title: Epi-iPSC cells, HC-treated control day 9 kidney organoid differentiation, biol rep 3

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

description: Library name: HC_rep_3

data_processing:
Raw data was run through the NextFlow nf-core/rnaseq pipeline version 3.18.0-gb96a753 using Homo sapiens genome assembly GRCh38, annotation version GRCh38.113.
Softward utilized and their respective versions and excecution parameters can be found in the supplemental files; nf_core_rnaseq_software_mqc_versions.yml and params_2025-03-07_17-39-07.json respectively.
Assembly: GRCh38.113
Supplementary files format and content: Count matrix file

source_name: Gibco episomal iPSC

growth_protocol: Gibco episomal iPSCs were maintained in DMEM/F12 media supplemented with StemFlex supplement and antibiotics in humidified atmostphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen). 1μg of total RNA was used for the construction of sequencing libraries.
Isolation of Poly(A) mRNA was conducted using the NEBNext Poly(A) Magnetic Isolation Module. Following isolation of poly(a) mRNA, library preparation was conducted using the NEBNext Ultra II RNA Library Prep Kit for Illumina per manufacturer’s instructions, individual samples were barcoded using NEBNext Multiplex Oligos for Illumina, and equal sample volumes were pooled prior to sample QC.

treatment_protocol:
Day 0 cells, plated on Day -1 at ~40,000 cells/cm2, were washed with pre-warmed 1X dPBS and switched to differentiation media Advanced RPMI 1640 + 1% L-Glutamine + 0.5% KnockOut Serum Replacement, containing 7μM CHIR and 5ng/mL noggin on days 0-3 with media changes every 2 days. On days 4-6, cells received differentiation media containing 10ng/mL Activin A  and 1μg/mL heparin. Days 7-8, media was replaced with differentiation media containing 10ng/mL FGF9 and 1μg/mL heparin. On days 9-10, cells received media containing 10ng/mL FGF9, 3μM CHIR, and 1μg/mL heparin. On day 11, cells were dissociated into single-cell suspensions using Accutase, pelleted at 300g for 3 minutes, then resuspended in differentiation medium containing 0.1% polyvinyl alcohol (PVA), 0.1% methylcellulose (MC), 1μg/mL heparin, and 10μM Y-27632  equivalent to a splitting ratio of 1:2-1:4 depending on cell density. Cells were then transferred to cell repellent dishes and placed on an orbital shaker at 60-80rpm in a cell culture incubator overnight to form spheroids. Day 12 spheroids were collected in 15mL conical tubes, centrifuged at 10g for 1 minute, and treated with fresh differentiation medium containing 0.1% PVA and 0.1% MC, without Y-27632 or growth factors. Subsequent media changes were conducted every other day until collection.
Organoid culture media was supplemented with 1μg/mL hydrocortisone or an equivalent volume of vehicle (DMSO) during daily media changes on days 4-9.

value: Gibco episomal iPSC

value: Epi-iPSC cells

value: WT


title: Epi-iPSC cells, HC-treated control day 9 kidney organoid differentiation, biol rep 4

status: Public on Mar 01 2026

type: SRA

country: USA

description: Library name: HC_rep_4

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Epi-iPSC cells, HC-treated control day 9 kidney organoid differentiation, biol rep 2

description: Library name: HC_rep_2


title: replicate 2 of CK13 CUT&Tag in HeLa

city: Changsha

first: Kewei

last: Zheng

address: Lushan Road

department: School of Biomedical Sciences

country: China

institute: Hunan University

description: Library name: Hela_CK13_R2

library_source: genomic

data_processing:
The clean paired-end sequencing data were analyzed using the human genome (version hg38) as a reference. Reads were aligned with bowtie2 using --fast-local. Normalized (RPGC) coverage tracks were generated by deepTools bamCoverage using parameters --binSize 50 --normalize --extendReads --ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: cervical cancer tissue

growth_protocol: HeLa and HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
The CUT&Tag method was constructed following the described protocol (32) with some modifications. A total of 105 cells were washed twice with 100 µL wash buffer (20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). Next, 10 µL of pre-activated concanavalin A coated magnetic beads were added to the cells in 100 µL wash buffer and incubated on a rotator for 10 min at room temperature. The supernatant was removed, and the bead-bound cells were resuspended in 100 µL of dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1× protease inhibitors) containing 250 nM of G4P, 200 nM of CK13, 2 µL of anti-NCL antibody (ab70493, Abcam), or 1 µL of anti-Top1 antibody (ab109374, Abcam), respectively. After 2 hours rotation at room temperature, the cells incubated with G4P or CK13 were washed twice with 100 µL of dig-wash buffer and resuspended with 100 µL of dig-wash buffer containing 2 µL of anti-FLAG M2 antibody (Sigma-Aldrich), or 2 µL of anti-V5 tag antibody (ab15828, Abcam), incubated for another 1 hour at room temperature. The buffer containing primary antibodies was then removed from the cells, and 100 µL of dig-wash buffer containing 1 µL of Goat anti-mouse IgG (AP124, Sigma-Aldrich) or 1 µL of Goat anti-rabbit IgG (AP132, Sigma-Aldrich) was mixed with the cells and incubated for 1 hour at room temperature. After washing three times with dig-wash buffer, a 1:100 dilution of pAG-Tn5 adapter complex (~0.2 µM) was prepared in 100 µL of dig-wash buffer and added to the cells, which were then rotated for 1 hour at room temperature. After five washes with dig-wash buffer, the bead-bound cells were resuspended with 50 µL of tagmentation buffer (20 mM HEPES–KOH (pH 7.5), 150 mM KCl, 10 mM MgCl2, 0.5 mM spermidine, 1× protease inhibitors) and incubated at 37 ℃ for 1 hour. To terminate the tagmentation reaction, 2.5 µL of 0.5 M EDTA and 1 µL of 20 mg/mL proteinase K were added and incubated at 55 ℃ for 30 min. The DNA was then extracted using 120 µL of Ampure XP beads (Beckman Counter) for library preparation. DNA was eluted in 40 µL of 5 mM Tris−HCl (pH 8.0).
To amplify the libraries, 16 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer and amplified using Q5 high-fidelity 2 × master mix (New England Biolabs). The PCR cycles for G4P and CK13 groups were 16 to 18, and those for Top1, NCL, and IgG groups were 15, 17, and 22, respectively. The libraries were purified with 1.3 × volume of Ampure XP beads and eluted in 20 µL of 10 mM Tris−HCl (pH 8.0).

tag: tissue

value: cervical cancer tissue

value: HeLa


title: Epi-iPSC cells, DMSO-treated control day 9 kidney organoid differentiation, biol rep 4

description: Library name: DMSO_rep_4


title: Epi-iPSC cells, HC-treated control day 9 kidney organoid differentiation, biol rep 1

description: Library name: HC_rep_1


title: replicate 1 of NCL CUT&Tag in HeLa

description: Library name: Hela_NCL_R1


title: Epi-iPSC cells, DMSO-treated control day 9 kidney organoid differentiation, biol rep 3

description: Library name: DMSO_rep_3


title: Breast Benign Disease [Patient 026_SH06F30_Cell1]

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.

hyb_protocol: Hybridized for 17 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

source_name: serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: The whole blood specimens were collected and processed at each institution using red/gray topped gel barrier tubes (Becton Dickinson Vacutainer® SST™ Tubes 367988, Franklin Lakes, NJ). The blood specimens were allowed to clot for 30 - 35 minutes at room temperature. The tubes were then centrifuged at either 4°C or room-temperature at 1,100 – 1,300 g for 10 minutes. After centrifugation, aliquots of 0.5 mL of serum were stored at or below -80 °C within 90 minutes of collection.

tag: Sex

value: female

tag: age

tag: category

value: Training


title: PhiX control library

description: Library name: PhiX_control

source_name: PhiX control library

value: PhiX control library


title: replicate 2 of NCL CUT&Tag in HeLa

description: Library name: Hela_NCL_R2


title: replicate 1 of TOP1 CUT&Tag in HeLa

description: Library name: HeLa_TOP1_R1


title: Breast Benign Disease [Patient 025_SH11R05_Cell1]


title: Epi-iPSC cells, DMSO-treated control day 9 kidney organoid differentiation, biol rep 2

description: Library name: DMSO_rep_2


title: Epi-iPSC cells, DMSO-treated control day 9 kidney organoid differentiation, biol rep 1

description: Library name: DMSO_rep_1


title: hfPSCs_2_ATAC

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

description: Library name: hfPSCs_2_ATAC

data_processing:
After removal of reads with poor quality and adapters, reads from ATAC-seq datasets were mapped to the human genome (hg19) using Bowtie2 v. 2.2.2. The UCSC genome browser was used to visualize ATAC-seq data.
Assembly: hg19
Supplementary files format and content: bw format; bw files

source_name: hfPSCs

extract_protocol:
After cell passage, the cells were washed once with PBS, and 50,000 cells from each group were used for subsequent library preparation.
The library construction was carried out following the manufacturer’s protocol for the Vazyme Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711). In brief, cells were resuspended in freshly prepared lysis buffer and lysed accordingly. The lysate was then mixed with the fragmentation master mix and incubated at 37 °C for 30 minutes to achieve chromatin fragmentation. Following fragmentation, the reaction was terminated, and the resulting fragments were immediately purified using ATAC DNA Extract Beads. The purified DNA fragments were subsequently used for PCR amplification to generate the final libraries. All libraries were sequenced on an Illumina NovaSeq X Plus platform according to the manufacturer's instructions.

value: hfPSCs

value: human formative pluripotent stem cells (hfPSCs)


title: Breast Benign Disease [Patient 024_SH0ZE14_Cell3]


title: Breast Benign Disease [Patient 023_SH09X59_Cell4]


title: hfPSCs_1_ATAC

description: Library name: hfPSCs_1_ATAC


title: PTCY2, pooledSeq

city: Stanford

first: Cameron

middle: Scott

last: Bader

state: California

address: 269 Campus Drive, CCSR Room 2250

department: BMT and Cell Therapy

institute: Stanford University

description: Library name: PTCY2

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned using standard BD processing pipelines on SevenBridges Genomics cloud computing platform.
Processing output files were combined using custom code which can be found at https://github.com/csbader/Bader-CS-et-al-2025.
Assembly: GRCh38
Supplementary files format and content: all_sample_rna is a Seurat object .rds with all sample counts and associated metadata.
Supplementary files format and content: all_samples_vdj is an .rds dataframe with all sample VDJ information and matching barcodes to all_sample_rna.

source_name: PBMC

extract_protocol:
Cells were captured and lysed using the BD Rhapsody platform.
Targeted Human Immune Response Panel and VDJ libraries were generated according to manufactuer instructions.

treatment_protocol: Patients either received Orca-T immunotherapy or PBSC grafts ~3 weeks before PBMC isolation, sorting, and capture.

value: PBMC

value: Sorted lymphocytes


title: replicate 2 of TOP1 CUT&Tag in HeLa

description: Library name: HeLa_TOP1_R2


title: 293T-shNC-ERCC

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description:
Library name: sample1
293T-mRNA-ERCC-NC-RK.txt

