title: ST615 LEP

status: Public on Jul 11 2025

city: Dublin

first: Karsten

last: Hokamp

state: Dublin

address: Stephen's Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
reference genomes and annotation files were downloaded from GenBank
read mapping against the reference genomes was carried out through bowtie2 version 2.4.2 with the flag ‘--very-sensitive-local'; hits with an XS:i tag (indicating detection of additional alignments for a read) were excluded to focus only on uniquely mapped reads
reads were aggregated into read-count matrices for each strain through featureCounts version 2.0.3 in stranded mode
read counts from all four strains were combined into a single file based on homology prediction by Panaroo version 1.5.0 with the settings ‘--clean-mode sensitive --refind-mode off --remove-invalid-genes’
Assembly: NC_008533 (D39), CP071871 (ST217), FQ312039 (ST306), NZ_LN831051 (ST615)
Supplementary files format and content: tab-delimited text file contains raw read counts for each sample and homology mappings between the four strains

organism: Streptococcus pneumoniae

source_name: Serotype 2 strain ST615

growth_protocol: Each pneumococcal strain was inoculated at a density of 2.5x10^6 in 250ml of Brain Heart Infusion (BHI) broth and incubated at 37ºC in a water bath for a pre-determined duration, depending on the targeted growth phase.

extract_protocol:
Ribonucleic acid (RNA) from each phase was stabilised by incubating the bacteria in a 5% phenol (Invitrogen) and 95% ethanol solution for 30 minutes on ice. Following stabilisation, RNA was extracted using a phase separation method using TRIzol® (Invitrogen). Briefly, the cells were centrifuged and re-suspended in TRIzol® to allow bacterial lysis. The lysed bacteria were mixed with chloroform to separate the RNA from DNA, lipids and proteins. Once the aqueous phase was collected (RNA), the sample was washed and the RNA was precipitated using ethanol. Finally, the RNA was re-suspended in DNase/RNase free distilled water (Invitrogen). The RNA extraction was done in an RNase-free area and using RNase-free materials to avoid RNA degradation. The quantity of RNA was determined using the Qubit® Fluorometer (Thermo Scientific). A 2100 Bioanalyzer (Agilent Technologies, Stanta Clara, USA) was used to assess the quality of the RNA.
RNA libraries for samples 1-5 were assumably prepared for sequencing using standard Illumina protocols. RNA samples 6-20  were fragmented with ultrasound (4 pulses of 30 sec at 4°C) followed by a treatment with antarctic phosphatase and re-phosphorylated with polynucleotide kinase (PNK). Afterwards, the RNA fragments were poly(A)-tailed using poly(A) polymerase and a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit. The cDNA samples were pooled in equimolar amounts in three different pools. The cDNA in the size range of 150 – 500 bp was eluted from preparative agarose gels. Aliquots of the size fractionated cDNAs were analyzed by capillary electrophoresis.

treatment_protocol: Ribonucleic acid (RNA) from each sample was stabilised to avoid sacrificing the integrity of the RNA by incubating the bacterial pellet with a solution of 5% phenol (Invitrogen) and 95% ethanol for a minimum of 30min in ice. Following this stabilisation step, the RNA was extracted.

value: Serotype 2 strain ST615

tag: growth phase

value: Late exponential phase


title: ST615 LSP

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype

value: WT

value: Late stationary phase


title: L. plantarum derived EV treated HEK295T cells

status: Public on Jul 12 2025

type: RNA

city: Pyeongchag

first: seoah

last: Park

address: 1447-1, Pyeongchang-daero, Daehwa-myeon, Pyeongchang-gun, Gangwon-do, Republic of Korea

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEK293T cell line (ATCC, Manassas, VA) was maintained in DMEM (Gibco) with 10% Fetal Bovine Serum (FBS) (Gibco) under 5% CO2 condition at 37°C

extract_protocol: After washing and lysing the cells with Buffer RLT, the complete RNA was extracted using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) as instructed by the manufacturer, including the on-column DNA digestion stage (RNase-Free DNase Set; QIAGEN).

treatment_protocol: HEK293T cell line (ATCC, Manassas, VA) was treated in DMEM with 10% FBS (Gibco) and Pk2 (10 nM) or not after reaching 80%fluence.

tag: cell line

tag: treatment


title: L. rhamnosus derived EV treated HEK294T cells


title: ST615 MEP

value: Mid-exponential phase


title: C_C57BL/6J mice

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

description: Library name: Sample 5

data_processing:
Sequencing was performed on an MGI DNBSEQ-G400 platform in a 100-base paired-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
Sequence quality of the FASTQ files was assessed using FastQC, and reads were trimmed based on quality scores using Trimmomatic. Trimmed reads were aligned to the mouse reference genome sequences (GRCm38) using Hisat2.
SAM files were converted to BAM format with Samtools, and gene-level read counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes count values for each Sample

organism: Mus musculus

source_name: intestinal tract

extract_protocol:
A moderate amount of intestinal tract was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a TruSeq Stranded mRNA sample preparation kit (Illumina) without RPB (mRNA Purification Beads) process.

tag: tissue

value: intestinal tract

value: fed normal diet until day 13


title: ST615 EEP

value: Early exponential phase


title: ST217 LSP

source_name: Serotype 2 strain ST217

value: Serotype 2 strain ST217


title: ST306 ESP

source_name: Serotype 2 strain ST306

value: Serotype 2 strain ST306

value: Early stationary phase


title: ST306 LSP


title: L. acidophilus derived EV treated HEK293T cells


title: TNR_BALB/c mice

description: Library name: Sample 3

value: fed TNR diet until day 13


title: ST217 ESP


title: ST306 LEP


title: ST306 MEP


title: ST306 EEP


title: MR_BALB/c mice

description: Library name: Sample 2

value: fed MR diet until day 13


title: Liver, HFD, KO, rep5

city: Edmonton

first: René

last: Jacobs

state: Alberta

address: Room 4002E, Li Ka Shing Building, 11300 87 Ave NW

department: Department of Agricultural, Food and Nutritional Science

country: Canada

institute: University of Alberta

description:
Library name: KO5
females

data_processing:
STAR[1] (version 2.5.2b) was used to align RNA-Seq data to the genome reference; RSEM[2] (version 1.3.0) was used to quantify gene and isoform expression; Ensembl gene annotation GTF[3] was used to build the RSEM reference, and add gene and transcript specific information to the .results file
Differential expression (DE) analysis was performed using R[4] (version R-4.0.2) and DESeq2[5] package (version 1.28.1), using raw read count (gene-level abundances) as input data. When applying DESeq2, the functions DESeqDataSetFromMatrix and DESeq were used.
When performing DE analysis, genes were filtered out if the median counts from either test group or control group < 25. An expected Benjamini-Hochberg (FDR) adjusted p-value less than 0.05 as regarded as significant
Fold enrichment analysis was performed to determine biological processes that were up or down regulated.
GO terms were determined with the online DAVID resource with default parameters,with an FDR cutoff of 0.05 for ontology and pathway terms
Assembly: mm10
Supplementary files format and content: Tab delimited text files, with columns for NCBI official gene symbol, Ensembl gene ID, and FPKM values, for all samples

molecule: polyA RNA

source_name: Liver

growth_protocol: Full body Etnppl knockout (KO) and wild type (WT) female mice were fed a standard chow diet for 8 weeks, then fed a HFD containing 45% kcal fat for 10 weeks.

