger single-cell gene expression output archive

source_name: Tissue

value: Tissue


title: AB4462

description:
Library name: Sample662
MARS


title: AB4461

description:
Library name: Sample661
MARS


title: CAMR34_T

description:
Library name: sample6
processed Cell Ranger single-cell gene expression output archive


title: CAMR33_T

description:
Library name: sample5
processed Cell Ranger single-cell gene expression output archive


title: CAMR19_T

description:
Library name: sample4
processed Cell Ranger single-cell gene expression output archive


title: AB4262

description:
Library name: Sample660
MARS


title: AB4261

description:
Library name: Sample659
MARS


title: AB4260

description:
Library name: Sample658
MARS


title: CAMR16_T

description:
Library name: sample3
processed Cell Ranger single-cell gene expression output archive


title: CAMR14_T

description:
Library name: sample2
processed Cell Ranger single-cell gene expression output archive


title: AB4257

description:
Library name: Sample657
MARS


title: CAMR12_T

description:
Library name: sample1
processed Cell Ranger single-cell gene expression output archive


title: AB4256

description:
Library name: Sample656
MARS


title: RWPE1 cell line exogenously expressing ERG and myristoylated AKT

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Biology 200

country: USA

institute: Indiana University

description:
Library name: REMA
10x Genomics

data_processing:
Cells were quantified using Cell Ranger 7.1.0. Genes with less than 5 cells with expression were removed. Quality control protocols for cells include requiring a minimum of 200 and a maximum of 2500 expressed genes per cell. Cells with a Mitochondrial percent less than 7.5 were also filtered out. The R package Harmony was used to integrate the two existing datasets  after normalization and both UMAP and PCA dimension reduction was performed and used for visualization and clustering. A Wilcoxon Rank Sum test was performed per gene and marker genes were defined as having a Benjamini-Hochberg adjusted p-value less than 0.05.
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Prostate

extract_protocol:
Cell were trypsinized, pelleted at 300 rcf, 5min, resuspended in 1xPBS with 0.04% BSA
10,000 cells were used as input to the 10X Genomics Chromium system using the Chromium Next GEM Single Cell 3' Kit v3.1

value: Prostate

tag: cell line

tag: cell type

value: Epithelial

tag: genotype

value: ERG, mAKT


title: AB4255

description:
Library name: Sample655
MARS


title: AB4254

description:
Library name: Sample654
MARS


title: RWPE1 cell line

description:
Library name: RWPE1
10x Genomics

value: Vector only control


title: HeLa, FBS-SM, biological replicate 3

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

description: Library name: Hela_S_3

data_processing:
Raw FASTQ reads were screened for rRNA-derived sequences using RiboDetector (v0.2.7); reads classified as rRNA were removed prior to downstream processing.
Non-rRNA reads were quality filtered and adapter trimmed using fastp (v0.20.0) with sliding-window trimming (minimum base quality Q20); short reads (<80 bp) were removed.
High-quality reads were aligned to the human reference genome (UCSC hg38) using STAR (v2.7.10b) within the Sentieon® secondary analysis framework (release 202503) with two-pass mapping; Eurofins parameterization included splice junction and fusion read detection.
Alignment and mapping QC were generated using Qualimap (v2.2.2-dev; strand-specific-reverse)
Gene- and transcript-level abundance estimates were generated using RSEM (v1.3.3).
Assembly: hg38 (UCSC)
Supplementary files format and content: Tab-delimited text file (TSV) containing gene_id, gene_name, and integer raw read counts for each library (raw_counts.tsv).
Supplementary files format and content: Tab-delimited text file (TSV) containing gene_id, gene_name, and DESeq2 size-factor normalized counts for each library (normalized_counts.tsv).

source_name: cervix

growth_protocol: HepaRG and HuH7 were maintained under two parallel culture conditions: a conventional FBS-supplemented medium (FBS-SM) and a serum-free chemically defined medium (CDM), using cell line–specific formulations. HeLa cells were included as a non-hepatic outgroup and cultured under matched FBS-SM and CDM conditions. For each cell line, FBS-SM and CDM cultures were passaged in parallel for five consecutive passages prior to RNA isolation.

extract_protocol:
Total RNA was isolated using the QIAwave RNA Kit (50) (74534, Qiagen) according to the manufacturer’s instructions. Adherent monolayers were washed with PBS and lysed directly in RLT buffer supplemented with β-mercaptoethanol (1% v/v). For pooled PHH, cryovials were thawed (37 °C, 2 min), diluted in nine volumes of ice-cold PBS, pelleted (100 × g, 5 min, 4 °C), supernatant removed, and pellets lysed in RLT buffer. RNA concentration and purity (A260/280 and A260/230) were assessed using a NanoDrop 2000 UV-Vis spectrophotometer.
RNA-seq libraries were prepared and sequenced by Eurofins Genomics (INVIEW™ Transcriptome Discover service). mRNA was enriched using bead-based poly(A) selection, followed by library preparation (Eurofins standard pipeline). Libraries were sequenced on an Illumina NovaSeq platform as paired-end 2 × 150 bp reads (NovaSeq PE150) with a target yield of 30 million read pairs per sample (±3%).

treatment_protocol: The primary experimental factor was culture medium composition (CDM versus FBS-SM) within each cell model. HepaRG differentiation was performed identically in both media: 14 days in growth medium, 24 h in the corresponding medium containing 1% DMSO, followed by 14 days in the corresponding medium containing 1.7% DMSO. HuH7 were directly adapted to CDM without gradual serum withdrawal

value: cervix

value: HeLa

value: cervical adenocarcinoma cells

tag: treatment

value: FBS-supplemented medium (FBS-SM)


title: AB3710

description:
Library name: Sample653
MARS


title: HeLa, FBS-SM, biological replicate 2

description: Library name: Hela_S_2


title: AB3709

description:
Library name: Sample652
MARS


title: HeLa, FBS-SM, biological replicate 1

description: Library name: Hela_S_1


title: AB3708

description:
Library name: Sample651
MARS


title: HeLa, CDM, biological replicate 3

description: Library name: Hela_C_3

value: chemically defined medium (CDM)


title: AB3707

description:
Library name: Sample650
MARS


title: AB4736

description:
Library name: Sample716
MARS


title: HeLa, CDM, biological replicate 2

description: Library name: Hela_C_2


title: Gene expression library of B cell  rxn 3 replicate 2

city: La Jolla

first: Bryan

last: Briney

state: CA

address: 10550 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

description:
Library name: Bcell2.3_GEX
10x Genomic HT, Gene Expression

data_processing:
FASTQ files were generated from raw base call files using CellRanger, and downstream analyses were performed with scab (Hurtado et al. 2022). Matrices of VDJ contigs and counts were assembled by alignment to VDJ and transcriptome reference genomes, outputting full-length per cell VDJ sequences as FASTA files and expression profiles (cells x genes) as an .h5 file, differentiating individual cells by barcode. Antibody sequences were annotated using abstar (Briney and Burton 2018) and integrated with gene expression and cellhash data using scab. Donors were demultiplexed by cellhash using scab. Because samples had different read depths, cell hash thresholds were incorrectly high for some of the samples with fewer reads per cell. Reads were thus normalized to ensure equal representation from each donor. To further refine the expression matrix, cells with fewer than 200 and greater than 6000 genes were removed. Genes which appeared in fewer than 50 cells were also removed. Normalization, log plus one transformation, and scaling were performed using scab and scanpy. Scab’s dimensionality reduction tool performed principle component analysis, neighborhood graphing, and cell clustering according to the Leiden algorithm and utilized UMAP for embedding (Traag, Waltman, and van Eck 2019; Becht et al. 2018; McInnes, Healy, and Melville 2018). Doublets were identified using Scrublet (Wolock, Lopez, and Klein 2019) and all doublets, including entire clusters containing primarily doublets, were removed. Cells were then re-clustered without doublets and identified as lymphoid, myeloid, erythroid, plasma cells, T cells, or B cells according to gene expression profiles. B cells were then separated out, clustered again for granularity, and subset into developmental phases also according to gene expression profiles.
Assembly: gene expression assembly - refdata-gex-GRCh38-2020-A, for V(D)J assembly - refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, all_contig_annotations.csv
Library strategy: CITE-seq

source_name: Bone marrow

extract_protocol:
Bone marrow samples from four healthy adult donors were obtained through our commercial clinical partner (ALLCELLS). Lymphocytes were isolated by density gradient centrifugation using Lymphoprep (StemCell Technologies). To ensure representation of early progenitors and developing B cell populations, donor samples were individually enriched for B cells and hematopoietic stem cells by EasySep Human B Cell Enrichment and Human CD34+ Selection Kits (StemCell Technologies).
Single-cell RNA sequencing (scRNAseq) was performed on over 3.8x105 cells from bone marrow and enriched samples with the 10x Genomics 5’ Single Cell Immune Profiling Kit (v2). Briefly, donor samples were individually labelled with Totalseq Anti-Human Hashtags (Biolegend) and pooled prior to overloading the 10x Genomic reaction, targeting 4-6x104 cells per run (Stoeckius et al. 2018). Single-cell emulsion generation, barcoding, V(D)J enrichment, and sequencing library construction were carried out according to theChromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000330 Rev A). Final libraries were sequenced on a NovaSeq 6000 using a 26-10-10-90 read configuration, with minimum target sequencing depths of 5,000 reads per cell for Cell Surface Protein libraries, 10,000 reads per cell for V(D)J libraries, and 30,000 reads per cell for Gene expression libraries.