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads. Clean Reads were then aligned to the reference genome (Human: hg19; C. elegans: ce10)Bowtie2. For linear RNA, read counts were generated using BEDTools. For poly(A)-selected RNA-seq with ERCC spike-in, clean reads were aligned to a combined reference consisting of the human/C. elegans genome and ERCC spike-in sequences. Read counts for endogenous genes and ERCC transcripts were obtained using standard counting procedures. ERCC read counts were modeled using a negative binomial distribution to estimate sample-specific scaling factors, which were subsequently applied to normalize endogenous gene expression levels for assessment of global mRNA abundance.
Assembly: hg19(human), ce11(C. elegans)
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer’s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For poly(A)-selected RNA-seq, external RNA Control Consortium (ERCC) spike-in RNA controls (Invitrogen, 4456740) were diluted and added according to the manufacturer’s instructions. Specifically, 1 μL of 1:100 diluted ERCC spike-in RNA mix was added to 5 μg total RNAs prior to enrichment using oligo(dT) magnetic beads and library preparation.


title: Breast Benign Disease [Patient 027_SH06Y49_Cell2]


title: replicate 1 of CK13 CUT&Tag in HeLa

description: Library name: Hela_CK13_R1


title: PTCY3, pooledSeq

description: Library name: PTCY3


title: Breast Benign Disease [Patient 022_SH08L23_Cell3]


title: CASM34 ChIP S1

city: Umeå

first: Lixiao

state: Sverige

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

department: Department of Medical Biosciences

country: Sweden

institute: Umeå University

description: Library name: IP34P1

data_processing:
Adapter trimming using Trim Galore, aligning sequencing reads to reference sequences using Bowtie2
Create normalised bigWig files scaled to 1 million mapped reads were performed by using BEDTools and bedGraphToBigWig.
Peaks were called using MACS 2 with the significant cut-off q-value 0.05
NarrowPeak files were generate using MACS 2 with default settings.
Assembly: GRCh38
Supplementary files format and content: BigWig, narrowPeak

growth_protocol: Cells were cultured in RPMI 1640 medium (31870074, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (A3160502, Thermo Fisher Scientific), 100 U.mL-1 penicillin and 100 mg. mL-1 streptomycin (15140122, Thermo Fisher Scientific) and 2 mM L-glutamine (25030081, Thermo Fisher Scientific) and maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
p53 ChIP-seq was performed using a SimpleChIP® Plus Enzymatic Chromatin IP Kit (9005, Cell Signalling technology) following the manufacturer’s instructions. Briefly, cells were fixed and nuclei was purified as described in DNA-ChIP. DNA was then fragmented by treating with Micrococcal Nuclease for 20 min at 37°C and sonicated. Fragmented DNA was subjected to IP as described above using DO-1 p53 antibody (2mg/ml) and ChIP-Grade Protein G Magnetic Beads.
Quality of the purified ChIP DNA was analyzed by Agilent 2100 Bioanalyzer according to the manufacturer’s instructions and proceeded for library preparation and deep-sequencing using PE150 strategy on Ilumina platform (Novogene, Cambridge, UK).

value: non-small-cell lung carcinoma cells

value: ChIP antibody DO-1 p53


title: Breast Benign Disease [Patient 028_SH06Y29_Cell2]


title: PTCY1, pooledSeq

description: Library name: PTCY1


title: replicate 1 of IgG CUT&Tag in HeLa

description: Library name: Hela_IgG_R1


title: CASM34 ChIP S2

description: Library name: IP34P2


title: Breast Benign Disease [Patient 021_SH06Y35_Cell3]


title: Breast Benign Disease [Patient 020_SH11R17_Cell4]


title: p53WT ChIP S2

description: Library name: IPWT2


title: Breast Benign Disease [Patient 019_SH05T42_Cell4]


title: BAMS9

city: Singapore

first: Vanitha

middle: Venkoba

last: Rao

address: National University of Singapore Department of Biological Sciences  14 Science Drive 4 Block S1A, #05-05

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Library name: Sample 6

data_processing:
High quality reads were obtained and short read alignment was performed using Hisat2 (v2.0.1) with default parameters. FPKM (Fragments per kilo bases per million reads) was calculated based on read counts from HT-seq (v0.6.1)
Assembly: GRCh38.p13
Supplementary files format and content: xls files include FPKM values for each sample

source_name: patient derived iPSC

extract_protocol:
RNA from Day12 differentiated Cranial placodes cells was extracted using RNeasy mini kit (Qiagen) with DNase digestion on column
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BAMS

value: Cranial Placode cells


title: p53WT RNA S2

description: Library name: RNAWT2

data_processing:
RNA sequencing analysis using STAR, RSEM
Sequence reads were trimmed for adptor sequence/low-quality sequence using trim_galore
aligning sequencing reads to reference sequence and quantification were performed using star and rsem
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file inculdes raw counts, TPM, and FPKM values for each sample.

extract_protocol:
Total RNAs were isolated from H1299 cells expressing p53-WT/CASM34 using RNeasy Mini Kit (74104, Qiagen) following the manufacturer's protocol. Quality of isolated RNAs were assessed by Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.
RNAs were then subjected to polyA purification, library preparation and massive parallel sequencing (Novogene, UK).


title: CASM34 RNA S2

description: Library name: RNA34P2


title: p53WT ChIP S1

description: Library name: IPWT1


title: p53WT RNA S1

description: Library name: RNAWT1


title: BAMS1

description: Library name: Sample 4


title: BAMS2

description: Library name: Sample 5


title: SKBR3 cells, SPDEF knockdown 4

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

description: Library name: Sample 16

data_processing:
The raw sequencing reads files in Fastq format were assessed for quality with FastQC.
Pseudo-alignment was achieved using Salmon (version 1.9) with hg38 referece genome.
Subsequent analysis were performed using DESeq2 (version 3.16) with output quantification files.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: MCF7, SKBR3 control and SPDEF knockdown cells were cultured in DMEM +GlutaMAX-1 containing 10% Fetal bovine serum and pen/strep at 37˚C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. RNA sequencing was performed using Illumina NextSeq550 system, with paired-end 2 x 101 bp read length.
RNA-seq libraries were constructed following Illumina NextSeq 550 standard mRNA protocol.

value: Human breast cancer

value: SPDEF knockdown


title: Control3

description: Library name: Sample 3

value: Control


title: replicate 2 of IgG CUT&Tag in HeLa

description: Library name: Hela_IgG_R2


title: Breast Benign Disease [Patient 018_SH06Y53_Cell2]


title: Control2

description: Library name: Sample 2


title: Breast Benign Disease [Patient 017_SH05T56_Cell4]


title: Control1

description: Library name: Sample 1


title: SKBR3 cells, SPDEF knockdown 2

description: Library name: Sample 14


title: Breast Benign Disease [Patient 015_SH11R09_Cell2]


title: Breast Benign Disease [Patient 016_SH0ZE14_Cell1]


title: SKBR3 cells, Control WT 2

description: Library name: Sample 10

value: WT


title: SKBR3 cells, Control WT 4

description: Library name: Sample 12


title: SKBR3 cells, SPDEF knockdown 1

description: Library name: Sample 13


title: SKBR3 cells, Control WT 3

description: Library name: Sample 11


title: SKBR3 cells, Control WT 1

description: Library name: Sample 9


title: SKBR3 cells, SPDEF knockdown 3

description: Library name: Sample 15


title: Breast Benign Disease [Patient 014_SH09X49_Cell3]


title: CASM34 RNA S1

description: Library name: RNA34P1


title: syN-CAR-exo

city: Changchun

first: Jiayi

last: chen

state: 吉林Jilin

address: School of Life Sciences

institute: Jilin University

description:
Library name: sample B
10x Genomics

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by marker gene.
KEGG (Kanehisa M, 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumour

extract_protocol:
10x Genomics® Cell Preparation Guide describes best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).

value: tumour


title: MCF7 cells, SPDEF knockdown 3

description: Library name: Sample 7


title: MCF7 cells, SPDEF knockdown 4

description: Library name: Sample 8


title: PBS

description:
Library name: sample A
10x Genomics


title: MCF7 cells, SPDEF knockdown 2

description: Library name: Sample 6


title: MCF7 cells, Control WT 3

description: Library name: Sample 3


title: Breast Benign Disease [Patient 011_SH06Y52_Cell4]


title: MCF7 cells, Control WT 4

description: Library name: Sample 4


title: BB22_005, Lung, IPF

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

description:
Library name: BB22_005
FFPE spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ragering Pipline
Sequences were aligned to Human reference (GRCh38) to gene expression count using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: Space Ranger output folder "outs"
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
FFPE
Followed 10XGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacutre's construction

value: Lung

tag: group

value: IPF


title: Breast Benign Disease [Patient 010_SH11R05_Cell4]

value: female

value: Training


title: MCF7 cells, Control WT 2

description: Library name: Sample 2


title: MCF7 cells, Control WT 1

description: Library name: Sample 1


title: Breast Benign Disease [Patient 012_SH11M29_Cell2]


title: Breast Benign Disease [Patient 013_SH06Y38_Cell3]


title: cc003-20, Lung, Donor

description:
Library name: cc003-20
FFPE spatial transcriptome sequencing

value: Donor


title: cc0005-19, Lung, Donor

description:
Library name: cc0005-19
FFPE spatial transcriptome sequencing


title: SKBR3_SPDEFKD_02

description: Library name: SKBR3_SPDEFKD_02

data_processing:
The quality of sequenced ATAC-seq data was evaluated with FastQC. All sequencing data were mapped onto the hg38 human genome assembly using Bowtie2.
SAMtools was used to remove duplicate reads, only non-duplicate reads kept in the BAM format were used for the subsequent analysis. Peak calling on nucleosome-free reads was performed by MACS2 using the module ‘‘callpeak’’.
Picard Tools and ggplot2 were used to analyze and plot the distribution of paired-end sequencing fragment sizes. For data normalization and visualization, the BAM files were converted to the bigWig format using the “bamCoverage”.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
After a wash step in cold cell wash buffer, outer membranes were disrupted in lysis buffer for 2 min on ice. After a centrifugation step at 1,500g for 10 min, pelleted nuclei were kept for the next step. In a 50-μl final volume, tagmentation was performed for 30 min at 37 °C, using the Nextera DNA library prep kit. After addition of SDS to 0.2% final concentration, DNA was purified on AMPure XP beads using a 2:1 ratio (v/v) of beads:tagmented DNA.
Freshly eluted DNA was barcoded and amplified in 110-μl PCR volume to generate a library with the following PCR program: 65 °C, 5 min; 98 °C, 30 s; 11 cycles of (98 °C, 10 s ramping to 65 °C, 30 s), 4 °C hold. ATAC libraries were then pooled at equimolar concentration and were sequenced multiplexed on the Illumina NextSeq550 with 50-bp paired-ends


title: SKBR3_02

description: Library name: SKBR3_02


title: cc07-18, Lung, Donor

description:
Library name: cc07-18
FFPE spatial transcriptome sequencing


title: SKBR3_01

description: Library name: SKBR3_01


title: SKBR3_SPDEFKD_01

description: Library name: SKBR3_SPDEFKD_01


title: MCF7_SPDEFKD_02

description: Library name: MCF7_SPDEFKD_02


title: Day 6 suppressed ATAC

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

description: Library name: d6-suppressed_ATAC

data_processing:
Cell Ranger Arc
Assembly: GRch38
Supplementary files format and content: Cell ranger output files: barcode.tsv.gz, matrix.tsv.gz, features.tsv.gz

source_name: Blood

extract_protocol:
T cells magnetically separated from DCs
10x Multiome

treatment_protocol: Activated T cells (control) or yMSC-suppressed T cells (suppressed). Suppressed T cells exposed to yMSC on the bottom of a transwell for 48 hours before being placed back into fresh media for the remaining activation period (6 days).

