title: Control

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description:
RNA was isolated from the spinal cords of 4 mice.
total mRNA
3' RNAseq

data_processing:
Illumina bcl2fastq software used for basecalling.
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: *.tar archives contain the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: spinal cord

extract_protocol:
10x Genomics Chromium single-cell preparation.
NGS Illumina Next Seq.

treatment_protocol: Before being assigned to surgery, the body weight of mice was assessed and mice lighter than 19 grams were removed. Mice were anesthetized with a ketamine (100 mg kg-1)–xylazine (10 mg kg-1) mixture. The hair on the back was shaved and cleaned with betadine and alcohol. A 15-mm midline skin incision was performed over the T6-T13 vertebra, and the connective and muscle tissues were bluntly dissected to expose the lamina. A laminectomy was performed using rongeurs at T9 to expose the dorsal spinal cord. The vertebral column was stabilized with angled clamps attached to the T7 and T12 and a calibrated contusion injury of the spinal cord was induced at T9 by an Infinite Horizon Impactor (IH-0400 Impactor Precision Systems and Instrumentation) at a force of 80K dynes. After the injury, the muscles and skin were sutured separately and mice were allowed to recover from anesthesia on heating pads. After recovering from anesthesia, mice were injected intra-subcutaneously with buprenorphine (0.05 mg kg-1) daily for the first three days. Water containing sulfamethoxazole and trimethoprime oral suspension (200 mg/ 40 mg L-1) was supplied. Soft food and nutra-gel diet (S5769-TRAY, Bio-Serv) were supplied daily. Bladders of all mice were manually voided twice a day during the experiments.

value: spinal cord

tag: gender

value: female

tag: age

value: 2-3 months

value: spinal cord injury + PBS


title: Cp

status: Public on Jul 23 2024

type: SRA

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: treatment

value: spinal cord injury + Cp clonal T cells


title: Plate2_N16

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

library_source: transcriptomic

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
the following steps were undertaken to filter out low-count genes and samples across the entire dataset: 1) Genes with fewer than 10 mean counts across all samples (n = 4558) were excluded, 2) Samples with an average expression across all genes lower than 15 were also removed. Principal component analysis (PCA) was conducted on vehicle controls from all samples across 16 plates to assess potential plate effects. Outliers in vehicle control samples were identified and excluded using a mean correlation threshold of <0.85, ensuring the reliability of the subsequent transcriptomic dose-response and differential expression analyses.
Assembly: Whole transcriptome assay
Supplementary files format and content: with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: meta data of the QC samples

organism: Homo sapiens

source_name: iPSC-Cardiomyocytes

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

tag: cell type

value: iPSC-Cardiomyocytes


title: Plate2_N05


title: PBS

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw sequencing data were processed using the 10x Genomics’s Cell Ranger analysis pipeline (v.7.1.0) for sample demultiplexing, barcode processing, alignment with mm10 mouse genome, filtering, and UMI counting. The scRNA-seq data were analyzed using R Seurat Package (v4). The low quality cells are further filtered by three quality control filters: >10% mitochondrial reads, <5% ribosomal reads or <200 detected features. The doublets were identified and removed using DoubletFinder. The normalization and variance stabilization was performed with SCTransform (v2) with regressing out percentage of mitochondrial reads. 2,000 most variable genes were selected to calculate the first 40 PCs for the downstream analysis. The expression profiles were clustered using Leiden algorithm and visualized using two-dimensional UMAP. The cell type of each cell cluster was identified and annotated using known maker genes. The differentially expressed genes of each cell cluster were found with pseudo-bulk method using Deseq2. The pathway enrichment analysis was done using fGSEA with Kegg, Reactome and GO BP databases.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CMM

growth_protocol: CMM (GFP+) cells IV engrafted in C57BL/6 mice

extract_protocol:
Total RNA was extracted from sorted GFP+c-Kit+ CMM cells using Maxwell RSC simplyRNA tissue kit (Promega)
Library was performed using Single Cell-3 Solution kit v3.1 following the manufacture’s protocol. The final library size was determined using a High Sensitivity DNA Chip (Agilent). The libraries were sequenced with the paired end setting of 28 Read1 and 101 Read2 cycles, 10 index i7 and i5 cycles on NovaSeq 6000 platform (Illumina) using S4 Reagent kit v1.5 (Illumina).

treatment_protocol: start treatment when %GFP+ leukemia cells reached ~1% in blood, treat mice IV with PBS or CpG-STAT3dODN every other day for 3 times

value: AML

value: CMM


title: Spleen H11

description: RNA was isolated from 6 mice.

data_processing:
Demultiplexing with custom Python and perl script.
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Assembly: mm10
Supplementary files format and content: all.gene_counts.csv: Comma-separated text file with raw gene counts for all cells.

source_name: Spleen

extract_protocol: See 'overall design' on Series record.

value: Spleen

value: T cells

value: 3 months

value: spinal cord injury


title: epsilonPLCDs bladder

city: Tianjin

first: Chunhui

last: Miao

address: 22 Qixiangtai Road, Heping District

department: Immunology

country: China

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm39
Supplementary files format and content: Excel files include RAW counts for each sample.
Supplementary files format and content: Excel files include TPM values for each sample.

source_name: bladder

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bladder

tag: genotype

value: wild type

value: epsilonPLCDs


title: Spleen H12

description: RNA was isolated from 6 mice.


title: Plate2_N17


title: Plate2_N18


title: Plate2_N20


title: Spleen H9

description: RNA was isolated from 6 mice.


title: Spleen H8

description: RNA was isolated from 6 mice.


title: Plate2_N21


title: Spleen H7

description: RNA was isolated from 6 mice.


title: Plate2_N22


title: Plate2_N23


title: Plate2_H13


title: Spleen H4

description: RNA was isolated from 6 mice.


title: Spleen H3

description: RNA was isolated from 6 mice.


title: Plate2_H14

value: Monobenzyl phthalate_0.2_uM


title: Plate2_H15

value: 3,3',5,5'-Tetrabromobisphenol A_0.2_uM


title: Spleen H2

description: RNA was isolated from 6 mice.


title: Spleen H10

description: RNA was isolated from 6 mice.


title: Spleen G12

description: RNA was isolated from 6 mice.


title: Plate2_N19


title: Spleen G11

description: RNA was isolated from 6 mice.


title: Spleen H1

description: RNA was isolated from 6 mice.


title: Plate2_H21


title: Plate2_H18


title: Spleen G10

description: RNA was isolated from 6 mice.


title: Plate2_H19


title: Spleen G9

description: RNA was isolated from 6 mice.


title: Spleen G8

description: RNA was isolated from 6 mice.


title: Plate2_H22


title: Spleen H6

description: RNA was isolated from 6 mice.


title: Spleen G7

description: RNA was isolated from 6 mice.


title: Spleen G6

description: RNA was isolated from 6 mice.


title: Plate2_H23


title: Plate2_I03


title: Spleen H5

description: RNA was isolated from 6 mice.


title: Spleen G5

description: RNA was isolated from 6 mice.


title: Plate2_I02


title: Spleen G4

description: RNA was isolated from 6 mice.


title: Plate2_I04


title: Plate2_H16


title: Spleen G2

description: RNA was isolated from 6 mice.


title: Plate2_I05


title: Plate2_I06


title: Plate2_H17


title: Spleen G1

description: RNA was isolated from 6 mice.


title: Plate2_H20


title: Spleen F12

description: RNA was isolated from 6 mice.


title: Plate2_I07


title: Plate2_I10

value: Di-n-octyl phthalate_10_uM


title: Spleen F11

description: RNA was isolated from 6 mice.

value: female


title: Plate2_I08


title: Spleen F10

description: RNA was isolated from 6 mice.


title: Spleen F8

description: RNA was isolated from 6 mice.


title: Spleen F6

description: RNA was isolated from 6 mice.


title: Spleen F9

description: RNA was isolated from 6 mice.


title: Plate2_I13


title: Plate2_I11

value: tert-Butylhydro-quinone (TBHQ)_10_uM


title: Spleen F7

description: RNA was isolated from 6 mice.


title: Plate2_I12


title: Spleen F5

description: RNA was isolated from 6 mice.


title: Plate2_I14

value: Monobenzyl phthalate_10_uM


title: Spleen F4

description: RNA was isolated from 6 mice.


title: Spleen G3

description: RNA was isolated from 6 mice.


title: Plate2_I18


title: Plate2_I17


title: Spleen F1

description: RNA was isolated from 6 mice.


title: Plate2_I19


title: Plate2_I09


title: Spleen E12

description: RNA was isolated from 6 mice.


title: Plate2_I20


title: Plate2_I21


title: Spleen E11

description: RNA was isolated from 6 mice.


title: Plate2_I22


title: Spleen E8

description: RNA was isolated from 6 mice.


title: Spleen E9

description: RNA was isolated from 6 mice.


title: Plate2_I23


title: Plate2_I16


title: Spleen E10

description: RNA was isolated from 6 mice.


title: Spleen F3

description: RNA was isolated from 6 mice.


title: Plate2_I15

value: 3,3',5,5'-Tetrabromobisphenol A_10_uM


title: Spleen E5

description: RNA was isolated from 6 mice.


title: Spleen F2

description: RNA was isolated from 6 mice.


title: Plate2_J07

value: iPSC-Cardiomyocytes


title: Plate2_J05


title: Plate2_J03


title: Spleen E2

description: RNA was isolated from 6 mice.


title: Plate2_J04


title: Plate2_J02


title: Spleen E3

description: RNA was isolated from 6 mice.


title: Plate2_J08


title: Spleen E7

description: RNA was isolated from 6 mice.


title: Spleen E4

description: RNA was isolated from 6 mice.


title: Plate2_J06


title: Spleen E1

description: RNA was isolated from 6 mice.


title: Spleen D12

description: RNA was isolated from 6 mice.


title: Plate2_J10

value: Di-n-octyl phthalate_1_uM


title: Spleen D11

description: RNA was isolated from 6 mice.


title: Spleen D10

description: RNA was isolated from 6 mice.


title: Plate2_J11

value: tert-Butylhydro-quinone (TBHQ)_1_uM


title: Plate2_J12


title: Spleen D9

description: RNA was isolated from 6 mice.

value: Spleen


title: Spleen E6

description: RNA was isolated from 6 mice.

value: T cells


title: Plate2_J13


title: Spleen D8

description: RNA was isolated from 6 mice.

value: 3 months


title: Spleen D7

description: RNA was isolated from 6 mice.

value: spinal cord injury


title: Spleen D6

description: RNA was isolated from 6 mice.


title: Plate2_J14

value: Monobenzyl phthalate_1_uM


title: Plate2_J15

value: 3,3',5,5'-Tetrabromobisphenol A_1_uM


title: Spleen D5

description: RNA was isolated from 6 mice.


title: Plate2_J17


title: Plate2_J19


title: Spleen D4

description: RNA was isolated from 6 mice.


title: Plate2_J18


title: Plate2_J09


title: Plate2_J16


title: Spleen D3

description: RNA was isolated from 6 mice.


title: Spleen D1

description: RNA was isolated from 6 mice.


title: Spleen D2

description: RNA was isolated from 6 mice.


title: Plate2_J22


title: Spleen C11

description: RNA was isolated from 6 mice.


title: Plate2_J20


title: Plate2_J23


title: Plate2_J21


title: Spleen C12

description: RNA was isolated from 6 mice.


title: Spleen C10

description: RNA was isolated from 6 mice.


title: Spleen C8

description: RNA was isolated from 6 mice.


title: Plate2_K03


title: Spleen C9

description: RNA was isolated from 6 mice.