value: Bone marrow

value: B-cell

tag: library type

value: mRNA


title: AB3700

description:
Library name: Sample648
MARS

value: BM

value: PC


title: Pooled primary human hepatocytes, replicate 2

description: Library name: PHH_2

source_name: liver

value: liver

value: primary human hepatocytes


title: HeLa, CDM, biological replicate 1

description: Library name: Hela_C_1


title: AB3701

description:
Library name: Sample649
MARS


title: Pooled primary human hepatocytes, replicate 1

description: Library name: PHH_1


title: AB3699

description:
Library name: Sample647
MARS


title: AB3698

description:
Library name: Sample646
MARS


title: AB4729

description:
Library name: Sample710
MARS


title: AB3697

description:
Library name: Sample645
MARS


title: Gene expression library of B cell  rxn 1 replicate 2

description:
Library name: Bcell2.1_GEX
10x Genomic HT, Gene Expression


title: HuH7, FBS-SM, biological replicate 3

description: Library name: Hu_S_3

value: hepatocellular carcinoma cells


title: HuH7, FBS-SM, biological replicate 2

description: Library name: Hu_S_2


title: AB3696

description:
Library name: Sample644
MARS


title: HuH7, FBS-SM, biological replicate 1

description: Library name: Hu_S_1


title: AB3695

description:
Library name: Sample643
MARS


title: HuH7, CDM, biological replicate 3

description: Library name: Hu_C_3


title: AB3551

description:
Library name: Sample642
MARS


title: HuH7, CDM, biological replicate 2

description: Library name: Hu_C_2


title: HuH7, CDM, biological replicate 1

description: Library name: Hu_C_1


title: AB3550

description:
Library name: Sample641
MARS


title: AB3549

description:
Library name: Sample640
MARS


title: HepaRG, FBS-SM, biological replicate 3

description: Library name: RG_S_3

value: HepaRG

value: differentiated hepatocyte-like cells


title: AB3548

description:
Library name: Sample639
MARS


title: HepaRG, FBS-SM, biological replicate 2

description: Library name: RG_S_2


title: AB3547

description:
Library name: Sample638
MARS


title: HepaRG, FBS-SM, biological replicate 1

description: Library name: RG_S_1


title: AB3546

description:
Library name: Sample637
MARS


title: HepaRG, CDM, biological replicate 3

description: Library name: RG_C_3


title: AB3474

description:
Library name: Sample636
MARS


title: HepaRG, CDM, biological replicate 2

description: Library name: RG_C_2


title: HepaRG, CDM, biological replicate 1

description: Library name: RG_C_1


title: AB3473

description:
Library name: Sample635
MARS


title: AB3472

description:
Library name: Sample634
MARS


title: AB3471

description:
Library name: Sample633
MARS


title: AB3470

description:
Library name: Sample632
MARS


title: AB3468

description:
Library name: Sample631
MARS


title: ONS_Sh5_4

city: Orsay

first: Sabine

last: Druillennec

address: Bat 110 centre universitaire

country: France

institute: Institut Curie

description: Library name: P118T359

data_processing:
Raw sequencing reads were first checked for quality with Fastqc (0.12.0) and trimmed for adapter sequences with cutadapt using the TrimGalore (0.6.11) wrapper.
Trimmed reads were subsequently aligned to the complete human ribosomal RNA sequence with bowtie1 (1.3.0).
Reads that did not align to rRNA were then mapped to the human reference genome hg38 and read counts per gene were generated with STAR mapper (2.7.6a).
The bioinformatics pipelines used for these tasks are available online (RNAseq v4.2.2 : https://gitlab.curie.fr/data-analysis/RNA-seq, doi: 10.5281/zenodo.7443721).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: ONS

growth_protocol: D458, D425, ONS and RPE cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles were seeded 72h after infection and total RNA was isolated 48h after.  RNA-sequencing data were used to compare gene expression profiles upon HSPA5 knockdown.

extract_protocol:
Total RNAs were isolated using the RNeasy plus mini kit for RNA purification (Qiagen). RNA Quality was evaluated by Bioanalyzer (Agilent Technologies) and samples with RNA integrity > 7 were used for library construction.
RNA-sequencing libraries were prepared from 1µg of total RNA following the Illumina stranded mRNA prep Ligation protocol.