extract_protocol:
Total RNA was extracted with Trizol, cleaned up with RNEasy columns.mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA was synthesized from heat-denaturated purified mRNA using the following kits: a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) to synthesize first-strand cDNA; PCR Clean DX (Aline Biosciences) bead purification; and the NEBNext Ultra 12 Directional Second Strand cDNA Synthesis protocol (New England Biolabs)

treatment_protocol: High fat diet containing 45% kcal fat for 10 weeks.

value: Liver

value: Etnppl KO

value: high fat diet


title: Liver, HFD, KO, rep2

description:
Library name: KO2
females


title: Liver, HFD, KO, rep4

description:
Library name: KO4
females


title: Liver, HFD, KO, rep3

description:
Library name: KO3
females


title: Liver, HFD, KO, rep1

description:
Library name: KO1
females


title: Liver, HFD, WT, rep5

description:
Library name: WT5
females

value: Etnppl WT


title: Liver, HFD, WT, rep4

description:
Library name: WT4
females


title: ST615 ESP

value: Serotype 2 strain ST615


title: Liver, HFD, WT, rep3

description:
Library name: WT3
females


title: Liver, HFD, WT, rep2

description:
Library name: WT2
females


title: HEK293T control 1

source_name: HEK293T cells


title: DSP-1001660015236-G-H06

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ files were processed using the GeoMx NGS Pipeline v2.0 software.
All downstream processing and analysis was performed using the GeoMxTools (v3.4.0) R package.
Assembly: mm10
Supplementary files format and content: geomx_metadata.tsv.gz, processed GeoMx metadata used for final analysis.
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc, probe annotation file for the Nanostring mouse whole transcriptome atlas.
Supplementary files format and content: Hesselberth_02-SO-90138_v1.0.pkc, probe annotation file for custom probes targeting ova-psDNA tags.
Supplementary files format and content: Tamburini_061423_20230619T1930_LabWorksheet.txt, worksheet produced by the GeoMx NGS pipeline, needed for downstream analysis.
Library strategy: GeoMx DSP

source_name: lymph node

extract_protocol:
The popliteal lymph nodes were harvested either 21 or 42 days after immunization with 20mg of one or both ova-psDNA GeoMx tags and 1E4 pfu per foot of vaccinia virus. Lymph nodes were fixed for 24-hours in 10% phosphate buffered formalin, and then placed in 70% Ethanol until embedding. The lymph nodes were embedded in paraffin wax, 7 uM sections were cut using a microtome. Slides were stained with Lyve-1-647 (clone: EPR21771), CD11c-Biotin (clone: D1V9Y), CD4 (clone: 4SM95). The nuclei were counterstained with SYTO™ 82 Orange Fluorescent Nucleic Acid Stain (S11363). Biotinylated antibodies were visualized with Streptavadin-AF594 (S32356) and the CD4 antibody was visualized with OPAL 520 (FP1487001KT, Akoya Biosciences). The ROI’s selected to undergo GeoMx DSP spatial transcriptomics were chosen based on Lyve-1 staining, CD11c staining and CD4 staining. Regions were selected based on the size of the area or the maximum size allowed for the R01.
Sequencing libraries were generated following the Nanostring GeoMx NGS protocol.

treatment_protocol: 6–8-week-old C57BL/6 (CD45.2) mice were immunized with 1E4 plaque-forming units (PFU) of Vaccinia Western Reserve and 20 µg of ova-psDNA in footpad.

value: lymph node

value: ova-GeoMX+VV 6week LN4

tag: slide

value: Slide 2

tag: segment


title: DSP-1001660015236-G-H05


title: DSP-1001660015236-G-H09

value: ova-GeoMX+VV 6week and 3week LN4


title: DSP-1001660015236-G-H07


title: DSP-1001660015236-G-H11


title: DSP-1001660015236-G-H10


title: DSP-1001660015236-G-H12


title: DSP-1001660015236-G-H03


title: DSP-1001660015236-G-H02


title: DSP-1001660015236-G-G11

value: ova-GeoMX+VV 3week LN4


title: DSP-1001660015236-G-G12


title: DSP-1001660015236-G-G10


title: DSP-1001660015236-G-G09


title: DSP-1001660015236-G-G07


title: DSP-1001660015236-G-G08


title: DSP-1001660015236-G-G05


title: DSP-1001660015236-G-G06


title: DSP-1001660015236-G-F11

value: ova-GeoMX+VV 6week LN5


title: DSP-1001660015236-G-G03


title: DSP-1001660015236-G-G04


title: DSP-1001660015236-G-F09

value: ova-GeoMX+VV 3week LN2

value: Slide 1


title: DSP-1001660015236-G-H08


title: DSP-1001660015236-G-G02


title: Liver, HFD, WT, rep1

description:
Library name: WT1
females


title: DSP-1001660015236-G-G01


title: DSP-1001660015236-G-F10


title: DSP-1001660015236-G-H04


title: DSP-1001660015236-G-H01


title: DSP-1001660015236-G-F12


title: DSP-1001660015236-G-F07


title: DSP-1001660015236-G-F05

value: ova-GeoMX+VV 6week LN3


title: DSP-1001660015236-G-E08

value: ova-GeoMX+VV 6week and 3week LN3


title: DSP-1001660015236-G-F08

value: Other


title: DSP-1001660015236-G-E09

value: ova-GeoMX+VV 6week and 3week LN1


title: DSP-1001660015236-G-E12

value: ova-GeoMX+VV 6week and 3week LN2


title: DSP-1001660015236-G-E07


title: DSP-1001660015236-G-E06


title: DSP-1001660015236-G-E05

value: naive LN 2


title: DSP-1001660015236-G-F04


title: DSP-1001660015236-G-E03


title: DSP-1001660015236-G-F01


title: DSP-1001660015236-G-F02


title: DSP-1001660015236-G-F06


title: DSP-1001660015236-G-E02


title: DSP-1001660015236-G-E04


title: DSP-1001660015236-G-E01

value: naive LN 1


title: DSP-1001660015236-G-D11


title: DSP-1001660015236-G-D09

value: ova-GeoMX+VV 6week LN2


title: DSP-1001660015236-G-D12


title: DSP-1001660015236-G-D10


title: DSP-1001660015236-G-D08


title: DSP-1001660015236-G-D07


title: DSP-1001660015236-G-E11


title: DSP-1001660015236-G-F03


title: DSP-1001660015236-G-D05


title: DSP-1001660015236-G-D04


title: DSP-1001660015236-G-D06


title: DSP-1001660015236-G-E10


title: DSP-1001660015236-G-D01

value: ova-GeoMX+VV 3week LN1


title: DSP-1001660015236-G-C12

value: lymph node


title: DSP-1001660015236-G-D02


title: DSP-1001660015236-G-C10


title: DSP-1001660015236-G-D03


title: DSP-1001660015236-G-C07

value: ova-GeoMX+VV 3week LN3


title: DSP-1001660015236-G-C08


title: DSP-1001660015236-G-C11


title: DSP-1001660015236-G-C09


title: DSP-1001660015236-G-C03


title: DSP-1001660015236-G-C02


title: DSP-1001660015236-G-C06


title: DSP-1001660015236-G-C01


title: DSP-1001660015236-G-B12


title: DSP-1001660015236-G-B11


title: DSP-1001660015236-G-B10


title: DSP-1001660015236-G-B09


title: DSP-1001660015236-G-B08


title: DSP-1001660015236-G-B06


title: DSP-1001660015236-G-B07


title: DSP-1001660015236-G-B05


title: DSP-1001660015236-G-B02


title: DSP-1001660015236-G-B04


title: DSP-1001660015236-G-B03


title: DSP-1001660015236-G-B01

value: ova-GeoMX+VV 6week LN1


title: DSP-1001660015236-G-A10


title: DSP-1001660015236-G-A12


title: DSP-1001660015236-G-C04


title: DSP-1001660015236-G-A11


title: DSP-1001660015236-G-A09


title: DSP-1001660015236-G-A05


title: DSP-1001660015236-G-C05


title: DSP-1001660015236-G-A06


title: DSP-1001660015236-G-A04


title: DSP-1001660015236-G-A03


title: DSP-1001660015236-G-A07


title: DSP-1001660015236-G-A08


title: DSP-1001660015236-G-A01

value: No template control

value: No Template Control


title: DC-P4-P2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
DC_P4_P2-JH300_6
cd45pos
dc