title: Plate2_K02


title: Plate2_K04


title: Spleen C5

description: RNA was isolated from 6 mice.


title: Plate2_K05


title: Spleen C7

description: RNA was isolated from 6 mice.


title: Plate2_K06


title: Plate2_K09


title: Spleen C3

description: RNA was isolated from 6 mice.


title: Spleen C6

description: RNA was isolated from 6 mice.


title: Plate2_K08


title: Spleen C2

description: RNA was isolated from 6 mice.


title: Plate2_K12


title: Spleen C1

description: RNA was isolated from 6 mice.


title: Plate2_K07


title: Spleen B12

description: RNA was isolated from 6 mice.


title: Plate2_K11

value: tert-Butylhydro-quinone (TBHQ)_0.2_uM


title: Spleen B10

description: RNA was isolated from 6 mice.


title: Plate2_K14

value: Monobenzyl phthalate_0.2_uM


title: Plate2_K13


title: Plate2_K10

value: Di-n-octyl phthalate_0.2_uM


title: Plate2_K17


title: Spleen B7

description: RNA was isolated from 6 mice.


title: Spleen B11

description: RNA was isolated from 6 mice.


title: Plate2_K18


title: Plate2_K15

value: 3,3',5,5'-Tetrabromobisphenol A_0.2_uM


title: Spleen B8

description: RNA was isolated from 6 mice.

value: female


title: Plate2_K16


title: Spleen B6

description: RNA was isolated from 6 mice.


title: Spleen B5

description: RNA was isolated from 6 mice.


title: Spleen C4

description: RNA was isolated from 6 mice.


title: Plate2_K19


title: Spleen B4

description: RNA was isolated from 6 mice.


title: Plate2_K20


title: Spleen B3

description: RNA was isolated from 6 mice.


title: Spleen B2

description: RNA was isolated from 6 mice.


title: Plate2_K21


title: Spleen B1

description: RNA was isolated from 6 mice.


title: Spleen A12

description: RNA was isolated from 6 mice.


title: Plate2_K22


title: Plate2_L02


title: Spleen B9

description: RNA was isolated from 6 mice.


title: Spleen A11

description: RNA was isolated from 6 mice.


title: Plate2_L03


title: Plate2_L04


title: Spleen A9

description: RNA was isolated from 6 mice.


title: Spleen A10

description: RNA was isolated from 6 mice.


title: Spleen A8

description: RNA was isolated from 6 mice.


title: Spleen A6

description: RNA was isolated from 6 mice.


title: Spleen A7

description: RNA was isolated from 6 mice.


title: Spleen A5

description: RNA was isolated from 6 mice.


title: Plate2_L10


title: Spleen A4

description: RNA was isolated from 6 mice.


title: Plate2_L07


title: Plate2_L06


title: Plate2_L08


title: Spleen A3

description: RNA was isolated from 6 mice.


title: Plate2_L11

value: Diphenolic acid_10_uM


title: Plate2_L09


title: Plate2_L12


title: Spleen A2

description: RNA was isolated from 6 mice.


title: Plate2_K23


title: Spleen A1

description: RNA was isolated from 6 mice.


title: Plate2_L13


title: Spinal Cord H12

description: RNA was isolated from 6 mice.

source_name: Spinal cord

value: Spinal cord

value: 24 months


title: Spinal Cord H11

description: RNA was isolated from 6 mice.


title: Plate2_L15

value: iPSC-Cardiomyocytes


title: Plate2_L05


title: Spinal Cord H10

description: RNA was isolated from 6 mice.


title: Plate2_L17


title: Plate2_L16


title: Spinal Cord H9

description: RNA was isolated from 6 mice.


title: Spinal Cord H8

description: RNA was isolated from 6 mice.


title: Plate2_L18


title: Spinal Cord H7

description: RNA was isolated from 6 mice.


title: Spinal Cord H6

description: RNA was isolated from 6 mice.


title: Spinal Cord H5

description: RNA was isolated from 6 mice.


title: Plate2_L20


title: Plate2_L21


title: Plate2_L23


title: Plate2_M02


title: Spinal Cord H3

description: RNA was isolated from 6 mice.


title: Plate2_L14


title: Spinal Cord H1

description: RNA was isolated from 6 mice.


title: Spinal Cord H4

description: RNA was isolated from 6 mice.


title: Plate2_M03


title: Spinal Cord G12

description: RNA was isolated from 6 mice.


title: Spinal Cord G11

description: RNA was isolated from 6 mice.


title: Plate2_M05


title: Plate2_M06


title: Spinal Cord G10

description: RNA was isolated from 6 mice.


title: Spinal Cord G8

description: RNA was isolated from 6 mice.


title: Spinal Cord G9

description: RNA was isolated from 6 mice.


title: Plate2_M07


title: Plate2_M08


title: Plate2_L19


title: Spinal Cord G7

description: RNA was isolated from 6 mice.


title: Spinal Cord G6

description: RNA was isolated from 6 mice.


title: Plate2_M11

value: Diphenolic acid_1_uM


title: Plate2_M10


title: Plate2_L22


title: Spinal Cord G4

description: RNA was isolated from 6 mice.


title: Spinal Cord H2

description: RNA was isolated from 6 mice.


title: Plate2_M12


title: Spinal Cord G5

description: RNA was isolated from 6 mice.


title: Spinal Cord G2

description: RNA was isolated from 6 mice.


title: Plate2_M14


title: Spinal Cord G1

description: RNA was isolated from 6 mice.


title: Plate2_M04


title: Plate2_M15


title: Plate2_M16


title: Spinal Cord F12

description: RNA was isolated from 6 mice.


title: Plate2_C05


title: Spinal Cord F11

description: RNA was isolated from 6 mice.


title: Plate2_C07


title: Spinal Cord F10

description: RNA was isolated from 6 mice.


title: Plate2_C06


title: Spinal Cord F7

description: RNA was isolated from 6 mice.


title: Spinal Cord F9

description: RNA was isolated from 6 mice.


title: Plate2_C08


title: Spinal Cord F8

description: RNA was isolated from 6 mice.


title: Plate2_C09


title: Spinal Cord G3

description: RNA was isolated from 6 mice.


title: Spinal Cord F6

description: RNA was isolated from 6 mice.


title: Plate2_M13


title: Plate2_C12


title: Spinal Cord F5

description: RNA was isolated from 6 mice.


title: Spinal Cord F4

description: RNA was isolated from 6 mice.


title: Plate2_C14

value: Monobenzyl phthalate_10_uM


title: Spinal Cord F2

description: RNA was isolated from 6 mice.


title: Plate2_C13


title: Spinal Cord F1

description: RNA was isolated from 6 mice.


title: Spinal Cord F3

description: RNA was isolated from 6 mice.


title: Spinal Cord E12

description: RNA was isolated from 6 mice.


title: Plate2_C15

value: 3,3',5,5'-Tetrabromobisphenol A_10_uM


title: Plate2_C16


title: Plate2_C17


title: Plate2_C18


title: Spinal Cord E11

description: RNA was isolated from 6 mice.

value: T cells


title: Spinal Cord E10

description: RNA was isolated from 6 mice.


title: Plate2_C10

value: Di-n-octyl phthalate_10_uM


title: Spinal Cord E9

description: RNA was isolated from 6 mice.

value: spinal cord injury


title: Plate2_C19


title: Spinal Cord E7

description: RNA was isolated from 6 mice.


title: Plate2_C20


title: Spinal Cord E6

description: RNA was isolated from 6 mice.


title: Plate2_C22


title: Spinal Cord E8

description: RNA was isolated from 6 mice.


title: Plate2_C21


title: Plate2_C11

value: tert-Butylhydro-quinone (TBHQ)_10_uM


title: Plate2_C23


title: Spinal Cord E4

description: RNA was isolated from 6 mice.


title: Spinal Cord E5

description: RNA was isolated from 6 mice.


title: Spinal Cord E3

description: RNA was isolated from 6 mice.


title: Plate2_D03


title: Plate2_D02


title: Spinal Cord E1

description: RNA was isolated from 6 mice.


title: Spinal Cord E2

description: RNA was isolated from 6 mice.


title: Plate2_D04


title: Plate2_D05


title: Plate2_D06


title: Spinal Cord D12

description: RNA was isolated from 6 mice.


title: Spinal Cord D10

description: RNA was isolated from 6 mice.


title: Spinal Cord D9

description: RNA was isolated from 6 mice.


title: Plate2_D07


title: Plate2_D09


title: Plate2_D08


title: Plate2_D10

value: Di-n-octyl phthalate_1_uM


title: Plate2_D11

value: tert-Butylhydro-quinone (TBHQ)_1_uM


title: Spinal Cord D8

description: RNA was isolated from 6 mice.


title: Spinal Cord D7

description: RNA was isolated from 6 mice.


title: Plate2_D13


title: Plate2_D12


title: Spinal Cord D5

description: RNA was isolated from 6 mice.


title: Spinal Cord D4

description: RNA was isolated from 6 mice.


title: Spinal Cord D6

description: RNA was isolated from 6 mice.


title: Spinal Cord D3

description: RNA was isolated from 6 mice.


title: Spinal Cord D2

description: RNA was isolated from 6 mice.


title: Plate2_D14

value: Monobenzyl phthalate_1_uM


title: Spinal Cord D1

description: RNA was isolated from 6 mice.


title: Plate2_D19


title: Plate2_D17


title: Spinal Cord C12

description: RNA was isolated from 6 mice.


title: Plate2_D18


title: Spinal Cord C11

description: RNA was isolated from 6 mice.


title: Plate2_D15

value: 3,3',5,5'-Tetrabromobisphenol A_1_uM


title: Spinal Cord D11

description: RNA was isolated from 6 mice.


title: Spinal Cord C10

description: RNA was isolated from 6 mice.


title: Spinal Cord C9

description: RNA was isolated from 6 mice.


title: Plate2_D20


title: Plate2_M09


title: Spinal Cord C8

description: RNA was isolated from 6 mice.


title: Spinal Cord C7

description: RNA was isolated from 6 mice.


title: Plate2_D22


title: Plate2_D21


title: Plate2_D23


title: Spinal Cord C6

description: RNA was isolated from 6 mice.


title: Spinal Cord C5

description: RNA was isolated from 6 mice.


title: Plate2_E05


title: Plate2_E03


title: Spinal Cord C4

description: RNA was isolated from 6 mice.


title: Plate2_E04


title: Spinal Cord C2

description: RNA was isolated from 6 mice.


title: Plate2_D16


title: Plate2_E06


title: Spinal Cord B12

description: RNA was isolated from 6 mice.


title: Plate2_E08


title: Plate2_E07


title: Plate2_E10

value: Di-n-octyl phthalate_0.2_uM


title: Plate2_E09


title: Spinal Cord C1

description: RNA was isolated from 6 mice.

value: female


title: Spinal Cord B11

description: RNA was isolated from 6 mice.


title: Spinal Cord B9

description: RNA was isolated from 6 mice.


title: Plate2_E11

value: tert-Butylhydro-quinone (TBHQ)_0.2_uM


title: Plate2_E02


title: Spinal Cord B6

description: RNA was isolated from 6 mice.

value: Spinal cord


title: Plate2_E15

value: 3,3',5,5'-Tetrabromobisphenol A_0.2_uM


title: Plate2_E14

value: iPSC-Cardiomyocytes

value: Monobenzyl phthalate_0.2_uM


title: Spinal Cord B8

description: RNA was isolated from 6 mice.

value: 24 months


title: Plate2_E13


title: Spinal Cord B5

description: RNA was isolated from 6 mice.