value: Blood

tag: library type

value: ATAC

value: T cells


title: MCF7_02

description: Library name: MCF7_02


title: MCF7_SPDEFKD_01

description: Library name: MCF7_SPDEFKD_01


title: Breast Benign Disease [Patient 008_SH09X57_Cell4]


title: BB22_19, Lung, IPF

description:
Library name: BB22_19
FFPE spatial transcriptome sequencing


title: Breast Benign Disease [Patient 009_SH11M32_Cell4]


title: Day 6 suppressed RNA

description: Library name: d6-suppressed_GEX

value: mRNA


title: MCF7_01

description: Library name: MCF7_01


title: Brain_HTL_08

city: São Paulo

first: Arthur

middle: Barbarini

last: Yoshida

state: SP

address: Dr. Arnaldo, 455 – 4º andar – sala 4110 - Cerqueira César

department: Neurology

country: Brazil

institute: Faculdade de Medicina da Universidade de São Paulo

description: Library name: X63_S63

data_processing:
Alignment: Raw sequence data were aligned to the GRCh38 reference genome. The alignment software used was STAR.
BAM File Processing: The resultant BAM files were sorted and merged using biobambam2’s bamsort.
Read Quantification: Gene-level reads were quantified using the software featureCounts against Ensembl GFF annotations.
Quality Control Assessment: Quality metrics were assessed using the software FastQC and RNA-SeQC.
Assembly: Reference Genome: GRCh38.
Supplementary files format and content: Format and Content: Primary processed data format consists of gene-level read counts. These counts were subsequently processed into log₂-normalized RNA-seq counts. The data were also presented after gene-wise z-score scaling of these log₂-normalized counts. Downstream results include statistical outputs such as BH-adjusted p-values.

source_name: Autopsy brain tissue

extract_protocol:
Tissue Quality Assessment and Nucleic Acid Extraction: Tissue quality was initially assessed by haematoxylin–eosin staining of 6 µm cryostat sections. Up to 40 mg of frozen tissue was lysed in Qiagen RLT Plus buffer and homogenized by repeated passage through an insulin syringe. DNA and RNA were co-extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol.
RNA-seq Library Preparation and Sequencing: RNA-seq libraries were prepared using the QuantSeq 3′ mRNA‑Seq Library Prep FWD kit (Lexogen, Vienna, Austria). This process generated approximately 5 million 75 bp reads per sample. Sequencing was performed on an Illumina NextSeq 550 (Illumina, San Diego, CA) at the SELA facility (USP).

value: Autopsy brain tissue


title: MCF7 cells, SPDEF knockdown 1

description: Library name: Sample 5


title: Breast Benign Disease [Patient 006_SH06Y56_Cell2]


title: Breast Benign Disease [Patient 007_SH08L32_Cell3]


title: Breast Benign Disease [Patient 004_SH09X53_Cell1]


title: Breast Benign Disease [Patient 005_SH09X59_Cell2]


title: Day 6 conrol ATAC

description: Library name: d6-control_ATAC


title: Brain_HTL_06

description: Library name: X61_S61


title: Brain_HTL_07

description: Library name: X62_S62


title: Brain_HCP_06

description: Library name: X58_S58


title: Brain_HCP_07

description: Library name: X59_S59


title: Day 6 control RNA

description: Library name: d6-control_GEX


title: Brain_HPC_08

description: Library name: X60_S60


title: Brain_HCP_05

description: Library name: X57_S57


title: Day 5 suppressed ATAC

description: Library name: d5-suppressed_ATAC


title: Brain_HCP_04

description: Library name: X56_S56


title: Brain_HCP_02

description: Library name: X54_S54


title: Breast Benign Disease [Patient 003_SH0ZE24_Cell4]


title: Day 5 suppressed RNA

description: Library name: d5-suppressed_GEX


title: Brain_HCP_03

description: Library name: X55_S55


title: control

city: Sakai

first: Kosuke

last: Murakami

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

institute: Kindai University

description: Library name: TakamuraWTA12

data_processing:
Raw reads were trimmed using Cutadapt v2.10, annotated using BD Biosciences–provided Python scripts, and mapped to the reference transcriptome using Bowtie2 v2.4.2. Cell barcode information was added to BAM files, and read counts for each gene in each cell were calculated using mawk.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: tumor

extract_protocol:
Recombinant mouse IL-17A was administered to OCCC-bearing mice, and ovarian tumors were harvested 7 days after treatment. Tumor tissues were finely minced with scissors and enzymatically digested with Collagenase D (1.25 mg/mL; Merck, Darmstadt, Germany) at 37°C for 30 minutes. The resulting single-cell suspensions were stained with an anti-CD45 antibody (clone 30-F11, 1:800; BioLegend, San Diego, CA, USA) and 7-aminoactinomycin D (7-AAD, 1:200; BioLegend), and viable CD45⁺7-AAD⁻ cells were sorted using a BD FACSAria II cell sorter (BD Biosciences, San Jose, CA, USA). Sorted cells were loaded onto a BD Rhapsody Cartridge and processed using the BD Rhapsody Cartridge Reagent Kit (BD Biosciences) according to the manufacturer’s instructions. Single-cell cDNA synthesis was performed by Immunogeneteqs (Chiba, Japan) using the BD Rhapsody cDNA Kit (BD Biosciences). Whole Transcriptome Analysis (WTA) libraries were generated using the Immune Response Panel Mm and sequenced on a NovaSeq 6000 S4 flow cell (NovaSeq 6000 S4 Kit v1.5; Illumina, San Diego, CA, USA), with a sequencing depth of approximately 20,000 reads per cell.
Sorted cells were loaded onto a BD Rhapsody Cartridge and processed using the BD Rhapsody Cartridge Reagent Kit (BD Biosciences) according to the manufacturer’s instructions. Single-cell cDNA synthesis was performed by Immunogeneteqs (Japan) using the BD Rhapsody cDNA Kit (BD Biosciences). Whole Transcriptome Analysis (WTA) libraries were generated using the Immune Response Panel Mm and sequenced on a NovaSeq 6000 S4 flow cell (NovaSeq 6000 S4 Kit v1.5; Illumina).

value: tumor


title: Brain_HCP_01

description: Library name: X53_S53


title: control, IL-17

description: Library name: TakamuraWTA10


title: Brain_FRO_06

description: Library name: X50_S50


title: Brain_FRO_07

description: Library name: X51_S51


title: Brain_FRO_08

description: Library name: X52_S52


title: Day 5 control RNA

description: Library name: d5-control_GEX


title: Brain_FRO_05

description: Library name: X49_S49


title: Day 4 suppressed ATAC

description: Library name: d4-suppressed_ATAC


title: Breast Benign Disease [Patient 001_SH08L40_Cell1]


title: AngII+LY-4

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

description:
Library name: Sample-14
colname in normalized_counts.txt: COMBINE_GD014

data_processing:
Gene expression levels were quantified with feature Counts and differential expression analysis was conducted using DESeq2. The differentially expressed genes (DEGs) between different conditions were determined using the Wald test with a cut-off for absolute log2 fold change greater than 0.5 and adjusted p-values less than 0.05. Volcano plots and pathway analyses were generated with Ingenuity Pathway Analysis (IPA) (Qiagen), and the heatmaps were generated using RStudio’s Shiny app.
Assembly: GRCm39
Supplementary files format and content: tap-delimited txt file for normalized data

source_name: aortic valve leaflets

growth_protocol: All mice were fed with Breslow Western Diet during the study.

extract_protocol:
RNA extracted from aortic leaflets and purified using Qiagen Rneasy kit.
Bulk RNA-seq raw fast files were first subjected to quality control using FastQC  (v0.12.1) to identify potential issues such as contamination and adapter sequences (Figure S2). After trimming low-quality sequences, FastQC was rerun on the cleaned reads to ensure that all major quality issues were resolved. The sequencing reads were then aligned to the mouse reference genome (GRCm39) using HISAT2.

treatment_protocol: Mice were treated with AngII at 1000 ng/kg/min rate in minipumps or LY272015 every other day at 3mg/kg rate.

value: aortic valve leaflets

value: C57BL/6 wild type

value: Angiotensin II + LY272018


title: Brain_FRO_04

description: Library name: X48_S48


title: Day 4 suppressed RNA

description: Library name: d4-suppressed_GEX


title: Day 5 control ATAC

description: Library name: d5-control_ATAC


title: Brain_FRO_02

description: Library name: X46_S46


title: AngII+LY-2

description:
Library name: Sample-12
colname in normalized_counts.txt: COMBINE_GD012

value: Angiotensin II + LY272016


title: Breast Benign Disease [Patient 002_SH06Y54_Cell2]


title: Brain_FRO_01

description: Library name: X45_S45


title: Brain_PAR_16

description: Library name: X44_S44


title: AngII-4

description:
Library name: Sample-10
colname in normalized_counts.txt: ANG2_GD010

value: Angiotensin II


title: Day 4 control RNA

description: Library name: d4-control_GEX


title: Brain_PAR_13

description: Library name: X41_S41


title: Brain_PAR_14

description: Library name: X42_S42


title: AngII+LY-3

description:
Library name: Sample-13
colname in normalized_counts.txt: COMBINE_GD013

value: Angiotensin II + LY272017


title: AngII-3

description:
Library name: Sample-9
colname in normalized_counts.txt: ANG2_GD009


title: Day 3 control ATAC

description: Library name: d3-control_ATAC


title: Day 3 suppressed ATAC

description: Library name: d3-suppressed_ATAC


title: AngII-2

description:
Library name: Sample-8
colname in normalized_counts.txt: ANG2_GD008


title: Brain_PAR_11

description: Library name: X39_S39


title: Brain_PAR_12

description: Library name: X40_S40


title: Day 3 control RNA

description: Library name: d3-control_GEX


title: AngII-1

description:
Library name: Sample-7
colname in normalized_counts.txt: ANG2_GD007


title: Brain_FRO_03

description: Library name: X47_S47


title: Day 4 control ATAC

description: Library name: d4-control_ATAC


title: Brain_PAR_10

description: Library name: X38_S38


title: Brain_PAR_07

description: Library name: X35_S35


title: LY-2

description:
Library name: Sample-6
colname in normalized_counts.txt: LY_GD006


title: Day 3 suppressed RNA

description: Library name: d3-suppressed_GEX


title: Brain_PAR_09

description: Library name: X37_S37


title: Day 2 suppressed ATAC

description: Library name: d2-suppressed_ATAC


title: Brain_PAR_05

description: Library name: X33_S33


title: Brain_PAR_04

description: Library name: X32_S32


title: LY-1

description:
Library name: Sample-5
colname in normalized_counts.txt: LY_GD005


title: Brain_PAR_06

description: Library name: X34_S34


title: Day 2 suppressed RNA

description: Library name: d2-suppressed_GEX


title: AngII+LY-1

description:
Library name: Sample-11
colname in normalized_counts.txt: COMBINE_GD011