library_source: other

data_processing:
Reads were aligned and count matrices were generated using the 10x Genomics Cell Ranger software.
Downstream analysis including ova-psDNA quantification, gene expression normalization, sample integration, and cell clustering was performed using the Seurat R package.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5, raw count matrix from Cell Ranger in HDF5 format.
Supplementary files format and content: count_matrix.h5, processed count matrix in HDF5 format, matrices are provided for all CD45- cells, all CD45+ cells, LECs, and DCs.
Supplementary files format and content: metadata.tsv.gz, cell metadata for count_matrix.h5 matrices.
Supplementary files format and content: feature_reference.csv, ova-psDNA feature barcodes.
Supplementary files format and content: sample_info.xlsx, sample and ova-psDNA barcode information used for analysis.
Library strategy: CITE-seq

molecule: protein

extract_protocol:
21 or 42 days following vaccination, popliteal lymph nodes were harvested from 13 mice, with 4 lymph nodes mechanically separated with 22-gauge needles in 2 mL of EHAA media. 8 LNs were digested in collagenase D and DNase 1 for isolation of dendritic cells. The other 18 LNs were digested with Liberase DL with DNase 1 to isolate the stromal cell population. The 8 LNs digested for dendritic cell isolation were then stained with CD11c, CD11b and B220, and a live/dead dye. Live cells were then sorted into four tubes on a FACS Aria Cell Sorter: sorted CD11c-APC Cy7+ cells, sorted CD11b PE-Cy7+ cells, sorted B220 PE+ cells and Fixable Viability Stain 510 ungated live cells, which were recombined at a 4:4:1:1 ratio, respectively. For the remaining lymph nodes in the stromal cell digest, cells were stained with CD45-PE and Ter119-PE followed by magnetic bead isolation using the Miltenyi bead isolation kit. CD45-negative cells that passed through the column were then washed and counted using a hemocytometer.
Cells were assayed using the 10x Genomics v3 single-cell 3’ expression kit or v3 single-cell 3’ HT kit according to manufacturer’s instructions and CITE-seq protocol.

tag: cell type

value: CD45+ LN cells

tag: experiment

value: Immunized 21 and 42 days prior to harvest, CD45+ cells

tag: library type

value: ADT


title: DC-P2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
DC_P2-JH300_4
cd45pos
dc

value: Immunized 21 days prior to harvest, CD45+ cells


title: DSP-1001660015236-G-A02

value: Slide 1


title: LEC-P4-P2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
stromal_P4_P2-JH300_3
cd45neg
lec

value: CD45- LN cells

value: Immunized 21 and 42 days prior to harvest, CD45- cells


title: DC-P4_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
DC_P4-JH300_5
cd45pos
dc

value: Immunized 42 days prior to harvest, CD45+ cells


title: LEC-P4_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
stromal_P4-JH300_2
cd45neg
lec

value: Immunized 42 days prior to harvest, CD45- cells


title: LEC-P2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and captured using the 10x Chromium X
stromal_P2-JH300_1
cd45neg
lec

value: Immunized 21 days prior to harvest, CD45- cells


title: DC-1_DC-2_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_6-BT_ADT_6
cd45pos
dc

value: Immunized 21 and 42 days prior to harvest, CD45+ cells, capture 1


title: DC-1_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_7-BT_ADT_7
cd45pos
dc

value: Immunized 42 days prior to harvest, CD45+ cells, capture 1


title: DC-2_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_8-BT_ADT_8
cd45pos
dc

value: lymph node

value: Immunized 21 days prior to harvest, CD45+ cells, capture 1


title: LEC-1_LEC-2_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_1-BT_ADT_1
cd45neg
lec

value: Immunized 21 and 42 days prior to harvest, CD45- cells, capture 1


title: LEC-2_r2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_4-BT_ADT_4
cd45neg
lec

value: Immunized 21 days prior to harvest, CD45- cells, capture 2


title: LEC-1_LEC-2_r2_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_2-BT_ADT_2
cd45neg
lec

value: Immunized 21 and 42 days prior to harvest, CD45- cells, capture 2


title: DC-P4-P2

value: CD45+ LN cells

value: mRNA


title: DC-P4


title: DC-P2


title: LEC-P2


title: DC-2_r1


title: LEC-1_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_5-BT_ADT_5
cd45neg
lec

value: Immunized 42 days prior to harvest, CD45- cells, capture 1

value: ADT


title: LEC-P4-P2


title: DC-1_r1


title: LEC-1_LEC-2_r2


title: LEC-1_r1


title: LEC-1_LEC-2_r1


title: LEC-P4


title: LEC-2_r2


title: WT_E14.5_FL_LK_2

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

data_processing:
RNA-seq reads were aligned by STAR (version 2.5.2b) to the mouse genome (version mm10) with GENCODE basic gene annotations (version M22).
Gene expression levels were quantified by RSEM (version 1.3.0)
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

source_name: E14.5 FL LK (Lin-c-Kit+) Cells

extract_protocol:
Total RNA was purified from sorted E14.5 fetal liver LK (Lin-c-Kit+ )cells using RNeasy Micro kit (Qiagen)
Sequencing libraries were prepared by using Takara SMART-Seq V4 Ultra-Low Input according to the manufacturer’s specifications

value: E14.5 FL LK (Lin-c-Kit+) Cells

value: Vav-Cre


title: WT_E14.5_FL_LK_1


title: YY1_KO_E14.5_FL_LK_3

value: Yy1f/f Vav-Cre


title: YY1_KO_E14.5_FL_LK_2


title: YY1_KO_E14.5_FL_LK_1


title: YY1_17

library_source: genomic

data_processing:
CUT&Tag FASTQ files were first processed by removing the adapter ‘CTGTCTCTTATACACATCT’ using the Cutadapt software (version 4.5) and then aligned to the mouse genome (version mm10) by Bowtie2 (version 2.5.1). Duplicated fragments were marked and removed by Picard (version 3.1.1). Peaks were called by MACS2 (version 2.2.9.1) for each replicate under a q-value cutoff of 10-6. Only peaks from Chromosome 1-19, X, or Y, and not overlapping with any of the ENCODE problematic genomic regions (https://www.encodeproject.org/files/ENCFF547MET/) were kept. Peaks are defined as the genomic regions belonging to peaks called in all 4 replicates and with a minimum genomic span of 10 base pairs (bp).
Assembly: mm10
Supplementary files format and content: bigWig files of CUT&Tag signals
Supplementary files format and content: bigBed files of CUT&Tag peaks
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: E14.5 Fetal Liver Lin- Cells

extract_protocol:
B6 Lin- fetal liver cells were extracted using the EasySep ™ magnet system (StemCell™ Technologies) with antibodies against CD3, CD4, CD5, CD8, B220, CD19, IgM, CD127, AA4.1 and Ter119 (eBioscience). Around 300,000 cells were used for each CUT&Tag reaction with antibodies against H3K4me3 (Abcam ab213224) and YY1 (Active Motif 61780).
The library was constructed following the published protocol (Li, Yuefeng et al. “Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag.” STAR protocols vol. 2,3 100751. 19 Aug. 2021). The library is amplified with barcoded i5 and i7 primer using NEBNext High-Fidelity 2X PCR Master Mix (M0541). The quality of the tagmented DNA library is assessed using Bioanalyzer High Sensitivity DNA Analysis (Agilent).