value: ONS

value: Medulloblastoma cell line

value: HSPA5 knockdown


title: RPE_Sh5_4

description: Library name: P118T360

source_name: RPE

value: RPE

value: Retinal Pigment Epithelium cell  line


title: D458_Sh5_4

description: Library name: P118T358


title: D425_Sh5_4

description: Library name: P118T357


title: AB3466

description:
Library name: Sample630
MARS


title: AB3465

description:
Library name: Sample629
MARS


title: RPE_Sh2_4

description: Library name: P118T355


title: ONS_Sh2_4

description: Library name: P118T354


title: AB3464

description:
Library name: Sample628
MARS


title: D458_Sh2_4

description: Library name: P118T353


title: AB3463

description:
Library name: Sample627
MARS


title: D425_Sh2_4

description: Library name: P118T352


title: RPE_ShCTL_4

description: Library name: P118T350

value: WT


title: AB3462

description:
Library name: Sample626
MARS


title: AB3461

description:
Library name: Sample625
MARS


title: ONS_ShCTL_4

description: Library name: P118T349


title: D458_ShCTL_4

description: Library name: P118T348


title: AB3458

description:
Library name: Sample623
MARS


title: D425_ShCTL_4

description: Library name: P118T347


title: AB3459

description:
Library name: Sample624
MARS


title: AB3457

description:
Library name: Sample622
MARS


title: RPE_Sh5_3

description: Library name: P118T345


title: ONS_Sh5_3

description: Library name: P118T344


title: AB3456

description:
Library name: Sample621
MARS


title: AB3455

description:
Library name: Sample620
MARS


title: D458_Sh5_3

description: Library name: P118T343


title: AB3454

description:
Library name: Sample619
MARS


title: RPE_Sh2_3

description: Library name: P118T340


title: D425_Sh5_3

description: Library name: P118T342


title: AB3453

description:
Library name: Sample618
MARS


title: AB3452

description:
Library name: Sample617
MARS


title: ONS_Sh2_3

description: Library name: P118T339


title: AB3451

description:
Library name: Sample616
MARS


title: D458_Sh2_3

description: Library name: P118T338


title: AB3448

description:
Library name: Sample615
MARS


title: D425_Sh2_3

description: Library name: P118T337


title: AB3447

description:
Library name: Sample614
MARS


title: RPE_ShCTL_3

description: Library name: P118T335


title: ONS_ShCTL_3

description: Library name: P118T334


title: AB3446

description:
Library name: Sample613
MARS


title: D458_ShCTL_3

description: Library name: P118T333


title: AB3445

description:
Library name: Sample612
MARS


title: AB3444

description:
Library name: Sample611
MARS


title: AB3333

description:
Library name: Sample609
MARS


title: RPE_Sh5_2

description: Library name: P118T330


title: D425_ShCTL_3

description: Library name: P118T332


title: AB3337

description:
Library name: Sample610
MARS


title: ONS_Sh5_2

description: Library name: P118T329


title: D458_Sh5_2

description: Library name: P118T328


title: D425_Sh5_2

description: Library name: P118T327


title: AB3332

description:
Library name: Sample608
MARS


title: AB3331

description:
Library name: Sample607
MARS


title: RPE_Sh2_2

description: Library name: P118T325


title: AB3329

description:
Library name: Sample605
MARS


title: AB3330

description:
Library name: Sample606
MARS


title: AB3328

description:
Library name: Sample604
MARS


title: D458_Sh2_2

description: Library name: P118T323


title: AB3326

description:
Library name: Sample603
MARS


title: AB3324

description:
Library name: Sample602
MARS


title: RPE_ShCTL_2

description: Library name: P118T320


title: D425_Sh2_2

description: Library name: P118T322


title: AB3196

description:
Library name: Sample601
MARS


title: D458_ShCTL_2

description: Library name: P118T318


title: AB3194

description:
Library name: Sample600
MARS


title: ONS_ShCTL_2

description: Library name: P118T319


title: AB3192

description:
Library name: Sample599
MARS


title: D425_ShCTL_2

description: Library name: P118T317


title: AB3191

description:
Library name: Sample598
MARS


title: RPE_Sh5_1

description: Library name: P118T315


title: AB3190

description:
Library name: Sample597
MARS


title: ONS_Sh5_1

description: Library name: P118T314


title: AB3189

description:
Library name: Sample596
MARS


title: D458_Sh5_1

description: Library name: P118T313


title: AB3188

description:
Library name: Sample595
MARS


title: AB3187

description:
Library name: Sample594
MARS


title: D425_Sh5_1

description: Library name: P118T312


title: RPE_Sh2_1

description: Library name: P118T310


title: ONS_Sh2_1

description: Library name: P118T309


title: AB3186

description:
Library name: Sample593
MARS


title: AB3184

description:
Library name: Sample592
MARS


title: AB3183

description:
Library name: Sample591
MARS


title: D458_Sh2_1

description: Library name: P118T308


title: D425_Sh2_1

description: Library name: P118T307


title: AB3182

description:
Library name: Sample590
MARS


title: RPE_ShCTL_1

description: Library name: P118T305


title: ONS_ShCTL_1

description: Library name: P118T304


title: AB3181

description:
Library name: Sample589
MARS


title: AB3180

description:
Library name: Sample588
MARS


title: D458_ShCTL_1

description: Library name: P118T303


title: D425_ShCTL_1

description: Library name: P118T302


title: AB3179

description:
Library name: Sample587
MARS


title: AB3154

description:
Library name: Sample586
MARS


title: AB9948

description:
Library name: Sample2111
MARS_v2


title: AB3153

description:
Library name: Sample585
MARS


title: AB9947

description:
Library name: Sample2110
MARS_v2


title: AB3152

description:
Library name: Sample584
MARS


title: AB9946

description:
Library name: Sample2109
MARS_v2


title: AB3151

description:
Library name: Sample583
MARS


title: AB9945

description:
Library name: Sample2108
MARS_v2


title: AB3150

description:
Library name: Sample582
MARS


title: AB9944

description:
Library name: Sample2107
MARS_v2


title: AB3149

description:
Library name: Sample581
MARS


title: AB3148

description:
Library name: Sample580
MARS


title: AB9941

description:
Library name: Sample2106
MARS_v2


title: AB9940

description:
Library name: Sample2105
MARS_v2


title: AB3147

description:
Library name: Sample579
MARS


title: AB9939

description:
Library name: Sample2104
MARS_v2


title: AB3146

description:
Library name: Sample578
MARS


title: AB9938

description:
Library name: Sample2103
MARS_v2


title: AB3145

description:
Library name: Sample577
MARS


title: AB9937

description:
Library name: Sample2102
MARS_v2


title: AB9936

description:
Library name: Sample2101
MARS_v2


title: AB3144

description:
Library name: Sample576
MARS


title: AB3073

description:
Library name: Sample575
MARS


title: AB9920

description:
Library name: Sample2100
MARS_v2


title: AB3072

description:
Library name: Sample574
MARS


title: AB9919

description:
Library name: Sample2099
MARS_v2


title: AB3071

description:
Library name: Sample573
MARS


title: AB9918

description:
Library name: Sample2098
MARS_v2


title: AB3070

description:
Library name: Sample572
MARS


title: AB9917

description:
Library name: Sample2097
MARS_v2


title: AB3069

description:
Library name: Sample571
MARS


title: AB9916

description:
Library name: Sample2096
MARS_v2


title: AB3068

description:
Library name: Sample570
MARS


title: AB9914

description:
Library name: Sample2094
MARS_v2


title: AB3067

description:
Library name: Sample569
MARS


title: AB3066

description:
Library name: Sample568
MARS


title: ONS_Sh2_2

description: Library name: P118T324


title: AB9913

description:
Library name: Sample2093
MARS_v2


title: AB3065

description:
Library name: Sample567
MARS


title: AB9912

description:
Library name: Sample2092
MARS_v2


title: AB9915

description:
Library name: Sample2095
MARS_v2


title: AB3064

description:
Library name: Sample566
MARS


title: AB9911

description:
Library name: Sample2091
MARS_v2


title: AB3063

description:
Library name: Sample565
MARS


title: AB9910

description:
Library name: Sample2090
MARS_v2


title: AB3061

description:
Library name: Sample564
MARS


title: AB9909

description:
Library name: Sample2089
MARS_v2


title: AB9908

description:
Library name: Sample2088
MARS_v2


title: AB3060

description:
Library name: Sample563
MARS


title: AB3058

description:
Library name: Sample562
MARS


title: AB9907

description:
Library name: Sample2087
MARS_v2


title: AB9906

description:
Library name: Sample2086
MARS_v2


title: AB3057

description:
Library name: Sample561
MARS


title: AB9896

description:
Library name: Sample2085
MARS_v2


title: AB3055

description:
Library name: Sample559
MARS


title: AB3056

description:
Library name: Sample560
MARS


title: AB9895

description:
Library name: Sample2084
MARS_v2


title: AB3001

description:
Library name: Sample558
MARS


title: AB3000

description:
Library name: Sample557
MARS


title: AB9894

description:
Library name: Sample2083
MARS_v2


title: AB9893

description:
Library name: Sample2082
MARS_v2


title: AB2972

description:
Library name: Sample556
MARS


title: AB2971

description:
Library name: Sample555
MARS


title: AB9892

description:
Library name: Sample2081
MARS_v2


title: AB2970

description:
Library name: Sample554
MARS


title: AB9891

description:
Library name: Sample2080
MARS_v2


title: AB9890

description:
Library name: Sample2079
MARS_v2


title: AB2968

description:
Library name: Sample552
MARS


title: AB9889

description:
Library name: Sample2078
MARS_v2


title: AB2969

description:
Library name: Sample553
MARS


title: AB9774

description:
Library name: Sample2077
MARS_v2


title: AB2967

description:
Library name: Sample551
MARS


title: AB9773

description:
Library name: Sample2076
MARS_v2


title: AB2966

description:
Library name: Sample550
MARS


title: AB9772

description:
Library name: Sample2075
MARS_v2


title: AB9574

description:
Library name: Sample2074
MARS_v2


title: AB2964

description:
Library name: Sample549
MARS


title: AB2962

description:
Library name: Sample548
MARS


title: AB9573

description:
Library name: Sample2073
MARS_v2


title: AB2961

description:
Library name: Sample547
MARS


title: AB2960

description:
Library name: Sample546
MARS


title: AB9572

description:
Library name: Sample2072
MARS_v2


title: AB9571

description:
Library name: Sample2071
MARS_v2


title: AB2959

description:
Library name: Sample545
MARS


title: AB9570

description:
Library name: Sample2070
MARS_v2


title: AB2958

description:
Library name: Sample544
MARS


title: AB9569

description:
Library name: Sample2069
MARS_v2


title: AB9568

description:
Library name: Sample2068
MARS_v2


title: AB2956

description:
Library name: Sample543
MARS


title: AB2955

description:
Library name: Sample542
MARS


title: AB9567

description:
Library name: Sample2067
MARS_v2


title: AB2953

description:
Library name: Sample540
MARS


title: AB2954

description:
Library name: Sample541
MARS


title: AB9565

description:
Library name: Sample2065
MARS_v2


title: AB2952

description:
Library name: Sample539
MARS


title: AB9563

description:
Library name: Sample2063
MARS_v2


title: AB2951

description:
Library name: Sample538
MARS


title: AB9562

description:
Library name: Sample2062
MARS_v2


title: AB2947

description:
Library name: Sample536
MARS


title: AB2946

description:
Library name: Sample535
MARS


title: AB2945

description:
Library name: Sample534
MARS


title: AB9560

description:
Library name: Sample2060
MARS_v2


title: AB9559

description:
Library name: Sample2059
MARS_v2


title: AB9558

description:
Library name: Sample2058
MARS_v2


title: AB2839

description:
Library name: Sample533
MARS


title: AB2838

description:
Library name: Sample532
MARS


title: AB9557

description:
Library name: Sample2057
MARS_v2


title: AB2837

description:
Library name: Sample531
MARS


title: AB9556

description:
Library name: Sample2056
MARS_v2


title: AB2836

description:
Library name: Sample530
MARS


title: AB9555

description:
Library name: Sample2055
MARS_v2


title: AB9554

description:
Library name: Sample2054
MARS_v2


title: AB2835

description:
Library name: Sample529
MARS


title: AB9552

description:
Library name: Sample2052
MARS_v2


title: AB9551

description:
Library name: Sample2051
MARS_v2


title: AB2831

description:
Library name: Sample525
MARS


title: AB9550

description:
Library name: Sample2050
MARS_v2


title: AB9026

description:
Library name: Sample2048
MARS_v2


title: AB2830

description:
Library name: Sample524
MARS


title: AB9549

description:
Library name: Sample2049
MARS_v2


title: AB2708

description:
Library name: Sample522
MARS


title: AB9025

description:
Library name: Sample2047
MARS_v2


title: AB2707

description:
Library name: Sample521
MARS


title: AB9024

description:
Library name: Sample2046
MARS_v2


title: AB9023

description:
Library name: Sample2045
MARS_v2


title: AB2706

description:
Library name: Sample520
MARS


title: AB9022

description:
Library name: Sample2044
MARS_v2


title: AB2704

description:
Library name: Sample518
MARS


title: AB9021

description:
Library name: Sample2043
MARS_v2


title: AB2701

description:
Library name: Sample516
MARS


title: AB9020

description:
Library name: Sample2042
MARS_v2


title: AB2700

description:
Library name: Sample515
MARS


title: AB8893

description:
Library name: Sample2040
MARS_v2


title: AB2699

description:
Library name: Sample514
MARS


title: AB8892

description:
Library name: Sample2039
MARS_v2


title: AB2698

description:
Library name: Sample513
MARS


title: AB8891

description:
Library name: Sample2038
MARS_v2


title: AB9553

description:
Library name: Sample2053
MARS_v2


title: AB2697

description:
Library name: Sample512
MARS


title: AB2832

description:
Library name: Sample526
MARS


title: AB2833

description:
Library name: Sample527
MARS


title: AB8890

description:
Library name: Sample2037
MARS_v2


title: AB8889

description:
Library name: Sample2036
MARS_v2


title: AB2695

description:
Library name: Sample510
MARS


title: AB8888

description:
Library name: Sample2035
MARS_v2


title: AB2694

description:
Library name: Sample509
MARS


title: AB2693

description:
Library name: Sample508
MARS


title: AB8886

description:
Library name: Sample2033
MARS_v2


title: AB2692

description:
Library name: Sample507
MARS


title: AB2691

description:
Library name: Sample506
MARS


title: AB8884

description:
Library name: Sample2031
MARS_v2


title: AB2690

description:
Library name: Sample505
MARS


title: AB8883

description:
Library name: Sample2030
MARS_v2


title: AB2565

description:
Library name: Sample504
MARS


title: AB8882

description:
Library name: Sample2029
MARS_v2


title: AB2564

description:
Library name: Sample503
MARS


title: AB8881

description:
Library name: Sample2028
MARS_v2


title: AB2563

description:
Library name: Sample502
MARS


title: AB8880

description:
Library name: Sample2027
MARS_v2


title: AB2562

description:
Library name: Sample501
MARS


title: AB8879

description:
Library name: Sample2026
MARS_v2


title: AB2560

description:
Library name: Sample500
MARS


title: AB8878

description:
Library name: Sample2025
MARS_v2


title: AB2696

description:
Library name: Sample511
MARS


title: AB2559

description:
Library name: Sample499
MARS


title: AB8877

description:
Library name: Sample2024
MARS_v2


title: AB8887

description:
Library name: Sample2034
MARS_v2


title: AB2558

description:
Library name: Sample498
MARS


title: AB2557

description:
Library name: Sample497
MARS


title: AB8876

description:
Library name: Sample2023
MARS_v2


title: AB8867

description:
Library name: Sample2022
MARS_v2


title: AB8885

description:
Library name: Sample2032
MARS_v2


title: U937 cells, control, rep2

city: Hefei

first: Mengqing

last: Gao

state: Anhui

department: Department of Hematology

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

data_processing:
Raw fastq reads were processed using fastp to remove low-quality reads, resulting in clean reads for subsequent data analysis.
HISAT2 was used for alignment to the reference genome hg38.
Gene expression levels were calculated in FPKM and the read counts for each gene were obtained using HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: U937 cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA from U937 cells was extracted with TRIzol reagent (Invitrogen, 15596026CN). RNAs from primary samples were extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Cat# 80004) according to the manufacturer’s instructions.
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme) for AML primary samples and Fast RNA-seq Lib Prep Kit V2 (ABclonal) for cell lines according to the manufacturer's instructions

treatment_protocol: U937 NT, KO1, KO2 were deprived of glutamine for 6 hours. U937 cells were treated with 0.5 μM JQ1 for 24 hours.

value: acute myeloid leukemia cell lines

value: DMSO


title: AB2556

description:
Library name: Sample496
MARS


title: AB8866

description:
Library name: Sample2021
MARS_v2


title: AB2555

description:
Library name: Sample495
MARS


title: AB8865

description:
Library name: Sample2020
MARS_v2


title: AB2554

description:
Library name: Sample494
MARS


title: AB9566

description:
Library name: Sample2066
MARS_v2


title: AB8722

description:
Library name: Sample2018
MARS_v2


title: AB2315

description:
Library name: Sample493
MARS


title: AB2314

description:
Library name: Sample492
MARS


title: AB8864

description:
Library name: Sample2019
MARS_v2


title: AB9564

description:
Library name: Sample2064
MARS_v2


title: AB8721

description:
Library name: Sample2017
MARS_v2


title: AB2313

description:
Library name: Sample491
MARS


title: AB8720

description:
Library name: Sample2016
MARS_v2


title: AB9561

description:
Library name: Sample2061
MARS_v2


title: AB2312

description:
Library name: Sample490
MARS


title: AB2948

description:
Library name: Sample537
MARS


title: AB8719

description:
Library name: Sample2015
MARS_v2


title: AB8391

description:
Library name: Sample2014
MARS_v2


title: AB8390

description:
Library name: Sample2013
MARS_v2


title: AB2310

description:
Library name: Sample488
MARS


title: AB2309

description:
Library name: Sample487
MARS


title: AB8389

description:
Library name: Sample2012
MARS_v2


title: AB8388

description:
Library name: Sample2011
MARS_v2


title: AB2308

description:
Library name: Sample486
MARS


title: AB2307

description:
Library name: Sample485
MARS


title: AB2306

description:
Library name: Sample484
MARS


title: AB8387

description:
Library name: Sample2010
MARS_v2


title: AB2834

description:
Library name: Sample528
MARS


title: AB8386

description:
Library name: Sample2009
MARS_v2


title: AB2305

description:
Library name: Sample483
MARS


title: AB8204

description:
Library name: Sample2008
MARS_v2


title: AB2304

description:
Library name: Sample482
MARS


title: AB8203

description:
Library name: Sample2007
MARS_v2


title: AB2303

description:
Library name: Sample481
MARS


title: AB8202

description:
Library name: Sample2006
MARS_v2


title: AB2302

description:
Library name: Sample480
MARS


title: AB8201

description:
Library name: Sample2005
MARS_v2


title: AB7975

description:
Library name: Sample2004
MARS_v2


title: AB2301

description:
Library name: Sample479
MARS


title: AB2153

description:
Library name: Sample478
MARS


title: AB2829

description:
Library name: Sample523
MARS


title: AB2152

description:
Library name: Sample477
MARS


title: AB7974

description:
Library name: Sample2003
MARS_v2


title: AB7973

description:
Library name: Sample2002
MARS_v2


title: AB2151

description:
Library name: Sample476
MARS


title: AB9019

description:
Library name: Sample2041
MARS_v2


title: AB7971

description:
Library name: Sample2000
MARS_v2


title: AB7972

description:
Library name: Sample2001
MARS_v2


title: AB2150

description:
Library name: Sample475
MARS


title: AB7970

description:
Library name: Sample1999
MARS_v2


title: AB2149

description:
Library name: Sample474
MARS


title: AB2142

description:
Library name: Sample473
MARS


title: AB7969

description:
Library name: Sample1998
MARS_v2


title: AB2141

description:
Library name: Sample472
MARS


title: AB7968

description:
Library name: Sample1997
MARS_v2


title: AB2705

description:
Library name: Sample519
MARS


title: AB2140

description:
Library name: Sample471
MARS


title: AB7967

description:
Library name: Sample1996
MARS_v2


title: AB7966

description:
Library name: Sample1995
MARS_v2


title: AB2138

description:
Library name: Sample469
MARS


title: AB2139

description:
Library name: Sample470
MARS


title: AB7965

description:
Library name: Sample1994
MARS_v2


title: AB2137

description:
Library name: Sample468
MARS


title: AB7964

description:
Library name: Sample1993
MARS_v2


title: AB7963

description:
Library name: Sample1992
MARS_v2


title: AB2136

description:
Library name: Sample467
MARS


title: AB7962

description:
Library name: Sample1991
MARS_v2


title: chordoid glioma snRNAseq

city: Paris

first: Franck

last: Bielle

address: 47-83 Bd de l'Hôpital

institute: Paris Brain Institute

data_processing:
The Cell Ranger  Single-cell Software suite (4.0.0) was used to process the data with default parameters on GRCh38-1.2.0_premrna reference genome.
Assembly: GRCh38-1.2.0_premrna
Supplementary files format and content: _barcodes.tsv.gz a compressed text file that contains cell barcodes
Supplementary files format and content: _features.tsv.gz a compressed text file with feilds separated by a tabulation that contains informations on genes used to generate counts data
Supplementary files format and content: _matrix.mtx.gz a compressed text file with fields separated by a space that contains 3 columns correspondind to features, barcodes and read count