value: Angiotensin II + LY272015


title: Brain_PAR_03

description: Library name: X31_S31


title: Brain_PAR_01

description: Library name: X29_S29


title: Brain_HTL_05

description: Library name: X28_S28


title: Brain_PAR_15

description: Library name: X43_S43


title: Brain_HTL_03

description: Library name: X26_S26


title: Brain_HTL_01

description: Library name: X24_S24


title: Brain_HTL_02

description: Library name: X25_S25


title: Brain_PAR_08

description: Library name: X36_S36


title: Brain_HTL_04

description: Library name: X27_S27


title: Brain_PAR_02

description: Library name: X30_S30


title: Day 2 control RNA

description: Library name: d2-control_GEX


title: Control-2

description:
Library name: Sample-2
colname in normalized_counts.txt: CTRL_GD002

value: Untreated


title: Day 2 control ATAC

description: Library name: d2-control_ATAC


title: Control-3

description:
Library name: Sample-3
colname in normalized_counts.txt: CTRL_GD003


title: Control-4

description:
Library name: Sample-4
colname in normalized_counts.txt: CTRL_GD004


title: Day 1 ATAC

description: Library name: d1-Tcells_ATAC


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, cLTP, rep 3

city: Wako

first: Nayan

last: Suryawanshi

state: Saitama

address: Hirosawa 2-1

department: Center for Brain Science

institute: RIKEN

description:
Library name: cLTP3.Bulk.Ribo
cLTP3-Ribo-seq

library_source: other

data_processing:
For Bulk-Ribo-seq, samples were demultiplexed and adapters were trimmed, aligned to rRNA using Bowtie, aligned to mouse transcriptome and genome using Bowtie and STAR, respectively. And furhter processed with samtools and bedtools.
For Ribo-seq (HALO IP-RIbo-seq), adapters were trimmed using cutadapt -a CTGTAGGCACCATCAAT -u 1 -m 11, aligned to rRNA using Bowtie, aligned to mouse transcriptome and genome using Bowtie and STAR, respectively. And furhter processed with samtools and bedtools.
Assembly: mm39 and nucleotide sequences of all transcripts on the reference chromosomes
Supplementary files format and content: A tab-delimited text file contains normalised counts for all predicted mORFs with columns for transcript id (V7), Bulk-Ribo-seq normalised counts from each samples: TTX1, TTX2, tTTX3, cLTP1, cLTP2, and cLTP3

molecule: other

source_name: Hippocampus

growth_protocol: Organotypic hippocampal slice cultures were prepared as described previously by Stoppini et al 49. In brief, hippocampal slices of 325 μm thickness were dissected from both male and female C57BL/6N mice (SLC) at the postnatal day 5-6 (P5-6) using a McIlwain tissue chopper (The Mickle Laboratory Engineering), and were plated on hydrophilic PTFE membranes (Millicell, Millipore). The slices were maintained in a culture medium containing MEM (Sigma-Aldrich), 20% heat-inactivated horse serum (GIBCO), 1 mM glutamax (GIBCO), 1 mM CaCl2, 2 mM MgSO4, 12.9 mM D-Glucose, 5.2 mM NaHCO3, 30 mM HEPES, 0.075% ascorbic acid, 1 µg/ml insulin at 37℃ in a 5% CO2 humidified at-mosphere. The culture medium was exchanged with fresh medium every other day.

extract_protocol:
RNA extraction was performed as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012)
Library construction was performed as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012). For RNA-seq, RNA was used to purify mRNA using Takara Oligotex-dT30 kit according to manufac-turer’s instructions. Purified RNA was fragmented using alkaline fragmentation buffer containing 27 mM Na2CO3 , 72 mM NaHCO3 , 2 mM EDTA, at 95 ℃ for 40 min. Fragments corresponding the length of 25 to 34 nt were used for NGS sequencing library preparation.

treatment_protocol: At day in vitro 2 (DIV2), cultured slices were divided into the two groups and AAV vectors at a titer of 0.5 x 1013 GC were directly added onto cultures, as follows: AAV-DJ-hSyn1-EGFP-L10a and AAV-DJ-hSyn1-HA-GFP-nanobody-HALO-PEST for control group and AAV-DJ-hSyn1-EGFP-L10a and AAV-DJ-ESARE-HA-GFP-nanobody-HALO-PEST for stimulation group. At DIV15-16, the culture medium was replaced by media containing 1 µM TTX (Tocris and Wako). At DIV16-17, slices were either treated with cLTP cocktail or 1 µM TTX for 15 min. cLTP cocktail containing 50 µM forskolin (Abcam), 0.1 µM rolipram (Sigma), 50 µM (+)-bicuculline (Tocris), and 100 µM 4-aminopyridine (Tocris) was prepared in artificial cerebrospinal fluid (ACSF) composed of 15 mM Hepes pH 7.3, 125 mM NaCl, 20 mM Glucose, 5 mM KCl, and 4 mM CaCl2. After the stimulation, the slices were al-lowed to recover for 1 h in normal culture media. Slices were then briefly washed with ice-cold PBS, immediately frozen in liquid nitrogen and stored at -80℃ until processed for Ribo-seq and RNA-seq.

value: Hippocampus

value: No genetic modification

value: cLTP

tag: batch


title: Day 0 RNA

description: Library name: d0-Tcells_GEX

value: Blood


title: Brain_SUB_01

description: Library name: X19_S19


title: Control-1

description:
Library name: Sample-1
colname in normalized_counts.txt: CTRL_GD001


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, cLTP, rep 2

description:
Library name: cLTP2.Bulk.Ribo
cLTP2-Ribo-seq


title: Day 0 ATAC

description: Library name: d0-Tcells_ATAC

value: ATAC


title: Brain_TEMP_05

description: Library name: X18_S18


title: Brain_SUB_04

description: Library name: X22_S22


title: Brain_SUB_05

description: Library name: X23_S23


title: MCF-7 Tam1, Si-NSUN7, biol rep2

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description: Library name: GE33.H43.S32

data_processing:
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic]. Transcript-level mapping and quantification were performed by Salmon using the human transcriptome database (Gencode version H43). Flags -seqBias and -gcBias were applied during mapping to correct systematic biases commonly present in batch RNA-seq data. Quality of RNA-seq, mapping and quantification was assessed using FastQC (Babraham Bioinformatics, UK) and MultiQC tools
Gene-level quantification and annotation were done using Tximeta utility.
Assembly: Gencode H43/GRCh38.p13
Supplementary files format and content: tab-delimited text file includes Salmon aligner quantification.
Supplementary files format and content: Columns: Name — This is the name of the target transcript provided in the input transcript database (FASTA file). Length —the length of the target transcript in nucleotides. EffectiveLength —the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias. TPM —salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads —salmon’s estimate of the number of reads mapping to each transcript that was quantified.

source_name: MCF-7 Tam1

growth_protocol: MCF-7 Tam1 were grown in DMEM with 4.5 g/l glucose and supplemented with 1 mM sodium pyruvate, 10 µg/mL human insulin, 10% (v/v) fetal bovine serum (FBS) and antibiotics at 37ºC in 5% CO2. Cells were continuously cultured in 1 µM 4-OH tamoxifen to maintain resistance.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were prepared using standard TruSeq Stranded mRNA library preparation protocol

treatment_protocol: Transfection was achieved using Lipofectamine™ RNAiMAX transfection reagent.

value: MCF-7 Tam1

value: Epithelial Cells

value: NSUN7 Knockdown


title: Brain_SUB_02

description: Library name: X20_S20

value: Autopsy brain tissue


title: Day 1 RNA

description: Library name: d1-Tcells_GEX

value: mRNA

value: T cells


title: Brain_SUB_03

description: Library name: X21_S21


title: Brain_TEMP_03

description: Library name: X16_S16


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, TTX, rep 3

description:
Library name: TTX3.Bulk.Ribo
TTX3-Ribo-seq

value: TTX


title: MCF-7 Tam1, Si-NSUN7, biol rep1

description: Library name: GE33.H43.S31


title: Brain_TEMP_02

description: Library name: X15_S15


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, cLTP, rep 1

description:
Library name: cLTP1.Bulk.Ribo
cLTP1-Ribo-seq


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, TTX, rep 2

description:
Library name: TTX2.Bulk.Ribo
TTX2-Ribo-seq


title: Brain_OCC_04

description: Library name: X13_S13


title: Brain_TEMP_01

description: Library name: X14_S14


title: Brain_OCC_02

description: Library name: X11_S11


title: Brain_OCC_03

description: Library name: X12_S12


title: MCF-7 Tam1, Si-Control , biol rep1

description: Library name: GE33.H43.S29

value: WT


title: MCF-7 Tam1, Si-Control , biol rep2

description: Library name: GE33.H43.S30


title: Brain_OCC_05

description: Library name: X9_S9


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, TTX, rep 1

description:
Library name: TTX1.Bulk.Ribo
TTX1-Ribo-seq


title: Brain_CER_08

description: Library name: X8_S8


title: HEK293T cells-K700E_rep3

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

description: Library name: Sample 12

data_processing:
Raw data of fastq format were firstly trimmed through trim_galore (version 0.6.4). In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean Reads were mapped to genome(hg38) using hisat2(version 2.2.0)
circRNAs were identified and quantified using CIRI2(version 2.0.6)
Annotate circRNA using the circBase database. Counts per million(CPM) were used to calculate circRNA expression levels
Differential expression analysis of two groups was performed using the edge R package(version 3.36.0).
Assembly: ensembl CRCh38
Supplementary files format and content: tab-delimited text files include reads for each Sample

growth_protocol: Hela and HEK293T cell line was cultured in DMEM (Gibco) supplemented with 10% FBS and streptomycin/penicillin (100 U/mL) at 37˚C in an atmosphere of 5% CO2.

extract_protocol:
Hela and HEK293T cells with or without SF3B1-K700E mutation was harvested using Trizol reagent.Total RNA was extracted using the RNeasy Mini Kit (Cat#74106, Qiagen).Total RNA was depleted ribosomal RNA and then useds RNase R to digest linearRNA.The RNA was fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T cells were transiently transfected with pIRES2-SF3B1 WT (WT) or pIRES2-SF3B1 K700E (K700E) plasmid for 48h using Lipofectamine 2000.

