title: Ccx_1-Ccx_6, Cc_1-Cc_6, Hi_1-Hi_6

description: Library name: Sample 1-18

source_name: Sample 1-18

extract_protocol:
The mouse brains were isolated from the sacrificed mice and washed with PBS, followed by embedding in optimal cutting temperature compound (OCT) and stored at −80 °C before cry sectioning. The embedded surface of fresh frozen mouse brain tissue was trimmed and sliced by using microtome, and the obtained tissue sections were deposited on polydimethylsiloxane (PDMS) membrane slides. Then the sections were fixed with 4% paraformaldehyde briefly, rinsed with H2O to remove OCT, and dehydrated using isopropyl alcohol for 2 min. After that the treated tissue sections were stained with hematoxylin and eosin (H&E) according to previously reported literature37. The processed tissue sections could be directly used for microneedle sampling or stored at -80 °C freezer for further processing. Before tissue sampling, the PCR tubes or plates pre-added with lysis buffer according to the above described. The home-built microneedle capturing system originated from our group was used for tissue micro-sampling. The microneedle capturing system was consisted of four parts including a 3D translation stage for position control, a system control unit, a microscopic camera system for monitoring the sampling process, and a tapered glass capillary tube for tissue capturing operation. Among this, the capillary tube was fabricated by heating and stretching a glass capillary (200 µm i.d., 360 µm o.d.) in micropipette puller instrument (P-1000, Sutter, USA) to produce a tapered tip. The obtained tissue samples were blown into microtubes by connecting a capillary tube with a compatible syringe. Finally, the tissue samples were centrifuged at 500 g for 2 min to ensure them at the bottom of the tube and were directly analyzed or frozen at -20 °C until library preparation.
microregion tissue samples were removed from the −80 °C storage and thawed at room temperature for 10 min to facilitate sample lysis and RNA release, then transferred to a preheated PCR thermocycler, incubated for 3 min at 72 °C and immediately placed on ice afterwards. Next, 10 µl of RT-PCR mix containing 1.2 µL dNTP mix (10 mM), 0.252 µL RNase Inhibitor (40 U/µl), 0.1 µL DTT (100 mM), 0.328 µL MgCl2 (279 mM), 0.18 µL dCTP (100 mM), 2 µL Betaine (5 M), 0.368 µL CBTi-TSO (50 µM), 0.172 µL of Superscript Ⅳ / Maxima H (200 U/µL, ThermoFisher Scientific) and 5 µL of KAPA HiFi HotStart Ready Mix (2×, Roche) were added to synthesis full-length dsDNA. The following RT-PCR program was set to: 60 min at 50 °C, 98 °C for 3 min, then 20 cycles of (98 °C for 20 s, 67 °C for 20 s, 72 °C for 6 min). The cDNA concentration was quantified using the Qubit 4.0 fluorimeter, and size distribution was assessed using capillary electrophoresis on a Fragment Analyzer system (Agilent Bioanalyzer). 1 μl unpurified amplified cDNA working dilution (5 ng/µl) of each sample was transferred to a new plate before adding tagmentation reaction mix as described above. Of note, each sample used unique combination barcoding. Samples were incubated for 10 min at 55 °C. Then, all tagmented products were mixed into 1.5- or 2 ml PCR tube, purified with 1.5× AMPure XP beads for termination of the tagmented reaction and collection, followed by elution with 20 µl nuclease-free water.

value: brain

value: cerebral cortex neuron, corpus callosum neuron, hippocampal neuron


title: Patient 21, GBM, replicate 1

status: Public on Jan 01 2026

type: SRA

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description: Library name: sample91

library_source: transcriptomic

data_processing:
First, the raw FASTQ files were run with FastQC (v0.11.9) to assess the overall sequencing quality and possible adapter sequence contamination
Skewer (v0.11.9) was used to remove Illumina TruSeq adapter sequences (read 1: 5’-AGATCGGAAGAGCACACGTCTGAACTC-CAGTCA-3’, read 2: 5’-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’) from the read files.
Followingly, the reads were aligned to the GRCh38 (hg38) reference genome using STAR aligner (v2.7.10a) to generate coordinate-sorted BAM files.
FeatureCounts (v2.0.3) was used to generate the gene expression count table, which is further normalized in transcripts per million (TPM) criterion with R (v4.3.3).
Differential expression (DE) analyses were performed using the DESeq2 R package, and the genes that met the following threshold were considered significant: |Log2 fold change| > 0.5 & BH-adjusted P-value < 0.05.
Pathway enrichment analyses for GO Biological Process were then conducted using the clusterProfiler R package.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Glioblastoma tissue

extract_protocol:
RNA was extracted with Rneasy mini plus kit (Qiagen).
The samples for RNAseq were processed with Aglient SureSelect Human Alll Exon v6 + UTR kit to build sequence libraries under maufacturer's protocols.

tag: tissue

value: Glioblastoma tissue


title: Heart left ventricle_Sham_S30_rep5

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Boulevard Gambetta

country: France

institute: Unversity of Rouen Normandy

description: Library name: S_30

data_processing:
Reads were aligned to the mouse genome build mm10 using Hisat2 version 2.0.541
mm10
Assembly: Transcript quantification was performed with feature Counts from the subread package42. Differential analysis, including normalization, was performed with DESeq2 bioconductor package version 1.22.143 using R version 3.5.1.
Supplementary files format and content: gene_fpkm.xls contains FPKM counts far all samples

molecule: total RNA

organism: Mus musculus

source_name: Heart left ventricle

growth_protocol: Commercial C57BL/6JRj (Janvier Labs)female mice, 20–22 g (12–18 weeks), were maintained at the EU0477 animal care facility in ventilated cages with softly lit, environmental enrichment, ad libitum access to normal chow diet (Altromin International Cat#1310) and water (automated watering system), subjected to a standard 12-hour light-dark cycle at a constant temperature of 22 °C and a relative humidity kept between 45 and 65%. A two-week acclimatization period was observed for mice provided by Janvier Laboratories.

extract_protocol:
total RNA isolated from left ventricles of 5 independent sham or MI mice previously treated either with GSK-343 (20 mg/kg, Interchim Cat# XLR94D) or vehicle (20% captisol), 8 days post-MI using NucleoSpin RNA XS kit (Macherley-Nagel Cat# 740902)
1 000 ng of total RNA with a concentration >20 ng/ml and a RIN ratio >8 were used for Poly-A mRNA-seq, sequencing length of 150 nt paired end (PE150) with the Illumina NovaSeq 6000

treatment_protocol: Left ventricular (LV) MI was induced in 20–22 g (12–18 weeks) C57BL/6JRj (Janvier Labs) female mice by permanent ligation of the left descending coronary artery. GSK-343 (20 mg/kg, Interchim Cat# XLR94D) was dissolved in cyclodextrin-based Captisol® as a solubilization vehicle at 20% final concentration, as advised by the manufacturer to perform daily intraperitoneal injections starting from 6 h after surgery and daily until 7 days post-MI. Control mice received a vehicle solution (Captisol® 20%) injection of the same volume at the same time as treated mice.

value: Heart left ventricle


title: Patient 21, Tumor-free SVZ, replicate 1

description: Library name: sample49

source_name: Tumor-free subventricular zone

value: Tumor-free subventricular zone


title: L929 cells, 3' control groups

city: nanjing

first: Liyong

last: He

state: Not US or Canada

address: 南京市玄武区东南大学

country: China

institute: State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering

description: Library name: control-250425

library_source: transcriptomic single cell

data_processing:
The sequencing data was processed using the SSH (Secure Shell) client MobaXterm within a Linux operating system. The overall processing workflow was performed according to the following:
1) Quality control: FastQC was used to assess the quality of the sequencing data fastq.gz format. Indicators such as “Per base sequence quality,” “Per base sequence content,” and “Sequence Duplication Levels” were used to make a preliminary judgment of the quality of the sequencing library.
2) Barcode B and UMI swapping: The fastq.gz files were decompressed using the zcat command to convert them into “fq” files. Following the process shown in Supplementary Fig. 15, a Python script was written to swap the Barcode B and UMI from Read 2 to the beginning of Read 1. Additionally, 33 bp from the 5’ end of Read 2 was deleted. The Final_R1/R2.fq.gz files were then compressed.
3) Data preprocessing: The FastqToSam function in Picard tools were invoked to convert the “fq” file into query-name sorted bam file. Run the TagBamWithReadSequenceExtended function from Drop-seq_tools-3.0.2-0 twice to extract Barcode and UMI sequences at different locations, then invoke FilterBam function to filter low-quality Barcode and UMI sequences, and finally use the PolyATrimmer function to remove the Poly A sequence at the capture end. After preprocessing, the SamToFastq function from Picard tools was used to convert the bam files back into fastq files for subsequent sequence alignment.
4) Sequence alignment: Reference genome indices for mouse GRCm38 (https://www.ncbi.nlm.nih.gov/grc/mouse) and human GRCh38 (https://www.ncbi.nlm.nih.gov/grc/human) were constructed from NCBI Genome Reference Consortium, respectively. Sequence alignment was then performed using STAR software (version 2.7.11b).
5) Expression matrix: After alignment, the SortSam and MergeBamAlignment functions in Picard were called to sort and integrate the results. Finally, the DigitalExpression function in Drop-seq_tools-3.0.2-0 was employed with specified filtering conditions to select the digital expression matrix corresponding to the specified Barcode.
Assembly: GRCm38
Supplementary files format and content: matrixed files

source_name: connective tissue

extract_protocol:
cells were detached with trypsin treatment after the supernatant was removed. Perform cell aggregate dissociation with strong pipetting. Cells were then rinsed three times with ice-cold phosphate buffer solution (PBS), pelleted by centrifugation at 500 ×g for 10 min at 4 °C to remove the supernatant containing excess trypsin and culture media thoroughly. The home-built microneedle capturing system described above was employed for picking up single cells into 8- or 96-well plates containing lysis buffer. Specifically, under the optimized diameter of the capillary tip (30 μm), the conical tip of the capillary probe was controlled to be aligned with the target cells, and the target cell was sucked into the probe under capillary force. The CBTi-seq lysis buffer consisted of 0.13 µl recombinant RNase inhibitor (40 U/µl, Takara), 0.25 µl of Takara lysis buffer (10 ×) and 0.5 µl CBTi-Oligo dT primer (10 µM), and ddH2O to 2.5 µl final volume. The plates were centrifuged at 1000 ×g immediately after sorting and stored at −80 °C until use.
Sorted single-cell or microregion tissue samples were removed from the −80 °C storage and thawed at room temperature for 10 min to facilitate sample lysis and RNA release, then transferred to a preheated PCR thermocycler, incubated for 3 min at 72 °C and immediately placed on ice afterwards. Next, 10 µl of RT-PCR mix containing 1.2 µL dNTP mix (10 mM), 0.252 µL RNase Inhibitor (40 U/µl), 0.1 µL DTT (100 mM), 0.328 µL MgCl2 (279 mM), 0.18 µL dCTP (100 mM), 2 µL Betaine (5 M), 0.368 µL CBTi-TSO (50 µM), 0.172 µL of Superscript Ⅳ / Maxima H (200 U/µL, ThermoFisher Scientific) and 5 µL of KAPA HiFi HotStart Ready Mix (2×, Roche) were added to synthesis full-length dsDNA. The following RT-PCR program was set to: 60 min at 50 °C, 98 °C for 3 min, then 20 cycles of (98 °C for 20 s, 67 °C for 20 s, 72 °C for 6 min). The cDNA concentration was quantified using the Qubit 4.0 fluorimeter, and size distribution was assessed using capillary electrophoresis on a Fragment Analyzer system (Agilent Bioanalyzer). 1 μl unpurified amplified cDNA working dilution (5 ng/µl) of each sample was transferred to a new plate before adding tagmentation reaction mix as described above. Of note, each sample used unique combination barcoding. Samples were incubated for 10 min at 55 °C. Then, all tagmented products were mixed into 1.5- or 2 ml PCR tube, purified with 1.5× AMPure XP beads for termination of the tagmented reaction and collection, followed by elution with 20 µl nuclease-free water.