molecule: nuclear RNA

source_name: chordoid glioma

extract_protocol:
Frozen tissues (3 mm3 ), still frozen, were minced in 1 mL of cold lysis buffer (10-mM TrisHCl, 10-mM NaCl, 3-mM MgCl2 and 0.1% NP40solution in Nuclease-Free Water) with scissors for 1 min and then incubated for 9 min at 4C, with gently regular shaking. One millilitreof lysing buffer was added, and samples lysates were transferred into2-mL Kimble homogeniser dounce (Dominique Dutscher, Issy-Les-Moulineaux, France) on ice and the A and B pestle gently lowered and raised 15 times each successively avoiding too much pressure. After being transferred to 5-mL eppendorf tubes, each lysate was completed with 3-mL washing buffer containing 1X PBS (Gibco, Life technologies SAS, Courtaboeuf, France), 2% bovine serum albumin and0.2 U/μL of Protector RNase Inhibitor (reference 2313A, Takara BioEurope SAS, Saint-Germain-En-Laye, France) before being filtered through 100-μm cell strainers (VWR, Fontenay-sous-Bois, France).Nuclei suspensions were centrifuged at 500g for 10 min at 4C with gentle acceleration and braking, and the pellet was resuspended in 3-mL washing buffer. After the same centrifugation, pellets were re-suspended in 250 μL of wash buffer. Nuclei were then incubated with Alexa Fluor® 647 anti-Nuclear Pore Complex Proteins AntibodyMab414 (BioLegend, Amsterdam, The Netherlands) at 2 μg/μL for15 min at 4C, washed with 3 mL of washing buffer and filtered through the 35-μm cell strainer 332235 Falcon (Dominique Dutscher)before sorting using a BD FACSAria III (BD Biosciences, Le-Pont-De-Claix, France) with the 85-μm nozzle and the BD FACSDIVA software. One hundred thousand nuclei were collected in a tube containing20 μL of wash buffer. The nuclei suspension was passed through a nucleocounter (ChemoMetec, Allerod, Denmark). The concentration of nuclei after FACS was approximately 280 nuclei/μL. For the nuclei extraction, all the products (except where indicated) came from SigmaAldrich (St. Louis, MO).
For each sample, 10,000 nuclei were loaded on the controller to generate single-cell gel bead-in-emulsions (Chromium, 10 Genomics).The mRNA was reverse transcribed and sample indexed to barcoded cDNA, purified using DynaBeads and amplified by PCR. To construct the 50 gene expression library, the amplified barcoded cDNA was fragmented, end-repaired, A-tailed, sample indexed and double-sized selected with SPRI beads (average size 450 bp). The DNA was quantified, and fragment size distribution of the libraries was determined using the Qubit dsDNA HS assay kit (Thermo, Q32851) and Agilent2100 BioAnalyzer High Sensitivity DNA kit (Agilent Technologies,5067-4626). Pooled libraries were then sequenced on an IlluminaNextseq 500 sequencing platform to a minimum sequencing depth of20,000 reads per nuclei using reads lengths of 26 bp read 1, 10 bp double indexes and 90 bp read 2

value: chordoid glioma

value: tumoral

value: PKCalpha D463H


title: RICTOR knock down with TGF-β1 treatment replicate 3

city: London

first: Manuela

last: Platé

state: Greater London

address: Rayne Institute, 5, University Street

department: UCL Respiratory

country: United Kingdom

institute: University College London

description: Male former smoker

data_processing:
Data analysis was performed with Galaxy and in R.
Reads pre-processing and alignment to the genome (Homo sapiens UCSC hg38) were performed using HISAT2, and counts files for each individual sample were generated with Featurecounts.
Assembly: hg38
Supplementary files format and content: Processed data files are in tab-delimited txt or FASTQ format.

source_name: Lung

growth_protocol: Primary human lung fibroblasts were grown in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% Fetal bovine serum (FBS), 1% Penicillin/Streptomycin and 1% L-glutamine. They were maintained at 37 degC and at 10% CO2. Cells were passaged when 80% confluent.

extract_protocol:
RNA was extracted using Rneasy Mini Kit
Poly(A)-taled RNA enrichment and library preparation were performed using the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPABiosystems), following the manufacturer's instructions.

treatment_protocol: 90% confluent cells were serum starved for 24h before treatment. Cells were treated with 1ng/mL TGFβ1  and incubated for 24h.

value: Lung

value: primary

value: fibroblast


title: RICTOR knock down with TGF-β1 treatment replicate 2

description: Male former smoker


title: AB7961

description:
Library name: Sample1990
MARS_v2

value: BM

value: PC


title: AB7960

description:
Library name: Sample1989
MARS_v2


title: AB2703

description:
Library name: Sample517
MARS


title: RICTOR knock down with TGF-β1 treatment replicate 1

description: Male former smoker


title: AB7958

description:
Library name: Sample1987
MARS_v2


title: AB7959

description:
Library name: Sample1988
MARS_v2


title: RICTOR knock down not treated replicate 2

description: Male former smoker

value: control


title: RICTOR knock down not treated replicate 1

description: Male former smoker


title: RICTOR knock down not treated replicate 3

description: Male former smoker


title: AB7956

description:
Library name: Sample1985
MARS_v2


title: RPTOR knock down with TGF-β1 treatment replicate 3

description: Male former smoker


title: AB7957

description:
Library name: Sample1986
MARS_v2


title: AB7955

description:
Library name: Sample1984
MARS_v2


title: RPTOR knock down with TGF-β1 treatment replicate 2

description: Male former smoker


title: RPTOR knock down not treated replicate 3

description: Male former smoker


title: AB7953

description:
Library name: Sample1982
MARS_v2


title: AB7954

description:
Library name: Sample1983
MARS_v2


title: RPTOR knock down with TGF-β1 treatment replicate 1

description: Male former smoker


title: AB7952

description:
Library name: Sample1981
MARS_v2


title: RPTOR knock down not treated replicate 2

description: Male former smoker


title: AB7950

description:
Library name: Sample1979
MARS_v2


title: RPTOR knock down not treated replicate 1

description: Male former smoker


title: AB7951

description:
Library name: Sample1980
MARS_v2


title: CRISPR control with TGF-β1 treatment replicate 3

description: Male former smoker


title: AB7949

description:
Library name: Sample1978
MARS_v2


title: CRISPR control with TGF-β1 treatment replicate 2

description: Male former smoker


title: AB7948

description:
Library name: Sample1977
MARS_v2


title: CRISPR control with TGF-β1 treatment replicate 1

description: Male former smoker


title: AB7947

description:
Library name: Sample1976
MARS_v2


title: CRISPR control not treated replicate 3

description: Male former smoker


title: CRISPR control not treated replicate 2

description: Male former smoker


title: AB7945

description:
Library name: Sample1975
MARS_v2


title: AB7944

description:
Library name: Sample1974
MARS_v2


title: CRISPR control not treated replicate 1

description: Male former smoker


title: AB7943

description:
Library name: Sample1973
MARS_v2


title: KP-H3WT-Ctrl in vivo tumors, mouse 34107

city: Philadelphia

first: Amy

middle: C

last: Gladstein

state: Pennsylvania

address: 421 Curie Blvd Rm 729

department: Cancer Biology

institute: University of Pennsylvania

description:
Library name: H3WT_34107
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34107

library_source: genomic

data_processing:
Raw paired-end sequencing reads were demultiplexed and quality checked.
Demultiplexed reads were matched and aligned against the custom pooled sgRNA library reference sequence.
Guide cassette counting and abundance quantification were performed across all samples using the MAGeCK software pipeline.
Individual sample counts were compiled into a single unified tab-delimited text matrix file. Raw counts were preserved without library-size normalization to allow downstream differential enrichment analysis.
Assembly: Custom sgRNA Library Reference
Supplementary files format and content: Tab-delimited text matrix (.txt) containing raw guide counts per sgRNA (rows) across 18 in vivo tumor samples and 2 baseline control cell lines (columns).
Supplementary files format and content: Tab-delimited text matrix (results.gene_summary.txt) containing MAGeCK gene-level summary statistics—including positive/negative selection scores, p-values, FDR, and log-fold changes—evaluating the knockout effects of dsRNA sensing and immunity-related genes (e.g., Ifih1, Ddx58, mb21d1, Setd2) across the in vivo screen groups.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Kras-G12D; p53-/- (KP) lung cancer cell lines expressing either mutant H3K36M or wild-type H3WT were cultured in vitro using standard DMEM medium supplemented with 10% fetal bovine serum (FBS) and 1% gentamycin. For the in vivo arm of the screen, cells were harvested, resuspended in sterile PBS, and delivery was achieved via tail-vein injection into athymic nude mice to initiate pulmonary tumor colonization. Mice were monitored and tumors were allowed to develop under in vivo selective pressure until the experimental endpoint.

extract_protocol:
Genomic DNA (gDNA) was isolated from harvested lung tumor nodules and baseline parental cell line pellets. Tissue dissociation was performed followed by purification using a standard column-based genomic DNA extraction kit (DNeasy Blood & Tissue Kit, Qiagen) according to the manufacturer's instructions. DNA concentration and purity were verified using a NanoDrop spectrophotometer and Qubit fluorometric quantification to ensure sufficient gDNA yield for representative sgRNA library amplification.
Sequencing libraries were prepared using a targeted amplicon strategy to capture the integrated sgRNA cassettes from the genomic DNA. Universal primers flanking the sgRNA region were utilized in a high-fidelity PCR amplification workflow (using Q5 Hot Start High-Fidelity DNA Polymerase). This step isolated and amplified the specific sgRNA target sequence while incorporating Illumina-compatible adapter sequences and unique sample index barcodes, following standard high-throughput pooled CRISPR screening library preparation protocols (Genewiz/Azenta Amplicon-EZ workflow). Final libraries were pooled and quantified prior to sequencing.

treatment_protocol: No exogenous chemical treatments or drug therapies were administered. The baseline parental cell line samples represent the pre-injection control pool (time zero reference for initial sgRNA library representation). For the experimental groups, the treatment condition consists entirely of physiological, in vivo selection and tumor microenvironment pressure during colonization in the mouse lung.