value: Transient transfection with pIRES2-SF3B1 K700E plasmid


title: Brain_CER_07

description: Library name: X7_S7


title: WT Ep300 for RA differentiation

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

description:
Library name: WT-RA-Ep300
WT E14 cell for RA differentiation

data_processing:
Using bowtie2 to map fastq reads data to mm10
MACS3 were used to call Ep300 peaks
Bamcoverage to calculate the bigwig peaks file
Assembly: mm10
Supplementary files format and content: Bw files

source_name: ES

extract_protocol:
Cells were wash twice with PBS containing 5% FBS. Then Cuttag targeting Ep300 was using to generate library
Cuttag libraries for were prepared usingNovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) following manufacturer's protocols.

value: ES

value: E14 cell line

value: RA-induced differentiation


title: DKO Ep300 for RA differentiation

description:
Library name: DKO-RA-Ep300
Rara and Rxra deletion E14 cell for RA differentiation

value: Rara and Rxra deletion


title: HEK293T cells-K700E_rep2

description: Library name: Sample 11


title: HEK293T cells-K700E_rep1

description: Library name: Sample 10


title: Brain_CER_05

description: Library name: X5_S5


title: Brain_CER_06

description: Library name: X6_S6


title: Brain_OCC_01

description: Library name: X10_S10


title: AP1

city: Shanghai

first: Yuankai

last: Hao

address: No. 1954, Huashan Road

institute: Shanghai Jiao Tong University

description: Library name: Sample 16

data_processing:
Data Quality Control by RseQC 4.0.0
Gene Expression Level Annotation and Statistics by htseq-count 0.11.2
Intra-sample Correlation Test
Principal Component Analysis
Cluster Analysis
Assembly: tab-delimited text includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Tumor

extract_protocol:
Lysis: Homogenize samples in TRIzol® (tissue/cells) for complete RNA release. Phase Separation: Add chloroform, centrifuge to isolate RNA in the aqueous phase. Precipitation: Mix with isopropanol, incubate, and centrifuge to pellet RNA. Wash: Remove contaminants with 75% ethanol. Column Purification: Use silica columns (e.g., Zymo Kit) for DNase treatment and high-purity RNA elution.
RNA-seq libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit. For sequencing and analysis

value: Tumor

value: Resection of untreated tumors after combined cryo-thermal and anti-PD-1 therapy


title: AP2

description: Library name: Sample 17


title: A3

description: Library name: Sample 15

value: Resection of untreated tumors after cryo-thermal therapy


title: HEK293T cells-WT_rep3

description: Library name: Sample 9

value: Transient transfection with pIRES2-SF3B1 WT plasmid


title: HEK293T cells-WT_rep2

description: Library name: Sample 8


title: Brain_CER_02

description: Library name: X2_S2


title: Brain_CER_01

description: Library name: X1_S1


title: Brain_CER_03

description: Library name: X3_S3


title: Brain_CER_04

description: Library name: X4_S4


title: A2

description: Library name: Sample 14


title: C_60

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

data_processing:
Reads were aligned to the human genome using STAR.
STAR alignments were counted using Salmon.
Assembly: hg38
Supplementary files format and content: Salmon quant file (.sf)

source_name: iNPC

growth_protocol: DMEM/F12, 1xB27, heparin, EGF, bFGF grown on Matrigel or Cultrex basement membrane

extract_protocol:
Adherent cells were detached with Accutase. mRNA was extracted using the Qiagen RNeasy Plus Kit.
mRNA libraries were prepared using the KAPA mRNA HyperPrep and Illumina TruSeq adapters. Libraries were quantified using a Qubit Fluorometer validated using the Agilent High Sensitivity D1000 Tapestation Kit. Libraries were pooled 12/sequencing run and sequenced on 75 cycle High Output v2.5 Illumina kits.

value: iNPC

tag: h3.3 status

tag: pdgfra status

value: iPSC-derived neural progenitor cells


title: C_55


title: AP3

description: Library name: Sample 18


title: HEK293T cells-WT_rep1

description: Library name: Sample 7


title: C_54


title: A1

description: Library name: Sample 13


title: Hela cells-K700E_rep2

description: Library name: Sample 5

source_name: Hela

value: Hela

value: CRISPR/Cas9 introduces endogenous SF3B1-K700E mutation


title: C_51


title: RP3

description: Library name: Sample 12

value: Resection of untreated tumors after combined radiofrequency ablation and anti-PD-1 therapy


title: C_52


title: C_49


title: RP2

description: Library name: Sample 11


title: C_50


title: Hela cells-K700E_rep1

description: Library name: Sample 4


title: Hela cells-WT_rep3

description: Library name: Sample 3

value: Without any treatment


title: C_46


title: R3

description: Library name: Sample 9

value: Resection of untreated tumors after radiofrequency ablation


title: C_45

source_name: iDMG

value: iDMG

value: iPSC-derived high grade glioma model tumor cells


title: C_48

value: WT


title: C_43


title: RP1

description: Library name: Sample 10


title: Hela cells-WT_rep2

description: Library name: Sample 2


title: R2

description: Library name: Sample 8


title: C_53


title: C_3


title: Hela cells-K700E_rep3

description: Library name: Sample 6


title: Hela cells-WT_rep1

description: Library name: Sample 1


title: C_34


title: AS9LRN (3')

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description:
Library name: AS9LRN
10X genomics

data_processing:
Sequenced data were processed into expression matrices with the Cell Ranger Single Cell Software (v 6.1.2) of 10X Genomics against the GRCh38 human reference genome with default parameters.
Assembly: GRCh38
Supplementary files format and content: 10X Cellranger format

source_name: aortic valve

extract_protocol:
Samples were washed, chopped into small pieces, and digested in an enzymatic digestion buffer containing 3 mg/ml collagenase type II (#LS004176, Worthington Biochemical Corp, NJ, USA), 0.15 mg/ml collagenase type XI (#H3506, Sigma Aldrich, MO, USA), 0.25 mg/ml soybean trypsin inhibitor (#LS003571, Worthington Biochemical Corp), 0.1875 mg/ml elastase lyophilized (#LS002292, Worthington Biochemical Corp), 0.24 mg/ml hyaluronidase type I (#H3506, Sigma Aldrich), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES, #H4034, Sigma Aldrich) in PBS with Ca2+ and Mg2+, at 37°C for 90 minutes with shaking. The digested samples were filtered through 40 μm cell strainers (#352340, BD Biosciences, NJ, USA), washed, and centrifuged at 3000 × g for 10 minutes.
ScRNA-seq (3’) libraries were prepared using the Single Cell 3’Reagent Kits v3 for scRNA-seq (10x Genomics, CA, USA). Sequencing libraries were generated following the User Guide (CG000388).

value: aortic valve

value: immune cells


title: R1

description: Library name: Sample 7


title: C_36


title: C_32


title: C_27


title: CP3

description: Library name: Sample 6

value: Resection of untreated tumors after combined cryoablation and anti-PD-1 therapy


title: AS8N (3')

description:
Library name: AS8N
10X genomics


title: C_21


title: C_25


title: AS8LR (3')

description:
Library name: AS8LR
10X genomics


title: C_1


title: AS7R (3')

description:
Library name: AS7R
10X genomics


title: CP1

description: Library name: Sample 4

value: Tumor


title: C_18


title: C_19


title: C3

description: Library name: Sample 3

value: Resection of untreated tumors after cryoablation


title: C_31


title: C_15


title: B_65


title: CP2

description: Library name: Sample 5


title: A_9


title: AS7L (3')

description:
Library name: AS7L
10X genomics


title: B_61


title: C_17


title: C1

description: Library name: Sample 1


title: AS6R (3')

description:
Library name: AS6R
10X genomics


title: C2

description: Library name: Sample 2


city: Chengdu

first: Lei

last: Zhao

state: Sichuan

address: Guoxue Alley 37

department: Department of Hematology

institute: West China Hospital, Sichuan Universtiy

description:
Library name: T125_62
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, IMP125 treatment 3

data_processing:
Sequencing reads were processed using the Cell Ranger pipeline (10x Genomics) for demultiplexing, alignment to mm10 genome, and gene-barcode matrix generation.
Assembly: Mouse genome assembly mm10 (GRCm38)
Supplementary files format and content: Processed data files include gene-barcode matrices (matrix.mtx.gz), cell barcodes (barcodes.tsv.gz), features/genes annotation (features.tsv.gz)

source_name: spleen

growth_protocol: BALB/c mice were maintained under standard conditions. AML syngeneic model was established by intravenous injection of WEHI-3-luc cells.

extract_protocol:
Spleens were harvested from mice. Single-cell suspensions were prepared using mechanical dissociation and filtered through a 40 μm strainer. Cells were washed and counted before library preparation.
Single-cell RNA-seq libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 following manufacturer’s instructions.

treatment_protocol: Treatment started on day 9 post-transplant. IMP125 (5 mg/kg), doxorubicin (DOX) were administered intravenously twice weekly for 4 doses. Control mice received vehicle only.

value: spleen

value: mixed splenocytes

value: BALB/c


title: A_8


title: A_6

value: iNPC

value: iPSC-derived neural progenitor cells


title: B_59


description:
Library name: T125_54
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, IMP125 treatment 2


title: AS6N (3')

description:
Library name: AS6N
10X genomics


title: A_5


title: AS6L (3')

description:
Library name: AS6L
10X genomics


title: AS7N (3')

description:
Library name: AS7N
10X genomics


title: A_48


title: AS5R (3')

description:
Library name: AS5R
10X genomics


title: A_46


title: A_44


title: AS5N (3')

description:
Library name: AS5N
10X genomics


title: AS5L (3')

description:
Library name: AS5L
10X genomics


description:
Library name: H_1
Single-cell RNA-seq of spleen cells from healthy BALB/c mouse


description:
Library name: T125_01
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, IMP125 treatment 1


title: A_42


description:
Library name: DOX_64
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, doxorubicin treatment 3

value: doxorubicin


title: A_35


title: A_43


title: AS4NR (3')

description:
Library name: AS4NR
10X genomics


title: A_34


title: A_45


description:
Library name: DOX_02
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, doxorubicin treatment 2


title: AS3N (3')

description:
Library name: AS3N
10X genomics


description:
Library name: DOX_01
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, doxorubicin treatment 1


title: A_32


title: A_28


description:
Library name: CON_43
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, vehicle control 3

value: vehicle control


title: AS4L (3')

description:
Library name: AS4L
10X genomics


title: A_33


title: Brain_TEMP_04

description: Library name: X17_S17

value: Autopsy brain tissue


title: A_29


description:
Library name: CON_02
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, vehicle control 2


title: A_30


title: A_31


title: A_23


description:
Library name: CON_01
Single-cell RNA-seq of spleen cells from syngeneic AML BALB/c mouse, vehicle control 1


title: AS3L (3')

description:
Library name: AS3L
10X genomics


title: A_21


title: AS2N (3')

description:
Library name: AS2N
10X genomics


title: AS3R (3')

description:
Library name: AS3R
10X genomics


title: A_19


title: A_18


title: AS2LR (3')

description:
Library name: AS2LR
10X genomics


title: Metastatic lymph node BECs, replicate 1, scRNAseq

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

description: Library name: Sample 1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38.91
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Briefly, lymph nodes from six C57BL/6J mice were collected, washed with Hanks Balanced Salt Solution three times and minced into small pieces using surgical scissors.The lymph node tissues were digested with RPMI-1640 medium containing 0.2 mg/ml collagenase P (Sigma Aldrich, #11213857001), 0.8 mg/ml dispase Ⅱ (Sigma Aldrich, #D4693) and 0.01 mg/ml DNase (Sigma Aldrich, #DN25) for 1 h at 37 °C under constant shaking. FBS (final concentration 30%) was added to stop the digestion. Dissociated cell suspensions were then passed through 100 μM and 40 μM filter. Cells were pelleted at 250 g for 5 min, and treated with 2ml of 1× RBC lysis buffer (Biolegend, #420301) on ice for 10 min. The washing buffer was then added and the cells were centrifuged at 1000 rpm for 5 min and was resuspended in PBS.
The single-cell suspension was converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10× Genomics) according to the manufacturer’s protocol. Briefly, the single-cell suspension was loaded into each reaction. The RNA transcripts were uniquely barcoded and reverse-transcribed. Complementary DNA (cDNA) was generated, amplified, fragmented, end repaired, and ligated with adaptors to generate sequencing libraries.