value: connective tissue

tag: cell line

tag: cell type

value: fibroblasts


title: L929 cells, CBTis-seq control groups and knock groups

description: Library name: 20MIX-250304


title: Patient 19, GBM, replicate 1

description: Library name: sample26


title: Patient 19, Cortex, replicate 1

description: Library name: sample25

source_name: Brain cortex

value: Brain cortex


title: Patient 17, GBM, replicate 1

description: Library name: sample913


title: Heart left ventricle_Sham_S3_S6_mixed_rep1

description: Library name: S3_S6_mixed


title: CD45+ cells from the A101 CAR T+ aPDL1 treatment group_biol rep 4

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

country: USA

institute: national institutes of health

description:
Library name: CD45_pos_16
10x Genomics (scFlex 4-plex)

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.2.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.2.0 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A) and probe set (Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
344SQ tumors from CAR-T-, mock-T- and saline-treated mice were harvested on day 12 post-treatment. Tumors from 3 different mice were harvested per treatment group. Tumor tissue was harvested in cold DMEM media supplemented with 10% FBS. Tissue was dissected and digested with 0.25 mg/mL Liberase (Sigma) plus 0.5 mg/mL DNase I (Sigma) in DMEM media (Thermo Fisher) for 30 min at 37 °C. Digestion mixture was passed through 100 μm cell strainer (FALCON) to prepare single cell suspension and washed with cold media. Dead cells were removed (Miltenyi kit) and CD45- and CD45+ cells were column sorted using Miltenyi kits according to manufacturer’s instructions. Samples were fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics) in preparation for 10x Genomics singe cell RNA-FLEX sequencing according to the manufacturer’s instructions. Samples were stored at -80 oC until they were ready for sequencing. Samples were thawed, pelleted, and resuspended in 0.5X PBS + 0.02% BSA for cell counting on the LunaFX7 and probe hybridization. Sample quality was determined based on single cellular suspension and homogeneity of cellular solution. A series of wash cycles and normalization pooling was performed to allow for 4x4 multiplexing. Capabilities of scFLEX 4-Plex include 8 capture lanes with 4-plex capture and an expected target recovery of 20,000 cells per lane (5,000 cells per sample). A total of 32 samples were 4x4 multiplexed and the pools were then loaded in 8 capture lanes according to the 10X Genomics Chromium Fixed RNA Profiling User Guide.These consisted of 3 biological replicates of CD45- and 3 biological replicates of CD45+ cells per treatment group (CAR-T, mock-T, saline). Cell partitioning completed successfully with uniform emulsion consistency and the reverse transcription PCR was run overnight. The pre amplification and library construction were completed successfully. Single-cell suspension and droplet-based sequencing was performed. Three NovaSeq runs for FRP were performed.
Whole-transcriptome, probe-based single-cell gene expression libraries were prepared following the 10x Genomics Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527). Briefly, isolated and enriched single-cell samples, which had been fixed and stored according to the 10x Genomics User Guide (CG000478), were thawed and hybridized with a mouse probe panel containing unique sample-specific indices. After post-hybridization washes, cells were quantified, pooled into sets of four, and then partitioned and single-cell barcoded using the 10x Genomics Chromium X Controller. Multiplexed single-cell libraries were generated with additional pooled sample indices and adapters for downstream Illumina sequencing on the NovaSeq 6000 platform.

treatment_protocol: CAR-T cell treatment

value: lung

tag: tumor model_type

value: lung adenocarcinoma

tag: mouse strain

tag: Sex

value: Female

tag: age

value: 8-10 weeks old

tag: lane

tag: scan date


title: Patient 16, GBM, replicate 2

description: Library name: sample74


title: Asrij high_3

city: Bengaluru

first: Maneesha

middle: S

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur

department: MBGU

country: India

institute: JNCASR

description: Library name: BPLT_3

data_processing:
Quality check of the sequenced FASTQ files was done using the FastQC tool, followed by trimming, which removes the adaptor sequences and low-quality bases (Q < 20) using the Fastp tool. UCSC mm10 was used as the reference genome and indexed using Hisat2. Trimmed reads were aligned to the indexed genome using Hisat2. The resulting Sequence Alignment/Map (SAM) files were sorted by coordinates and converted to Binary Alignment/Map (BAM) files using Samtools. Gene expression values were calculated using the Feature counts package of the Subread R package, and summarised counts for each gene were obtained.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each gene

source_name: Bone marrow

extract_protocol:
RNA was isolated from FACS-sorted Asrijlow and Asrijhigh LT-HSCs using the RNeasy mini kit (#74104, Qiagen) and quantified using a Qubit high-sensitivity assay kit (#Q32852, Invitrogen) on a Qubit 4 fluorimeter (Invitrogen).
RNA was isolated using RNeasy mini kit (#74104, Qiagen) and quantified using a Qubit high-sensitivity assay kit (#Q32852, Invitrogen) on a Qubit 4 fluorimeter (Invitrogen). Samples were run on the TapeStation system (Agilent) with high-sensitivity RNA Screen Tape analysis (Agilent, #5067-5579) for RNA quality control (QC). Ribosomal RNA (rRNA) depletion was performed using NEBNext rRNA depletion kit v2 with RNA sample purification beads (NEB, #E7405X). cDNA libraries were constructed utilizing the NEBNext Ultra II Directional RNA Library Prep (stranded) kit with sample purification beads (NEB, #E7765L).

value: Bone marrow

value: Hematopoietic stem cells

tag: genotype


title: Asrij high_1

description: Library name: BPLT_1


title: Patient 16, GBM, replicate 1

description: Library name: sample73


title: CD45+ cells from the Saline_aPDL1 treatment group_biol rep 3

description:
Library name: CD45_pos_15
10x Genomics (scFlex 4-plex)


title: Patient 20, Tumor-free SVZ, replicate 1

description: Library name: sample894


title: Asrij low_3

description: Library name: BNLT_3


title: CD45- cells from the Saline_aPDL1 treatment group_biol rep 3

description:
Library name: CD45_neg_15
10x Genomics (scFlex 4-plex)


title: CD45+ cells from the Saline_aPDL1 treatment group_biol rep 1

description:
Library name: CD45_pos_13
10x Genomics (scFlex 4-plex)


title: Patient 21, Cortex, replicate 1

description: Library name: sample90


title: Patient 20, GBM, replicate 1

description: Library name: sample893


title: Patient 20, Cortex, replicate 1

description: Library name: sample892


title: Asrij high_2

description: Library name: BPLT_2


title: Patient 18, GBM, replicate 1

description: Library name: sample33


title: Asrij low_1

description: Library name: BNLT_1


title: CD45+ cells from the Saline_aPDL1 treatment group_biol rep 2

description:
Library name: CD45_pos_14
10x Genomics (scFlex 4-plex)


title: CD45- cells from the Saline_aPDL1 treatment group_biol rep 1

description:
Library name: CD45_neg_13
10x Genomics (scFlex 4-plex)


title: Patient 15, GBM, replicate 1

description: Library name: sample931


title: Patient 16, Tumor-free SVZ, replicate 1

description: Library name: sample922


title: Asrij low_2

description: Library name: BNLT_2


title: Patient 15, Tumor-free SVZ, replicate 1

description: Library name: sample932


title: CD45- cells from the Saline_aPDL1 treatment group_biol rep 2

description:
Library name: CD45_neg_14
10x Genomics (scFlex 4-plex)


title: CD45- cells from the A101 CAR T+ aPDL1 treatment group_biol rep 4

description:
Library name: CD45_neg_16
10x Genomics (scFlex 4-plex)


title: CD45- cells from the Saline treatment group_biol rep 3

description:
Library name: CD45_neg_12
10x Genomics (scFlex 4-plex)


title: Patient 14, GBM, replicate 1

description: Library name: sample899


title: Patient 16, GBM, replicate 3

description: Library name: sample921


title: Patient 13, GBM, replicate 1

description: Library name: sample367


title: Patient 14, Tumor-free SVZ, replicate 1

description: Library name: sample900


title: CD45- cells from the Mock T treatment group_biol rep 3

description:
Library name: CD45_neg_9
10x Genomics (scFlex 4-plex)


title: Patient 12, GBM, replicate 1

description: Library name: sample72


title: Patient 1, Cortex, replicate 1

description: Library name: sample119


title: Patient 13, Tumor-free SVZ, replicate 1

description: Library name: sample368


title: CD45- cells from the A101 CAR T+ aPDL1 treatment group_biol rep 2

description:
Library name: CD45_neg_2
10x Genomics (scFlex 4-plex)


title: CD45- cells from the A101 CAR T treatment group_biol rep 3

description:
Library name: CD45_neg_6
10x Genomics (scFlex 4-plex)


title: CD45- cells from the Mock T treatment group_biol rep 2

description:
Library name: CD45_neg_8
10x Genomics (scFlex 4-plex)


title: Patient 12, Cortex, replicate 1

description: Library name: sample71


title: Patient 9, GBM, replicate 1

description: Library name: sample371


title: Patient 10, GBM, replicate 1

description: Library name: sample550


title: CD45- cells from the Saline treatment group_biol rep 1

description:
Library name: CD45_neg_10
10x Genomics (scFlex 4-plex)


title: CD45- cells from the A101 CAR T treatment group_biol rep 2

description:
Library name: CD45_neg_5
10x Genomics (scFlex 4-plex)


title: CD45- cells from the Mock T treatment group_biol rep 1

description:
Library name: CD45_neg_7
10x Genomics (scFlex 4-plex)


title: Patient 11, GBM, replicate 1

description: Library name: sample270


title: Patient 1, Tumor-free SVZ, replicate 1

description: Library name: sample122


title: Patient 7, GBM, replicate 1

description: Library name: sample9


title: CD45- cells from the A101 CAR T+ aPDL1 treatment group_biol rep 1

description:
Library name: CD45_neg_1
10x Genomics (scFlex 4-plex)


title: CD45- cells from the A101 CAR T+ aPDL1 treatment group_biol rep 3

description:
Library name: CD45_neg_3
10x Genomics (scFlex 4-plex)


title: CD45+ cells from the A101 CAR T treatment group_biol rep 3

description:
Library name: CD45_pos_6
10x Genomics (scFlex 4-plex)


title: CD45- cells from the A101 CAR T treatment group_biol rep 1

description:
Library name: CD45_neg_4
10x Genomics (scFlex 4-plex)


title: CD45- cells from the Saline treatment group_biol rep 2

description:
Library name: CD45_neg_11
10x Genomics (scFlex 4-plex)