value: E14.5 Fetal Liver Lin- Cells


title: LEC-2_r1_ADT

description:
Mice were vaccinated with ova-psDNA +VV, LN cells were sorted and divided between multiple captures using the 10x Chromium controller
BT_GEX_3-BT_ADT_3
cd45neg
lec

value: CD45- LN cells

value: Immunized 21 days prior to harvest, CD45- cells, capture 1


title: YY1_13


title: YY1_14


title: H3K4me3_14


title: H3K4me3_13


title: DC-1_DC-2_r1

value: Immunized 21 and 42 days prior to harvest, CD45+ cells, capture 1


title: WT_E14.5_FL_LK_3


title: WT_E14.5_FL_LK_4


title: 12-week TH Akap11 -/- snRNA-seq Sample 3

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

description:
10x Genomics
akap11_12wTH_snRNAseq_meta.csv

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, including introns
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Thalamus

extract_protocol:
Nuclei extraction was performed within 16 hours of brain tissue dissection to avoid freeze-thaw cycles, which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe).
Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer’s protocol.

value: Thalamus

tag: age


title: 12-week TH Akap11 -/- snRNA-seq Sample 2


title: LEC-2_r1

value: lymph node


title: 12-week TH Akap11 -/- snRNA-seq Sample 1


title: 12-week TH Akap11 WT snRNA-seq Sample 1

value: WT


title: 12-week TH Akap11 WT snRNA-seq Sample 2


title: 12-week TH Akap11 +/- snRNA-seq Sample 3


title: 12-week TH Akap11 -/- snRNA-seq Sample 4


title: 12-week TH Akap11 WT snRNA-seq Sample 3


title: YY1_KO_E14.5_FL_LK_4


title: 12-week TH Akap11 WT snRNA-seq Sample 4


title: 12-week TH Akap11 +/- snRNA-seq Sample 4


title: 12-week STR Akap11 WT snRNA-seq Sample 3

description:
10x Genomics
akap11_12wSTR_snRNAseq_meta.csv

source_name: Striatum

value: Striatum


title: 12-week STR Akap11 WT snRNA-seq Sample 4


title: 12-week STR Akap11 -/- snRNA-seq Sample 3


title: 12-week TH Akap11 +/- snRNA-seq Sample 2


title: 12-week STR Akap11 -/- snRNA-seq Sample 4


title: 12-week TH Akap11 +/- snRNA-seq Sample 1


title: YY1_08


title: 12-week STR Akap11 WT snRNA-seq Sample 1


title: 12-week STR Akap11 WT snRNA-seq Sample 2


title: 12-week STR Akap11 -/- snRNA-seq Sample 2


title: 12-week STR Akap11 -/- snRNA-seq Sample 1


title: 12-week STR Akap11 +/- snRNA-seq Sample 3


title: 12-week STR Akap11 +/- snRNA-seq Sample 1


title: 12-week STR Akap11 +/- snRNA-seq Sample 2


title: 4-week STR Akap11 WT snRNA-seq Sample 5

description:
10x Genomics
akap11_4wSTR_snRNAseq_meta.csv


title: 4-week STR Akap11 WT snRNA-seq Sample 2


title: 4-week STR Akap11 WT snRNA-seq Sample 4


title: 4-week STR Akap11 WT snRNA-seq Sample 3


title: 4-week STR Akap11 WT snRNA-seq Sample 1


title: 4-week STR Akap11 -/- snRNA-seq Sample 3


title: 4-week STR Akap11 -/- snRNA-seq Sample 4


title: 4-week STR Akap11 -/- snRNA-seq Sample 2


title: 4-week STR Akap11 -/- snRNA-seq Sample 1


title: 4-week STR Akap11 +/- snRNA-seq Sample 2


title: 4-week STR Akap11 +/- snRNA-seq Sample 1


title: 4-week STR Akap11 +/- snRNA-seq Sample 3


title: 12-week PFC Akap11 WT snRNA-seq Sample 4

description:
10x Genomics
akap11_12wPFC_snRNAseq_meta.csv

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: 12-week PFC Akap11 WT snRNA-seq Sample 1


title: 12-week PFC Akap11 -/- snRNA-seq Sample 1


title: 12-week PFC Akap11 -/- snRNA-seq Sample 2


title: 12-week PFC Akap11 +/- snRNA-seq Sample 1


title: 12-week STR Akap11 +/- snRNA-seq Sample 4


title: 12-week PFC Akap11 -/- snRNA-seq Sample 3


title: 12-week PFC Akap11 WT snRNA-seq Sample 2


title: 4-week PFC Akap11 WT snRNA-seq Sample 4

description:
10x Genomics
akap11_4wPFC_snRNAseq_meta.csv


title: 12-week PFC Akap11 +/- snRNA-seq Sample 4


title: 12-week PFC Akap11 WT snRNA-seq Sample 3


title: 12-week PFC Akap11 +/- snRNA-seq Sample 2


title: 4-week STR Akap11 +/- snRNA-seq Sample 4


title: 4-week PFC Akap11 WT snRNA-seq Sample 1


title: 12-week PFC Akap11 +/- snRNA-seq Sample 3


title: 4-week PFC Akap11 WT snRNA-seq Sample 2


title: 4-week PFC Akap11 -/- snRNA-seq Sample 4


title: 4-week PFC Akap11 -/- snRNA-seq Sample 2


title: 4-week PFC Akap11 -/- snRNA-seq Sample 3


title: 4-week PFC Akap11 -/- snRNA-seq Sample 1


title: 12-week PFC Akap11 -/- snRNA-seq Sample 4


title: 4-week PFC Akap11 +/- snRNA-seq Sample 4


title: 12-week TH Akap11 WT Bulk RNA-seq Sample 5

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Akap11 mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.


title: 4-week PFC Akap11 +/- snRNA-seq Sample 2


title: 4-week PFC Akap11 +/- snRNA-seq Sample 1


title: 12-week TH Akap11 WT Bulk RNA-seq Sample 4


title: 4-week PFC Akap11 +/- snRNA-seq Sample 3


title: 4-week PFC Akap11 WT snRNA-seq Sample 3


title: 12-week TH Akap11 WT Bulk RNA-seq Sample 3


title: 12-week TH Akap11 -/- Bulk RNA-seq Sample 5


title: 12-week TH Akap11 WT Bulk RNA-seq Sample 2


title: 12-week TH Akap11 -/- Bulk RNA-seq Sample 4


title: 12-week TH Akap11 -/- Bulk RNA-seq Sample 2


title: 12-week TH Akap11 WT Bulk RNA-seq Sample 1


title: 12-week TH Akap11 +/- Bulk RNA-seq Sample 5


title: 12-week TH Akap11 -/- Bulk RNA-seq Sample 3


title: 12-week TH Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week TH Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week TH Akap11 +/- Bulk RNA-seq Sample 4


title: 12-week TH Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 6


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 5


title: 12-week TH Akap11 -/- Bulk RNA-seq Sample 1


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 3


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 2


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 1


title: 4-week TH Akap11 WT Bulk RNA-seq Sample 4


title: 4-week TH Akap11 -/- Bulk RNA-seq Sample 4


title: 4-week TH Akap11 -/- Bulk RNA-seq Sample 5


title: 4-week TH Akap11 -/- Bulk RNA-seq Sample 2


title: 4-week TH Akap11 -/- Bulk RNA-seq Sample 3


title: 4-week TH Akap11 -/- Bulk RNA-seq Sample 1


title: 4-week TH Akap11 +/- Bulk RNA-seq Sample 6


title: 4-week TH Akap11 +/- Bulk RNA-seq Sample 4


title: 4-week TH Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week STR Akap11 WT Bulk RNA-seq Sample 3