title: Spinal Cord C3

description: RNA was isolated from 6 mice.


title: Plate2_E16


title: Plate2_E17


title: Plate2_E18


title: Spinal Cord B1

description: RNA was isolated from 6 mice.


title: Spinal Cord B3

description: RNA was isolated from 6 mice.


title: Spinal Cord B10

description: RNA was isolated from 6 mice.


title: Spinal Cord A12

description: RNA was isolated from 6 mice.


title: Plate2_E12


title: Spinal Cord A11

description: RNA was isolated from 6 mice.


title: Plate2_E22


title: Plate2_E20


title: Spinal Cord A9

description: RNA was isolated from 6 mice.


title: Plate2_E21


title: Spinal Cord A10

description: RNA was isolated from 6 mice.


title: Plate2_E23


title: Spinal Cord B4

description: RNA was isolated from 6 mice.


title: Spinal Cord A8

description: RNA was isolated from 6 mice.


title: Spinal Cord B7

description: RNA was isolated from 6 mice.


title: Plate2_F03


title: Plate2_F02


title: Spinal Cord A7

description: RNA was isolated from 6 mice.


title: Plate2_F05


title: Spinal Cord A5

description: RNA was isolated from 6 mice.


title: Plate2_F04


title: Spinal Cord A4

description: RNA was isolated from 6 mice.


title: Spinal Cord A3

description: RNA was isolated from 6 mice.


title: Plate2_F07


title: Spinal Cord B2

description: RNA was isolated from 6 mice.


title: Plate2_E19


title: Plate2_F08


title: Spinal Cord A1

description: RNA was isolated from 6 mice.


title: Plate2_F09


title: mouse dentate gyrus cells sample, cKO

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
Cellranger/4.0.0 was used for alignment, filtering barcode counting, and UMI counting.
Output files of cellranger aggregation pipeline (barcodes.tsv.gz,features.tsv.gz and matrix.mtx.gz) are processed using scanpy (version 1.7.0) for downstream analyses
Genome_build: Mouse reference (mm10)
Supplementary_files_format_and_content: Tab delimited file of barcodes metadata
Supplementary_files_format_and_content: Tab delimited file of gene names metadata
Supplementary_files_format_and_content: matrix of count values in mtx format
Supplementary_files_format_and_content: scanpy object

source_name: P30 mouse dentate gyrus

extract_protocol:
PHF2 control (n=4) and cKO (n=4) mice were euthanized by isoflurane, followed by transcardially perfusion using phosphate-buffered saline (1x PBS), and brains were immediately immersed into ice cold HBSS with 0.01% BSA. The dissected dentate gyrus was dissociated into single cells following manufacturer's instructions of the Adult Brain Dissociation Kit (Miltenyi Biotec, Neural Tissue Dissociation Kit (P) 130-092-628). Directly after dissociation, cell quantity, and viability of cells were measured, and a cell suspension volume equivalent to 1x106 target cells was used for further processing.
Libraries were constructed using Chromium Next GEM Single Cell 3' GEM, Library$ Gel Bead Kit v3.1 (Cat# CG000204) by 10x Genomics.

value: Nestin-Cre (B6.Cg-Tg(Nes-cre)1Kln/J) mice (JAX stock #003771)

value: dentate gyrus

value: post natal day 30

value: conditional knockout (Nestin-Cre Tg, Phf2flox/flox)


title: Plate2_F10

value: Di-n-octyl phthalate_10_uM


title: Spinal Cord A2

description: RNA was isolated from 6 mice.

value: T cells

value: spinal cord injury


title: Plate2_F11

value: tert-Butylhydro-quinone (TBHQ)_10_uM


title: mouse dentate gyrus cells sample, control

value: wild type(Nestin-Cre Tg, Phf2+/+)


title: Spinal Cord A6

description: RNA was isolated from 6 mice.


title: Plate2_F12


title: Plate2_F14

value: Monobenzyl phthalate_10_uM


title: Plate2_F13


title: Plate2_F16


title: Plate2_F15

value: 3,3',5,5'-Tetrabromobisphenol A_10_uM


title: Plate2_F18


title: Plate2_F06


title: Plate2_F17


title: Plate2_F19


title: Nephrectomy 4

city: Guangzhou

first: Jing-Fu

last: Bao

address: 1838 North Guangzhou Ave

institute: Southern Medical University

data_processing:
Quality examination and data cleansing of the raw data were finished by SOAPnuke (v1.5.6)
Clean data were aligned to the reference genome Mus musculus GCF_000001635.26_GRCm38.p6 through HISAT2 (v2.1.0)
Differential expression analysis was carried out based on the matrix of read counts through DESeq2 (v1.4.5)
Assembly: mm10
Supplementary files format and content: gene expression table.txt includes raw counts of each sample

molecule: polyA RNA

source_name: Left ventricular tissues

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific, Inc.)
Sequencing libraries were prepared using the MGIEasy RNA Library Prep Set (MGI Tech Co., Ltd.)

treatment_protocol: Mice with adnine-diet were treated with 5-week 0.25% adenine diet and 2-week normal diet, and mice were sacrificed. Mice with nephrectomy were treated with subtotal nephrectomy at left kidney; One week later, right kidney was removed; 5 week after surgery, mice were sacrificed.

value: Left ventricular tissues

value: WT

value: Modeified Nephrectomy


title: Adenine 3

value: Adenine and normal diet


title: Adenine 4


title: Nephrectomy 1


title: Adenine 1


title: Nephrectomy 2


title: Plate2_F21

value: iPSC-Cardiomyocytes


title: Adenine 5


title: Adenine 2


title: Plate2_F20


title: Nephrectomy 5


title: Plate2_F23


title: Control 5

value: Sham operation


title: Control 3


title: Control 2


title: Nephrectomy 3


title: Control 1


title: Plate2_G03


title: Control 4


title: Plate2_G02


title: Plate2_G04


title: GAS WT rep3

city: 上海

first: yang

middle: ji

last: ding

address: 淞沪路2005号

institute: fudan university

data_processing:
The clean reads were mapped to the reference genome (mm10) using STAR (2.7.10a).
Quantification of gene expression was calculated using RSEM (v1.2.28).
Differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expression genes.
Assembly: mm10
Supplementary files format and content: csv files include counts values for each samples

source_name: Gastrocnemius

extract_protocol:
The gastrocnemius samples from each group were collected for RNA sequencing
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: Gastrocnemius

value: room temperature housing


title: GAS BKO rep3

value: BAT MSTNKO


title: GAS WT rep1


title: Plate2_G08


title: GAS WT rep2


title: Plate2_G06


title: Plate2_G09


title: BAT WT rep2

source_name: Brown Adipose Tissue

extract_protocol:
The BAT samples from each group were collected for RNA sequencing
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: Brown Adipose Tissue


title: Plate2_G07


title: Plate2_G11

value: tert-Butylhydro-quinone (TBHQ)_1_uM


title: GAS BKO rep2


title: Plate2_G13


title: Plate2_F22


title: Plate2_G05


title: Plate2_G10

value: Di-n-octyl phthalate_1_uM


title: BAT WT rep3


title: BAT BKO rep4


title: Plate2_G12


title: GAS BKO rep1


title: BAT BKO rep3


title: Plate2_G18


title: Plate2_G19


title: BAT WT rep1


title: Plate2_G14

value: Monobenzyl phthalate_1_uM


title: Plate2_G15

value: 3,3',5,5'-Tetrabromobisphenol A_1_uM


title: WT, replicate 3_R1, scRNAseq

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

data_processing:
Demultiplex, raw paired-end scRNA-seq data were processed using the Cell Ranger (v. 7.1.0) from the 10x Genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest).
‘Cell ranger count’ function was used to align reads to the human genome and generate a digital gene expression (DGE) matrices for each sample.
DGEs were further processed in R (v. 4.2.2) using Seurat (v. 5.0.2).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Regionalized midbrain organoid

growth_protocol: NPC-derived midbrain organoids were generated following a protocol by Renner H, Grabos M, Becker KJ, Kagermeier TE, Wu J, Otto M, Peischard S, Zeuschner D, TsyTsyura Y, Disse P, Klingauf J, Leidel SA, Seebohm G, Scholer HR, Bruder JM (2020). A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids. Elife. 9,

extract_protocol:
Midbrain organoids were dissociated using the Papain Dissociation System (Worthington Biochemical, USA). The cell suspension withh added 800 µL of freezing-cold 100% methanol were stored at -80°C until further analysis.
Samples after rehydration were subjected to scRNA-seq using the 10× Genomics Chromium Single Cell 3’ Gene Expression system with feature barcoding technology for cell multiplexing.
Libraries were generated using 10x Chromium

value: Regionalized midbrain organoid

tag: cell line

value: midbrain organoid

value: WT/WT


title: Plate2_G21


title: WT, replicate 1_R1, scRNAseq

description: 10× Genomics Chromium Single Cell 3’ Gene Expression system


title: Plate2_G17


title: Plate2_G16


title: BAT BKO rep2


title: Plate2_G22


title: HD, replicate 1_R1, scRNAseq


title: WT, replicate 2_R1, scRNAseq


title: DHBC_wk8_nonTfh

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10, build NCBI:GCA_003339765.3) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10
Supplementary files format and content: raw gene count file

organism: Macaca mulatta

source_name: lymph node

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on NovaSeq 6000 (Illumina).

value: lymph node

value: non-Tfh

value: DEL bNAb Tx

tag: animal id

value: DHBC

tag: timepoint


title: Plate2_H02

value: iPSC-Cardiomyocytes


title: Plate2_H03


title: Plate2_G20


title: HD, replicate 3_R1, scRNAseq


title: Plate2_H05


title: DHBC_wk8_GCTfh

value: GCTfh


title: Healthy control PMN, rep7

city: Helsinki

first: Tomas

last: Strandin

address: Haartmaninkatu 3

department: Virology

country: Finland

institute: University of Helsinki

data_processing:
Conversion: Illumina Bcl2fastq2 Conversion Software (version v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.
Quality Control: FastQC (version 0.11.9) and MultiQC (v1.9) were used to check the quality of the data.
Trimming: Sample-specific read files were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences using Trimmomatic (v0.39).
Alignment: Trimmed reads were aligned to the human genome using STAR aligner (v2.7.6a) in two-pass mode.
Reference Genome: Reference genome and gene annotations were based on GENCODE release v38 (GRCh38.p13).
Counting: Counts per gene were collected using featureCounts from the Subread package (v2.0.1).
Assembly: GENCODE release v38 (GRCh38.p13)
Supplementary files format and content: Gene expression table (.txt): A table with gene expression levels for each sample. The table includes gene identifiers and normalized read counts for each gene across all samples.
Supplementary files format and content: FeatureCounts: generated by the featurecounts tool.Text files (format). Contains raw read counts for each gene in each sample, summary of read assignment results including counts of successfully assigned reads and unassigned reads, and log file with details of the featureCounts run, parameters used, and summary of the process.

source_name: Peripheral blood neutrophils

growth_protocol: Neutrophils and low-density granulocytes (LDGs) were isolated from peripheral blood samples of patients and healthy controls. Blood samples were collected and processed according to standard clinical procedures.