title: Patient 1, GBM, replicate 1

description: Library name: sample121


title: Patient 6, GBM, replicate 1

description: Library name: sample943


title: CD45+ cells from the A101 CAR T+ aPDL1 treatment group_biol rep 3

description:
Library name: CD45_pos_3
10x Genomics (scFlex 4-plex)


title: Patient 6, Tumor-free SVZ, replicate 1

description: Library name: sample944


title: CD45+ cells from the Saline treatment group_biol rep 2

description:
Library name: CD45_pos_11
10x Genomics (scFlex 4-plex)


title: Patient 5, GBM, replicate 1

description: Library name: sample945


title: Patient 8, GBM, replicate 1

description: Library name: sample206


title: CD45+ cells from the Mock T treatment group_biol rep 3

description:
Library name: CD45_pos_9
10x Genomics (scFlex 4-plex)


title: CD45+ cells from the A101 CAR T treatment group_biol rep 2

description:
Library name: CD45_pos_5
10x Genomics (scFlex 4-plex)


title: CD45+ cells from the Mock T treatment group_biol rep 2

description:
Library name: CD45_pos_8
10x Genomics (scFlex 4-plex)


title: CD45+ cells from the Saline treatment group_biol rep 3

description:
Library name: CD45_pos_12
10x Genomics (scFlex 4-plex)


title: Patient 5, Tumor-free SVZ, replicate 1

description: Library name: sample925


title: Patient 3, GBM, replicate 2

description: Library name: sample269


title: CD45+ cells from the Saline treatment group_biol rep 1

description:
Library name: CD45_pos_10
10x Genomics (scFlex 4-plex)


title: Patient 2, GBM, replicate 1

description: Library name: sample16


title: CD45+ cells from the Mock T treatment group_biol rep 1

description:
Library name: CD45_pos_7
10x Genomics (scFlex 4-plex)


title: Patient 2, Cortex, replicate 1

description: Library name: sample15


title: Patient 2, Tumor-free SVZ, replicate 1

description: Library name: sample17


title: Patient 4, GBM, replicate 1

description: Library name: sample69


title: BT-474_Trastuzumab_Resistance_3

city: Madrid

first: Eduardo

last: Pérez-Gómez

state: Madrid

address: José Antonio Novais 12

department: Biochemistry and Molecular Biologý

country: Spain

institute: Universidad Complutense de Madrid)

description: Library name: TR3

data_processing:
Generation of sequencing libraries and sequencing were performed by Novogene Co Ltd (Cambridge, UK).
Sequencing libraries were constructed using amplified cDNAs with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using the Illumina Novaseq6000 system in 150-bp paired-end mode. Bioinformatic analysis was performed by DREAMGENICS S.L. (Oviedo, Spain). First, sequenced reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The RNA reads were then aligned to the reference sequences of the Ensemble’s 2019 version of the human genome (GRCh38) using the Salmon algorithm, and relative gene expression was quantified as transcript per million (TPM).
For the analysis of differences in gene expression between conditions, the DESeq2 algorithm was used.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast

growth_protocol: Human Breast Cancer cell line BT-474 were obtained from the American Type Culture Collection (ATCC).BT-474 cells were cultured in DMEM/F12 medium (Sigma-Aldrich) with 10 % fetal bovine serum (FBS, Gibco) and 1 % penicillin/streptomycin (Lonza). BT-474 cells were maintained at 37 °C in a humidified atmosphere of 5 % CO2.  and routinely tested for Mycoplasma spp. contamination.

extract_protocol:
RNA was isolated with Nucleozol™ (Macherey-Nagel) following the extraction protocol suggested by the manufacturer. RNA was isolated as described above and resuspended in ultrapure water. Concentration and RNA integrity number > 7 were determined and 1 µg per sample was utilized for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human HER2+ breast cancer cell lines BT474 TS (trastuzumab-sensitive) and TR (trastuzumab-resistant) were obtained from the American Type Culture Collection (ATCC, Manassas, VI, USA). The CB2R knockout (KO) cell line was generated by knocking out CB2R expression in TS cells using CRISPR/Cas9. The following RNA guide targeting CB2R exon 3 was cloned into the pLv-puro-sgRNA lentiviral plasmid: TCC GGA ATC ATC TAC ACC TA (TGG) (Addgene #7140, Watertown, MA, USA). TS cells stably expressing Cas9 (via infection with a pCLIP-hCMV-Cas9-Nuclease-Blast lentiviral plasmid, kindly donated by Dr. Markus Müschen, City of Hope Comprehensive Cancer Center, Duarte, CA, USA) were infected with the CB2R-targeting guide. Cells incorporating both Cas9 and guide were selected via antibiotic resistance, and CB2R knockout was confirmed by genomic PCR. The scramble control (SCR) cell line was generated using the same protocol but with a scramble guide (CCT AAG GTT AAG TCG CCC TCG CTC GAG CGA GGG CGA CTT AAC CT TAGG). The CB2R rescue (RESC) and TR CB2R cell lines were derived from CB2R KO and TR cells, respectively, via lentiviral transduction of the pLv-neo-CMV-hCNR2 plasmid. Briefly, lentiviral particles were produced by transfecting HEK293T cells with envelope (pMD2.G, Addgene #12259), packaging (psPAX2, Addgene #12260), and donor plasmids (CB2R, pLv-neo-hCNR2, Vector Builder, Neu-Isenburg, Germany). Conditioned medium containing recombinant lentiviruses was collected, filtered, and used to infect CB2R KO and TR cells.

value: Breast

value: epithelial cell

value: WT

tag: treatment

value: Trastuzumab


title: Ribo-Seq Eif5a SKO round spermatids_rep2

city: Jinan

first: Yuling

last: Cai

state: Shandong

address: Qianfoshan Street

department: CCenter of reproductive medicine

institute: Shandong University

description: Library name: Sample 5

data_processing:
Ribo-seq data processing Raw reads were trimmed with cutadapt v4.563 with parameters: cutadapt -u 16 -n 3 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -o <output.file> <input.file>, and the trimmed reads were sequentially mapped to mouse rRNA sequences (mm10) using Bowtie2 v2.2.564 with parameters –seedlen=23. Those aligned to rRNA were discarded, and the remaining reads were mapped to transcriptome of mm10 using STAR v2.7.10b65 with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression levels were then calculated by cufflinks v2.2.166 based on the annotation of CDS region, defined by mm10 refFlat database from the UCSC genome browser. We next calculated average FPKM for replicates and as long as expression is detected in one duplicate sample, it is regarded as genes detected by Ribo-lite. Spearman correlations were calculated between duplicate samples and different samples. 3-nt periodicity was assessed and the offset was determined. The 3-nt periodicity of RPF reads based on their P-site alignment was used as strong evidence for activated translation. We evaluated the 3-nt periodicity of all Ribo-seq samples using the RiboCode v1.2.15 program67. RiboCode v1.2.15 also calculated the percentage of periodic reads and identified all translated ORFs, including new, unannotated ORFs such as uORFs. Metagene analyses of ribosome profiling data Metagene analyses of ribosome profiling data were performed by MetageneAnalysis of RiboMiner v0.2.3.268 with “-u 0 -d 500 -l 100 -n 10 -m 1” parameters. Specifically, for genes that exhibited more than one transcript, only the longest transcript was used in all analyses. Only the transcripts with length over 100 codons and RPKM more than 10 in the whole CDS region were considered. The ribosome densities were normalized to reads per million mapped reads (RPM). Codon optimality analysis. To observe whether there are differences between different codons or amino acids (AA), we calculated the ribosome density at each codon or AA by RiboDensityAtEachKindAAOrCodon of RiboMiner v0.2.3.268. In order to select those triplete amino acid (tri-AA) motifs that are rich in ribosomes, we used the ProcessPausingScore function to complete this work and output the position weight matrix (PWM) of the E, P, and A sites of triplete amino acid (tri-AA) motif, and then used Seq2Logo69 to perform motif Logo drawing. Polarity calculation To estimate ribosome tracking the mean score was calculated by RiboMiner. We used the PolarityCalculation of RiboMiner v0.2.3.268 to evaluate the ribosomes of all genes for each reconstructed version and analyzed the changes in scores after knocking out Eif5a by comparing the scores in the SKO group and scores. Here p value is calculated by t test from the mean of repeated samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw FPKM for each Sample
Library strategy: Ribo-Seq

source_name: testis

extract_protocol:
Round sperm samples were lysed in ice-cold lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100, 25 U/ml Turbo DNase) for 4 hours on ice. Lysates were clarified at 20,000 ×g for 10 minutes at 4°C, treated with RNase I (1 µl of 100 U/µl) at room temperature for 45 minutes, and the reaction terminated with 10 μl SUPERase•In. Samples were layered onto a 700 µl sucrose cushion (1 M sucrose, 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 20 U/ml SUPERase•In) and centrifuged at 260,000 ×g, 4°C for 4 hours. Pellets were resuspended in 50 µl precipitate buffer, and RPFs were extracted using TRIzol and chloroform. RPFs were precipitated with isopropanol and glycogen at -20°C and resuspended in nuclease-free water. RPFs were separated on a 15% TBE-urea polyacrylamide gel (200 V, 65 min), and RNA was extracted from gel slices using RNA extraction buffer, precipitated, and resuspended in nuclease-free water. Sequencing libraries were prepared using the CATS Small RNA-seq Kit or D-Plex Small RNA-seq Kit, followed by purification with AMPure XP. Barcoded libraries were pooled and sequenced on Illumina platforms, generating 150 bp paired-end reads.
Round sperm samples were lysed in ice-cold lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100, 25 U/ml Turbo DNase) for 4 hours on ice. Lysates were clarified at 20,000 ×g for 10 minutes at 4°C, treated with RNase I (1 µl of 100 U/µl) at room temperature for 45 minutes, and the reaction terminated with 10 μl SUPERase•In. Samples were layered onto a 700 µl sucrose cushion (1 M sucrose, 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 20 U/ml SUPERase•In) and centrifuged at 260,000 ×g, 4°C for 4 hours. Pellets were resuspended in 50 µl precipitate buffer, and RPFs were extracted using TRIzol and chloroform. RPFs were precipitated with isopropanol and glycogen at -20°C and resuspended in nuclease-free water. RPFs were separated on a 15% TBE-urea polyacrylamide gel (200 V, 65 min), and RNA was extracted from gel slices using RNA extraction buffer, precipitated, and resuspended in nuclease-free water. Sequencing libraries were prepared using the CATS Small RNA-seq Kit or D-Plex Small RNA-seq Kit, followed by purification with AMPure XP. Barcoded libraries were pooled and sequenced on Illumina platforms, generating 150 bp paired-end reads.

value: testis

value: Round spermatids

value: Eif5a SKO


title: BT-474_Trastuzumab_Resistance_1

description: Library name: TR1


title: CD45+ cells from the A101 CAR T+ aPDL1 treatment group_biol rep 2

description:
Library name: CD45_pos_2
10x Genomics (scFlex 4-plex)


title: Patient 3, GBM, replicate 1

description: Library name: sample885

value: Glioblastoma tissue


title: Wild type round spermatids_rep3

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly quality control analyzed using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were trimmed to remove low-quality bases by Trim Galore (version 0.6.4)(https://github.com/FelixKrueger/TrimGalore) in PAIRED-end mode.  All the downstream analyses were based on clean data with high quality. Paired-end clean reads were aligned to the reference genome (GRCm38) by HISAT2 (version 2.0.5)60. FeatureCounts (version 1.5.0-p3)61 of the subread package was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated by R script based on the length of genes and reads count.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
For Smart-seq2, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Following this, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.
For Smart-seq2, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Following this, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.