title: 4-week TH Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week STR Akap11 WT Bulk RNA-seq Sample 4


title: 12-week STR Akap11 WT Bulk RNA-seq Sample 5


title: 12-week STR Akap11 -/- Bulk RNA-seq Sample 3


title: 12-week STR Akap11 -/- Bulk RNA-seq Sample 4


title: 12-week STR Akap11 WT Bulk RNA-seq Sample 2


title: 12-week STR Akap11 -/- Bulk RNA-seq Sample 5


title: 12-week STR Akap11 WT Bulk RNA-seq Sample 1


title: 12-week STR Akap11 +/- Bulk RNA-seq Sample 5


title: 12-week STR Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week STR Akap11 -/- Bulk RNA-seq Sample 1


title: 12-week STR Akap11 -/- Bulk RNA-seq Sample 2


title: 4-week STR Akap11 WT Bulk RNA-seq Sample 6


title: 12-week STR Akap11 +/- Bulk RNA-seq Sample 3


title: 12-week STR Akap11 +/- Bulk RNA-seq Sample 4


title: 4-week STR Akap11 WT Bulk RNA-seq Sample 4


title: 4-week STR Akap11 WT Bulk RNA-seq Sample 5


title: 4-week STR Akap11 WT Bulk RNA-seq Sample 1


title: 4-week STR Akap11 WT Bulk RNA-seq Sample 3


title: 4-week STR Akap11 -/- Bulk RNA-seq Sample 4


title: 4-week TH Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week STR Akap11 -/- Bulk RNA-seq Sample 5


title: 4-week STR Akap11 -/- Bulk RNA-seq Sample 1


title: 4-week STR Akap11 -/- Bulk RNA-seq Sample 2


title: 4-week STR Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week STR Akap11 +/- Bulk RNA-seq Sample 6


title: 4-week STR Akap11 +/- Bulk RNA-seq Sample 4


title: 4-week STR Akap11 +/- Bulk RNA-seq Sample 2


title: 4-week STR Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week SSC Akap11 WT Bulk RNA-seq Sample 4

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: 12-week SSC Akap11 WT Bulk RNA-seq Sample 3


title: 12-week SSC Akap11 WT Bulk RNA-seq Sample 2


title: 12-week SSC Akap11 WT Bulk RNA-seq Sample 1


title: 12-week STR Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week SSC Akap11 -/- Bulk RNA-seq Sample 3


title: 12-week SSC Akap11 -/- Bulk RNA-seq Sample 5


title: 12-week SSC Akap11 -/- Bulk RNA-seq Sample 2


title: 12-week SSC Akap11 +/- Bulk RNA-seq Sample 5


title: 12-week SSC Akap11 +/- Bulk RNA-seq Sample 4


title: 12-week SSC Akap11 -/- Bulk RNA-seq Sample 1


title: 4-week SSC Akap11 WT Bulk RNA-seq Sample 6


title: 12-week SSC Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week SSC Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week SSC Akap11 WT Bulk RNA-seq Sample 1


title: 4-week SSC Akap11 WT Bulk RNA-seq Sample 2


title: 4-week SSC Akap11 WT Bulk RNA-seq Sample 4


title: 12-week SSC Akap11 -/- Bulk RNA-seq Sample 4


title: 4-week SSC Akap11 -/- Bulk RNA-seq Sample 3


title: 4-week SSC Akap11 -/- Bulk RNA-seq Sample 4


title: 12-week SN Akap11 WT Bulk RNA-seq Sample 3

source_name: Substantia Nigra

value: Substantia Nigra


title: 4-week SSC Akap11 -/- Bulk RNA-seq Sample 5


title: 4-week SSC Akap11 -/- Bulk RNA-seq Sample 2


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week SN Akap11 WT Bulk RNA-seq Sample 4


title: 12-week SN Akap11 WT Bulk RNA-seq Sample 1


title: 12-week SSC Akap11 WT Bulk RNA-seq Sample 5


title: 4-week SSC Akap11 -/- Bulk RNA-seq Sample 1


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 6


title: 12-week SSC Akap11 +/- Bulk RNA-seq Sample 1


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 5


title: 4-week SSC Akap11 WT Bulk RNA-seq Sample 5


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 4


title: 12-week SN Akap11 +/- Bulk RNA-seq Sample 5


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week SN Akap11 WT Bulk RNA-seq Sample 2


title: 12-week SN Akap11 -/- Bulk RNA-seq Sample 2


title: 12-week SN Akap11 +/- Bulk RNA-seq Sample 2


title: 12-week SN Akap11 +/- Bulk RNA-seq Sample 1


title: 12-week SN Akap11 -/- Bulk RNA-seq Sample 1


title: 12-week SN Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week SN Akap11 WT Bulk RNA-seq Sample 5


title: 12-week SN Akap11 WT Bulk RNA-seq Sample 5


title: 12-week SN Akap11 -/- Bulk RNA-seq Sample 5


title: 12-week SN Akap11 +/- Bulk RNA-seq Sample 4


title: 4-week SN Akap11 WT Bulk RNA-seq Sample 3


title: 4-week SN Akap11 WT Bulk RNA-seq Sample 4


title: 4-week SSC Akap11 +/- Bulk RNA-seq Sample 3


title: 4-week SN Akap11 -/- Bulk RNA-seq Sample 6


title: 4-week SN Akap11 -/- Bulk RNA-seq Sample 5


title: epididymis epithelium organoids

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: AXH016

data_processing:
CellRanger 9.0
GRCh38
Supplementary files format and content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

source_name: epididymis epithelium organoids

growth_protocol: Human epididymis tissues were digested with collagenase to isolated human epididymis epithelial (HEE) cells. The HEE cells were resuspended in the culture media, mixed 1:1 with Matrigel and seeded on a 24-well plate.

extract_protocol:
A total of 2500–3000 cells were used for scRNA-seq using the 10X Genomics Chromium system.
Chromium Single Cell 3ʹ Library kit

treatment_protocol: No treatment

value: epididymis epithelium organoids


title: 4-week SN Akap11 -/- Bulk RNA-seq Sample 3


title: 4-week SN Akap11 WT Bulk RNA-seq Sample 2


title: 12-week SN Akap11 -/- Bulk RNA-seq Sample 4


title: 12-week SN Akap11 -/- Bulk RNA-seq Sample 3


title: 4-week SN Akap11 WT Bulk RNA-seq Sample 1


title: MCF-7 cells, Ibp3

city: Ningxia

first: feng

middle: xu

last: fu

address: Shengli Street

country: China

institute: Ningxia Medical University

description: Library name: Sample 6

data_processing:
The first-strand of complementary DNA (cDNA) was synthesized using a random hex‐ amer primer and reverse transcriptase (ribonuclease H (RNase H)), and the second-strand was subsequently synthesized using DNA polymerase I and RNase H.
The library quality of PCR products was assessed using an Agilent Bioanalyzer 2100 system. Library fragments were sequenced on an Illumina Novaseq platform according to the manufacturer’s instructions.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: Human breast cancer cell lines

growth_protocol: MCF-7 cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) fetal bovine serum  and 1% (v/v) penicillin/streptomycin solution. Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from the control group and the group treated with 8.0 mg/mL LBP (n=3) using TRIzol reagent , following the manufacturer's protocol.
Sequencing libraries were constructed using an RNA Library Prepare Kit for Illumina New England Biolabs  according to the manufacturer’s instruc‐ tions.