value: Lymph node

value: Endothelial cells


title: A_17

value: iDMG

value: iPSC-derived high grade glioma model tumor cells


title: A_16

value: WT


title: Hepa1-6  cells, sgNT, rep3

first: Yunyi

last: Zhou

address: 1954 Huashan Road, Xuhui District

description: Library name: Hepa1-6-sgNT-rep3

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.5 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
The read length was 2×150 bp.Clean reads were aligned to the mm10 using STAR.
The expression of the transcript was calculated by normalized count using Perl.Differentially expression genes (DEGs) were determined using the Random Sampling (MARS) model in the DESeq2 package. The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.
Then DEGs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database. The significantly enriched pathways were determined when P < 0.05 and at least two affiliated genes were included.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

growth_protocol: MC38, AKR, LLC1, and Hepa1-6 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using HiPure Unviersal RNA Mini Kit(Magen).1.3 ug of total RNA was uesd for the construction of sequencing libraries.
Strand-specific libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: hepatocellular carcinoma cells

value: total RNA

value: paired-end


title: AS1LNR (3')

description:
Library name: AS1LNR
10X genomics

value: aortic valve

value: immune cells


title: A_11


title: Hepa1-6 cells , sgB2m, rep3

description: Library name: Hepa1-6-sgB2m-rep3


title: A_20


title: AR4N (3')

description:
Library name: AR4N
10X genomics


title: AR3N (3')

description:
Library name: AR3N
10X genomics


title: AR3L (3')

description:
Library name: AR3L
10X genomics


title: Hepa1-6 cells , sgB2m, rep2

description: Library name: Hepa1-6-sgB2m-rep2


title: Hepa1-6 cells , sgNT, rep2

description: Library name: Hepa1-6-sgNT-rep2


title: AR4L (3')

description:
Library name: AR4L
10X genomics


title: Hashed, Cas9-CROPseq AML cells ex vivo, day 10, 3' mRNA library

city: Barcelona

first: Alejo

middle: E

last: Rodriguez-Fraticelli

state: Barcelona

address: Carrer Baldiri Reixac 10

department: Aging and Metabolism

country: Spain

institute: IRB Barcelona and ICREA

description:
Library name: CROPseq_PLSTC_GEX
Feature-reference file contains CROPseq and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

data_processing:
CloneRanger (https://github.com/dfernandezperez/cloneRanger)
Assembly: GRCm38 (mm10)
Supplementary files format and content: CellRanger output files (matrix files, barcodes files, features files) - TotalSeq barcode, CROPseq guide RNAs, and LARRY barcode counts are included as additional features in the matrix
Library strategy: CITE-seq

source_name: Hematopoietic cell culture

growth_protocol: Bone marrow AML cells were grown in PLSTC (HemEx type 9O) or Stemspan-based media.

extract_protocol:
Samples were incubated with TotalSeq-B cell hashing antibodies (2 ul per 1M cells) for 30 minutes on ice, washed, and then sorted using a Beckman Coulter CytoFlex SRT sorter. Live GFP+ cells were sorted, centrifuged 800g for 10 minutes at 4ºC, and then resuspended in PBS-0.01%BSA buffer, counted for viability and concentration, and then single-cell processed using Chromium X (3' Gene Expression + Feature Barcoding kits).
10x 3' Gene Expression with Feature Barcoding v3.1 following manufacturer instructions. LARRY and CROPseq barcoding libraries were prepared as previously published (Datlinger et al. Nat Methods 2017, doi: 10.1038/nmeth.4177, and Singh et al. Cell Stem Cell 2025, doi: 10.1016/j.stem.2025.01.012)

treatment_protocol: Cells were transplanted by tail-vein injection in sublethally irradiated mice (typically 10000 cells per animal).

value: Hematopoietic cell culture

value: primary AML cells

value: Acute Myeloid Leukemia

value: Npm1-cA, Flt3-ITD

value: CRISPR in culture

value: mRNA


title: Hashed, Cas9-CROPseq AML cells ex vivo, day 10, Hashing antibodies library

description:
Library name: CROPseq_PLSTC_FB
Feature-reference file contains CROPseq and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

molecule: protein

value: HTO

tag: hto

value: TotalSeq


title: Hashed, PLSTC and Stemspan cultured AML cells ex vivo, day 30, 3' mRNA library

description:
Library name: D30_PLSTC_vs_Stemspan_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: cell culture


title: Hashed, PLSTC and Stemspan cultured AML cells ex vivo, day 30, Hashing antibodies library

description:
Library name: D30_PLSTC_vs_Stemspan_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations


title: Hashed, LARRY-barcoded AML cells in vivo, treated mice, day 40, Hashing antibodies library

description:
Library name: D40_invivo_treated_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

source_name: Bone Marrow and Spleen

value: Bone Marrow and Spleen

value: transplantation and chemotherapy


title: Hashed, LARRY-barcoded AML cells in vivo, treated mice, day 40, LARRY barcodes library

description:
Library name: D40_invivo_treated_LARRY
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: LARRY

tag: lentiviral barcode

value: LARRY-EGFP and LARRY-Tsapphire


title: Hashed, LARRY-barcoded AML cells in vivo, treated mice, day 40, 3' mRNA library

description:
Library name: D40_invivo_treated_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations


title: Hashed, LARRY-barcoded AML cells in vivo, control mice, day 40, 3' mRNA library

description:
Library name: D40_invivo_control_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations


title: Hashed, LARRY-barcoded AML cells in vivo, control mice, day 40, Hashing antibodies library

description:
Library name: D40_invivo_control_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations


title: AR1LRN (3')

description:
Library name: AR1LRN
10X genomics


title: AKR cells, sgNT, rep2

description: Library name: AKR-sgNT-rep2

source_name: AKR

value: AKR

value: esophageal carcinoma cells

value: total RNA


title: Hashed, LARRY-barcoded AML cells in vivo, control mice, day 40, LARRY barcodes library

description:
Library name: D40_invivo_control_LARRY
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations


title: AR2LNR (3')

description:
Library name: AR2LNR
10X genomics

value: aortic valve

value: immune cells


title: IGF2BP3-IP_rep2

city: Kyoto

first: Masahiro

last: Inoue

address: Shimoadachi-cho 46, Sakyou-ku

institute: Kyoto University, Graduate School of Medicine

description: Library name: PR3495_06

data_processing:
Filtered reads were aligned to the human genome (GRCh38) using STAR with default splice-aware settings. Gene expression was quantified using featureCounts with annotation from GENCODE v41.
Raw reads were quality-checked using FastQC and trimmed with Trimmomatic to remove adapters and low-quality bases.
Assembly: hg38
Supplementary files format and content: tab-delimitated text file includes raw counts, gene names, and gene IDs for each samples

source_name: patient-derived adenoma organoids

extract_protocol:
RIP was performed using a Magna RIP RNA-Binding Protein Immunoprecipitation Kit (EMD Millipore, Billerica, MA, USA) according to the manufacturer’s protocol.
Sequence library preparation and next-generation sequencing were performed by Takara Bio, Inc. (Kusatsu, Japan). Briefly, the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) was used to prepare the sequencing library and 150-base pair-end sequence analysis was performed using a NovaSeq 6000 instrument (Illumina).

value: patient-derived adenoma organoids


title: Hashed, LARRY-barcoded AML cells in vivo, day 20, 3' mRNA library

description:
Library name: D20_invivo_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

source_name: Bone Marrow

value: Bone Marrow

value: primary AML cells

value: Acute Myeloid Leukemia

value: transplantation


title: Hashed, Cas9-CROPseq AML cells ex vivo, day 10, CROPseq library

description:
Library name: CROPseq_PLSTC_CROP
Feature-reference file contains CROPseq and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: Hematopoietic cell culture

value: Npm1-cA, Flt3-ITD

value: CRISPR in culture

value: CROPseq

value: CROPseq sgRNA


title: Hashed, LARRY-barcoded AML cells in vivo, day 20, LARRY barcodes library

description:
Library name: D20_invivo_LARRY
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: LARRY

value: LARRY-EGFP


title: AKR cells, sgNT, rep1

description: Library name: AKR-sgNT-rep1

value: AKR

value: paired-end


title: Hashed, LARRY-barcoded AML cells in vivo, day 20, Hashing antibodies library

description:
Library name: D20_invivo_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: HTO

value: TotalSeq


title: Hashed, LARRY-barcoded AML cells ex vivo, day 40, LARRY barcodes library

description:
Library name: D40_exvivo_LARRY
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: cell culture

value: LARRY-EGFP and LARRY-Tsapphire


title: AKR cells, sgNT, rep3

description: Library name: AKR-sgNT-rep3

value: esophageal carcinoma cells

value: total RNA


title: IGF2BP3-IP_rep1

description: Library name: PR3495_04

value: patient-derived adenoma organoids


title: Hepa1-6 cells, sgB2m, rep1

description: Library name: Hepa1-6-sgB2m-rep1

value: hepatocellular carcinoma cells


title: Hashed, LARRY-barcoded AML cells ex vivo, day 40, Hashing antibodies library

description:
Library name: D40_exvivo_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: Hematopoietic cell culture

value: primary AML cells

value: Acute Myeloid Leukemia


title: AKR cells, sgB2m, rep3

description: Library name: AKR-sgB2m-rep3


title: Hepa1-6 cells, sgNT, rep1

description: Library name: Hepa1-6-sgNT-rep1


title: Hashed, LARRY-barcoded AML cells ex vivo, day 40, 3' mRNA library

description:
Library name: D40_exvivo_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: Npm1-cA, Flt3-ITD

value: mRNA


title: IgG_ctrl_rep3

description: Library name: PR3495_03


title: Hashed, LARRY-barcoded AML cells ex vivo, day 20, LARRY barcodes library

description:
Library name: D20_exvivo_LARRY
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: LARRY


title: AKR cells, sgB2m, rep2

description: Library name: AKR-sgB2m-rep2


title: M2_BLZ_Stroke_tdT-

city: Freiburg

first: Maximilian

last: Fliegauf

address: Breisacherstraße 113

department: Institute for Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description:
Library name: S603_24_275plus283_C_neg_S24_R1_001.fastq.gz
tdT- BLZ