value: KP lung adenocarcinoma cells

value: Wild Type

value: in vivo selection (lung colonization)

value: Batch 1


title: KP-H3WT-Ctrl in vivo tumors, mouse 34106

description:
Library name: H3WT_34106
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34106


title: AB7942

description:
Library name: Sample1972
MARS_v2


title: AB7941

description:
Library name: Sample1971
MARS_v2


title: KP-H3WT-Ctrl in vivo tumors, mouse 34104

description:
Library name: H3WT_34104
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34104


title: AB7940

description:
Library name: Sample1970
MARS_v2


title: AB7939

description:
Library name: Sample1969
MARS_v2


title: KP-H3WT-Ctrl in vivo tumors, mouse 34105

description:
Library name: H3WT_34105
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34105


title: KP-H3WT-Ctrl in vivo tumors, mouse 34103

description:
Library name: H3WT_34103
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34103


title: AB7938

description:
Library name: Sample1968
MARS_v2


title: AB7937

description:
Library name: Sample1967
MARS_v2


title: AB7936

description:
Library name: Sample1966
MARS_v2


title: KP-H3WT-Ctrl in vivo tumors, mouse 34101

description:
Library name: H3WT_34101
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34101


title: KP-H3WT-Ctrl in vivo tumors, mouse 34100

description:
Library name: H3WT_34100
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34100


title: KP-H3WT-Ctrl in vivo tumors, mouse 34102

description:
Library name: H3WT_34102
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34102


title: KP-H3WT-Ctrl in vivo tumors, mouse 34099

description:
Library name: H3WT_34099
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34099


title: AB7935

description:
Library name: Sample1965
MARS_v2


title: KP-H3WT-Ctrl in vivo tumors, mouse 34098

description:
Library name: H3WT_34098
In vivo CRISPR screen sample, derived from H3WT lung tumor tissue of mouse 34098


title: AB7934

description:
Library name: Sample1964
MARS_v2


title: AB7933

description:
Library name: Sample1963
MARS_v2


title: AB7932

description:
Library name: Sample1962
MARS_v2


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34117

description:
Library name: H3K36M_34117
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34117

value: H3K36M mutant


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34115

description:
Library name: H3K36M_34115
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34115


title: AB7931

description:
Library name: Sample1961
MARS_v2


title: AB7929

description:
Library name: Sample1960
MARS_v2


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34112

description:
Library name: H3K36M_34112
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34112


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34113

description:
Library name: H3K36M_34113
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34113


title: AB7928

description:
Library name: Sample1959
MARS_v2


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34111

description:
Library name: H3K36M_34111
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34111


title: AB7927

description:
Library name: Sample1958
MARS_v2


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34110

description:
Library name: H3K36M_34110
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34110


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34109

description:
Library name: H3K36M_34109
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34109


title: AB7926

description:
Library name: Sample1957
MARS_v2


title: AB7925

description:
Library name: Sample1956
MARS_v2


title: KP-H3K36M-Ctrl in vivo tumors, mouse 34108

description:
Library name: H3K36M_34108
In vivo CRISPR screen sample, derived from H3K36M lung tumor tissue of mouse 34108


title: AB7924

description:
Library name: Sample1955
MARS_v2


title: Baseline parental cell line KP-H3WT-Ctrl

description:
Library name: Control_H3WT
Pre-injection parental cell line reference for sgRNA library representation

value: none (pre-injection baseline)


title: AB7923

description:
Library name: Sample1954
MARS_v2


title: Baseline parental cell line KP-H3K36M-Ctrl

description:
Library name: Control_H3K36M
Pre-injection parental cell line reference for sgRNA library representation


title: AB7922

description:
Library name: Sample1953
MARS_v2


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 007_BL | Full ROI

city: Chapel hill

first: Brent

last: Hanks

state: North Carolina

address: 450 West Dr

department: Medicine

institute: UNC at Chapel Hill

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.007.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

data_processing:
A pan-cytokeratin IF marker was used to identify epithelial tumor tissue while CD8 and elastase IF markers were used to assess tumor-infiltrating CD8+ T cell and PMN/neutrophil cell populations
Human Whole Transcriptome Atlas probe was hybridized overnight, slides were washed twice in fresh 2X saline-sodium citrate (SSC, Sigma-Aldrich, S6639-1L) and loaded onto the GeoMx DSP.
UV light was used to cleave oligos that were then collected in a 96-well plate for library preparation and were sequenced on an Illumina NextSeq2000 by the UNC High-Throughput Sequencing Facility (HTSF)
All transcriptional data was analyzed using GeoMx DSP Data Analysis software
dimensionality reduction (PCA) and normalization techniques (Q3 normalization) were used to identify potential outliers
Assembly: GRCh38
Supplementary files format and content: Quantitative counts of genes or proteins  ( .dcc files)
Supplementary files format and content: GE_counts.csv
Supplementary files format and content: Hs_R_NGS_CTA_v1.0.pkc
Library strategy: Spatial Transcriptomics

source_name: Gastric tumor tissue

extract_protocol:
library preparation and were sequenced on an Illumina NextSeq2000
FFPE tissue samples were prepared

value: Gastric tumor tissue

tag: cd8+ count

value: High

tag: neutrophil count

value: Low

tag: clinical response

value: PR

value: baseline


title: AB7921

description:
Library name: Sample1952
MARS_v2

tag: tissue


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 006_BL | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.006.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7920

description:
Library name: Sample1951
MARS_v2


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 005_BL | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.005.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 004_Tx | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.004.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 003_Tx | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.003.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7919

description:
Library name: Sample1950
MARS_v2


title: AB7918

description:
Library name: Sample1949
MARS_v2


title: AB7917

description:
Library name: Sample1948
MARS_v2


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 002_Tx | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.002.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 141 baseline and 141 on-Tx Bond 2KXX_1 | 001_Tx | Full ROI

description:
Library name: GE_141baselineand141on-TxBond2KXX.1.001.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7915

description:
Library name: Sample1946
MARS_v2


title: AB7916

description:
Library name: Sample1947
MARS_v2


title: 140 On-Tx Bond 2JJD_1 | 005 | Full ROI

description:
Library name: GE_140On-TxBond2JJD.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

value: PD

value: on-Treatment


title: AB7914

description:
Library name: Sample1945
MARS_v2


title: 140 On-Tx Bond 2JJD_1 | 004 | Full ROI

description:
Library name: GE_140On-TxBond2JJD.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7833

description:
Library name: Sample1944
MARS_v2


title: 140 On-Tx Bond 2JJD_1 | 003 | Full ROI

description:
Library name: GE_140On-TxBond2JJD.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7832

description:
Library name: Sample1943
MARS_v2


title: 140 On-Tx Bond 2JJD_1 | 002 | Full ROI

description:
Library name: GE_140On-TxBond2JJD.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 140 On-Tx Bond 2JJD_1 | 001 | Full ROI

description:
Library name: GE_140On-TxBond2JJD.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7831

description:
Library name: Sample1942
MARS_v2


title: 140 Baseline Bond 2JJC_1 | 005 | Full ROI

description:
Library name: GE_140BaselineBond2JJC.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7156

description:
Library name: Sample1940
MARS_v2


title: AB7830

description:
Library name: Sample1941
MARS_v2


title: 140 Baseline Bond 2JJC_1 | 004 | Full ROI

description:
Library name: GE_140BaselineBond2JJC.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7155

description:
Library name: Sample1939
MARS_v2


title: AB7154

description:
Library name: Sample1938
MARS_v2


title: 140 Baseline Bond 2JJC_1 | 003 | Full ROI

description:
Library name: GE_140BaselineBond2JJC.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 140 Baseline Bond 2JJC_1 | 002 | Full ROI

description:
Library name: GE_140BaselineBond2JJC.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7153

description:
Library name: Sample1937
MARS_v2


title: 140 Baseline Bond 2JJC_1 | 001 | Full ROI

description:
Library name: GE_140BaselineBond2JJC.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7152

description:
Library name: Sample1936
MARS_v2


title: 139 On-Tx Bond 2JJE_1 | 008 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.008
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 On-Tx Bond 2JJE_1 | 007 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.007
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7151

description:
Library name: Sample1935
MARS_v2


title: 139 On-Tx Bond 2JJE_1 | 006 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 On-Tx Bond 2JJE_1 | 005 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7148

description:
Library name: Sample1932
MARS_v2


title: 139 On-Tx Bond 2JJE_1 | 004 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7146

description:
Library name: Sample1930
MARS_v2


title: AB7147

description:
Library name: Sample1931
MARS_v2


title: AB7149

description:
Library name: Sample1933
MARS_v2


title: 139 On-Tx Bond 2JJE_1 | 003 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB7150

description:
Library name: Sample1934
MARS_v2


title: AB7145

description:
Library name: Sample1929
MARS_v2


title: 139 On-Tx Bond 2JJE_1 | 002 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 On-Tx Bond 2JJE_1 | 001 | Full ROI

description:
Library name: GE_139On-TxBond2JJE.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6735

description:
Library name: Sample1928
MARS_v2


title: 139 Baseline Bond 2JJB_1 | 007 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.007
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB2311

description:
Library name: Sample489
MARS


title: 139 Baseline Bond 2JJB_1 | 006 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6733