treatment_protocol: MCF-7 cells were seeded into 10 cm cell culture dishes at a density of 5,000 cells/well and subsequently treated with LBP(8.0 mg/mL) for 48 h.

value: Human breast cancer cell lines


title: MCF-7 cells, Ibp1

description: Library name: Sample 4


title: MCF-7 cells, Ibp2

description: Library name: Sample 5


title: 4-week SN Akap11 +/- Bulk RNA-seq Sample 6


title: 4-week SN Akap11 -/- Bulk RNA-seq Sample 2


title: MCF-7 cells, Con2

description: Library name: Sample 2


title: MCF-7 cells, Con3

description: Library name: Sample 3


title: 4-week SN Akap11 +/- Bulk RNA-seq Sample 4


title: MCF-7 cells, Con1

description: Library name: Sample 1


title: 4-week SN Akap11 -/- Bulk RNA-seq Sample 4


title: 4-week SN Akap11 +/- Bulk RNA-seq Sample 2


title: iGluta, sample3

city: La Jolla

first: Anne

middle: G

last: Bang

state: CA

address: 10901 North Torrey Pines Road

department: Prebys Center

institute: Sanford Burnham Prebys Medical Discovery Insititute

description: Library name: iCell-Gluta-sample-3

data_processing:
Bulk RNA-seq samples were processed using nf-core rnaseq pipeline version 3.17.0 using parameters “--aligner star_rsem” to perform read trimming, quality control, alignment, gene quantification, and normalization.
genome build/assembly: We used human genome version GRCh38.p14 sequence and GENCODE gene annotations version 47.
processed data files format and content: Matrix table with counts for every gene and every sample
processed data files format and content: Matrix table with normalized expression (TPM) for every gene and every sample

source_name: iCell GlutaNeurons (iGluta), FujiFilm Cellular Dynamics Inc.

extract_protocol:
Triplicate samples were prepared . Total RNA was isolated using an RNeasy mini kit (Qiagen, 74104) and treated with DNase (Qiagen 79254). Invitrogen Qubit and Agilent TapeStation were used to determine RNA concentration and RNA integrity numbers respectively prior to library preparation.
Polyadenylated RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, and barcoded, strand-specific libraries were prepared using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA). Libraries were sequenced as paired-end 151 bp reads on an Illumina NovaSeq platform.

treatment_protocol: untreated

value: human induced pluripotent stem cell derived glutamatergic neurons

value: untreated


title: LS174T, 1

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

description: Library name: Ctrl1_rep1

data_processing:
Raw, not normalized counts where retrieved using Salmon and the reference transcriptome (hg38)
Import of raw counts into the R environment using the tximport package. Differential expression analysis performed using the DESeq2 package
Assembly: GRCH38
Supplementary files format and content: Salmon quant.sf raw counts in xlsx format

growth_protocol: Human colorectal carcinoma HCT8 cells were maintained in high glucose Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin, and 1% L-glutamine. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C. PHGDH-silenced HCT8 cells were established by transfection with PHGDH human shRNA plasmid or scrambled shRNA using Lipofectamine 3000 according to the manufacturer's protocol, followed by selection with 2 μM puromycin.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's protocol. The amount and purity of RNA were determined with a NanoDrop Microvolume Spectrophotometer and Fluorometer. RNA quality was assessed by FastQC to ensure that the sequencing data met predefined quality standards prior to downstream analyses.
Total RNA-sequencing (RNA-seq) library preparation was performed from high-quality total RNA extracted from wild-type and PHGDH-silenced HCT8 cells. Following RNA quality control, libraries were constructed according to standard protocols for next-generation sequencing. The resulting libraries were subjected to deep sequencing on a high-throughput sequencing platform to generate transcriptome-wide expression data.

treatment_protocol: Cells were grown to sub-confluence in standard culture conditions. For experimental analyses, wild-type HCT8 cells and PHGDH-silenced HCT8 clones were harvested in their basal state without additional treatment. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality and quantity were assessed using a NanoDrop Microvolume Spectrophotometer and Fluorometer prior to library preparation for RNA-sequencing.

value: human colorectal carcinoma cell line

value: silenced


title: iGluta, sample2

description: Library name: iCell-Gluta-sample-2

value: iCell GlutaNeurons (iGluta), FujiFilm Cellular Dynamics Inc.


title: 4-week SN Akap11 +/- Bulk RNA-seq Sample 3


title: LS174T, 3

description: Library name: Ctrl1_rep3


title: 12-week PFC Akap11 WT Bulk RNA-seq Sample 5


title: Tail tissue at E80

first: Jiangang

last: Han

address: 59 Donnybrook Manor, Dublin 4

institute: University College Dublin

description: 10x Genomics

data_processing:
We employed the Cell Ranger Toolkit (version 6.0, 10x Genomics) to align sequencing reads onto the ovine reference genome (Oar_rambouillet_v1.0) with default parameters. The output documents, including "barcode.tsv", "features.tsv" and "matrix.mtx", were used to perform data normalization, cell quality control, clustering analysis, dimension reduction, differentially expressed genes analysis, annotation and visualization in the Seurat R package.
The provided processed data files include barcode information, gene information and gene expression matrix, which can be read by Seurat directly in R. Notably, the steps of cell quality control for generated raw cell-feature count matrix are necessary in downstream analyses.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: barcode.tsv, features.tsv, and matrix.mtx

organism: Ovis aries

source_name: Embryonic tail

extract_protocol:
The ovine embryonic tail tissues collected at nine stages were promptly stored in 5 ml tubes filled with MACS Tissue Storage Solution (Miltenyi, Germany) and immediately placed on ice. They were then transported to the lab within an hour and underwent independent dissociation and digestion. This process involved three washes in PBS (Gibco, Waltham, USA), mincing into approximately 1mm³ pieces, and treatment with a mixture of  collagenase IV, DNase I, and trypsin, while shaking at 37°C for at least 60 minutes. After sufficient dissociation, the cell/tissue suspension was filtered using a 70 µm strainer (Merck Millipore, Darmstadt, Germany) to remove large clumps and then centrifuged at 400 × g for 5 minutes. Resuspending the cell pellet in erythrocyte lysis buffer (Solarbio, Beijing, China) for 5 minutes at room temperature to lyse red blood cells, followed by another round of filtering and centrifuging. Finally, the cell pellet was resuspended in 0.04% BSA–PBS. The quality of the single cell suspension was evaluated using a Count Star device (Alit Biotech, China).
The steps for cell capture, cDNA synthesis, library construction, and sequencing were carried out at CapitalBio Technology Co., Ltd (Beijing, China). Briefly, 8,700 cells were loaded onto a Chromium Single Cell Controller (10x Genomics) to obtain 5,000 target cells and create single-cell gel beads in emulsion (GEMs) using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and Chromium Single Cell A Chip Kit (10x Genomics) according to manufacturer’s instructions. This was followed by cell lysis, RNA barcoding, and reverse transcription in a C1000 Touch Thermal Cycler (Bio-Rad) to generate cDNA. GEMs were then broken down, and the single-strand cDNA was isolated and purified using DynaBeads (Thermo Fisher Scientific). The cDNA library underwent further amplification to create a sequencing library, the quality of which was assessed using an Agilent 4200 device. Lastly, sequencing was performed on an Illumina Novaseq6000 with a PE150 model and a depth of at least 100,000 reads per cell (approximately 150GB of data per sample).