value: Wild type


title: BT-474_CB2R_KO_3

description: Library name: KO3

value: CB2R KO


title: Wild type  round spermatids_rep2

description: Library name: Sample 5


title: Ribo-Seq Eif5a SKO round spermatids_rep1

description: Library name: Sample 4


title: Ribo-Seq Wild type round spermatids_rep3

description: Library name: Sample 3


title: BT-474_CB2R_KO_2

description: Library name: KO2


title: BT-474_Trastuzumab_Resistance_2

description: Library name: TR2


title: BT-474_Trastuzumab_Sensible_3

description: Library name: TS3


title: Wild type round spermatids_rep1

description: Library name: Sample 4


title: Patient 5, GBM, replicate 2

description: Library name: sample946


title: CD45+ cells from the A101 CAR T treatment group_biol rep 1

description:
Library name: CD45_pos_4
10x Genomics (scFlex 4-plex)


title: BT-474_CB2R_KO_1

description: Library name: KO1


title: Ribo-Seq Wild type  round spermatids_rep2

description: Library name: Sample 2


title: Ribo-Seq Eif5a SKO round spermatids_rep3

description: Library name: Sample 6


title: Eif5a SKO round spermatids_rep2

description: Library name: Sample 2


title: BT-474_SCR_3

description: Library name: SCR3


title: BT-474_Trastuzumab_Sensible_1

description: Library name: TS1


title: Eif5a SKO round spermatids_rep3

description: Library name: Sample 3


title: BT-474_SCR_1

description: Library name: SCR1


title: BT-474_SCR_2

description: Library name: SCR2


title: Ribo-Seq Wild type round spermatids_rep1

description: Library name: Sample 1


title: CD45+ cells from the A101 CAR T+ aPDL1 treatment group_biol rep 1

description:
Library name: CD45_pos_1
10x Genomics (scFlex 4-plex)


title: Eif5a SKO round spermatids_rep1

description: Library name: Sample 1


title: BT-474_Trastuzumab_Sensible_2

description: Library name: TS2


title: Tumor tissues, PS473@NKMOF-102-[Mn] 3

city: Tianjin

first: Yijin

last: Liu

address: Haihe Education Park, 38 Tongyan Road, Tianjin 300071, China

institute: Nankai University

description: Library name: Sample 18

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was usedfor the construction of sequencing libraries.
After the RNA samples pass the quality inspection, magnetic beads coated with Oligo(dT) are used to enrich the mRNA of eukaryotes. Subsequently, fragmentation buffer is added to break the mRNA into short fragments. Using the mRNA as a template, first-strand cDNA is synthesized with random hexamers. Then, buffer, dNTPs, DNA polymerase I, and RNase H are added to synthesize second-strand cDNA. After that, AMPure XP beads are used to purify the double-stranded cDNA. The purified double-stranded cDNA undergoes end repair, A-tailing, and sequencing adapter ligation. Then, AMPure XP beads are used for fragment size selection. Finally, PCR amplification is performed, and the PCR products are purified with AMPure XP beads to obtain the final sequencing library.

treatment_protocol: B16F10 cells (1 × 10⁵ cells in 50 μL of PBS) were subcutaneously injected into the right flank of C57BL/6 female mice. On day 6, when the tumor volume reached approximately 50 mm³, the mice were randomly divided into 6 groups and treated every 2 days with intratumoral injections of PBS, free PS473, PS473@CPs, NKMOF-101-[Mn], M5@ NKMOF-101-[Mn], or PS473@NKMOF-101-[Mn].

value: Tumor

value: mouse melanoma cells


title: LNCaP-ENZR-3

city: Shanghai

first: Zehua

last: Ma

address: Pujian road 160

institute: Shanghai Jiaotong university

description:
Library name: sample6
LNCaP-ENZR-3

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to GRCh38 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: The clean reads were mapped to GRCh38 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: prostate

growth_protocol: Cells were grown in RPMI medium 1640 with 10% fetal bovine serum in a humidified atmosphere of 5% (v/v) CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.

treatment_protocol: LNCaP cells were gradually exposed to increased concentration of enzalutamide (ranging from 5 μM to 50 μM) in media supplemented with 10% charcoal-stripped FBS (CSS) (HyClone; SH30068) for over 12 months

value: prostate

value: LNCaP

value: Human prostate cancer cells

value: resistant to enzalutamide


title: LNCaP-ENZR-2

description:
Library name: sample5
LNCaP-ENZR-2

value: LNCaP cells were gradually exposed to increased concentration of enzalutamide (ranging from 5 μM to 50 μM) in media supplemented with 10% charcoal-stripped FBS (CSS) (HyClone; SH30068) for over 12 months


title: Tumor tissues, PS473@NKMOF-102-[Mn] 1

description: Library name: Sample 16


title: LNCaP-WT-3

description:
Library name: sample3
LNCaP-WT-3


title: LNCaP-ENZR-1

description:
Library name: sample4
LNCaP-ENZR-1


title: Tumor tissues, PS473@NKMOF-102-[Mn] 2

description: Library name: Sample 17


title: LNCaP-WT-1

description:
Library name: sample1
LNCaP-WT-1


title: Scr_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

description: Library name: GA69622

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Tumor tissue of pancreatic cancer

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Tumor tissue of pancreatic cancer

value: transfection with negative control (scramble) oligonucleotides


title: Tumor tissues, M5@NKMOF-101-[Mn] 2

description: Library name: Sample 14


title: Tumor tissues, NKMOF-101-[Mn] 2

description: Library name: Sample 11


title: Tumor tissues, M5@NKMOF-101-[Mn] 1

description: Library name: Sample 13


title: Tumor tissues, NKMOF-101-[Mn] 3

description: Library name: Sample 12


title: Scr_2

description: Library name: GA69621


title: Tumor tissues, PS473@CPs 3

description: Library name: Sample 9


title: Tumor tissues, NKMOF-101-[Mn] 1

description: Library name: Sample 10


title: Tumor tissues, M5@NKMOF-101-[Mn] 3

description: Library name: Sample 15


title: Tumor tissues, PS473@CPs 1

description: Library name: Sample 7


title: circ72309OE_3

description: Library name: GA69619

value: transfection with circ72309 vector


title: MG-63 cells on boronized Ti6Al4V/HA, rep 2, day 7

city: changsha

first: hong

middle: yi

last: chen

state: HuNan provience

address: 72 Xiangya Road

institute: Xiangya Stomatological HospitalCentral South University

description: Library name: C2

data_processing:
Adapter trimming: Cutadapt v2.10
Alignment: HISAT2 v2.2.1 to GRCh38
Assembly and quantification: StringTie v2.1.4
Read counting: featureCounts v2.0.1
DEG analysis: limma in R
Assembly: GRCh38
Supplementary files format and content: Processed data includes gene FPKM values in tab-delimited text format. Each row corresponds to a gene, and each column represents a sample.

growth_protocol: MG-63 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's protocol.
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were seeded on Ti6Al4V or boronized Ti6Al4V/HA composite surfaces and cultured in osteogenic induction medium for 7 days. The induction medium consisted of DMEM supplemented with 10 mM 尾-glycerophosphate, 50 碌g/mL ascorbic acid, and 100 nM dexamethasone.

value: Osteosarcoma (epithelial-like)

value: osteogenic induction

tag: batch


title: Tumor tissues, Free PS473 2

description: Library name: Sample 5


title: LNCaP-WT-2

description:
Library name: sample2
LNCaP-WT-2

value: WT


title: Tumor tissues, Free PS473 1

description: Library name: Sample 4


title: Scr_1

description: Library name: GA69620


title: circ72309OE_1

description: Library name: GA69617


title: MG-63 cells on boronized Ti6Al4V/HA, rep 3, day 7

description: Library name: C3


title: Tumor tissues, PBS 2

description: Library name: Sample 2


title: MG-63 cells on boronized Ti6Al4V/HA, rep 1, day 7

description: Library name: C1


title: MG-63 cells on Ti6Al4V+TiB2, rep 3, day 7

description:
Library name: B3
not included in final analysis


title: Tumor tissues, PS473@CPs 2

description: Library name: Sample 8


title: MG-63 cells on Ti6Al4V+TiB2, rep 1, day 7

description:
Library name: B1
not included in final analysis


title: MG-63 cells on Ti6Al4V, rep 3, day 7

description: Library name: A3


title: Tumor tissues, Free PS473 3

description: Library name: Sample 6


title: MG-63 cells on Ti6Al4V+TiB2, rep 2, day 7

description:
Library name: B2
not included in final analysis


title: Liver NPCs, Vaseline, biol rep 4

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

country: Germany

institute: University Hospital Mannheim

description: Library name: V4

data_processing:
The demultiplexing was done using bcl_convert
The cell calling and gene counting were done using the Cell Ranger software v7.0.0
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Livers were perfused via the portal vein, harvested, and processed into single-cell suspensions. Following hepatocyte depletion by ultracentrifugation, non-parenchymal cells (NPCs) were isolated.
Single-cell RNA sequencing libraries were constructed using the 10x Genomics 3' V3.1 Kit following the manufacturer's protocol.

value: Liver

value: female

value: Non-parenchymal cells (NPCs)

tag: strain

value: C57BL/6J wild-type mice

value: Vaseline


title: Tumor tissues, PBS 3

description: Library name: Sample 3

value: Tumor

value: mouse melanoma cells


title: MG-63 cells on Ti6Al4V, rep 1, day 7

description: Library name: A1


title: Liver NPCs, Imiquimod, biol rep 4

description: Library name: I4

value: Imiquimod


title: SK474, EtOH-RNA

city: Chicago

first: Sonia

last: Kupfer

state: IL

department: Human Genetics

institute: University of Chicago

description: Library name: KL-69

data_processing:
RNA-seq sequence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2 (v1.30.1) after first filtering for protein coding biotype and using DESeq's independent filtering.
ATAC-seq sequence alignment was performed with bwa (v0.7.17). Read filtering was performed with samtools (v1.10) with retained reads having mapping quality >=10. PCR duplicates were also removed using samtools.
Peak calling on mapped ATAC-seq sequences was performed with MACS2 (v.2.1.0).
Assembly: transcriptome reference was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF  (Release 29). ATAC-seq sequences were also mapped to hs37d5.
Supplementary files format and content: RSEM output files of transcript level abundances in tab-delimited plain text format
Supplementary files format and content: ATAC-seq alignment files are in compressed BAM format. MACS2 output peak files are in the narrowPeak plain text format.