description:
Library name: Sample1926
MARS_v2


title: AB6734

description:
Library name: Sample1927
MARS_v2


title: 139 Baseline Bond 2JJB_1 | 002 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 Baseline Bond 2JJB_1 | 003_Alt | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.003.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 Baseline Bond 2JJB_1 | 005 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6732

description:
Library name: Sample1925
MARS_v2


title: AB6731

description:
Library name: Sample1924
MARS_v2


title: 139 Baseline Bond 2JJB_1 | 004 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 139 Baseline Bond 2JJB_1 | 001 | Full ROI

description:
Library name: GE_139BaselineBond2JJB.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6730

description:
Library name: Sample1923
MARS_v2


title: AB6728

description:
Library name: Sample1921
MARS_v2


title: AB6729

description:
Library name: Sample1922
MARS_v2


title: AB6727

description:
Library name: Sample1920
MARS_v2


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 008_BL | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.008.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 009_BL | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.009.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6726

description:
Library name: Sample1919
MARS_v2


title: AB6725

description:
Library name: Sample1918
MARS_v2


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 007_BL | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.007.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 006_BL | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.006.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6722

description:
Library name: Sample1916
MARS_v2


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 005_BL | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.005.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 004_Tx | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.004.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB6724

description:
Library name: Sample1917
MARS_v2


title: AB6721

description:
Library name: Sample1915
MARS_v2


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 003_Tx | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.003.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: Feature Barcode library of Whole Bone Marrow  rxn 1 replicate 1

description:
Library name: BM1.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)

library_source: other

molecule: protein

value: Bone marrow

value: Lymphocyte

value: HTO


title: Feature Barcode library of B cell  rxn 1 replicate 1

description:
Library name: Bcell1.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)

value: B-cell


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 002_Tx | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.002.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB5600

description:
Library name: Sample1913
MARS_v2

value: BM

value: PC


title: Feature Barcode library of B cell  rxn 2 replicate 2

description:
Library name: Bcell2.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of B cell  rxn 2 replicate 1

description:
Library name: Bcell1.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: 129 baseline and 129 on-Tx Bond 2KXU_1 | 001_Tx | Full ROI

description:
Library name: GE_129baselineand129onTxBond2KXU.1.001.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB5599

description:
Library name: Sample1912
MARS_v2


title: AB5598

description:
Library name: Sample1911
MARS_v2


title: 127 On-Tx Bond 2JJF_1 | 006 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB5597

description:
Library name: Sample1910
MARS_v2


title: 127 On-Tx Bond 2JJF_1 | 004 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14520

description:
Library name: Sample1636
MARS_v2


title: AB14519

description:
Library name: Sample1635
MARS_v2


title: 127 On-Tx Bond 2JJF_1 | 002 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14518

description:
Library name: Sample1634
MARS_v2


title: 127 On-Tx Bond 2JJF_1 | 003 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14517

description:
Library name: Sample1633
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 010 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.010
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 127 On-Tx Bond 2JJF_1 | 001 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 127 Baseline Bond 2JJA_1 | 009 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.009
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14514

description:
Library name: Sample1631
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 007 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.007
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14513

description:
Library name: Sample1630
MARS_v2


title: AB14512

description:
Library name: Sample1629
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 006 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14509

description:
Library name: Sample1627
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 005 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14511

description:
Library name: Sample1628
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 004 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14361

description:
Library name: Sample1626
MARS_v2


title: AB14360

description:
Library name: Sample1625
MARS_v2


title: AB13215

description:
Library name: Sample1346
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 003 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14359

description:
Library name: Sample1624
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 001 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14358

description:
Library name: Sample1623
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 002 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 125 On-Tx Bond 2JJG_1 | 001 | Full ROI

description:
Library name: GE_125On-TxBond2JJG.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14357

description:
Library name: Sample1622
MARS_v2


title: 125 Baseline Bond 2JJ9_1 | 002 | Full ROI

description:
Library name: GE_125Baseline Bond2JJ9.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14356

description:
Library name: Sample1621
MARS_v2


title: AB14355

description:
Library name: Sample1620
MARS_v2


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 006_BL | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.006.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 007_BL_Alt | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.007.BL.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14353

description:
Library name: Sample1618
MARS_v2


title: AB14354

description:
Library name: Sample1619
MARS_v2


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 005_BL | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.005.BL
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 004_Tx | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.004.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14352

description:
Library name: Sample1617
MARS_v2


title: AB14351

description:
Library name: Sample1616
MARS_v2


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 002_Tx | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.002.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14348

description:
Library name: Sample1613
MARS_v2


title: 118 On-Tx Bond 2JJ5_1 | 008 | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.008
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14347

description:
Library name: Sample1612
MARS_v2


title: 118 On-Tx Bond 2JJ5_1 | 006 | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 118 On-Tx Bond 2JJ5_1 | 005 | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14344

description:
Library name: Sample1609
MARS_v2


title: 118 On-Tx Bond 2JJ5_1 | 004 | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14343

description:
Library name: Sample1608
MARS_v2


title: 118 On-Tx Bond 2JJ5_1 | 001 | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14179

description:
Library name: Sample1606
MARS_v2


title: 118 Baseline Bond 2JJ4_1 | 007 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.007
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14176

description:
Library name: Sample1603
MARS_v2


title: 118 Baseline Bond 2JJ4_1 | 006 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14027

description:
Library name: Sample1602
MARS_v2


title: 118 Baseline Bond 2JJ4_1 | 005 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 118 Baseline Bond 2JJ4_1 | 004 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13005

description:
Library name: Sample1324
MARS_v2


title: AB13012

description:
Library name: Sample1328
MARS_v2


title: AB14023

description:
Library name: Sample1599
MARS_v2


title: AB13199

description:
Library name: Sample1334
MARS_v2


title: 118 Baseline Bond 2JJ4_1 | 001 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 118 On-Tx Bond 2JJ5_1 | 007_Alt | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.007.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14345

description:
Library name: Sample1610
MARS_v2


title: 118 On-Tx Bond 2JJ5_1 | 003_Alt | Full ROI

description:
Library name: GE_118On-TxBond2JJ5.1.003.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 114 On-Tx Bond 2JJ3_1 | 008 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.008
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13230

description:
Library name: Sample1356
MARS_v2


title: AB14018

description:
Library name: Sample1596
MARS_v2


title: AB12993

description:
Library name: Sample1315
MARS_v2


title: AB14177

description:
Library name: Sample1604
MARS_v2


title: AB14016

description:
Library name: Sample1595
MARS_v2


title: 114 On-Tx Bond 2JJ3_1 | 007 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.007
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 118 Baseline Bond 2JJ4_1 | 008 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.008
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 114 On-Tx Bond 2JJ3_1 | 006 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14015

description:
Library name: Sample1594
MARS_v2


title: 114 On-Tx Bond 2JJ3_1 | 005 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14012

description:
Library name: Sample1592
MARS_v2


title: AB13003

description:
Library name: Sample1322
MARS_v2


title: 114 On-Tx Bond 2JJ3_1 | 004 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14010

description:
Library name: Sample1591
MARS_v2


title: 114 On-Tx Bond 2JJ3_1 | 003 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14024

description:
Library name: Sample1600
MARS_v2


title: 114 On-Tx Bond 2JJ3_1 | 002 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 114 On-Tx Bond 2JJ3_1 | 001 | Full ROI

description:
Library name: GE_114On-TxBond2JJ3.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14008

description:
Library name: Sample1589
MARS_v2


title: 114 Baseline Bond 2JJ2_1 | 005_Alt | Full ROI

description:
Library name: GE_114BaselineBond2JJ2.1.005.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 114 Baseline Bond 2JJ2_1 | 004_Alt | Full ROI

description:
Library name: GE_114BaselineBond2JJ2.1.004.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14005

description:
Library name: Sample1587
MARS_v2


title: AB14007

description:
Library name: Sample1588
MARS_v2


title: AB14004

description:
Library name: Sample1586
MARS_v2


title: AB14021

description:
Library name: Sample1598
MARS_v2


title: 114 Baseline Bond 2JJ2_1 | 002 | Full ROI

description:
Library name: GE_114BaselineBond2JJ2.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14003

description:
Library name: Sample1585
MARS_v2


title: 114 Baseline Bond 2JJ2_1 | 001 | Full ROI

description:
Library name: GE_114BaselineBond2JJ2.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 111 On-Tx Bond 2JJ1_1 | 007_Alt | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.007.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

value: CR


title: AB14001

description:
Library name: Sample1584
MARS_v2


title: AB14000

description:
Library name: Sample1583
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 006_Alt | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.006.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13999

description:
Library name: Sample1582
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 005 | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13998

description:
Library name: Sample1581
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 004 | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13997

description:
Library name: Sample1580
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 003 | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13996

description:
Library name: Sample1579
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 002 | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13995

description:
Library name: Sample1578
MARS_v2


title: AB5601

description:
Library name: Sample1914
MARS_v2


title: 111 On-Tx Bond 2JJ1_1 | 001 | Full ROI

description:
Library name: GE_111On-TxBond 2JJ1.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13994

description:
Library name: Sample1577
MARS_v2


title: 111 Baseline Bond 2JJ0_1 | 007_Alt | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.007.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 111 Baseline Bond 2JJ0_1 | 006 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.006
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13993