extract_protocol:
RNA extraction from isolated PMNs and LDGs was performed using the following steps: Neutrophils and LDGs were isolated from peripheral blood using density gradient centrifugation, then cells were lysed in Trizol, and finally RNA was extracted in the liquid phase using chloroform.
cDNA synthesis from total RNA was performed according to the Takara SMARTseq v4 Ultra-low input RNA kit for Sequencing user manual (Takara Bio, Mountain View, CA, USA). This was followed by Illumina Nextera XT Library preparation according to the Illumina Nextera XT Reference Guide (Illumina, San Diego, CA, USA). Unique Dual Index (UDI) setup was used for the Nextera XT libraries. Library quality check was performed using the LabChip GX Touch HT High Sensitivity assay (PerkinElmer, USA). Libraries were pooled based on concentrations acquired from the assay and quantified using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: For COVID-19 patients, the blood samples were collected at the time of diagnosis. Patients were categorized into severe and mild COVID-19 based on clinical criteria. Healthy control samples were obtained from individuals with no known history of COVID-19 or other significant illnesses.

value: Peripheral blood neutrophils

value: Neutrophils


title: BAT BKO rep1

value: BAT MSTNKO

value: room temperature housing


title: HD, replicate 2_R1, scRNAseq


title: Healthy control PMN, rep5


title: Plate2_H04


title: Plate2_G23


title: Healthy control PMN, rep4


title: DHBC_wk8_nonfCD8


title: Plate2_H06


title: Healthy control PMN, rep6


title: Plate2_H07


title: DHBC_wk8_fCD8


title: Healthy control PMN, rep3


title: DHBC_wk8_CD8CM

value: CD8+ central mem.


title: Plate2_H08


title: DHBC_wk8_CD8NA

value: CD8+ naive


title: Plate2_H09


title: Plate2_B05


title: Healthy control PMN, rep1


title: Plate2_H10

value: Di-n-octyl phthalate_0.2_uM


title: Plate2_H11

value: tert-Butylhydro-quinone (TBHQ)_0.2_uM


title: Plate2_H12


title: Plate2_B07


title: Severe COVID-19 PMN, rep15


title: Plate2_B03


title: DHBC_wk8_CD8

value: total CD8+


title: Healthy control PMN, rep2


title: Plate2_B02


title: Plate2_B04


title: Plate2_B10


title: Plate2_B06


title: Severe COVID-19 PMN, rep13


title: Severe COVID-19 PMN, rep14


title: Plate2_B09


title: Plate2_B08


title: DHBC_wk8_CD4

value: total CD4+


title: DHBC_pre_nonfCD8

value: pre


title: Plate2_B11


title: DHBC_wk8_CD8EM

value: lymph node

value: CD8+ effector mem.


title: Plate2_B12


title: Plate2_B13


title: Severe COVID-19 LDG, rep6


title: Plate2_B14


title: DHBC_wk8_CD4NA

value: CD4+ naive

value: DEL bNAb Tx


title: Severe COVID-19 LDG, rep5


title: Plate2_B15

value: iPSC-Cardiomyocytes


title: Plate2_B16


title: Severe COVID-19 PMN, rep12


title: DHBC_wk8_CD4MEM

value: CD4+ mem.

value: DHBC


title: Plate2_B18


title: Plate2_B19


title: Plate2_B22


title: DHBC_pre_nonTfh

value: non-Tfh


title: DHBC_pre_fCD8


title: Plate2_B17


title: Severe COVID-19 PMN, rep10

value: Peripheral blood neutrophils

value: Neutrophils


title: Severe COVID-19 LDG, rep4


title: DHBC_pre_CD8NA


title: Plate2_B20


title: DHBC_pre_CD8EM


title: Plate2_B21


title: Plate2_B23


title: Severe COVID-19 PMN, rep9


title: DHBC_pre_GCTfh

value: GCTfh


title: Plate2_C02


title: Severe COVID-19 PMN, rep11


title: DHBC_pre_CD8


title: Plate1_N03


title: Plate2_C03


title: Severe COVID-19 LDG, rep3


title: Plate2_C04


title: Plate1_N02


title: DHBC_pre_CD4NA


title: DHBC_pre_CD4MEM


title: Severe COVID-19 LDG, rep2


title: Plate1_N05


title: DHBC_pre_CD8CM

value: CD8+ central mem.


title: Plate1_N04


title: Plate1_N06


title: DHBC_pre_CD4


title: Plate1_N08


title: Severe COVID-19 PMN, rep8


title: Severe COVID-19 LDG, rep1


title: Mild COVID-19 PMN, rep8


title: Plate1_N09


title: DHBC_D14_nonTfh


title: DHBC_D14_GCTfh


title: Plate1_N11


title: Plate1_N12


title: DHBC_D14_fCD8


title: Plate1_N13


title: Mild COVID-19 PMN, rep6


title: Mild COVID-19 PMN, rep7


title: Plate1_N14


title: DHBC_D14_CD8NA

value: CD8+ naive


title: Mild COVID-19 PMN, rep5


title: Plate1_N15


title: DHBC_D14_CD8EM


title: Plate1_N16


title: Plate1_N17


title: Mild COVID-19 PMN, rep4


title: Plate1_N07


title: Plate1_N18


title: Plate1_N19


title: DHBC_D14_CD8CM


title: Mild COVID-19 PMN, rep3


title: DHBC_D14_CD8


title: Plate1_N10


title: Plate1_N20


title: Mild COVID-19 PMN, rep2


title: Plate1_K06


title: DHBC_D14_CD4NA


title: Plate1_N23


title: Mild COVID-19 PMN, rep1


title: DHBC_D14_CD4MEM


title: Severe COVID-19 PMN, rep7


title: DHBC_D14_CD4


title: Plate1_N22


title: Plate1_K07


title: Plate1_K08

value: Formetanate hydrochloride_0.2_uM


title: DH51_wk8_nonTfh

value: WT bNAb Tx


title: Plate1_K10


title: Plate1_K09


title: Severe COVID-19 PMN, rep5


title: Plate1_K13


title: Plate1_K12


title: DH51_wk8_nonfCD8


title: DH51_wk8_GCTfh


title: Severe COVID-19 PMN, rep4


title: Plate1_N21


title: Severe COVID-19 PMN, rep3


title: DH51_wk8_fCD8


title: Plate1_K15


title: Plate1_K14


title: Plate1_K16


title: Plate1_K18


title: Plate1_K17


title: Severe COVID-19 PMN, rep2


title: Plate1_K19


title: Severe COVID-19 PMN, rep1


title: Severe COVID-19 PMN, rep6


title: Plate1_K20


title: DH51_wk8_CD8EM


title: Plate1_K21


title: Plate1_K11


title: DH51_wk8_CD8CM


title: Plate1_K22


title: Plate1_L02


title: Plate1_K23


title: DH51_wk8_CD8

value: total CD8+


title: glioma, R7

city: Houston

first: Akdes

last: Serin Harmanci

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The Patch-seq reads were mapped using STAR72 to hg38 assemblies for humans. Read count matrices were generated using FeatureCounts73 with the latest gene annotations from GENCODE74 consortia
Assembly: hg38
Supplementary files format and content: matrix files
Library strategy: patch-Seq

source_name: glioma

extract_protocol:
RNA in the lysis buffer was denatured, reverse transcribed, amplified, and purified following the Smart-seq2-based protocol71.
Library was performed according to the manufacter’s instructions

value: glioma


title: glioma, R9


title: Plate1_L03


title: Plate1_L04


title: Plate1_L05


title: Plate1_L06


title: glioma, R5


title: DH51_wk8_CD4NA

value: lymph node


title: Plate1_L07


title: DH51_wk8_CD4MEM


title: glioma, R4


title: Plate1_L08


title: DH51_wk8_CD8NA


title: glioma, R6


title: glioma, R3


title: DH51_wk8_CD4

value: total CD4+


title: DH51_pre_nonTfh

value: pre


title: Plate1_L11


title: glioma, R31


title: glioma, R30


title: DH51_pre_nonfCD8


title: Plate1_L13


title: Plate1_L12


title: Plate1_L14


title: DH51_pre_fCD8


title: glioma, R98_S14


title: DH51_pre_GCTfh


title: Plate1_L15


title: glioma, R99_S15


title: Plate1_L16


title: Plate1_L17


title: Plate1_L09


title: Plate1_L18


title: Plate1_L10


title: Plate1_L19


title: glioma, R97_S13


title: Plate1_L21


title: DH51_pre_CD8EM

value: CD8+ effector mem.


title: glioma, R96_S12


title: Plate1_L22

value: iPSC-Cardiomyocytes


title: DH51_pre_CD8CM


title: glioma, R95_S11


title: glioma, R94_S10


title: DH51_pre_CD8


title: Plate1_M03


title: Plate1_L23


title: Plate1_M04


title: DH51_pre_CD4NA

value: CD4+ naive


title: glioma, R93_S9


title: Plate1_M02


title: DH51_pre_CD8NA


title: glioma, R92_S8


title: Plate1_M07


title: DH51_pre_CD4MEM

value: CD4+ mem.


title: Plate1_L20


title: glioma, R91_S7


title: DH51_D14_nonTfh

value: non-Tfh


title: Plate1_M09


title: Plate1_M06


title: glioma, R90_S6


title: Plate1_M11


title: Plate1_M10


title: Plate1_M08


title: Plate1_M13


title: DH51_D14_nonfCD8


title: Plate1_M15


title: glioma, R88_S4


title: Plate1_M14


title: Plate1_M17


title: glioma, R87_S3


title: DH51_D14_GCTfh


title: Plate1_M16


title: Plate1_M19


title: DH51_pre_CD4


title: glioma, R86_S2


title: DH51_D14_CD8EM


title: Plate1_M21


title: glioma, R85_S1


title: Plate1_M20


title: Plate1_M12


title: Plate1_M22


title: Plate1_M23


title: Plate1_H15


title: DH51_D14_CD8


title: glioma, R89_S5


title: Plate1_H16


title: glioma, R29


title: DH51_D14_CD4NA


title: Plate1_M18


title: Plate1_H18


title: Plate1_H17


title: Plate1_H19


title: DH51_D14_fCD8


title: DH51_D14_CD8NA


title: glioma, R28


title: Plate1_H20


title: DH51_D14_CD4


title: Plate1_H21


title: Plate1_H22


title: DH51_D14_CD8CM


title: glioma, R26


title: glioma, R8


title: DH41_wk8_nonTfh

value: DEL bNAb Tx


title: Plate1_H23


title: DH51_D14_CD4MEM


title: Plate1_I02


title: glioma, R25


title: Plate1_M05


title: Plate1_I03


title: glioma, R24


title: DH41_wk8_nonfCD8


title: glioma, R23


title: Plate1_I05


title: Plate1_I08

value: Formetanate hydrochloride_10_uM


title: DH41_wk8_GCTfh

value: GCTfh


title: Plate1_I09


title: DH41_wk8_CD8NA


title: Plate1_I10


title: Plate1_I07


title: Plate1_I06


title: Plate1_I11


title: glioma, R27


title: Plate1_I12


title: DH41_wk8_fCD8


title: Plate1_I15


title: Plate1_I04


title: glioma, R19


title: DH41_wk8_CD8EM


title: glioma, R21


title: glioma, R20


title: Plate1_I13


title: DH41_wk8_CD8CM

value: CD8+ central mem.