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: cells were treated using the Omni-ATAC protocol with some modifications. Briefly, cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA buffer, 5% TDE1 Tagment DNA Enzyme, 33% PBS) for 30 minutes.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina and sequenced using an Illumina NovaSeq6000 (paired end 100 bp). ATAC-seq libraries were prepared using the Nextera Index kit (Illumina #15055289) and were sequenced on the Hi-Seq 4000 platform (50 bp single end reads).

treatment_protocol: Organoids were treated with either 100nm/L 1α,25-dihydroxyvitamin D or vehicle control (0.1% ethanol) for 4 hours for ATAC-seq and 6 hours for RNA-seq.

value: colonic organoid

value: M

tag: ancestry

value: AA

value: EtOH


title: SK474, VD-RNA

description: Library name: KL-72

value: VD


title: circ72309OE_2

description: Library name: GA69618

value: Tumor tissue of pancreatic cancer

value: transfection with circ72309 vector


title: SK440, EtOH-RNA

description: Library name: KL-51


title: Liver NPCs, Vaseline, biol rep 3

description: Library name: V3


title: Tumor tissues, PBS 1

description: Library name: Sample 1


title: Liver NPCs, Imiquimod, biol rep 3

description: Library name: I3


title: SK440, VD-RNA

description: Library name: KL-54


title: Liver NPCs, Imiquimod, biol rep 1

description: Library name: I1


title: SK438, VD-RNA

description: Library name: KL-48

value: EA


title: SK438, EtOH-RNA

description: Library name: KL-45


title: SK226, VD-RNA

description: Library name: KL-12


title: Liver NPCs, Vaseline, biol rep 2

description: Library name: V2


title: Cortical nuclei, 2 pooled samples, 1 female het/ 1 male wt, biol rep 1

city: Davis

first: Stephanie

middle: A

last: Lozano

state: CA

address: 1544 Newton Ct

institute: University of California, Davis

description:
Library name: snRNA-seq_ctx4_FHET_MWT
10X Genomics 3' GEX v3.1

data_processing:
Demultiplexed FASTQ files were passed through the Cell Ranger count pipeline for alignment to the mouse mm10 genome, filtering, and creation of feature-barcode matrices. Ambient RNA removal was performed using SoupX (version 1.6.1), and Seurat objects were generated using Seurat (version 4.3.0). These Seurat objects were subjected to initial clustering, and each resulting cluster was filtered based on cluster-specific thresholds for UMI count, feature count, and percentage of mitochondrial reads, which were determined using standard deviation criteria. Mitochondrial genes were then removed from all objects. The DoubletFinder package (version 2.0.4) was used to assign nuclei as ‘Singlet’ or ‘Doublet’.  Predicted doublets were removed before proceeding with downstream analyses. Nuclei were next assigned as ‘male’ or ‘female’ using the sxreveal package (version 0.2.0), which uses X- and Y-linked marker gene expression to predict sex.  Chd8 genotype was assigned based on the predicted sex and pool-specific metadata. Because each pool consisted of only one male and one female of opposite genotype, all female nuclei in a pool were assumed to be one genotype and all males were assumed to be the other.  Seurat objects for each of the 5 samples were individually passed through SCTransform to normalize counts, then all 5 were integrated using IntegrateData. The ‘RNA’ assay of the integrated object was normalized and scaled using NormalizeData and ScaleData. Principal Components Analysis was performed on the ‘Integrated’ assay of the integrated data to identify top variable genes, and FindNeighbors was used to construct a KNN graph based on their euclidean distance in PCA space. The data were then passed through FindClusters to group cells into clusters using the Louvain algorithm. Clusters were visualized with uniform manifold approximation and projection (UMAP).  FindAllMarkers was used to identify cluster marker genes. Modules of cell type marker genes described in published scRNA-seq datasets from adult mouse cortex were constructed. Canonical marker genes were added to these modules, then AddModuleScore was used to calculate relative expression of each module in each cluster. The cell type associated with the marker gene module that had the highest expression in each cluster was assigned as that cluster’s identity.  All nuclei were assigned identities at 3 levels of classification, with ‘Cell_Type_1’ being the most specific and ‘Cell_Type_3’ the broadest.  Clusters that were poorly clustered, had a high percentage of mitochondrial reads relative to other clusters, or had ambiguous marker genes (i.e. markers for multiple distinct cell types) were removed before subsequent analysis. The filtered Seurat object was then re-normalized, re-scaled, and re-clustered as described previously.
Assembly: Mouse mm10
Supplementary files format and content: Filtered and quality-controlled Seurat object (.rds) containing single-nucleus gene expression matrices, cell-level metadata, dimensionality reductions (PCA, UMAP), and cluster cell type assignments. All samples have been integrated into one object.

molecule: nuclear RNA

source_name: P60 cortex

extract_protocol:
Frozen issue from the first 6 samples was processed into nuclei using 2mL glass dounce homogenizers containing 2mL of EZ Prep lysis buffer each. Tissue for 3 samples was dounced over ice, 25 times with pestle A and 35 times with pestle B. Each solution was transferred to a 15 mL conical tube, then the same douncing process was repeated for the second set of 3 samples. Solutions from the latter 3 samples were pooled with those of the first 3 such that each pool contained one male and one female of opposite genotype. An additional 6 mL of EZ Prep lysis buffer was added to each conical tube and the tubes were incubated on ice for 5 minutes. Homogenates were centrifuged at 500xg for 5 minutes at 4°C, the supernatant was discarded, and the pellet was washed twice in NSB (1X PBS with 0.01% BSA and 0.1% RNAse inhibitor). The final pellet was resuspended in 1mL NSB then passed through a 20uM cell strainer. Nuclei were counted using a LUNA-FL cell counter and Acridine Orange/ Propidium Iodide stain. The 10X Genomics nuclei isolation kit, with protocol as described, was used to isolate nuclei for the final 4 samples. These samples were combined into 2 pools, each containing one male and one female of opposite genotype, then nuclei were counted as described previously. Nuclei suspensions had concentrations adjusted to target 10,000 nuclei for sequencing per pool, then used as input for the 10X Genomics 3’ Gene Expression Assay.
Library preparation was performed according to the manufacturer’s instructions (Next GEM Single Cell 3' Gene Expression v3.1 protocol, 10X Genomics). Briefly, nuclei were resuspended in a reverse transcription master mix and loaded into a Chromium Next GEM Chip G along with barcoded gel beads and partitioning oil. The chip was run on a Chromium controller to generate Gel Beads-in-Emulsion (GEMs). Within each GEM, reverse transcription occurred, producing cDNA tagged with a cell barcode, UMI, and an Illumina Read 1 primer sequence. GEMs were then broken and the barcoded cDNA was purified using Dynabeads, amplified by PCR, and cleaned using SPRIselect beads. During library construction, cDNA was fragmented, end-repaired, A-tailed, and ligated to sequencing adapters that include the Illumina Read 2 primer binding site. After adapter ligation and SPRIselect cleanup, sample index PCR was performed to incorporate P5 and P7 sequences and sample indices, followed by a final SPRIselect cleanup. Libraries were QCed and sequenced on an Agilent BioAnalyzer, batches 1, 2, and 4 were sequenced on an Illumina NovaSeq 6000 and batches 5 and 6 were sequenced on an Element Biosciences AVITI.

value: P60 cortex

value: mixed nuclei

tag: genotype sex_1

tag: genotype sex_2


title: MG-63 cells on Ti6Al4V, rep 2, day 7

description: Library name: A2

value: Osteosarcoma (epithelial-like)

value: osteogenic induction


title: SK214, VD-RNA

description: Library name: KL-06


title: SK214, EtOH-RNA

description: Library name: KL-03


title: Cortical nuclei, 2 pooled samples, 1 male het/ 1 female wt, biol rep 2

description:
Library name: snRNA-seq_ctx2_MHET_FWT
10X Genomics 3' GEX v3.1


title: Cortical nuclei, 2 pooled samples, 1 male het/ 1 female wt, biol rep 1

description:
Library name: snRNA-seq_ctx1_MHET_FWT
10X Genomics 3' GEX v3.1


title: Cortex, whole cell synaptic fraction, male WT, biol rep 5

description:
Library name: RNA-seq_Ctx_28M_Syn
Chd8_P60_syn_nuc_final.txt

data_processing:
Reads were aligned to mouse genome (GRCm38/mm10) using STAR (version 2.5.4b), and gene counts were produced using featureCounts89. On average, 50 million paired-end reads (PE) aligned per sample, with a range of 32 to 84 million reads. Data quality was assessed using FastQC90, and principal component analysis (PCA) was used to determine presence of sample outliers. All 24 samples were qualified for the analysis. Bioinformatic analysis was performed using R programming language version 4.2.1 (R Development Core Team, 2015) and RStudio integrated development environment version 2023.06.0 (Team R, 2018). Plots were generated using ggplot2 R package version 3.4.0. Heatmaps were generated using pheatmap R package 1.0.12.
Assembly: Mouse mm10
Supplementary files format and content: Tab-delimited counts tables (*.txt) generated by featureCounts v2.0.0. One counts table for each batch, tables contain gene-level counts for each BAM file, with column headers indicating sample tissue and replicate.

extract_protocol:
Cellular fractionation into synaptic and nuclear fractions: Brains from Chd8+/5bpdel and wild-type littermates were collected on or around PND60. Following cervical dislocation, brains were sub-dissected to isolate Cortex. Flash frozen cortices were stored at -80C until further processing. On the day of cellular fractionation, samples were treated with Syn-Per reagent (ThermoFisher Scientific Catalog #87793) to obtain cytosol, synaptosome and flowthrough (“total”) fractions. The “total” fraction was then used treated with “NE-PER™ Nuclear and Cytoplasmic Extraction Reagents” (cat #78833) to obtain the nuclear, and a “cleaner cytosol” fractions. Total RNA from these fractions was then extracted using RNA RNAqueous™ Total RNA Isolation Kit (cat# AM1912 ThermoFisher Scientifics). Manufacturer protocols were followed with minor adjustments to increase RNA yield from cellular fractions. Adjustments included combining the cortex samples with 500μl of Syn-Per reagent and 5μl of protease inhibitors during homogenization, based on our starting sample amount, and adding 350μl of RNA extraction lysis buffer immediately after fractionation to the synaptosome and nuclear fractions.  Total RNA extraction: Mouse cortices were collected at around PND60 from the following groups: 16 wild-type (WT) mice and 16 Chd8+/- mice (8 males and 8 females in the WT group; 7 males and 9 females in the Chd8+/- group), as well as 6 WT and 8 Chd8+/flox control mice (4 males and 2 females in the WT group; 5 males and 4 females in the Chd8+/flox group). Samples were snap frozen on dry ice and stored at -80C until RNA preparation. Total RNA was obtained using RNAqueous Total RNA Isolation Kit (cat# AM1912 ThermoFisher Scientifics), and assayed via Agilent RNA 6000 Nano Bioanalyzer kit/instrument. Sample RIN scores ranged from 8 to 9.4.
Poly-A-enriched mRNA libraries were prepared at Novogene using Illumina reagents. Libraries were sequenced using Illumina NovaSeq 6000 S4 system, paired-end 150 (PE150) method.