description:
Library name: Sample1576
MARS_v2


title: AB13992

description:
Library name: Sample1575
MARS_v2


title: 111 Baseline Bond 2JJ0_1 | 005 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 127 On-Tx Bond 2JJF_1 | 005 | Full ROI

description:
Library name: GE_127On-TxBond2JJF.1.005
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13991

description:
Library name: Sample1574
MARS_v2


title: AB14014

description:
Library name: Sample1593
MARS_v2


title: 111 Baseline Bond 2JJ0_1 | 004 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.004
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13990

description:
Library name: Sample1573
MARS_v2


title: AB14516

description:
Library name: Sample1632
MARS_v2


title: 127 Baseline Bond 2JJA_1 | 008 | Full ROI

description:
Library name: GE_127BaselineBond2JJA.1.008
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 111 Baseline Bond 2JJ0_1 | 003 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13989

description:
Library name: Sample1572
MARS_v2


title: AB13988

description:
Library name: Sample1571
MARS_v2


title: 111 Baseline Bond 2JJ0_1 | 002 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 111 Baseline Bond 2JJ0_1 | 001 | Full ROI

description:
Library name: GE_111Baseline Bond2JJ0.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: Ribo-seq of Wild Type [WT_RPF2]

city: Beijing

first: Yanran

last: Wang

address: No.5, Dongdan Sanjiao, Dongcheng District, Beijing

department: State Key Laboratory of Medical Molecular Biology

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

description: Ribo-seq of Wild Type

data_processing:
library strategy: Ribo-seq
RNA-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic. Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene expression analysis.
Assembly: GENCODE Release 36, GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: bigWig, narrowPeak
Ribo-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic.Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene translation efficiency analysis. The TE (Translation Efficiency) value were calculated by taking the ratio of TPM in Ribo-seq over TPM in RNA-seq with R scripts.
acRIP-seq: Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were aligned to the Homo sapiens transcripts using bowtie2. ac4C peaks were detected by MACS2, and filtered by log10P < -3. Input samples were used as controls for peak calling. Screening of differential peaks using BEDTools map. ac4C sites that resided in protein coding genes were analyzed for downstream analysis. ChIPseeker was used for annotating the peaks.

growth_protocol: RNA-seq: k562 cells were grown in RPMI-1640 media supplemented with 10% FBS at 37°C in the presence of 5% CO2.

extract_protocol:
RNA-seq: Total RNA was extracted from NAT10 knockout and parental k562 cells using Trizol reagent(Invitrogen).
RNA-seq: RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacture's protocols.
Ribo-seq: Prepare the suspended cells to a density of 2 x 10^6 cells/mL in 10cm dishes.Incubate cells in growth media with cycloheximide at a final concentration of 100ug/ml for 15 minutes at 37°C with 5 % CO2, harvest, and wash twice with ice-cold PBS containing 100ug/ml cycloheximide.Discard supernatant and resuspend cells in 500 μl MCB lysis buffer(1 M MgCl2,100 % glycerol,1 M HEPES,20 % Triton X-100) combine with 1 M DTT, EDTA free RNase Inhibitor, EDTA free 50×cocktail,10mg/ml cycloheximide and vortex for 5 seconds followed by lysed on ice for 15mins, centrifuge lysates at 15000 rpm for 10 min at 4℃ and transfer supernatant to a new tube, prepare the 20％——50％ sucrose gradients. Remove 500 μl of sucrose gradients from the top and add the same volume of lysates onto each sucrose gradient. Centrifuge at 38000 rpm for 3 hours at 4°C in a Beckman Coulter Optima L-100XP with a SW41 Ti rotor. To collect different gradient ribosome fractions at 0.5ml/fraction, carefully remove tubes from the rotor and place them in the fraction collector. Add 750 μl of Trizol LS(Invitrogen) to each fraction and proceed with the RNA extraction as directed.
Ribo-seq: 12 PCR cycles were used for indexing of libraries and the finial PCR products were purified with RNA Clean & Concentrator-5 kit (Zymo research).
acRIP-seq: Total RNA was rRNA depleted with the NEBNext® rRNA Depletion Kit v2 (Promega) and then subjected to immunoprecipitation. Briefly, RNA was randomly fragmented to ~100 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody or Normal Rabbit IgG antibody by rotating at room temperature for 2 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
acRIP-seq: RNA libraries for IP,IgG and input samples were then constructed with NEBNext® Ultra™ RNA Library Prep Kit by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina).

value: wild type


title: AB13987

description:
Library name: Sample1570
MARS_v2


title: AB13986

description:
Library name: Sample1569
MARS_v2


title: Ribo-seq of Wild Type [WT_RPF1]

description: Ribo-seq of Wild Type


title: AB14009

description:
Library name: Sample1590
MARS_v2


title: Ribo-seq after NAT10 knock out [KO_RPF2]

description: Ribo-seq after NAT10 knock out

value: NAT10 knock out


title: AB13985

description:
Library name: Sample1568
MARS_v2


title: AB13983

description:
Library name: Sample1566
MARS_v2


title: Ribo-seq after NAT10 knock out [KO_RPF1]

description: Ribo-seq after NAT10 knock out


title: AB13984

description:
Library name: Sample1567
MARS_v2


title: RNA-seq of Wild Type [WT_input2]

description: RNA-seq of Wild Type

data_processing:
RNA-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic. Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene expression analysis.
Assembly: GENCODE Release 36, GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: bigWig, narrowPeak
Ribo-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic.Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene translation efficiency analysis. The TE (Translation Efficiency) value were calculated by taking the ratio of TPM in Ribo-seq over TPM in RNA-seq with R scripts.
acRIP-seq: Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were aligned to the Homo sapiens transcripts using bowtie2. ac4C peaks were detected by MACS2, and filtered by log10P < -3. Input samples were used as controls for peak calling. Screening of differential peaks using BEDTools map. ac4C sites that resided in protein coding genes were analyzed for downstream analysis. ChIPseeker was used for annotating the peaks.


title: AB13982

description:
Library name: Sample1565
MARS_v2


title: 114 Baseline Bond 2JJ2_1 | 003_Alt | Full ROI

description:
Library name: GE_114BaselineBond2JJ2.1.003.Alt
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: 125 Baseline Bond 2JJ9_1 | 001 | Full ROI

description:
Library name: GE_125Baseline Bond2JJ9.1.001
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: RNA-seq of Wild Type [WT_input1]

description: RNA-seq of Wild Type


title: AB13870

description:
Library name: Sample1564
MARS_v2


title: RNA-seq after NAT10 knock out [KO_input2]

description: RNA-seq after NAT10 knock out


title: AB13869

description:
Library name: Sample1563
MARS_v2


title: RNA-seq after NAT10 knock out [KO_input1]

description: RNA-seq after NAT10 knock out


title: AB14349

description:
Library name: Sample1614
MARS_v2


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 003_Tx | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.003.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB14350

description:
Library name: Sample1615
MARS_v2


title: 120 baseline and 120 on-Tx Bond 2KXT_1 | 001_Tx | Full ROI

description:
Library name: GE_120baselineand120on-TxBond2KXT.1.001.Tx
Formalin-fixed paraffin-embedded spatial transcriptome sequencing


title: AB13867

description:
Library name: Sample1561
MARS_v2


title: AB13868

description:
Library name: Sample1562
MARS_v2


title: AB13866

description:
Library name: Sample1560
MARS_v2


title: AB13865

description:
Library name: Sample1559
MARS_v2


title: AB13864

description:
Library name: Sample1558
MARS_v2


title: AB13863

description:
Library name: Sample1557
MARS_v2


title: HiC cerebellum, P6, rep1

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description: Library name: Hi-C_pnd6_1

data_processing:
Hi-C reads were aligned to the mm10 reference genome with Bowtie2 and HiC-Pro. Uniquely mapped paired-end reads were assigned to MboI restriction fragments and valid pairs with a minimum genomic distance of 1Kb were filtered for PCR duplicates. Interaction matrices were normalized using Knight-Ruiz (KR) matrix balancing and observed divided by expected (o/e) transformation and visualized using hic files in Juicebox
Assembly: mm10
Supplementary files format and content: hic files

source_name: cerebellum

extract_protocol:
The cerebellum from postnatal day 6 or 22 mice or cerebellar vermis from mice at day 1 to 28 after electroporation were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony). The genomic DNA was digested with MboI and re-ligated after the biotin fill-in reaction, followed by sonication. The fragmented DNA was then subjected to biotin-IP.
Hi-C libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 1 to 28 after electroporation.

value: cerebellum

value: cerebellar cells


title: HiC cerebellum, P6, rep3

description: Library name: Hi-C_pnd6_3


title: HiC cerebellum, P22, rep1

description: Library name: Hi-C_pnd22_1


title: HiC cerebellum, P22, rep2

description: Library name: Hi-C_pnd22_2


title: HiC cerebellum, P6, rep2

description: Library name: Hi-C_pnd6_2


title: HiC cerebellum, P22, rep3

description: Library name: Hi-C_pnd22_3


title: AB13862

description:
Library name: Sample1556
MARS_v2


title: AB14346

description:
Library name: Sample1611
MARS_v2