value: Embryonic tail

tag: breed

value: Tan sheep

value: Global cells

value: Embryonic day 80


title: 2nd replicate of primary unsorted cells derived from a RPN lung tumor initiated by SPC-Cre

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: Library name: RPNS_tumor_1_rep2

data_processing:
H5 files were generated in CellRanger v7.1.0
Assembly: modified mm10 genome with RIT1 transgene added
Supplementary files format and content: H5 files were generated in CellRanger v7.1.0

source_name: lung tumor

growth_protocol: Cell lines were cultured in DMEM+10% FBS and trypsinized and washed in PBS.

extract_protocol:
Tumors were processed using the Mouse Tumor Dissociation Kit (Miltenyi Biotech) and filtered through MACS SmartStrainer (Miltenyi Biotech). A red blood cell lysis was performed. No other sorting was performed.
10x Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (Dual Index)

value: lung tumor

value: SPC-Cre

tag: batch


title: LS174T, 2

description: Library name: Ctrl1_rep2


title: 12-week PFC Akap11 WT Bulk RNA-seq Sample 3

value: WT


title: HCT8, PHGDH-silenced clone 2 (shPHGDH), 3

description: Library name: shPHGDH_rep6

value: PHGDH silencing


title: Tail tissue at E72

description: 10x Genomics

value: Embryonic day 72


title: HCT8, PHGDH-silenced clone 2 (shPHGDH), 2

description: Library name: shPHGDH_rep5


title: Tail tissue at E69

description: 10x Genomics

value: Embryonic day 69


title: Tail tissue at E66

description: 10x Genomics

value: Embryonic day 66


title: 12-week PFC Akap11 WT Bulk RNA-seq Sample 4

value: Prefrontal Cortex


title: Tail tissue at E63

description: 10x Genomics

value: Embryonic day 63


title: 1st replicate of primary unsorted cells derived from a RPN lung tumor initiated by SPC-Cre

description: Library name: RPNS_tumor_1_rep1


title: 4-week SN Akap11 +/- Bulk RNA-seq Sample 5

value: Substantia Nigra


title: 12-week PFC Akap11 WT Bulk RNA-seq Sample 2


title: HCT8, PHGDH-silenced clone 1 (shPHGDH), 3

description: Library name: shPHGDH_rep3

value: human colorectal carcinoma cell line


title: 12-week PFC Akap11 WT Bulk RNA-seq Sample 1


title: 1st replicate of cells from a cell line culture derived from a RPN lung tumor initiated by SPC-Cre

description: Library name: RPNS_cell_line_rep1

source_name: RPNS

value: RPNS


title: iGluta, sample1

description: Library name: iCell-Gluta-sample-1

value: iCell GlutaNeurons (iGluta), FujiFilm Cellular Dynamics Inc.

value: human induced pluripotent stem cell derived glutamatergic neurons

value: untreated


title: Tail tissue at E60

description: 10x Genomics

value: Embryonic tail

value: Tan sheep

value: Global cells

value: Embryonic day 60


title: Tail tissue at E75

description: 10x Genomics

value: Embryonic day 75


title: 12-week PFC Akap11 -/- Bulk RNA-seq Sample 5


title: Adjacent normal lung from the same animal used for RPNS_lung_tumor_S1

description: Library name: RPNS_normal_lung_1

source_name: lung

value: lung

value: SPC-Cre


title: Second replicate of cells from a cell line culture derived from a RPN lung tumor initiated by SPC-Cre

description: Library name: RPNS_cell_line_rep2


title: Tail tissue at E50

description: 10x Genomics

value: Embryonic day 50


title: 12-week PFC Akap11 -/- Bulk RNA-seq Sample 4


title: HCT8, PHGDH-silenced clone 1 (shPHGDH), 1

description: Library name: shPHGDH_rep1

value: silenced

value: PHGDH silencing


title: HCT8, wild-type (shCTRL), 3

description: Library name: shCTRL_rep3

value: WT


title: Primary unsorted cells derived from a second RPN lung tumor initiated by SPC-Cre

description: Library name: RPNS_tumor_2

value: lung tumor


title: DNA sequencing from HPGC after GPCR treatment

city: Florence

first: Marta

last: Baragli

address: Via di S. Marta 3

department: Department of Information Engineering

institute: University of Florence

data_processing:
For DNA samples: sequencing reads were basecalled with Guppy and aligned to the GRCh37 reference genome version with minimap2. Methylation calling has been performed with Guppy with a methylation-compatible model.
For RNA samples: to perform transcripts counts we used featureCounts
Assembly: GRCh37
Supplementary files format and content: For RNAseq, we provide a gene count table for HPGC samples. Each row reports a single gene and each column reports counts for a specific replicate sample.
Supplementary files format and content: For WGS, we provide tables reporting methylation frequency and entropy for each sample. Each file contains 6 columns indicating respectively: chromosome, position, methylation entropy, number of reads supporting methylation entropy value, methylaiton frequency,  number of reads supporting methylation frequency value
Library strategy: WGS

source_name: Human Peripheral Glial Cells

extract_protocol:
HPGC: total DNA was extracted using DNeasy Blood Tissue Kit (69506, Qiagen) and total RNA was extracted using  RNeasy Mini Kit (74106, Qiagen).
HPGC: RNA library preparation was performed with PCR-cDNA Barcoding Kit (SQK-PCB111.24) and DNA library preparation was performed with Sequencing Kit SQK-LSK109-XL

value: Human Peripheral Glial Cells


title: DNA sequencing from HPGC before GPCR treatment


title: RtP2_R1_control

city: Los Angeles

first: Matthew

middle: D

last: Dean

address: 1050 Childs Way, Rm #308

department: Molecular Biology

institute: University of Southern California

description: Library name: RtP2_R1_control

data_processing:
We sequenced libraries on the NextSeq 2000 platform at the Georgia Genomics and Bioinformatics Core. Sequencing reads from the ChIP and input control libraries were aligned to the mouse genome (mm10) using BOWTIE 2 v2.4.5 with options “--end-to-end --very-sensitive” [124]. We only kept uniquely aligning reads with fewer than three sequence mismatches to the reference genome.
We identified AR peaks using MACS2 v2.7.1 [93] with the options “--bdg --SPMR --qvalue=0.01” and generated fold-enrichment over input control. We performed de novo motif analysis from sequences within 50 bp of AR peak summits, using HOMER (http://homer.ucsd.edu/), with 100k random genomic sequences as the background. HOMER uses hypergeometric optimization to detect short sequence motifs that are enriched in sample vs. control
To test enrichment of Gene Ontology annotations with associated AR ChIP-seq peaks, we used the R package CHIPENRICH
Assembly: Mouse mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Penis

extract_protocol:
We placed dissected tissue in ice cold 1x DPBS for ChIP-seq. We incubated penis, forelimb, and hindlimb tissues in Trypsin-EDTA for 5 minutes at 37°C to loosen up the tissue. We inactivated Trypsin-EDTA using DMEM + 10% FBS, then cross-linked DNA to bound proteins by adding 1% formaldehyde, incubated on a horizontal nutator for 20 minutes at room temperature. We quenched the crosslinking reaction using 2.5 M Glycine, spun down tissues at 4,000 rpm for 5 minutes at 4°C. We washed tissues twice in ice-cold PBS, then removed the tissue pellet. We sheared chromatin to a size of 100-300 bp in a bath-based sonicator (Diagenode Bioruptor 300).
We produced ChIP and input chromatin control libraries using the NEBNext Ultra II Library Prep Kit (NEB, catalog #E7645S).