value: mixed cortical cells

tag: genotype sex


title: SK464, VD-RNA

description: Library name: KL-65

tag: tissue


title: Cortex, whole cell synaptic fraction, male WT, biol rep 4

description:
Library name: RNA-seq_Ctx_25M_Syn
Chd8_P60_syn_nuc_final.txt


title: SK464, EtOH-RNA

description: Library name: KL-62

tag: cell line


title: Liver NPCs, Imiquimod, biol rep 2

description: Library name: I2

value: Liver

value: female

tag: cell type

value: Non-parenchymal cells (NPCs)

value: C57BL/6J wild-type mice


title: SK456, VD-RNA

description: Library name: KL-59

value: colonic organoid


title: SK456, EtOH-RNA

description: Library name: KL-56

value: M


title: Cortex, whole cell synaptic fraction, male WT, biol rep 3

description:
Library name: RNA-seq_Ctx_24M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, male WT, biol rep 6

description:
Library name: RNA-seq_Ctx_29M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, male WT, biol rep 7

description:
Library name: RNA-seq_Ctx_29M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK226, EtOH-RNA

description: Library name: KL-09


title: Cortex, whole cell nuclear fraction, female Chd8+/- germline HET, biol rep 5

description:
Library name: RNA-seq_Ctx_21F_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK470, VD-RNA

description: Library name: KL-71


title: Cortex, whole cell nuclear fraction, male WT, biol rep 6

description:
Library name: RNA-seq_Ctx_25M_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, female Chd8+/- germline HET, biol rep 4

description:
Library name: RNA-seq_Ctx_20F_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, male Chd8+/- germline HET, biol rep 4

description:
Library name: RNA-seq_Ctx_27M_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, male WT, biol rep 5

description:
Library name: RNA-seq_Ctx_24M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK406, VD-RNA

description: Library name: KL-17

value: AA


title: SK424, VD-RNA

description: Library name: KL-29


title: Cortex, whole cell nuclear fraction, male WT, biol rep 4

description:
Library name: RNA-seq_Ctx_23M_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, female Chd8+/- germline HET, biol rep 4

description:
Library name: RNA-seq_Ctx_19F_Syn
Chd8_P60_syn_nuc_final.txt


title: Liver NPCs, Vaseline, biol rep 1

description: Library name: V1

value: Vaseline


title: SK394, EtOH-RNA

description: Library name: KL-08

value: EtOH


title: SK394, VD-RNA

description: Library name: KL-11

value: VD


title: Cortex, whole cell nuclear fraction, male Chd8+/- germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_18M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK470, EtOH-RNA

description: Library name: KL-68


title: Cortex, whole cell synaptic fraction, male Chd8+/- germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_17M_Syn
Chd8_P60_syn_nuc_final.txt


title: SK406, EtOH-RNA

description: Library name: KL-14


title: SK424, EtOH-RNA

description: Library name: KL-26


title: SK382, VD-RNA

description: Library name: KL-58


title: Cortex, whole cell nuclear fraction, male Chd8+/- germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_16M_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, male Chd8+/- germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_17M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK340, VD-RNA

description: Library name: KL-52


title: SK408, VD-RNA

description: Library name: KL-70


title: SK408, EtOH-RNA

description: Library name: KL-67


title: Cortex, whole cell synaptic fraction, male WT, biol rep 2

description:
Library name: RNA-seq_Ctx_13M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, male Chd8+/- germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_16M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, male WT, biol rep 1

description:
Library name: RNA-seq_Ctx_12M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, male WT, biol rep 2

description:
Library name: RNA-seq_Ctx_12M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK318, EtOH-RNA

description: Library name: KL-31


title: Cortex, whole cell nuclear fraction, male WT, biol rep 3

description:
Library name: RNA-seq_Ctx_13M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK340, EtOH-RNA

description: Library name: KL-49


title: SK318, VD-RNA

description: Library name: KL-34


title: Cortex, whole cell synaptic fraction, male Chd8+/- germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_18M_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, female Chd8+/- germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_7F_Syn
Chd8_P60_syn_nuc_final.txt


title: SK248, VD-RNA

description: Library name: KL-10


title: Cortex, whole cell nuclear fraction, male WT, biol rep 1

description:
Library name: RNA-seq_Ctx_11M_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK430, VD-RNA

description: Library name: KML2_23


title: Cortex, whole cell synaptic fraction, female Chd8+/- germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_9F_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, female Chd8+/- germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_6F_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, female Chd8+/- germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_9F_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK248, EtOH-RNA

description: Library name: KL-07


title: Cortex, whole cell nuclear fraction, female Chd8+/- germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_8F_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK430, EtOH-RNA

description: Library name: KML2_24


title: Cortex, whole cell synaptic fraction, female Chd8+/- germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_6F_Syn
Chd8_P60_syn_nuc_final.txt


title: SK294, EtOH-RNA

description: Library name: KL-13


title: SK294, VD-RNA

description: Library name: KL-16


title: SK336, VD-RNA

description: Library name: KML2_17


title: SK344, VD-RNA

description: Library name: KML2_19

value: F


title: Cortex, whole cell synaptic fraction, female WT, biol rep 4

description:
Library name: RNA-seq_Ctx_4F_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, female WT, biol rep 5

description:
Library name: RNA-seq_Ctx_5F_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, female WT, biol rep 5

description:
Library name: RNA-seq_Ctx_5F_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell nuclear fraction, female WT, biol rep 4

description:
Library name: RNA-seq_Ctx_4F_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK326, VD-RNA

description: Library name: KML2_15

value: EA


title: SK336, EtOH-RNA

description: Library name: KML2_18


title: Cortex, whole cell nuclear fraction, female WT, biol rep 3

description:
Library name: RNA-seq_Ctx_3F_Nuc
Chd8_P60_syn_nuc_final.txt

value: P60 cortex


title: Cortex, whole cell synaptic fraction, female WT, biol rep 3

description:
Library name: RNA-seq_Ctx_3F_Syn
Chd8_P60_syn_nuc_final.txt


title: SK326, EtOH-RNA

description: Library name: KML2_16


title: SK344, EtOH-RNA

description: Library name: KML2_20


title: SK276, VD-RNA

description: Library name: KML2_7


title: Cortex, whole cell nuclear fraction, female WT, biol rep 2

description:
Library name: RNA-seq_Ctx_2F_Nuc
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell synaptic fraction, female WT, biol rep 2

description:
Library name: RNA-seq_Ctx_2F_Syn
Chd8_P60_syn_nuc_final.txt


title: SK382, EtOH-RNA

description: Library name: KL-55


title: Cortex, whole cell nuclear fraction, female WT, biol rep 1

description:
Library name: RNA-seq_Ctx_1F_Nuc
Chd8_P60_syn_nuc_final.txt


title: SK266, VD-RNA

description: Library name: KML2_5


title: SK300, EtOH-RNA

description: Library name: KML11


title: SK300, VD-RNA

description: Library name: KML23


title: Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 4

description:
Library name: RNA-seq_Ctx_23
Chd8_CaMK2_conditional_w_Cre.txt


title: SK278, VD-RNA

description: Library name: KML22


title: SK276, EtOH-RNA

description: Library name: KML2_8


title: Cortex, whole cell synaptic fraction, female WT, biol rep 1

description:
Library name: RNA-seq_Ctx_1F_Syn
Chd8_P60_syn_nuc_final.txt


title: Cortex, whole cell, female, Camk2a-CRE Chd8+/flox, biol rep 1

description:
Library name: RNA-seq_Ctx_21
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 3

description:
Library name: RNA-seq_Ctx_18
Chd8_CaMK2_conditional_w_Cre.txt


title: SK238, VD-RNA

description: Library name: KML18


title: Cortex, whole cell, female Chd8^+/flox, biol rep 2

description:
Library name: RNA-seq_Ctx_19
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, female Chd8^+/flox, biol rep 3

description:
Library name: RNA-seq_Ctx_20
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, male Chd8^+/flox, biol rep 4

description:
Library name: RNA-seq_Ctx_24
Chd8_CaMK2_conditional_w_Cre.txt


title: SK472, VD-RNA

description: Library name: KL-66


title: Cortex, whole cell, female, Camk2a-CRE Chd8+/flox, biol rep 2

description:
Library name: RNA-seq_Ctx_22
Chd8_CaMK2_conditional_w_Cre.txt


title: SK222, VD-RNA

description: Library name: KML13


title: SK222, EtOH-RNA

description: Library name: KML1


title: Cortex, whole cell, male Chd8^+/flox, biol rep 2

description:
Library name: RNA-seq_Ctx_14
Chd8_CaMK2_conditional_w_Cre.txt


title: SK446, VD-RNA

description: Library name: KL-60


title: Cortex, whole cell, male Chd8^+/flox, biol rep 3

description:
Library name: RNA-seq_Ctx_15
Chd8_CaMK2_conditional_w_Cre.txt


title: SK278, EtOH-RNA

description: Library name: KML10


title: SK472, EtOH-RNA

description: Library name: KL-63


title: Cortex, whole cell, male Chd8^+/flox, biol rep 5

description:
Library name: RNA-seq_Ctx_25
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 2

description:
Library name: RNA-seq_Ctx_17
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 1

description:
Library name: RNA-seq_Ctx_13
Chd8_CaMK2_conditional_w_Cre.txt


title: SK446, EtOH-RNA

description: Library name: KL-57


title: SK422, EtOH-RNA

description: Library name: KL-33


title: SK238, EtOH-RNA

description: Library name: KML6


title: SK416, VD-RNA

description: Library name: KL-30


title: SK266, EtOH-RNA

description: Library name: KML2_6


title: SK416, EtOH-RNA

description: Library name: KL-27


title: Cortex, whole cell, male Chd8^+/flox, biol rep 1

description:
Library name: RNA-seq_Ctx_12
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, female Chd8^+/flox, biol rep 1

description:
Library name: RNA-seq_Ctx_11
Chd8_CaMK2_conditional_w_Cre.txt


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 9

description:
Library name: RNA-seq_Ctx_353
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, male WT, biol rep 8

description:
Library name: RNA-seq_Ctx_345
Chd80456_featureCounts_final.txt


title: SK402, VD-RNA

description: Library name: KL-24


title: SK402, EtOH-RNA

description: Library name: KL-21


title: Cortex, whole cell, female WT, biol rep 7

description:
Library name: RNA-seq_Ctx_318
Chd80456_featureCounts_final.txt


title: SK400, EtOH-RNA

description: Library name: KL-15


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 8

description:
Library name: RNA-seq_Ctx_317
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, male WT, biol rep 7

description:
Library name: RNA-seq_Ctx_344
Chd80456_featureCounts_final.txt


title: SK442, VD-RNA

description: Library name: KL-47


title: Cortex, whole cell, male WT, biol rep 6

description:
Library name: RNA-seq_Ctx_394
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, female WT, biol rep 6

description:
Library name: RNA-seq_Ctx_311
Chd80456_featureCounts_final.txt


title: SK422, VD-RNA

description: Library name: KL-36


title: SK442, EtOH-RNA

description: Library name: KL-44


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 7

description:
Library name: RNA-seq_Ctx_316
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 6

description:
Library name: RNA-seq_Ctx_306
Chd80456_featureCounts_final.txt


title: SK428, VD-RNA

description: Library name: KL-41


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 7

description:
Library name: RNA-seq_Ctx_348
Chd80456_featureCounts_final.txt


title: SK426, EtOH-RNA

description: Library name: KL-32


title: SK428, EtOH-RNA

description: Library name: KL-38


title: SK372, EtOH-RNA

description: Library name: KL-02


title: Cortex, whole cell, male WT, biol rep 5

description:
Library name: RNA-seq_Ctx_315
Chd80456_featureCounts_final.txt


title: SK400, VD-RNA

description: Library name: KL-18


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 5

description:
Library name: RNA-seq_Ctx_314
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 5