title: Plate1_I14


title: glioma, R2


title: Plate1_I22


title: DH41_wk8_CD4


title: glioma, R16


title: DH41_pre_nonTfh


title: Plate1_I16


title: DH41_wk8_CD8


title: Plate1_I17


title: DH41_wk8_CD4NA


title: glioma, R22


title: Plate1_I18


title: glioma, R18


title: DH41_wk8_CD4MEM


title: Plate1_I20


title: glioma, R17


title: Plate1_I21


title: Plate1_J07


title: Plate1_I19


title: Plate1_I23


title: Plate1_J02


title: DH41_pre_fCD8


title: glioma, R15


title: Plate1_J08

value: Formetanate hydrochloride_1_uM


title: glioma, R146_S34


title: Plate1_J09


title: Plate1_J03


title: DH41_pre_CD8NA

value: CD8+ naive


title: Plate1_J04


title: Plate1_J10


title: glioma, R148_S36


title: DH41_pre_GCTfh


title: DH41_pre_nonfCD8


title: Plate1_J11


title: glioma, R147_S35


title: Plate1_J05


title: Plate1_J06


title: glioma, R143_S31


title: Plate1_J13


title: Plate1_J15


title: glioma, R142_S30


title: Plate1_J18


title: glioma, R145_S33


title: glioma, R141_S29


title: DH41_pre_CD4MEM


title: Plate1_J12


title: glioma, R144_S32


title: glioma, R140_S28


title: glioma, R14


title: DH41_D14_nonfCD8


title: Plate1_J23


title: Plate1_J14


title: DH41_pre_CD8CM


title: Plate1_K03


title: Plate1_J22


title: DH41_pre_CD4


title: Plate1_K04


title: DH41_pre_CD8


title: glioma, R139_S27


title: Plate1_J17


title: DH41_pre_CD4NA


title: Plate1_J16


title: glioma, R137_S25


title: glioma, R136_S24


title: Plate1_E10


title: Plate1_J20


title: Plate1_K02


title: DH41_pre_CD8EM


title: glioma, R135_S23


title: Plate1_E14


title: glioma, R138_S26


title: DH41_D14_CD8CM


title: Plate1_E16


title: Plate1_K05


title: glioma, R133_S21


title: Plate1_E17


title: Plate1_E18


title: DH41_D14_GCTfh


title: Plate1_E09


title: Plate1_E08

value: Formetanate hydrochloride_0.2_uM


title: Plate1_J19


title: Plate1_J21


title: DH41_D14_nonTfh


title: DH41_D14_CD4NA


title: DH41_D14_fCD8


title: Plate1_E11


title: glioma, R131_S19


title: Plate1_E12


title: DH41_D14_CD8NA


title: Plate1_E13


title: glioma, R130_S18


title: DH41_D14_CD8EM


title: glioma, R134_S22


title: DH41_D14_CD4


title: Plate1_E15


title: Plate1_F03


title: DH41_D14_CD8

value: total CD8+


title: DH28_wk8_nonTfh

value: UnTx


title: glioma, R132_S20

value: glioma


title: DH28_wk8_nonfCD8

value: lymph node


title: Plate1_F05


title: Plate1_E20


title: Plate1_E19


title: DH28_wk8_GCTfh


title: Plate1_E21


title: Plate1_F07


title: DH41_D14_CD4MEM


title: Plate1_E22


title: glioma, R13


title: Plate1_F02


title: Plate1_F04


title: glioma, R129_S17


title: glioma, R126_S14


title: glioma, R127_S15


title: Plate1_F06


title: glioma, R128_S16


title: glioma, R125_S13


title: Plate1_F08


title: Plate1_E23


title: Plate1_F09


title: Plate1_F10


title: DH28_wk8_CD8NA


title: glioma, R124_S12


title: Plate1_F14


title: DH28_wk8_CD8EM


title: Plate1_F13


title: Plate1_F15


title: DH28_wk8_CD8CM


title: Plate1_F16


title: glioma, R122_S10


title: glioma, R123_S11


title: Plate1_F12


title: DH28_wk8_fCD8


title: Plate1_F17


title: DH28_wk8_CD8


title: Plate1_F18


title: Plate1_F19


title: Plate1_F23


title: Plate1_G02


title: DH28_wk8_CD4NA


title: Plate1_F20


title: Plate1_F11


title: DH28_wk8_CD4

value: total CD4+


title: Plate1_F21


title: Plate1_F22


title: glioma, R121_S9


title: Plate1_G03


title: glioma, R120_S8


title: DH28_pre_nonfCD8

value: pre


title: glioma, R12


title: DH28_wk8_CD4MEM


title: glioma, R119_S7


title: DH28_pre_nonTfh


title: Plate1_G06

value: iPSC-Cardiomyocytes


title: Plate1_G05


title: Plate1_G09


title: glioma, R118_S6


title: Plate1_G07


title: DH28_pre_GCTfh


title: glioma, R116_S4


title: glioma, R117_S5


title: DH28_pre_CD8NA


title: Plate1_G13


title: Plate1_G11


title: DH28_pre_fCD8


title: Plate1_G10


title: Plate1_G04


title: Plate1_G12


title: glioma, R113_S1


title: glioma, R115_S3


title: DH28_pre_CD8


title: Plate1_G14


title: DH28_pre_CD8EM

value: CD8+ effector mem.


title: Plate1_G18


title: glioma, R114_S2


title: Plate1_G20


title: Plate1_G19


title: Plate1_G15


title: DH28_pre_CD8CM


title: Plate1_G16


title: Plate1_G23


title: Plate1_G08


title: Plate1_G17


title: Plate1_H02


title: DH28_pre_CD4


title: glioma, R112_S28


title: DH28_pre_CD4NA

value: CD4+ naive


title: Plate1_H05


title: glioma, R108_S24


title: Plate1_H06


title: DH28_pre_CD4MEM

value: CD4+ mem.


title: Plate1_H07


title: Plate1_G21


title: glioma, R107_S23


title: glioma, R110_S26


title: Plate1_H08


title: glioma, R111_S27


title: Plate1_G22


title: Plate1_H03


title: glioma, R11


title: glioma, R106_S22


title: Plate1_H04


title: glioma, R105_S21


title: DH28_D14_nonTfh

value: non-Tfh


title: glioma, R109_S25


title: glioma, R104_S20


title: DH28_D14_nonfCD8


title: DH28_D14_GCTfh


title: glioma, R103_S19


title: Plate1_H09


title: glioma, R102_S18


title: Plate1_B05


title: Plate1_H10


title: DH28_D14_fCD8


title: Plate1_H11


title: glioma, R101_S17


title: Plate1_H12


title: Plate1_B08


title: Plate1_H13


title: DH28_D14_CD8EM


title: Plate1_B09


title: DH28_D14_CD8NA


title: Plate1_H14


title: glioma, R100_S16


title: DH28_D14_CD4


title: Plate1_B03


title: glioma, R10


title: Plate1_B04


title: DH28_D14_CD8


title: Plate1_B02


title: Plate1_B13


title: Plate1_B06


title: DGX4_wk8_nonTfh

value: WT bNAb Tx


title: Plate1_B07


title: Plate1_B10


title: Plate1_B14


title: DH28_D14_CD8CM


title: DH28_D14_CD4MEM


title: DGX4_wk8_GCTfh

value: GCTfh


title: Plate1_B12


title: glioma, R1


title: DH28_D14_CD4NA


title: Plate1_B17


title: Plate1_B21


title: D-xyl@epsilonPLCDs [cell line]

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp software.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the FPKM method.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCh38.p13
Supplementary files format and content: Excel files include RAW counts for each sample.
Supplementary files format and content: Excel files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted from the cells using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bladder epithelial carcinoma cells


title: DGX4_wk8_nonfCD8


title: DGX4_wk8_CD8EM


title: epsilonPLCDs [cell line]

value: epsilonPLCDs


title: Plate1_B11


title: Plate1_B22


title: Plate1_B19


title: Plate1_B18


title: Plate1_B20


title: Control [cell line]

value: Control


title: DGX4_wk8_CD8NA

value: CD8+ naive


title: 70Q/70Q d49 cerebral organoids, rep1

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.6.0c
Reads counted on GENCODE release 27 gene models using htseq-count 0.9.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns

extract_protocol:
Total RNA was extracted using the Qiagen isolation kit
rRNA-depleted RNA was fragmented and processed into strand-specific cDNA libraries using TruSeq Stranded Total LT Sample Prep Kit (Illumina)

value: cerebral organoids


title: Plate1_B16


title: 70Q/70Q d49 cerebral organoids, rep2


title: Plate1_C04


title: DGX4_wk8_fCD8


title: Plate1_B23


title: Plate1_C02


title: Plate1_C06


title: Plate1_B15


title: 70Q/70Q d28 cerebral organoids, rep3


title: DGX4_wk8_CD8CM

value: CD8+ central mem.


title: PNF4 P4 corin 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
STAR (version 2.7.9a) was used to align sequence reads to human genome build hg38.
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.32.0).
Assembly: hg38
Supplementary files format and content: counts.txt: 60646 x 28 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 60646 x 28 matrix of variance-stabilizing-transformed (VST) expression values

growth_protocol: All cell lines and primary cells were cultured in Dulbecco’s modified eagle medium (DMEM) (ThermoFisher Scientific) with 10% fetal bovine serum (FBS) (ThermoFisher Scientific), 1% 100X L-glutamine (L-glut) (ThermoFisher Scientific), and 1% Penicillin-Streptomycin (P/S) (ThermoFisher Scientific) at 37 °C under 5% CO₂.

extract_protocol:
RNeasy® Plus Mini Kit (Qiagen, Germany) was used to isolate RNA following the manufacturer’s protocol. Once RNA isolation was complete, the RNA concentration was calculated using the NanoDrop™ (NanoDrop 2000 Spectrophotometer, ThermoScientific).
100 nanograms of total RNA from each sample was enriched for polyadenylated RNA and prepared for next-generation sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) according to the manufacturer’s instructions.

treatment_protocol: Fibroblasts were treated with 1 microm of corin and DMSO as a control for 24 hours.

value: normal

tag: passage

value: corin


title: Plate1_C03


title: 70Q/70Q d49 cerebral organoids, rep3


title: DGX4_wk8_CD8

value: lymph node

value: total CD8+


title: Plate1_C05

value: iPSC-Cardiomyocytes


title: PNF4 P4 DMSO 2

value: DMSO


title: DGX4_wk8_CD4MEM


title: 70Q/70Q d28 cerebral organoids, rep1


title: Plate1_C08

value: Formetanate hydrochloride_10_uM


title: DGX4_wk8_CD4

value: total CD4+


title: 70Q/70Q NPC, rep3

value: NPC


title: PNF4 P3 corin 1


title: PNF4 P3 DMSO 1


title: DGX4_pre_nonTfh

value: non-Tfh

value: WT bNAb Tx

value: pre


title: Plate1_C09


title: Plate1_C10


title: DGX4_pre_nonfCD8


title: DGX4_wk8_CD4NA

value: CD4+ naive


title: PK4 P2 corin 2

value: keloid


title: 70Q/70Q NPC, rep2


title: DGX4_pre_GCTfh

value: GCTfh


title: 70Q/70Q d28 cerebral organoids, rep2

value: cerebral organoids


title: Plate1_C11


title: Plate1_C12


title: DGX4_pre_fCD8


title: Plate1_C07


title: PK4 P2 corin 1


title: 70Q/70Q iPSC, rep2

value: hiPSC


title: 70Q/70Q iPSC, rep1


title: PK4 P2 DMSO 2


title: DGX4_pre_CD8EM

value: CD8+ effector mem.


title: DGX4_pre_CD8NA

value: CD8+ naive


title: PK3 P4 corin 2

value: corin


title: WT/WT d49 cerebral organoids, rep3

value: WT/WT


title: Plate1_C14

value: iPSC-Cardiomyocytes


title: Plate1_C15


title: DGX4_pre_CD8CM

value: lymph node

value: CD8+ central mem.