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M39. Counts were obtained using FeatureCounts v2.0.6. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M39
Supplementary files format and content: Processed counts are provided in the file Counts_Ccr2creERT2_repopulation_stroke.txt

source_name: Coronal brain slice devoid of choroid plexus

growth_protocol: SPF breeding facility

extract_protocol:
Cells were sorted into RNAprotect Cell Reagent (QIAGEN) according to the manufacturers recommendations. Total RNA was extracted from FACS sorted cells stabilized in RNAprotect Cell Reagent according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added, and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation and RNAseq were carried out as described in the SMART-Seq mRNA LP User Manual (Takara Bio, Inc., CA, USA), the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism Protocol (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). In brief, approximately 500 pg of total-RNA was used to generate first strand cDNA. Double stranded cDNA was amplified by LD-PCR (13 cycles) and purified via magnetic bead clean-up. After validating the quality and quantity, 250 pg of cDNA was enzymatically fragmented and stem-loop adapters were ligated. Then libraries were PCR amplified (16 cycles) and indexed, generating Illumina-compatible libraries with unique dual indexes (UDIs). After a magnetic bead purification, the libraries were quantified using the KAPA Library Quantification Kit. Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1. 5.0.42699, using two 100 cycles P2 Flow Cells with the dual index, single-read (SR) run parameters.

treatment_protocol: Mice were treated for seven consectutive days with BLZ 945 at 200 mg/kg BW and on the last day of gavage as well as +2 and +4 days injected with Tamoxifen 2 mg/day and 8 weeks after last oral gavage injected with Thrombin into the MCA to induce ischemic stroke. Brains were harvested one day after stroke induction.

value: Ccr2creERT2 R26tdT

value: CD45intCD11b+CD206int-high tdt-

value: Ccr2creERT2/+ R26tdT/tdT

value: BLZ 7 days - 8  weeks later stroke


title: IgG_ctrl_rep1

description: Library name: PR3495_01


title: IgG_ctrl_rep2

description: Library name: PR3495_02


title: R010, TCRseq

city: Stanford

first: Cameron

last: Bader

address: 269 Campus Drive, CCSR Room 2250

institute: Stanford University

description: Library name: R010-TCR

data_processing:
Raw reads were aligned using standard BD processing pipelines on SevenBridges Genomics cloud computing platform.
Processing output files were combined using custom code which can be found at https://github.com/csbader/Bader-CS-et-al-2025.
Assembly: GRCh38
Supplementary files format and content: all_sample_rna is a Seurat object .rds with all sample counts and associated metadata.
Supplementary files format and content: all_samples_vdj is an .rds dataframe with all sample VDJ information and matching barcodes to all_sample_rna.

source_name: PBMC

extract_protocol:
Cells were captured and lysed using the BD Rhapsody platform.
Targeted Human Immune Response Panel and VDJ libraries were generated according to manufactuer instructions.

value: PBMC

value: Sorted lymphocytes


title: F3_BLZ_Stroke_tdT+

description:
Library name: S603_19_273plus280_C_pos_S19_R1_001.fastq.gz
tdT+ BLZ

value: Coronal brain slice devoid of choroid plexus

value: CD45intCD11b+CD206int-high tdt+


title: M1_BLZ_Stroke_tdT-

description:
Library name: S603_21_274plus258_C_neg_S21_R1_001.fastq.gz
tdT- BLZ


title: M1_BLZ_Stroke_MG

description:
Library name: S603_20_274plus258_MG_S20_R1_001.fastq.gz
MG BLZ


title: LLC1 cells, ssgNT, rep1

description: Library name: LLC1-sgNT-rep1

value: Lewis Lung carcinoma cells

value: total RNA

value: paired-end


title: R010, sampleTag

description: Library name: R010-ST


title: M2_BLZ_Stroke_MG

description:
Library name: S603_23_275plus283_MG_S23_R1_001.fastq.gz
MG BLZ


title: LLC1 cells, sgNT, rep3

description: Library name: LLC1-sgNT-rep3


title: AKR cells, sgB2m, rep1

description: Library name: AKR-sgB2m-rep1

value: AKR

value: esophageal carcinoma cells


title: M2_BLZ_Stroke_tdT+

description:
Library name: S603_25_275plus283_C_pos_S25_R1_001.fastq.gz
tdT+ BLZ


title: F2_BLZ_Stroke_tdT+

description:
Library name: S603_16_258_C_pos_S16_R1_001.fastq.gz
tdT+ BLZ


title: LLC1 cells, sgNT, rep2

description: Library name: LLC1-sgNT-rep2


title: F3_BLZ_Stroke_tdT-

description:
Library name: S603_18_273plus280_C_neg_S18_R1_001.fastq.gz
tdT- BLZ


title: Hashed, LARRY-barcoded AML cells ex vivo, day 20, 3' mRNA library

description:
Library name: D20_exvivo_GEX
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: Hematopoietic cell culture

value: primary AML cells

value: Acute Myeloid Leukemia

value: cell culture


title: R010, BCRseq

description: Library name: R010-BCR


title: F3_BLZ_Stroke_MG

description:
Library name: S603_17_273plus280_MG_S17_R1_001.fastq.gz
MG BLZ

value: Ccr2creERT2 R26tdT


title: LLC1 cells, sgB2m, rep2

description: Library name: LLC1-sgB2m-rep2


title: F2_BLZ_Stroke_tdT-

description:
Library name: S603_15_258_C_neg_S15_R1_001.fastq.gz
tdT- BLZ

value: CD45intCD11b+CD206int-high tdt-


title: R010, mRNA

description: Library name: R010-mRNA


title: F2_BLZ_Stroke_MG

description:
Library name: S603_14_258_MG_S14_R1_001.fastq.gz
MG BLZ

value: Ccr2creERT2/+ R26tdT/tdT


title: F1_BLZ_Stroke_MG

description:
Library name: S603_11_257plus263_MG_S11_R1_001.fastq.gz
MG BLZ

value: BLZ 7 days - 8  weeks later stroke


title: R009, TCRseq

description: Library name: R009-TCR

value: PBMC


title: F1_BLZ_Stroke_tdT-

description:
Library name: S603_12_257plus263_C_neg_S12_R1_001.fastq.gz
tdT- BLZ


title: LLC1 cells, sgB2m, rep1

description: Library name: LLC1-sgB2m-rep1


title: R009, sampleTag

description: Library name: R009-ST

value: Sorted lymphocytes


title: R009, mRNA

description: Library name: R009-mRNA


title: M2_Veh_Stroke_MG

description:
Library name: S603_07_282_MG_S7_R1_001.fastq.gz
MG CTL

value: Coronal brain slice devoid of choroid plexus

value: Vehicle 7 days - 8  weeks later stroke


title: MC38 cells, sgNT, rep2

description: Library name: MC38-sgNT-rep2

value: colon adenocarcinoma cells


title: LLC1 cells, sgB2m, rep3

description: Library name: LLC1-sgB2m-rep3

value: Lewis Lung carcinoma cells

value: total RNA


title: F2_Veh_Stroke_tdT-

description:
Library name: S603_06_272_C_neg_S6_R1_001.fastq.gz
tdT- CTL


title: F3_Veh_Stroke_MG

description:
Library name: S603_09_286_MG_S9_R1_001.fastq.gz
MG CTL


title: F3_Veh_Stroke_tdT-

description:
Library name: S603_10_286_C_neg_S10_R1_001.fastq.gz
tdT- CTL


title: M2_Veh_Stroke_tdT-

description:
Library name: S603_08_282_C_neg_S8_R1_001.fastq.gz
tdT- CTL


title: F1_Veh_Stroke_MG

description:
Library name: S603_03_271_MG_S3_R1_001.fastq.gz
MG CTL


title: MC38 cells, sgNT, rep3

description: Library name: MC38-sgNT-rep3

value: paired-end


title: R009, BCRseq

description: Library name: R009-BCR


title: MC38 cells, sgNT, rep1

description: Library name: MC38-sgNT-rep1


title: F1_Veh_Stroke_tdT-

description:
Library name: S603_04_271_C_neg_S4_R1_001.fastq.gz
tdT- CTL


title: R008, mRNA

description: Library name: R008-mRNA


title: MC38 cells, sgB2m, rep3

description: Library name: MC38-sgB2m-rep3


title: R008, sampleTag

description: Library name: R008-ST


title: R008, TCRseq

description: Library name: R008-TCR


title: F2_Veh_Stroke_MG

description:
Library name: S603_05_272_MG_S5_R1_001.fastq.gz
MG CTL


title: M1_Veh_Stroke_tdT-

description:
Library name: S603_02_270_C_neg_S2_R1_001.fastq.gz
tdT- CTL


title: M1_Veh_Stroke_MG

description:
Library name: S603_01_270_MG_S1_R1_001.fastq.gz
MG CTL


title: MC38 cells, sgB2m, rep2

description: Library name: MC38-sgB2m-rep2


title: M3_BLZ_LPS_Dura_pos

description:
Library name: 61_D_pos
tdT+ LPS

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M38. Counts were obtained using FeatureCounts v2.0.6. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M38
Supplementary files format and content: Processed counts are provided in the file Counts_Ccr2creERT2_repopulation_dura_LPS.txt

source_name: Cranial dura mater

treatment_protocol: Mice were treated for seven consectutive days with BLZ 945 at 200 mg/kg BW and on the last day of gavage as well as +2 and +4 days injected with Tamoxifen 2 mg/day and 8 weeks after last oral gavage injected with LPS at 2.5 mg/kg BW or PBS solution. Dura maters were harvested 12 hours later.

value: Cranial dura mater

value: dCAMs CD45intCD11b+CD206int-high tdt+

value: BLZ 7 days - 8 weeks later LPS 2.5 mg/kg BW


title: MC38 cells, sgB2m, rep1

description: Library name: MC38-sgB2m-rep1


title: R007, TCRseq

description: Library name: R007-TCR


title: R008, BCRseq

description: Library name: R008-BCR


title: R007, sampleTag

description: Library name: R007-ST


title: M1_BLZ_LPS_Dura_neg

description:
Library name: 59_D_neg
tdT- LPS

value: dCAMs CD45intCD11b+CD206int-high tdt-


title: M3_BLZ_LPS_Dura_neg

description:
Library name: 61_D_neg
tdT- LPS


title: M1_BLZ_LPS_Dura_pos

description:
Library name: 59_D_pos
tdT+ LPS


title: M2_BLZ_LPS_Dura_neg

description:
Library name: 60_D_neg
tdT- LPS


title: C57BL6_1_CR_2

city: Chicago

first: Alireza

last: Khoddam

state: IL

address: 303 E Superior St 8-400

department: Cardiology

institute: Northwestern University

description: Library name: C57BL6_1_CR_2

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: Mouse mm10
Supplementary files format and content: csv contains raw counts for each sample (bullk RNA-seq)

source_name: Liver

extract_protocol:
For bulk RNA-seq: mice were perfused with PBS, whole livers minced. RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, North Rhine-Westphalia, Germany) using the manufacturer protocol.
Library preparation was performed using the KAPA mRNA HyperPrep Kit (Roche, Cat# KK8580), which includes poly(A) selection, cDNA synthesis, and ligation of sequencing adapters.