description:
Library name: RNA-seq_Ctx_308
Chd80456_featureCounts_final.txt


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 6

description:
Library name: RNA-seq_Ctx_309
Chd80456_featureCounts_final.txt


title: SK390, VD-RNA

description: Library name: KL-64


title: Cortex, whole cell, female WT, biol rep 5

description:
Library name: RNA-seq_Ctx_312
Chd80456_featureCounts_final.txt


title: SK354, VD-RNA

description: Library name: KL-46


title: SK426, VD-RNA

description: Library name: KL-35


title: SK390, EtOH-RNA

description: Library name: KL-61


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 4

description:
Library name: RNA-seq_Ctx_476
Chd807_featureCounts_final.txt


title: Cortex, whole cell, male WT, biol rep 4

description:
Library name: RNA-seq_Ctx_497
Chd807_featureCounts_final.txt


title: SK302, EtOH-RNA

description: Library name: KL-19


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_477
Chd807_featureCounts_final.txt


title: SK302, VD-RNA

description: Library name: KL-22


title: Cortex, whole cell, female WT, biol rep 3

description:
Library name: RNA-seq_Ctx_489
Chd807_featureCounts_final.txt


title: SK272, VD-RNA

description: Library name: KL-04


title: SK272, EtOH-RNA

description: Library name: KL-01


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_499
Chd807_featureCounts_final.txt


title: SK372, VD-RNA

description: Library name: KL-05


title: Cortex, whole cell, male WT, biol rep 3

description:
Library name: RNA-seq_Ctx_481
Chd807_featureCounts_final.txt


title: Cortex, whole cell, female WT, biol rep 4

description:
Library name: RNA-seq_Ctx_474
Chd807_featureCounts_final.txt


title: SK358, EtOH-RNA

description: Library name: KML2_22


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 4

description:
Library name: RNA-seq_Ctx_494
Chd807_featureCounts_final.txt


title: Cortex, whole cell, female WT, biol rep 2

description:
Library name: RNA-seq_Ctx_482
Chd807_featureCounts_final.txt


title: SK304, EtOH-RNA

description: Library name: KML2_12


title: SK288, VD-RNA

description: Library name: KML2_9


title: SK304, VD-RNA

description: Library name: KML2_11


title: Cortex, whole cell, female WT, biol rep 1

description:
Library name: RNA-seq_Ctx_495
Chd807_featureCounts_final.txt


title: Cortex, whole cell, male Chd8+/– germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_498
Chd807_featureCounts_final.txt


title: SK354, EtOH-RNA

description: Library name: KL-43


title: SK254, VD-RNA

description: Library name: KML2_3


title: SK254, EtOH-RNA

description: Library name: KML2_4


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 2

description:
Library name: RNA-seq_Ctx_473
Chd807_featureCounts_final.txt


title: Cortex, whole cell, male WT, biol rep 2

description:
Library name: RNA-seq_Ctx_479
Chd807_featureCounts_final.txt


title: AML12-FFA-SIN-3

city: changzhou

first: gang

last: zhou

address: gehu middle road No.68

department: nanjing medical university

institute: nanjing medical university

description: Library name: Sample9

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: GRCm39.110
Supplementary files format and content: processed data.xlsx

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: Mouse hepatocytes


title: SK316, EtOH-RNA

description: Library name: KML2_14


title: SK358, VD-RNA

description: Library name: KML2_21


title: AML12-FFA-SIN-2

description: Library name: Sample8


title: AML12-FFA-SIN-1

description: Library name: Sample7


title: Cortex, whole cell, male WT, biol rep 1

description:
Library name: RNA-seq_Ctx_496
Chd807_featureCounts_final.txt


title: AML12-FFA-2

description: Library name: Sample5


title: AML12-NC-3

description: Library name: Sample3


title: SK244, VD-RNA

description: Library name: KML20


title: AML12-FFA-3

description: Library name: Sample6


title: SK316, VD-RNA

description: Library name: KML2_13


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 1

description:
Library name: RNA-seq_Ctx_493
Chd807_featureCounts_final.txt


title: Cortex, whole cell, female Chd8+/– germline HET, biol rep 3

description:
Library name: RNA-seq_Ctx_475
Chd807_featureCounts_final.txt


title: SK288, EtOH-RNA

description: Library name: KML2_10


title: SK242, EtOH-RNA

description: Library name: KML7


title: SK252, VD-RNA

description: Library name: KML2_1


title: C57BL6/J hippocampus tissue6

city: Yinchuan City

first: guoyuan

last: he

address: 1160 Shengli Street, Xingqing District, Yinchuan City, Ningxia Autonomous Region

institute: Ningxia Medical University

description: Library name: sample6

data_processing:
CLc Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus;C57BL/6 male

extract_protocol:
RNA was harvested using Rneasy mini pius kit (Qiagen). 1.3 ug of total extract protocolal RNA was used for the construction ofsequencing libraries.
RNA llbrarles for RNA-seq were prepared usIng SMARTER mRNA.seq library construction protocol:g Library Prep Kit following manufacturer's protocols.

value: hippocampus;C57BL/6 male

value: WT


title: AML12-FFA-1

description: Library name: Sample4


title: SK236, EtOH-RNA

description: Library name: KML5


title: C57BL6/J hippocampus tissue5

description: Library name: sample5


title: C57BL6/J hippocampus tissue4

description: Library name: sample4


title: AML12-NC-2

description: Library name: Sample2


title: SK420, VD-RNA

description: Library name: KML24


title: SK242, VD-RNA

description: Library name: KML19


title: BXPC_3_cilia_3

city: 上海

first: Xiaona

last: Zhang

address: No.197 Ruijin Er Road, Huangpu District, Shanghai 200025, China

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 12

data_processing:
NovaSeq Control Software v1.7.5 was used for basecalling.
The SMARTER was used to build the adaptor, the Skewer software was used to dynamically remove the adaptor sequence fragments and low-quality fragments from the 3' end of the sequencing data, and the FastQC software was used to conduct quality control analysis on the preprocessed data and statistically calculate the base ratios of Q20 and Q30.
StringTie software was used to count the original sequence counts of known genes, and FPKM was used to calculate the normalized gene expression levels.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text included FPKM for every sample.

extract_protocol:
Total RNA was isolated from Cfpac-1 cells and BxPC-3 cells using TRIzolTM reagent (Invitogen, USA) according to the manufacturer’s instructions.
The RNA  library construction was processed  to use the standard illumina protocol.

value: PDAC


title: SK244, EtOH-RNA

description: Library name: KML8


title: SK420, EtOH-RNA

description: Library name: KML12


title: SK236, VD-RNA

description: Library name: KML17


title: C57BL6/J hippocampus tissue1

description: Library name: sample1


title: SK250, EtOH-RNA

description: Library name: KML9


title: C57BL6/J hippocampus tissue2

description: Library name: sample2


title: BXPC_3_cilia_2

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 11


title: SK228, VD-RNA

description: Library name: KML14


title: SK250, VD-RNA

description: Library name: KML21


title: SK228, EtOH-RNA

description: Library name: KML2


title: AML12-NC-1

description: Library name: Sample1


title: SK252, EtOH-RNA

description: Library name: KML2_2


title: C57BL6/J hippocampus tissue3

description: Library name: sample3


title: C57BL6/J hippocampus tissue7

description: Library name: sample7


title: 4SU_ctrl_rep1

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

description:
Library name: 4SU_ctrl_rep1
KO_readcounts.txt

data_processing:
Raw paired-end Slam-seq reads were first quality-trimmed using Trim Galore (v0.6.10) with default parameters. The cleaned reads were then aligned to the mm10 mouse reference genome (Mus musculus GRCm38 release 90 from ensembl) using STAR  (v2.7.10a) in end-to-end mapping mode with parameters (--outFilterMismatchNmax 20，--outFilterMultimapNmax 1，--outFilterScoreMinOverLread 0.4 , -- outFilterMatchNminOverLread 0.4), and indexed using Samtools (v1.12). Nascent RNA analysis was conducted using GRAND-SLAM (v2.0.7b) with the parameters(-snpConv 0.3, -trim5p 15, -double), followed by transcript abundance quantification through grandR (v0.2.1) to processing of the output tables.For each gene, we quantified raw read counts, FPKM, and NTR (Nascent-to-Total RNA ratio) in both total RNA and 4sU-labeled (Nascent) RNA.
Paired-end ATAC-seq reads were trimmed using Trim Galore with default parameters. Processed reads were aligned to the mm10 reference genome using Bowtie2 (v2.4.2) in end-to-end mode with parameters (--very-sensitive --no-mixed --no-discordant --phred33 --no-unal -I 10 -X 2000). Then sorted BAM files were created from raw alignment data through Samtools, and PCR duplicates were removed using MarkDuplicates (Picard v2.20.4).The sequencing coverage was normalized using bamCoverage (deeptools v3.5.4) by computing reads per kilobase per million mapped reads (RPKM) in consecutive 50bp genomic windows.
Assembly: mm10
Supplementary files format and content: TSV file for slam-seq readcounts
Supplementary files format and content: bigwig for ATAC-seq

source_name: embryo

growth_protocol: All mice were housed under specific pathogen-free (SPF) environmental conditions with free access to water and food, a temperature of 20-26°C, 30-70% humidity, and a 12-hour light/12-hour dark cycle at the Animal Core Facility of Nanjing Medical University.

extract_protocol:
For SLAM-seq, the collected embryos were washed six times with 1xPBS and then immediately placed in lysis buffer (Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor in a volume of 1 µl) and then frozen at -80℃;  For ATAC-seq, the collected embryos were lysed in 5 µl lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, and 0.01% digitonin) for 10 min on ice.
For SLAM-seq, samples were taken out from -80℃ freezer, and thawed on ice, 1 µl of alkylation mix was added to the lysis buffer for a final alkylation reaction of 50 mM Tris-HCl (pH 8.4), 10 mM IAA, 45% DMSO. After 15 min at 50 °C, the alkylation reaction was stopped by adding 2 µl of stop solution for a final alkylation reaction of 15 mM DTT, 2 mM dNTP mix (Thermo Fisher Scientific, R0192), 10 µM oligo-dT primer and 2 U µl–1 RNase inhibitor, incubating for 5 min at room temperature. Reverse transcription (RT) and the remaining library preparation were performed according to a modified version of Smart-seq2. The modification step was the removal of DTT from the RT mix. Full length cDNA libraries were fragmented and processed into sequencing libraries by using the TruePrep DNA Library Prep Kit for Illumina (Vazyme, TD503) following the manufacturer's instructions; For ATAC-seq, tagmentation and remaining library preparation were performed by using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) with minor modification. The tagmentation mix were modified by adding 2.5 µl TTE Mix V50.

treatment_protocol: Embryos in this study were derived from IVF( In Vitro Fertilization). Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. COCs were isolated. Embryos at different stages were collected after adding the sperm.About the collection of embryos for SLAM-seq, embryos were obtained by IVF and cultured in KSOM supplemented with 2 mM uridine analog 4-thiouridine (4SU) for 6 hours. IVF assay was modified for the 4SU labeling from 0-6 hpi (hours post insemination). Sperm were isolated and capacitated for 1 hours in HTF with 2 mM 4SU. Then, sperm were added to HTF with 2 mM 4SU containing COCs and co-incubated for 2 hours. Followed by presumptive zygotes were washed and transferred to into KSOM with 2 mM 4SU at once. After 6-hour labeling, the embryos were collected for further lysis.