title: PK3 P4 DMSO 2

value: DMSO


title: 70Q/70Q iPSC, rep3


title: WT/WT d49 cerebral organoids, rep2


title: PK4 P2 DMSO 1


title: DGX4_pre_CD8

value: total CD8+


title: PK3 P3 corin 1


title: Plate1_C13


title: Plate1_C16


title: Plate1_C17


title: 70Q/70Q NPC, rep1

value: NPC


title: PK3 P3 DMSO 1


title: PK2 P4 corin 2


title: WT/WT d28 cerebral organoids, rep3


title: WT/WT d28 cerebral organoids, rep2


title: DGX4_pre_CD4NA

value: WT bNAb Tx


title: DGX4_pre_CD4

value: total CD4+

value: pre


title: WT/WT d49 cerebral organoids, rep1


title: DGX4_pre_CD4MEM

value: CD4+ mem.


title: Plate1_C18


title: Plate1_C19


title: PK2 P4 DMSO 2

value: keloid


title: Plate1_C20


title: WT/WT NPC, rep3


title: DGX4_D14_nonTfh

value: non-Tfh


title: Plate1_C21


title: PK2 P8 corin 1


title: DGX4_D14_nonfCD8


title: PK2 P8 DMSO 1


title: Plate1_C22


title: WT/WT NPC, rep2


title: PK1 P7 corin 2


title: DGX4_D14_GCTfh

value: GCTfh


title: DGX4_D14_fCD8


title: WT/WT NPC, rep1


title: Plate1_D02


title: WT/WT iPSC, rep3

value: iPS


title: PK1 P7 DMSO 2


title: WT/WT iPSC, rep2


title: DGX4_D14_CD8NA

value: CD8+ naive


title: CRL-1762 P4 corin 2

value: corin


title: DGX4_D14_CD8EM

value: CD8+ effector mem.


title: PK1 P7 corin 1


title: PK1 P7 DMSO 1


title: WT/WT d28 cerebral organoids, rep1

value: cerebral organoids

value: WT/WT


title: DGX4_D14_CD8CM

value: lymph node

value: CD8+ central mem.


title: Plate1_D04

value: iPSC-Cardiomyocytes


title: Plate1_D03


title: Plate1_D05


title: WT/WT iPSC, rep1


title: CRL-1762 P4 DMSO 2

value: DMSO


title: DGX4_D14_CD8

value: total CD8+

value: WT bNAb Tx


title: MDA-MB-231 cells, UBIAD1OE, Replicate 4

city: Padova

first: Giovanni

last: Tosi

state: Padova

address: Via Ugo Bassi 58/B

country: Italy

institute: University of Padova

data_processing:
The raw data were analyzed by Next Generation Diagnostic srl proprietary NEGEDIA Digital mRNA-seq pipeline (v2.0) which involves a cleaning step by quality filtering and trimming, alignment to the reference genome, and counting by gene
The raw expression data were normalized, analyzed, and visualized by Rosalind HyperScale architecture (OnRamp BioInformatics, Inc.)
Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library
Assembly: GRCh38
Supplementary files format and content: Extension txt.gz; tab-delimited text files including Ensembl_transcript_ids and read count for each sample
Supplementary files format and content: Extension txt; tab-delimitaed text file including Symbol, GeneID, Alias, Description, ensembl_gene_id, ensembl_peptide_ids, ensembl_transcript_ids, Normalized reads count for each sample, baseMean, log2FoldChange, pvalue, padj comparing all UBIAD1OE samples vs Scramble samples

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 cells were maintained in DMEM, high glucose, GlutaMAX™ Supplement, pyruvate supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted according to TRIzol™ Reagent manufacturer’s instructions. 1μL of DNase I (Thermo Fisher Scientific, Cat. #18068015) was used for every 1μg of isolated RNA to digest any remaining genomic DNA. After DNase I inactivation, RNA Clean & Concentrator-5 kit (Euroclone, Cat. #R1015) was used to purify the RNA samples. RNA concentration and purity were determined using a NanoDrop spectrophotometer at A260 and A280/260, respectively, while integrity was verified by Tapestation System (AGILENT). Only samples with RIN > 8 were used for the following RNA-seq analysis.
For library preparation, total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl) which included library preparation, quality assessment, and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).

value: Breast; Mammary gland

value: MDA-MB-231 (ATCC #HTB-26)

value: epithelial cell

tag: disease

value: Metastatic adenocarcinoma

tag: Sex

value: Female

value: UBIAD1 overexpression


title: DGX4_D14_CD4NA

value: CD4+ naive


title: Plate1_D06


title: MDA-MB-231 cells, UBIAD1OE, Replicate 2


title: Plate1_C23


title: Plate1_D08

value: Formetanate hydrochloride_1_uM


title: Plate1_D07


title: CRL-1762 P4 corin 1

value: keloid

value: corin


title: DGX4_D14_CD4MEM

value: CD4+ mem.


title: CRL-1762 P4 DMSO 1


title: PCS-201-021 P4 corin 2

value: normal


title: MDA-MB-231 cells, Scramble, Replicate 4

value: WT


title: DGX4_D14_CD4

value: lymph node

value: total CD4+


title: MDA-MB-231 cells, UBIAD1OE, Replicate 1


title: Plate1_D10

value: iPSC-Cardiomyocytes


title: Plate1_D09


title: DGX0_wk8_nonTfh

value: non-Tfh

value: DEL bNAb Tx


title: PCS-201-021 P4 DMSO 2

value: DMSO


title: MDA-MB-231 cells, Scramble, Replicate 2

value: Breast; Mammary gland

value: MDA-MB-231 (ATCC #HTB-26)

value: epithelial cell


title: MDA-MB-231 cells, UBIAD1OE, Replicate 3

value: Metastatic adenocarcinoma

value: Female

value: UBIAD1 overexpression


title: MDA-MB-231 cells, Scramble, Replicate 3


title: DGX0_wk8_nonfCD8


title: DGX0_wk8_fCD8


title: PCS-201-021 P5 corin 1


title: DGX0_wk8_GCTfh

value: GCTfh


title: PCS-201-021 P5 DMSO 1


title: Plate1_D11


title: MDA-MB-231 cells, Scramble, Replicate 1


title: DGX0_wk8_CD8NA

value: CD8+ naive


title: RNA-Seq ER_SiPax5_3

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 instrument producing 50 bp pairedend reads running Control Software 1.7.0
The sequenced reads were controlled for quality of sequencing with FastQC and trimmed using Trim_Galore.
Trimmed reads were aligned to the reference genome using the STAR aligner version 2.7.0f
RNA abundance was estimated with featureCounts from the Subread package version 1.6.3
Normalization of counts and differential expression analysis were performed with the DESEQ2 R package version 1.26.0
Assembly: GRCh38/hg38
Supplementary files format and content: DESeq2 normalized matrix of counts

source_name: Human prostate cancer cell line

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Library preparation has been done with 770 ng of input RNA using: NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310)) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 (NEB# E6440)

value: Human prostate cancer cell line

value: Neuroendocrine like

value: Pax5 knockdown


title: RNA-Seq ER_SiPax5_2


title: IgG_E145_2_R3

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
NF-Core CUT&RUN pipeline v3.1
Adapter trimming with Trim-Galore
Genome alignment Bowtie2
Deduplication with Picard Mark_Duplicates where applicaple
Deeptools bamCoverage for bigWig files
Assembly: GRCm38
Supplementary files format and content: BigWig read coverage

molecule: genomic DNA

source_name: testis from ebryonic day 14.5

growth_protocol: Embryonic testis obtained from timed matings using the B6;129S4-Pou5f1tm2Jae/J mouse line (Oct4-EGFP). Presence of the vaginal plug was considered E0.5.

extract_protocol:
Chromatin profilling was performed by CUT&TAG and genomic DNA was extracted using the DNA Clean & Concentrator-5 (Zymo).
Libraries were constructed from genomic DNA by indexing PCR amplification, followed by size-exclusion cleanup with AMPure XP beads and quality control on a Tapestation device.
Libraries constructed with 16 cycles of amplification while incorporating unique dual indexes.

treatment_protocol: Embryonic testes were dissected in PBS and digested into a single cells supention using sequential collagenase and trypsin treatments at 37°C. Cells were washed in PBS and isolated by FACS based on the presence of GFP.

value: testis from ebryonic day 14.5

value: germ cells, prospermatogonia

value: wild type

tag: antibody

value: IgG


title: Plate1_D13

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
the following steps were undertaken to filter out low-count genes and samples across the entire dataset: 1) Genes with fewer than 10 mean counts across all samples (n = 4558) were excluded, 2) Samples with an average expression across all genes lower than 15 were also removed. Principal component analysis (PCA) was conducted on vehicle controls from all samples across 16 plates to assess potential plate effects. Outliers in vehicle control samples were identified and excluded using a mean correlation threshold of <0.85, ensuring the reliability of the subsequent transcriptomic dose-response and differential expression analyses.
Assembly: Whole transcriptome assay
Supplementary files format and content: with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: meta data of the QC samples

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

value: iPSC-Cardiomyocytes


title: Plate1_D14


title: DGX0_wk8_CD8EM

value: lymph node

value: CD8+ effector mem.

value: DEL bNAb Tx


title: IgG_E145_2_R2


title: IgG_E145_2_R1


title: Plate1_D16


title: Plate1_D15


title: Plate1_D12


title: RNA-Seq ER_scr3

value: control


title: DGX0_wk8_CD8CM

value: CD8+ central mem.


title: IgG_E145_R2


title: Plate1_D17


title: RNA-Seq ER_scr2


title: DGX0_wk8_CD8

value: total CD8+


title: DGX0_wk8_CD4NA

value: CD4+ naive


title: IgG_E145_R1


title: RNA-Seq ER_scr1


title: DGX0_wk8_CD4MEM

value: CD4+ mem.


title: SPIN1_E145_2_R3


title: Plate1_D18


title: RNA-Seq DKD_siPax5_3


title: DGX0_wk8_CD4

value: total CD4+


title: SPIN1_E145_R2


title: RNA-Seq ER_SiPax5_1

value: Human prostate cancer cell line


title: DGX0_pre_nonTfh

value: non-Tfh

value: pre


title: RNA-Seq DKD_siPax5_1

value: Neuroendocrine like

value: Pax5 knockdown


title: IgG_E145_R3

value: testis from ebryonic day 14.5

value: germ cells, prospermatogonia

value: wild type


title: Plate1_D20

value: iPSC-Cardiomyocytes


title: Plate1_D21


title: SPIN1_E145_R1


title: H3K9me3_E145_2_R2


title: DGX0_pre_nonfCD8

value: lymph node


title: Plate1_D22


title: H3K9me3_E145_2_R1


title: DGX0_pre_GCTfh

value: GCTfh

value: DEL bNAb Tx


title: Plate1_D23


title: H3K4me3_E145_2_R2


title: DGX0_pre_fCD8


title: RNA-Seq DKD_scr2

value: control


title: H3K4me3_E145_2_R1


title: Plate1_E02


title: DGX0_pre_CD8NA

value: CD8+ naive


title: RNA-Seq DKD_scr1


title: RNA-Seq C4-2BER-3

value: Wild type

value: Enzalutamide Resistance


title: RNA-Seq DKD_siPax5_2


title: Plate1_D19


title: GBM-07_CO

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Fresh glioma samplels were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3, 10x Genomics).

value: glioma


title: RNA-Seq C4-2BER-2

value: Human prostate cancer cell line


title: DGX0_pre_CD8EM

value: CD8+ effector mem.


title: Plate1_E04


title: Plate1_E05


title: RNA-Seq C4-2BER-1


title: GBM-06_CO

description: 10x Genomics


title: DGX0_pre_CD8CM

value: CD8+ central mem.