value: Liver

value: Caloric Restiction


title: F2_BLZ_LPS_Dura_pos

description:
Library name: 56_D_pos
tdT+ LPS

value: Ccr2creERT2 R26tdT


title: C57BL6_1_CR_3

description: Library name: C57BL6_1_CR_3


title: F2_BLZ_LPS_Dura_neg

description:
Library name: 56_D_neg
tdT- LPS

value: Ccr2creERT2/+ R26tdT/tdT


title: Hashed, LARRY-barcoded AML cells ex vivo, day 20, Hashing antibodies library

description:
Library name: D20_exvivo_FB
Feature-reference file contains LARRY and TotalSeq barcodes, refer to Table_config files for demultiplexing annotations

value: Hematopoietic cell culture

value: primary AML cells

value: Acute Myeloid Leukemia

value: Npm1-cA, Flt3-ITD

value: cell culture

value: HTO

value: TotalSeq


title: C57BL6_1_TM5614_3

description: Library name: C57BL6_1_TM5614_3


title: F1_BLZ_LPS_Dura_pos

description:
Library name: 54_D_pos
tdT+ LPS


title: F3_BLZ_PBS_Dura_neg

description:
Library name: 179_D_neg
tdT- CTL

value: BLZ 7 days - 8 weeks later PBS


title: R007, BCRseq

state: California

description: Library name: R007-BCR

value: PBMC

value: Sorted lymphocytes


title: R007, mRNA

description: Library name: R007-mRNA


title: C57BL6_1_CR_1

description: Library name: C57BL6_1_CR_1


title: C57BL6_1_TM5614_2

description: Library name: C57BL6_1_TM5614_2


title: M2_BLZ_PBS_Dura_neg

description:
Library name: 178_D_neg
tdT- CTL

value: Cranial dura mater


title: R004, TCRseq

description: Library name: R004-TCR


title: M2_BLZ_PBS_Dura_pos

description:
Library name: 178_D_pos
tdT+ CTL

value: dCAMs CD45intCD11b+CD206int-high tdt+


title: R004, sampleTag

description: Library name: R004-ST


title: M2_BLZ_LPS_Dura_pos

description:
Library name: 60_D_pos
tdT+ LPS

value: BLZ 7 days - 8 weeks later LPS 2.5 mg/kg BW


title: C57BL6_1_TM5614_1

description: Library name: C57BL6_1_TM5614_1

value: Liver


title: M1_BLZ_PBS_Dura_neg

description:
Library name: 177_D_neg
tdT- CTL

value: dCAMs CD45intCD11b+CD206int-high tdt-


title: C57BL6_1_Metformin_3

description: Library name: C57BL6_1_Metformin_3

value: Metformin


title: F1_BLZ_LPS_Dura_neg

description:
Library name: 54_D_neg
tdT- LPS

value: Ccr2creERT2 R26tdT

value: Ccr2creERT2/+ R26tdT/tdT


title: M1_BLZ_PBS_Dura_pos

description:
Library name: 177_D_pos
tdT+ CTL


title: F3_BLZ_PBS_Dura_pos

description:
Library name: 179_D_pos
tdT+ CTL


title: C57BL6_1_Metformin_2

description: Library name: C57BL6_1_Metformin_2


title: R004, mRNA

description: Library name: R004-mRNA


title: F2_BLZ_PBS_Dura_neg

description:
Library name: 175_D_neg
tdT- CTL


title: F2_BLZ_PBS_Dura_pos

description:
Library name: 175_D_pos
tdT+ CTL


title: F1_BLZ_PBS_Dura_neg

description:
Library name: 174_D_neg
tdT- CTL


title: F1_BLZ_PBS_Dura_pos

description:
Library name: 174_D_pos
tdT+ CTL


title: C57BL6_1_Metformin_1

description: Library name: C57BL6_1_Metformin_1


title: Macrophage_LPS_CGRP_5

city: Gold coast

first: Jiaying

last: Liu

address: G40, parkland drive

country: Australia

institute: Griffith university

description:
Library name: Sample30
Column names in counts_invitro_all_samples.txt:CGRP_23_1 and CGRP_23_2

data_processing:
Cutadapt
Reads of low quality, adapter contamination, and high content of unknown bases (N) were removed using the Cutadapt tool.
After obtaining clean reads, we used STAR to align the clean reads to the reference genome sequence
Assembly: Mus_musculus_mm10/GCF_000001635.20
Supplementary files format and content: TXT file includes count values for all samples listed

growth_protocol: Raw264.7 were cultured in DMEM supplemented with 10% FBS and 1% p/s. Cells were incubated with 5% CO2 at 37℃.

extract_protocol:
RNA was harvest with PureLink RNA extraction kit (Thermofisher). A total of 30μl at concentration above 10ng/μl RNA for each sample was used for the construction of sequencing libraries.
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Raw264.7 were treated with 100ng/ml LPS alone as control, or 100ng/ml LPS and 10nM CGRP as test for 6 hours.

value: macrophage

value: WT

value: LPS and CGRP stimulation


title: Macrophage_LPS_CGRP_4

description:
Library name: Sample29
Column names in counts_invitro_all_samples.txt:CGRP_22_1 and CGRP_22_2


title: R005, sampleTag

description: Library name: R005-ST


title: C57BL6_1_Rapamycin_3

description: Library name: C57BL6_1_Rapamycin_3

value: Rapamycin


title: Macrophage_LPS_CGRP_3

description:
Library name: Sample28
Column names in counts_invitro_all_samples.txt:CGRP_21_1 and CGRP_21_2


title: R005, mRNA

description: Library name: R005-mRNA


title: C57BL6_1_Rapamycin_2

description: Library name: C57BL6_1_Rapamycin_2


title: Macrophage_LPS_CGRP_2

description:
Library name: Sample27
Column names in counts_invitro_all_samples.txt:CGRP_20_1 and CGRP_20_2


title: Macrophage_LPS_CGRP_1

description:
Library name: Sample26
Column names in counts_invitro_all_samples.txt: CGRP_19_1 and CGRP_19_2


title: C57BL6_1_Rapamycin_1

description: Library name: C57BL6_1_Rapamycin_1


title: Macrophage_LPS_6

description:
Library name: Sample25
Column names in counts_invitro_all_samples.txt: LPS_18_1 and LPS_18_2

value: LPS stimulation


title: Macrophage_LPS_5

description:
Library name: Sample24
Column names in counts_invitro_all_samples.txt:  LPS_17_1 and LPS_17_2


title: R003, TCRseq

description: Library name: R003-TCR


title: Macrophage_LPS_2

description:
Library name: Sample21
Column names in counts_invitro_all_samples.txt: LPS_14_1 and LPS_14_2


title: Macrophage_LPS_3

description:
Library name: Sample22
Column names in counts_invitro_all_samples.txt: LPS_15_1 and LPS_15_2


title: R003, sampleTag

description: Library name: R003-ST


title: C57BL6_1_AL_5

description: Library name: C57BL6_1_AL_5

value: Ad Libitum Diet


title: Macrophage_LPS_4

description:
Library name: Sample23
Column names in counts_invitro_all_samples.txt: LPS_16_1 and LPS_16_2


title: 177_MG_Ccr2Cre

description:
Library name: S591_72_177_MG_S72_R1_001.fastq.gz
no_correction

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17 software, which resulted in .bcl files, which were converted into fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M36. Counts were obtained using FeatureCounts v2.0.8. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M36
Supplementary files format and content: Processed counts are provided in the files count_LPS_wildtype_GEO.txt, counts_Ccr2KO_GEO.txt, counts_LPS_Ccr2_GEO.txt for the respective genotypes

source_name: Brain devoid of choroid plexuses

extract_protocol:
Cells were sorted into RNAprotect Cell Reagent (QIAGEN) according to the manufacturers recommendations. Total RNA was extracted from FACS sorted cells stabilized in RNAprotect Cell Reagent according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added, and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation with Illumina Nextera XT Sample Preparation. The sequencing run was performed on a HiSeq 1000 instrument (Control Software v2.2.68) using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: Mice were either treated with Vehicle solution (CTL) or with BLZ945 and each group with LPS or left untreated and injected with PBS. Ccr2CreERT2 R26tdT mice were treated with 2 mg tamoxifen at 0, 2 and 4 days after CTL or BLZ945 treatment. 8 weeks after the end of the treatment, mice were either left untreated or injected with LPS (CTL and BLZ945 groups). 12 hours later, mice were perfused and CAMs and MG were harvested.

value: Brain devoid of choroid plexuses

value: MG


title: C57BL6_1_AL_6

description: Library name: C57BL6_1_AL_6


title: R003, mRNA

description: Library name: R003-mRNA

value: PBMC

value: Sorted lymphocytes


title: R004, BCRseq

description: Library name: R004-BCR


title: C57BL6_1_AL_4

description: Library name: C57BL6_1_AL_4


title: Macrophage_LPS_1

description:
Library name: Sample20
Column names in counts_invitro_all_samples.txt: LPS_13_1 and LPS_13_2


title: 177_neg_Ccr2Cre

description:
Library name: S591_71_177_CAMs_neg_S71_R1_001.fastq.gz
no_correction

value: CAMs


title: R005, BCRseq

description: Library name: R005-BCR


title: 175_MG_Ccr2Cre

description:
Library name: S591_69_175_MG_S69_R1_001.fastq.gz
no_correction


title: C57BL6_1_AL_2

description: Library name: C57BL6_1_AL_2


title: C57BL6_1_AL_1

description: Library name: C57BL6_1_AL_1


title: 175_neg_Ccr2Cre

description:
Library name: S591_68_175_CAMs_neg_S68_R1_001.fastq.gz
no_correction


title: R002, sampleTag

description: Library name: R002-ST


title: 174_MG_Ccr2Cre

description:
Library name: S591_66_174_MG_S66_R1_001.fastq.gz
no_correction


title: R002, mRNA

description: Library name: R002-mRNA


title: R003, BCRseq

description: Library name: R003-BCR


title: 174_neg_Ccr2Cre

description:
Library name: S591_65_174_CAMs_neg_S65_R1_001.fastq.gz
no_correction


title: C57BL6_1_AL_3

description: Library name: C57BL6_1_AL_3


title: 174_pos_Ccr2Cre

description:
Library name: S591_64_174_CAMs_pos_S64_R1_001.fastq.gz
no_correction


title: 177_pos_Ccr2Cre

description:
Library name: S591_70_177_CAMs_pos_S70_R1_001.fastq.gz
no_correction


title: R002, TCRseq

description: Library name: R002-TCR