value: embryo

value: 4SU labeling


title: BXPC-3_control_1

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 7


title: BXPC_3_cilia_1

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 10


title: 4SU_pKO_rep2

description:
Library name: 4SU_pKO_rep2
KO_readcounts.txt

value: Klf17 paternal KO


title: 4SU_pKO_rep1

description:
Library name: 4SU_pKO_rep1
KO_readcounts.txt


title: BXPC-3_control_3

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 9


title: 4SU_ctrl_rep3

description:
Library name: 4SU_ctrl_rep3
KO_readcounts.txt


title: BXPC-3_control_2

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 8


title: 4SU_ctrl_rep2

description:
Library name: 4SU_ctrl_rep2
KO_readcounts.txt


title: Cfpac-1_control_2

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 2


title: Cfpac-1_cilia_1

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 4


title: 4SU_mKO_rep3

description:
Library name: 4SU_mKO_rep3
KO_readcounts.txt

value: Klf17 maternal KO


title: Cfpac-1_cilia_3

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 6


title: 4SU_mKO_rep2

description:
Library name: 4SU_mKO_rep2
KO_readcounts.txt


title: 4SU_KO_rep3

description:
Library name: 4SU_KO_rep3
KO_readcounts.txt

value: Klf17 KO


title: WT_V-NPC_Sample3

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: Library name: WT V-NPC Sample3

library_source: genomic

data_processing:
Reads were trimmed using TrimGalore (v0.6.7) and aligned using bismark (v0.23.1). Aligned reads were filtered based on mapping quality (>=10) using samtools (v0.1.19) and PCR duplicates were removed using GATK/Picard MarkDuplicates (gatk v4.1.3.0). Methylation data at individual cytosines was extracted using MethylDackel extract (v0.6.01). Methylation read counts were merged across strands using a custom python script.
Assembly: hg38
Supplementary files format and content: Tab deliminated MethylDackel output file containing genome wide methylation data

molecule: genomic DNA

source_name: WT

growth_protocol: hPSCs were maintained in StemFlex Media on Vitronectin coated cultureware.

extract_protocol:
DNA was extracted using the the AllPrep DNA/RNA kit (Qiagen)
DNA was using the Covaris E220 sonicator, purified using SPRISelect Beads and DNA was bisulfite converted using the EZ DNA Methylation-Direct Kit (Zymo Research Corporation). Libraries were generated using the xGen™ Methyl-Seq Lib Prep Kit (IDT) with combinatorial dual indexes as instructed.

value: V-NPC

value: Control


title: WT_V-NPC_Sample4

description: Library name: WT V-NPC Sample4


title: Cfpac-1_control_3

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 3


title: Cfpac-1_cilia_2

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 5


title: ATAC-seq_Blastocyst_rep1

description: Library name: ATAC-seq_Blastocyst_rep1

value: no labeling


title: ATAC-seq_Blastocyst_rep2

description: Library name: ATAC-seq_Blastocyst_rep2


title: Cfpac-1_control_1

institute: 上海交通大学医学院附属瑞金医院

description: Library name: Sample 1


title: ATAC-seq_Morula_rep2

description: Library name: ATAC-seq_Morula_rep2


title: WT_V-NPC_Sample2

description: Library name: WT V-NPC Sample2


title: 4SU_mKO_rep1

description:
Library name: 4SU_mKO_rep1
KO_readcounts.txt


title: ATAC-seq_4C_rep2

description: Library name: ATAC-seq_4C_rep2


title: 4SU_KO_rep2

description:
Library name: 4SU_KO_rep2
KO_readcounts.txt


title: WT_V-IN_Sample4

description: Library name: WT V-IN Sample4

value: V-IN


title: ATAC-seq_L2C_rep2

description: Library name: ATAC-seq_L2C_rep2


title: WT_V-NPC_Sample1

description: Library name: WT V-NPC Sample1


title: ATAC-seq_4C_rep1

description: Library name: ATAC-seq_4C_rep1


title: ATAC-seq_Morula_rep1

description: Library name: ATAC-seq_Morula_rep1


title: WT_iGlut_Sample2

description: Library name: WT iGlut Sample2

value: iGlut


title: 4SU_KO_rep1

description:
Library name: 4SU_KO_rep1
KO_readcounts.txt


title: WT_V-IN_Sample2

description: Library name: WT V-IN Sample2


title: WT_iGlut_Sample3

description: Library name: WT iGlut Sample3


title: WT_V-IN_Sample1

description: Library name: WT V-IN Sample1


title: WT_iGlut_Sample1

description: Library name: WT iGlut Sample1


title: ATAC-seq_L2C_rep1

description: Library name: ATAC-seq_L2C_rep1


title: ATAC-seq_E2C_rep2

description: Library name: ATAC-seq_E2C_rep2


title: WT_D-IN_Sample4

description: Library name: WT D-IN Sample4

value: D-IN


title: WT_D-IN_Sample3

description: Library name: WT D-IN Sample3


title: ATAC-seq_E2C_rep1

description: Library name: ATAC-seq_E2C_rep1


title: ATAC-seq_M2C_rep1

description: Library name: ATAC-seq_M2C_rep1


title: 40 embryos_4SU_rep2

description:
Library name: 40_rep2
embryos_readcounts.txt


title: P904L_V-NPC_Sample4

description: Library name: P904L V-NPC Sample4

value: TBRS P904L


title: ATAC-seq_M2C_rep2

description: Library name: ATAC-seq_M2C_rep2


title: 10 embryos_4SU_rep2

description:
Library name: 10_rep2
embryos_readcounts.txt


title: WT_V-IN_Sample3

description: Library name: WT V-IN Sample3


title: 10 embryos_4SU_rep1

description:
Library name: 10_rep1
embryos_readcounts.txt


title: WT_D-IN_Sample2

description: Library name: WT D-IN Sample2


title: ATAC-seq_1C_rep1

description: Library name: ATAC-seq_1C_rep1


title: ATAC-seq_1C_rep2

description: Library name: ATAC-seq_1C_rep2


title: 100 embryos_4SU_rep1

description:
Library name: 100_rep1
embryos_readcounts.txt


title: 100 embryos_4SU_rep2

description:
Library name: 100_rep2
embryos_readcounts.txt


title: 90-96hpi_4SU_rep3

description:
Library name: 90-96hpi_4SU_rep3
slamseq_readcounts.txt


title: P904L_V-IN_Sample2

description: Library name: P904L V-IN Sample2


title: 90-96hpi_4SU_rep2

description:
Library name: 90-96hpi_4SU_rep2
slamseq_readcounts.txt


title: P904L_V-NPC_Sample3

description: Library name: P904L V-NPC Sample3


title: 70-76hpi_4SU_rep3

description:
Library name: 70-76hpi_4SU_rep3
slamseq_readcounts.txt


title: WT_D-IN_Sample1

description: Library name: WT D-IN Sample1


title: P904L_V-NPC_Sample2

description: Library name: P904L V-NPC Sample2


title: 40 embryos_4SU_rep1

description:
Library name: 40_rep1
embryos_readcounts.txt


title: P904L_V-IN_Sample4

description: Library name: P904L V-IN Sample4


title: 70-76hpi_4SU_rep2

description:
Library name: 70-76hpi_4SU_rep2
slamseq_readcounts.txt


title: 90-96hpi_4SU_rep1

description:
Library name: 90-96hpi_4SU_rep1
slamseq_readcounts.txt


title: P904L_iGlut_Sample1

description: Library name: P904L iGlut Sample1


title: P904L_V-IN_Sample3

description: Library name: P904L V-IN Sample3


title: P904L_D-IN_Sample4

description: Library name: P904L D-IN Sample4


title: P904L_iGlut_Sample2

description: Library name: P904L iGlut Sample2


title: 48-54hpi_4SU_rep2

description:
Library name: 48-54hpi_4SU_rep2
slamseq_readcounts.txt


title: P904L_D-IN_Sample3

description: Library name: P904L D-IN Sample3


title: 48-54hpi_4SU_rep3

description:
Library name: 48-54hpi_4SU_rep3
slamseq_readcounts.txt


title: P904L_V-IN_Sample1

description: Library name: P904L V-IN Sample1


title: P904L_V-NPC_Sample1

description: Library name: P904L V-NPC Sample1


title: 48-54hpi_4SU_rep1

description:
Library name: 48-54hpi_4SU_rep1
slamseq_readcounts.txt


title: 70-76hpi_4SU_rep1

description:
Library name: 70-76hpi_4SU_rep1
slamseq_readcounts.txt


title: 30-36hpi_4SU_rep1

description:
Library name: 30-36hpi_4SU_rep1
slamseq_readcounts.txt


title: P904L_D-IN_Sample2

description: Library name: P904L D-IN Sample2


title: 30-36hpi_4SU_rep3

description:
Library name: 30-36hpi_4SU_rep3
slamseq_readcounts.txt


title: MS9, CSF

city: San Francisco

first: Joseph

middle: J

last: Sabatino

address: 1651 4th St, Room 421A

institute: UCSF

description:
Library name: 9_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92218a

data_processing:
CellRanger v3.1.0
ImmCantation v3.1.0
Change-O v0.4.6
Assembly: GRCh38.v94
Supplementary files format and content: csv files
Library strategy: TCR-Seq

source_name: CSF

extract_protocol:
PBMC and CSF mononuclear cell isolation as described in https://www.biorxiv.org/content/10.1101/2024.09.07.611010v2
5' T cell V(D)J scTCR-seq (10X Genomics)

value: CSF

value: T cell

tag: disease state

value: MS


title: P904L_D-IN_Sample1

description: Library name: P904L D-IN Sample1


title: MS9, PB

description:
Library name: 9_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92218a

source_name: PBMC

value: PBMC


title: 24-30hpi_4SU_rep3

description:
Library name: 24-30hpi_4SU_rep3
slamseq_readcounts.txt

value: WT


title: MS8, PB

description:
Library name: 8_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92518a


title: MS8, CSF

description:
Library name: 8_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92518a


title: P904L_iGlut_Sample3

description: Library name: P904L iGlut Sample3


title: 18-24hpi_4SU_rep2

description:
Library name: 18-24hpi_4SU_rep2
slamseq_readcounts.txt

value: embryo


title: 24-30hpi_4SU_rep2

description:
Library name: 24-30hpi_4SU_rep2
slamseq_readcounts.txt

value: 4SU labeling


title: MS7, PB

description:
Library name: 7_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  90118a


title: OND4, PB

description:
Library name: 4_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  89018a


title: 30-36hpi_4SU_rep2

description:
Library name: 30-36hpi_4SU_rep2
slamseq_readcounts.txt


title: 12-18hpi_4SU_rep2

description:
Library name: 12-18hpi_4SU_rep2
slamseq_readcounts.txt


title: HC32, CSF

description:
Library name: 32_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  95019a


title: CIS31, PB

description:
Library name: 31_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  99119a


title: 6-12hpi_4SU_rep3

description:
Library name: 6-12hpi_4SU_rep3
slamseq_readcounts.txt


title: MS7, CSF

description:
Library name: 7_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  90118a


title: CIS31, CSF

description:
Library name: 31_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  99119a


title: HC32, PB

description:
Library name: 32_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  95019a


title: 12-18hpi_4SU_rep1

description:
Library name: 12-18hpi_4SU_rep1
slamseq_readcounts.txt


title: 24-30hpi_4SU_rep1

description:
Library name: 24-30hpi_4SU_rep1
slamseq_readcounts.txt