value: pre


title: DGX0_pre_CD8

value: total CD8+


title: DGX0_pre_CD4NA

value: CD4+ naive


title: RNA-Seq DKD_scr3

value: Neuroendocrine like


title: RNA-Seq C4-2B-2

value: Adenocarcinoma


title: GBM-05_LE

description: 10x Genomics


title: Plate1_E03

value: iPSC-Cardiomyocytes


title: OG-03_LE

description: 10x Genomics


title: DGX0_pre_CD4MEM

value: lymph node

value: CD4+ mem.


title: Plate1_E07


title: DGX0_pre_CD4

value: total CD4+

value: DEL bNAb Tx


title: RNA-Seq C4-2B-1


title: OG-02_CO

description: 10x Genomics


title: 13_C42B_Input_S5

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Resulting fastq files were aligned to the human genome (hg38) using the sequence aligner Bowtie2 (version 2.2.3).
Picard routine MarkDuplicates (http://broadinstitute.github.io/picard/ [broadinstitute.github.io]) was used to remove sequence duplications.
Peak calling, of ChIP enriched regions the THOR peak caller software of each ChIP to corresponding input DNA sample was used to determine binding regions based on a FDR adjusted p-value (q-value) <0.05.
BigWig files were generated using the resulting bam files and deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/ [deeptools.readthedocs.io]).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: cell line

extract_protocol:
Disuccinimidyl glutarate (DSG) was used at a final concentration of 2mM and incubated for 45 minutes at room temperature. At the end of fixation, cells were centrifuge at 1500 rpm for 10 minutes. The pellete was washed in PBS for 3 times and the treated with 1% formaldehyde for 10mins at room temperature.  After quenching and cell lysis, chromatin was sonicated using a Bioraptor (Diagenode)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: cell line

value: Human prostate adenocarcinoma


title: 14_C42BER-Input_S7

value: Human prostate Neuroendocrine like cells


title: DGX0_D14_nonTfh

value: non-Tfh


title: MT529_64_4_D10CNCC_ATAC_rep2

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

data_processing:
ATAC-seq data were aligned to hg19 using BWA-mem. Mapped reads were offset by +4 bp for the forward strand and -5bp for the reverse strand. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq
Supplementary files format and content: peak files for ChIP-seq and ATAC-seq

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factoer Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR1 medium in small clusters

extract_protocol: Barcoded libraries were made with the Illumina Tagment DNA Enzyme and Buffer Kit and amplified. A qPCR side reaction was performed to quantify the PCR cycle number for fully amplified DNA and purified via AMPure XP beads

treatment_protocol: iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days. After 14 full days of CNCC specification, the cells were maintained in an “early CNCC” state for up to 21 days for subsequent experiments, or immediately transitioned to CNCC late maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, 20 ng/ml EGF, 20 ng/ml hFGF, 3uM ChIRON 99021, and 50ng/mL BMP2.

value: day 10 cranial neural crest cell

value: cranial neural crest cell specification


title: DGX0_D14_nonfCD8


title: MT528_64_9_D10CNCC_ATAC_rep2


title: 8_C42BERH3K27Ac_S4

tag: chip antibody

value: Cell Signaling, 8173


title: RNA-Seq C4-2B-3

value: Human prostate cancer cell line

value: Wild type


title: Plate1_E06

source_name: iPSC-Cardiomyocytes


title: OG-03_CO

description: 10x Genomics

value: glioma


title: 7_C42BERH3K27Ac_S3


title: DGX0_D14_GCTfh

value: GCTfh


title: MT526_SV20_D10CNCC_ATAC_rep2

source_name: SV20 (CTRL1)

value: SV20 (CTRL1)


title: 6_C42B_H3K27Ac_S2


title: MT527_81_2_D10CNCC_ATAC_rep2


title: DGX0_D14_fCD8


title: DGX0_D14_CD8NA

value: CD8+ naive


title: 5_C42B_H3K27Ac_S1


title: MT497_64_4_D10CNCC_ATAC_rep1


title: DGX0_D14_CD8EM

value: lymph node

value: CD8+ effector mem.


title: MT496_64_9_D10CNCC_ATAC_rep1


title: 4_C4-2BERH3K18Ac_S4

value: Cell Signaling, 13998S


title: DGX0_D14_CD8CM

value: CD8+ central mem.

value: DEL bNAb Tx


title: 3_C4-2BERH3K18Ac_S3

value: cell line


title: 2_C4-2BH3K18Ac_S2

value: Human prostate adenocarcinoma


title: DGX0_D14_CD4NA

value: CD4+ naive


title: MT494_SV20_D10CNCC_ATAC_rep1

value: day 10 cranial neural crest cell


title: 1_C4-2BH3K18Ac_S1


title: DGX0_D14_CD4MEM

value: CD4+ mem.


title: ATAC-Seq C4-2B_Enza_Resist-2

data_processing:
ATAC-Seq libraries were sequenced in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq 6000, running NovaSeq Control Software version 1.6.0.
Quality control of sequencing reads was performed using FastQC.
Reads were aligned to the reference genome (hg38) obtained from the UCSC genome browser using Bowtie2.
Samples were filtered for regions blacklisted by the ENCODE project and deduplicated using Picard tool.
Alignment coordinates were converted to BED format using BEDTools v.2.17.
Peak calling was performed using MACS2 with customized parameters for ATAC-Seq data.
Assembly: hg38

extract_protocol:
Cells were centrifuged at 500g before nuclei extraction. Nuclei isolation was performed on an iodixanol gradient and then counted using trypan blue using a TC20 automated cell counter (Biorad). 50.000 counted nuclei were transferred to fresh tubes and were centrifuged at 500g before proceeding with the transposition reaction. Isolated nuclei were lysed and transposed for 30 minutes at 37°c using the prokaryotic Tn5 transposase system (Nextera DNA library kit, Illumina, FC-121–1030). Transposed DNA was then purified on Diapure columns (Diagenode, C03040001). The nuclei preparations were prepared using the above mentioned protocol (refer to material and methods) on the « test samples ». Two isolation conditions were tested: 0.1% Igepal CA-630, 0.1% Tween 20 for 0 or 3 min. The nuclei preparation was evaluated by visualization under the microscope (AE2000; Matic).
The ATAC-seq library preparation has been conducted by Diagenode ATAC-seq Profiling service (Diagenode Cat# G02060000). Libraries were prepared from purified transposed DNA using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) and Illumina indexing primers. The number of library amplification cycles was determined by qPCR analysis using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) on LightCycler® 96 System (Roche). After their amplification, the libraries were size selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analysed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.).

value: Human prostate Neuroendocrine like cells


title: MT764_64_4_D10CNCC_Dec2023_noEGS_ChIP_input

data_processing:
ChIP-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq
Supplementary files format and content: peak files for ChIP-seq and ATAC-seq

extract_protocol: Barcoded libraries were made with NEBNext UltraII DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq2000, producing 138 single-end reads

value: cranial neural crest cell specification


title: EG_FCS_1_p11

type: RNA

first: Kirsten

middle: R

last: McEwen

address: Du Cane Road

department: MRC Clinical Sciences Centre

hyb_protocol: 100 ng of total RNA was processed using the Ambion WT Expression kit and Affymetrix GeneChip WT Terminal Labelling and Hybridisation kit.

scan_protocol: The GeneChip scanner was used to scan all micorarrays.

data_processing: Data was preprocessed in R using robust multiarray averaging, variance stabilising transformation and Combat batch correction.

label: Biotin

source_name: Embryonic germ cells, FCS line 1, passage 11

growth_protocol: Serum culture conditions contain 15% FCS, 0.1 mM MEM nonessential amino acids, 2 mM l-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol and 1000 U/mL LIF in DMEM-F12 with maintenance on a mouse embryonic fibroblast (MEF) feeder layer. 2i culture conditions contain 1 μM PD0325901, 3 μM CHIR99021 and 1000 U/mL LIF in N2B27 medium, maintained on laminin (10 μg/ml). Cells were incubated at 5% CO2, 95% relative humidity.

extract_protocol: RNA (100 ng) was isolated using the Qiagen RNeasy Mini kit.

value: Female

tag: batch


title: DGX0_D14_CD4

value: total CD4+


title: EG_2is_3_p14

source_name: Embryonic germ cells, 2i line 3, passage 14

label_protocol: 100 ng of total RNA was processed using the Ambion WT Expression kit and Affymetrix GeneChip WT Terminal Labelling and Hybridisation kit.


title: EG_2is_1_p14

source_name: Embryonic germ cells, 2i line 1, passage 14

value: Male


title: MT763_64_9_D10CNCC_Dec2023_noEGS_ChIP_input


title: MT762_81_2_D10CNCC_Dec2023_noEGS_ChIP_input


title: DGX0_D14_CD8

value: total CD8+


title: ATAC-Seq C4-2B_Enza_Resist-1


title: EG_FCS_2_p11

source_name: Embryonic germ cells, FCS line 2, passage 11


title: MT761_SV20_D10CNCC_Dec2023_noEGS_ChIP_input

value: SV20 (CTRL1)


title: MT495_81_2_D10CNCC_ATAC_rep1


title: EG_2is_3_p17

source_name: Embryonic germ cells, 2i line 3, passage 17


title: EG_FCS_2_p17

source_name: Embryonic germ cells, FCS line 2, passage 17


title: DGM4_wk8_nonTfh

value: lymph node

value: non-Tfh

value: UnTx


title: EG_2is_1_p11

source_name: Embryonic germ cells, 2i line 1, passage 11


title: ATAC-Seq C4-2B-2


title: MT597_64_9_D10CNCC_INPUT_noEGS


title: MT598_64_4_D10CNCC_INPUT_noEGS


title: ATAC-Seq C4-2B-1


title: MT596_81_2_D10CNCC_INPUT_noEGS


title: EG_FCS_1_p17

source_name: Embryonic germ cells, FCS line 1, passage 17


title: DGM4_wk8_fCD8

source_name: lymph node


title: MT595_SV20_D10CNCC_INPUT_noEGS


title: DGM4_wk8_GCTfh

value: GCTfh


title: DLD1_LA_3

first: Hua-shan

last: Liu

state: Guangdong

address: 26 Yuancun Erheng Road

department: Department of Colorectal Surgery

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
HTseq0.11.3  was used to calculate the counts of the genes
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
The culture medium were removed, washed with PBS for 3 times, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human CRC cells

tag: disease state

value: colorectal cancer

value: With lactate treatment


title: DLD1_LA_2


title: EG_2is_1_p17

source_name: Embryonic germ cells, 2i line 1, passage 17


title: DGM4_wk8_CD8EM

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10, build NCBI:GCA_003339765.3) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10
Supplementary files format and content: raw gene count file

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on NovaSeq 6000 (Illumina).

value: CD8+ effector mem.


title: DGM4_wk8_nonfCD8


title: DGM4_wk8_CD8NA

value: CD8+ naive


title: DLD1_LA_1


title: MT456_64_4_D10CNCC_H3K27ac_ChIP_rep1_R1

value: H3K27ac abcam ab4729

value: day 10 cranial neural crest cell


title: EG_FCS_3_p14

source_name: Embryonic germ cells, FCS line 3, passage 14


title: EG_2is_2_p17

source_name: Embryonic germ cells, 2i line 2, passage 17


title: DLD1_NC_3

value: Without lactate treatment


title: EG_FCS_2_p14

source_name: Embryonic germ cells, FCS line 2, passage 14


title: DGM4_wk8_CD8CM

value: CD8+ central mem.


title: MT455_64_9_D10CNCC_H3K27ac_ChIP_rep1_R1

value: cranial neural crest cell specification


title: DLD1_NC_2


title: EG_FCS_1_p14

source_name: Embryonic germ cells, FCS line 1, passage 14

value: Female


title: EG_FCS_3_p11

source_name: Embryonic germ cells, FCS line 3, passage 11

value: Male


title: MT454_81_2_D10CNCC_H3K27ac_ChIP_rep1_R1


title: DLD1_NC_1


title: DGM4_wk8_CD8

value: total CD8+


title: EG_2is_2_p14

source_name: Embryonic germ cells, 2i line 2, passage 14


title: EG_2is_2_p11

source_name: Embryonic germ cells, 2i line 2, passage 11


title: EG_2is_3_p11

source_name: Embryonic germ cells, 2i line 3, passage 11


title: DGM4_wk8_CD4NA

value: lymph node

value: CD4+ naive


title: EG_FCS_3_p17

source_name: Embryonic germ cells, FCS line 3, passage 17


title: ES_FCS_4

source_name: Embryonic stem cells, FCS


title: MT453_SV20_D10CNCC_H3K27ac_ChIP_rep1_R1

source_name: SV20 (CTRL1)

value: SV20 (CTRL1)


title: DGM4_wk8_CD4MEM

value: CD4+ mem.

value: UnTx


title: MT760_64_4_D10CNCC_ZIC2_ChIP_rep2

value: ZIC2 abcam ab150404


title: MT759_64_9_D10CNCC_ZIC2_ChIP_rep2


title: SW480_LA_2

value: Human CRC cells

value: colorectal cancer

value: With lactate treatment


title: SW480_LA_1


title: DGM4_wk8_CD4

value: total CD4+


title: DGM4_pre_nonTfh

value: non-Tfh

value: pre


title: SW480_NC_3

value: Without lactate treatment


title: MT612_64_4_D10CNCC_ZIC2_ChIP_rep1

value: day 10 cranial neural crest cell

value: cranial neural crest cell specification


title: DGM4_pre_nonfCD8


title: MT611_64_9_D10CNCC_ZIC2_ChIP_rep1


title: SW480_LA_3


title: SW480_NC_2


title: MT452_64_4_D10CNCC_ARID1A_ChIP_rep1_R1

value: ARID1A Genetex GTX129433


title: SW480_NC_1


title: ES_2i_5

source_name: Embryonic stem cells, 2i

value: Male


title: ES_FCS_5


title: ES_FCS_3

value: Female


title: MT451_64_9_D10CNCC_ARID1A_ChIP_rep1_R1


title: MT450_81_2_D10CNCC_ARID1A_ChIP_rep1_R1


title: DGM4_pre_CD8NA

value: lymph node

value: CD8+ naive


title: DGM4_pre_fCD8


title: HZ9_wk8_pDCs

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10 build 102) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10 build 102
Supplementary files format and content: raw gene count file

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on either a HiSeq 4000 or a NovaSeq 6000 (Illumina).

value: pDCs

value: WT bNAb Tx


title: ES_2i_3


title: HZ9_wk8_NKcells

value: NK cells


title: ES_2i_4


title: DGM4_pre_CD8EM

value: CD8+ effector mem.

value: UnTx


title: ES_FCS_2


title: MT449_SV20_D10CNCC_ARID1A_ChIP_rep1_R1

value: SV20 (CTRL1)


title: EG_FCS_4

source_name: Embryonic germ cells, FCS


title: HZ9_wk8_monocytes

value: monocytes


title: HZ9_wk8_Bcells

value: B cells


title: MT642_64_4_D14CNCC_late_RNA_rep3

data_processing:
RNA-seq data were quanitfied using kallisto. Differential gene expression was determined using DESeq2 in R.
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq
Supplementary files format and content: peak files for ChIP-seq and ATAC-seq

extract_protocol: Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).

treatment_protocol:
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® Ultra II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1μg of total RNA input was used for each library. Libraries were sequenced on Illumina NextSeq2000, producing 138 single-end reads
iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days. After 14 full days of CNCC specification, the cells were maintained in an “early CNCC” state for up to 21 days for subsequent experiments, or immediately transitioned to CNCC late maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, 20 ng/ml EGF, 20 ng/ml hFGF, 3uM ChIRON 99021, and 50ng/mL BMP2.

value: day 14 cranial neural crest cell - late maintenance media


title: DGM4_pre_CD8CM

value: CD8+ central mem.

value: pre


title: EG_FCS_1


title: EG_2i_4

source_name: Embryonic germ cells, 2i


title: DGM4_pre_CD8

value: total CD8+


title: HZ9_pre_pDCs


title: MT641_64_9_D14CNCC_late_RNA_rep3

value: cranial neural crest cell specification


title: HZ9_pre_NKcells


title: MT640_81_2_D14CNCC_late_RNA_rep3


title: DGM4_pre_CD4NA

value: CD4+ naive


title: ES_2i_1

value: Female


title: EG_2is_4


title: HZ9_pre_monocytes

value: lymph node


title: MT639_64_4_D14CNCC_late_RNA_rep2


title: HZ9_pre_Bcells


title: MT637_81_2_D14CNCC_late_RNA_rep2


title: DGM4_D14_nonfCD8


title: MT636_64_4_D14CNCC_late_RNA_rep1


title: DGM4_D14_nonTfh

value: non-Tfh


title: HZ9_D14_monocytes


title: ES_2i_2

value: Male


title: HZ9_D14_Bcells

value: WT bNAb Tx


title: DGM4_D14_GCTfh

value: GCTfh


title: ES_FCS_1


title: EG_FCS_3


title: MT635_64_9_D14CNCC_late_RNA_rep1


title: EG_FCS_2


title: HZ2_wk8_pDCs

value: pDCs

value: Untreated


title: EG_2is_2


title: DGM4_D14_fCD8

value: UnTx


title: DGM4_pre_CD4

value: total CD4+


title: EG_2i_2


title: MT638_64_9_D14CNCC_late_RNA_rep2


title: DGM4_pre_CD4MEM

value: CD4+ mem.


title: MT634_81_2_D14CNCC_late_RNA_rep1

value: day 14 cranial neural crest cell - late maintenance media


title: EG_2i_3


title: DGM4_D14_CD8EM

value: CD8+ effector mem.


title: EG_2i_1


title: MT633_SV20_D14CNCC_late_RNA_rep1

value: SV20 (CTRL1)


title: HZ2_wk8_NKcells

value: NK cells


title: DGM4_D14_CD8NA

value: CD8+ naive


title: HZ9_D14_NKcells


title: HZ2_wk8_monocytes

value: monocytes


title: MT632_64_4_D14CNCC_early_RNA_rep3

value: day 14 cranial neural crest cell - early maintenance media

value: cranial neural crest cell specification


title: MT631_64_9_D14CNCC_early_RNA_rep3


title: CD11bplus_4

first: Haiqing

last: Li

address: 1500 E Durate Rd

data_processing:
To remove the adapter contamination and the artificial methylation due to the end repair reaction, the raw pair-end RRBS reads were trimmed using Trim Galore (v0.6.4) and Cutadapt (v2.7) with default setting. The Read1 sequences were trimmed a 2 bp from their 3' end and Read2 sequences were trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction.
The methylation status and type of each cytosine were analyzed using Bismark methylation extractor (v.22.4) with the default setting. To improve the methylation analysis quality, the first three and the last two bases from 5’ and 3’ ends of Read1, respectively, and the first and last two bases from both ends of Read2 were excluded from the methylation status call. The different methylated sites were analyzed using R methylKit package (v1.20.0). Only the methylation site detected in all samples were included in the different methylation analysis. The different methylation CG site between different treatment samples were detected using methylKit’s getMethylDiff feature with FDR<0.05 and 25% different methylation ratio cutoff. The different methylated CG site was annotated using R Genomation Package (v1.26.0) to identify the gene, gene region (exon, intron, or intergenic), and CpG island it located on.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, Bismark methylation extractor report

source_name: AML

extract_protocol:
Harvest spleen 1 day post last treatment and make single cell suspension, sort GFP+ cells from PBS group and GFP+CD11b- vs GFP+CD11b+ cells from CpG-STAT3dODN group using FACSAria III,  extract DNA using Promega Maxwell RSC Tissue DNA kit.
ChIP-seq libraries were prepared using the Illumina RRBS-seq library prep kit following vendor's protocol.

value: AML

value: CMM

tag: group

value: CpG-STAT3dODN-induced CD11b+ CMM cell subset


title: EG_2is_1

value: Male


title: DGM4_D14_CD8CM

source_name: lymph node

value: lymph node

value: CD8+ central mem.


title: DGM4_D14_CD8

value: total CD8+

value: UnTx


title: EG_2is_3

value: Female


title: HZ2_wk8_cDCs

value: cDCs

value: Untreated


title: CD11bplus_3


title: MT630_81_2_D14CNCC_early_RNA_rep3


title: DGM4_D14_CD4MEM

value: CD4+ mem.


title: HZ2_pre_NKcells

value: NK cells

value: pre


title: CD11bplus_2


title: MT629_SV20_D14CNCC_early_RNA_rep3

value: SV20 (CTRL1)


title: CD11bplus_1


title: DGM4_D14_CD4NA

value: CD4+ naive


title: MT628_64_4_D14CNCC_early_RNA_rep2

value: day 14 cranial neural crest cell - early maintenance media

value: cranial neural crest cell specification


title: HZ2_pre_monocytes

value: monocytes


title: CD11b_4

value: AML

value: CMM

value: bulk CD11b-CMM cells


title: DGM4_D14_CD4

value: lymph node

value: total CD4+


title: MT627_64_9_D14CNCC_early_RNA_rep2


title: DGL9_wk8_nonTfh

value: non-Tfh

value: WT bNAb Tx


title: HZ2_pre_cDCs

value: cDCs


title: CD11b_3


title: HRI_wk8_pDCs

value: pDCs

value: DEL bNAb Tx

value: HRI


title: MT626_81_2_D14CNCC_early_RNA_rep2


title: CD11b_2


title: MT625_SV20_D14CNCC_early_RNA_rep2


title: DGL9_wk8_nonfCD8


title: CD11b_1


title: DGL9_wk8_GCTfh

value: GCTfh


title: HRI_wk8_NKcells

value: NK cells


title: HZ2_wk8_Bcells

value: B cells

value: Untreated


title: MT624_64_4_D14CNCC_early_RNA_rep1

value: day 14 cranial neural crest cell - early maintenance media

value: cranial neural crest cell specification


title: MT623_64_9_D14CNCC_early_RNA_rep1


title: PBS_4

value: AML

value: untreated


title: HRI_wk8_Bcells


title: DGL9_wk8_CD8NA

value: CD8+ naive


title: MT622_81_2_D14CNCC_early_RNA_rep1


title: MT621_SV20_D14CNCC_early_RNA_rep1

value: SV20 (CTRL1)


title: HRI_wk8_cDCs

value: lymph node


title: DGL9_wk8_CD8EM

value: CD8+ effector mem.


title: PBS_1

value: CMM


title: HRI_pre_pDCs

value: pre


title: PBS_2


title: PBS_3


title: MT521_64_4_D10CNCC_RNA_rep3

value: day 10 cranial neural crest cell


title: MT520_64_9_D10CNCC_RNA_rep3


title: HRI_pre_monocytes

value: monocytes

value: DEL bNAb Tx


title: DGL9_wk8_CD8

value: total CD8+

value: WT bNAb Tx


title: DGL9_wk8_fCD8


title: DGL9_wk8_CD4NA

value: CD4+ naive


title: HRI_wk8_monocytes

value: HRI