value: Penis

tag: antibody

value: AR rabbit polyclonal, Millipore catalog #06-680; Lot #2967860


title: RNAseq Replicate 4 from HPGC after GPCR treatment

data_processing:
For DNA samples: sequencing reads were basecalled with Guppy and aligned to the GRCh37 reference genome version with minimap2. Methylation calling has been performed with Guppy with a methylation-compatible model.
For RNA samples: to perform transcripts counts we used featureCounts
Assembly: GRCh37
Supplementary files format and content: For RNAseq, we provide a gene count table for HPGC samples. Each row reports a single gene and each column reports counts for a specific replicate sample.
Supplementary files format and content: For WGS, we provide tables reporting methylation frequency and entropy for each sample. Each file contains 6 columns indicating respectively: chromosome, position, methylation entropy, number of reads supporting methylation entropy value, methylaiton frequency,  number of reads supporting methylation frequency value


title: HCT8, PHGDH-silenced clone 2 (shPHGDH), 1

description: Library name: shPHGDH_rep4

value: human colorectal carcinoma cell line


title: 12-week PFC Akap11 -/- Bulk RNA-seq Sample 1

value: Prefrontal Cortex


title: Tail tissue at E55

description: 10x Genomics

value: Embryonic tail

value: Embryonic day 55


title: RtP2_R1_ChIP

description: Library name: RtP2_R1_ChIP


title: HCT8, wild-type (shCTRL), 2

description: Library name: shCTRL_rep2


title: Second adjacent normal lung sample from the same animal used for RPNS_lung_tumor_S1

description: Library name: RPNS_normal_lung_2


title: RNAseq Replicate 3 from HPGC after GPCR treatment


title: mm_penis_P13_Input

description: Library name: mm_penis_P13_Input


title: 12-week PFC Akap11 -/- Bulk RNA-seq Sample 2


title: MCF7_CTRLN2

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: Library name: MCF7_CTRLN2

data_processing:
FastQC was used for quality assessment of raw Fastq reads.
Fastq files were mapped to human GRCh38 genome using STAR aligner.
For RNA-seq feature counts was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files with raw counts for each sample.

growth_protocol: MCF7 cells were cultured in media recommended by European Collection of Authenticated Cell Cultures in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
For RNA-seq, total RNA was extracted from normoxia and hypoxia treeated cells using TRIzol (Invitrogen, 15596026).
mRNA enrichment method was used as the library preparation strategy . Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: MCF7 cells were kept under Hypoxia (1% oxygen) before performing RNA-seq

value: Breast epithelium

value: Normoxia


title: 12-week PFC Akap11 +/- Bulk RNA-seq Sample 5


title: HCT8, wild-type (shCTRL), 1

description: Library name: shCTRL_rep1


title: 12-week PFC Akap11 +/- Bulk RNA-seq Sample 4


title: mm_penis_P13_ARChIP

description: Library name: mm_penis_P13_ARChIP


title: MCF7_CTRLN1

description: Library name: MCF7_CTRLN1


title: RNAseq Replicate 2 from HPGC after GPCR treatment


title: HCT8, PHGDH-silenced clone 1 (shPHGDH), 2

description: Library name: shPHGDH_rep2


title: RNAseq Replicate 1 from HPGC after GPCR treatment


title: 12-week PFC Akap11 +/- Bulk RNA-seq Sample 3


title: 12-week PFC Akap11 -/- Bulk RNA-seq Sample 3


title: MP6_R2_control

description: Library name: MP6_R2_control


title: MCF7_CTRLH2

description: Library name: MCF7_CTRLH2

value: Hypoxia


title: RNAseq Replicate 4 from HPGC before GPCR treatment


title: 12-week PFC Akap11 +/- Bulk RNA-seq Sample 2


title: MCF7_CTRLH1

description: Library name: MCF7_CTRLH1


title: RNAseq Replicate 3 from HPGC before GPCR treatment


title: MP6_R2_ChIP

description: Library name: MP6_R2_ChIP


title: 12-week PFC Akap11 +/- Bulk RNA-seq Sample 1


title: MP6_R1_control

description: Library name: MP6_R1_control


title: MP6_R1_ChIP

description: Library name: MP6_R1_ChIP


title: RNAseq Replicate 2 from HPGC before GPCR treatment


title: 4-week PFC Akap11 WT Bulk RNA-seq Sample 5


title: pATML1::GFP+CSLD5-csld5, rep3

city: Shanghai

first: yangxuan

last: liu

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS), Chinese Academy of Sciences

data_processing:
The raw reads were trimmed with Trimmomatic v.0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:50.
Clean reads were then aligned to the TAIR10 transcriptome using Hisat2 v2.2.1.
Expression levels were extracted for each gene using TPMCalculator v0.0.3 and featureCounts v2.0.6.
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

organism: Arabidopsis thaliana

source_name: inflorescence meristem

extract_protocol:
Total RNAs were extracted with the RNAprep Pure Plant Plus Kit Kit (TIANGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TransNGS Fast RNA-Seq Library Prep Kit for Illumina  following the manufacturer’s instructions.

value: inflorescence meristem


title: Single_nucleus_DS_3

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description: snRNA-seq

data_processing:
To ensure data quality, cells from individual replicates underwent stringent quality control filtering and were normalized using SCTransform. Cells with ≥ 5% mitochondrial genes, ≤ 200, and ≥ 2,500 unique feature counts were excluded from the datasets. Following, individual replicates were integrated and Harmony was used to correct for potential batch effects. Seurat v5 (R v4.2.1) was used to perform data normalization, dimensional reduction using PCA, and graph-based clustering with UMAP
Assembly: hg38
Supplementary files format and content: CellRanger output files: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz

source_name: Brain

growth_protocol: Ten prenatal human brain samples (n=5 euploid, n=5 Down Syndrome, 13-19 gestational weeks) were obtained from the Human Developmental Biology Resource (HDBR, United Kingdom), under a research ethics agreement from Clinical Trials Ontario (Study # 3227)

extract_protocol:
Nuclei were extracted from ten individual brain samples and processed using the 10x Genomics Chromium System.
Libraries were sequenced using the Novaseq 6000 on S1 flow cell at the Centre for Applied Genomics (TCAG; The Hospital for Sick Children) in Toronto, ON, Canada.

value: Brain

tag: developmental stage

tag: Sex

value: Male

value: Down Syndrome


title: Single_nucleus_DS_2

description: snRNA-seq


title: MP6a3

description: Library name: Sample 3

data_processing:
Data processing was performed using Cell Ranger v7.0.0 according to 10X technical support's recommendations. According to their recommendations, round 1 and round 2 sequencing of each of our samples were combined into one output.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
We placed dissected tissue in ice cold DMEM w/o Phenol Red (Hyclone #SH30284.02). We dissociated tissues using the gentleMACS Octo Dissociator using the soft tumor program 37C_m_TDK1. We placed the cell suspension in a MACS SmartStrainer (70 µM) placed in a 15 mL conical tube, then washed it in 10 mL of DMEM. We then centrifuged the sample at 300 G for 7 min. at 4°C, removed the supernatant, and resuspended cells in 100 µL of PBS w/ 0.04% BSA. We processed cell suspensions with a 10X Single Cell 3’ v3.1 kit, aiming to isolate ~10,000 cells
Libraries were prepared according to the 10X Genomics protocol


title: 4-week PFC Akap11 WT Bulk RNA-seq Sample 1


title: Single_nucleus_DS_5

description: snRNA-seq

value: 15 pcw


title: 4-week PFC Akap11 -/- Bulk RNA-seq Sample 6


title: Single_nucleus_DS_4

description: snRNA-seq


title: pATML1::GFP+CSLD5-csld5, rep1


title: MHe15

description: Library name: Sample 5

source_name: Hindlimb

value: Hindlimb


title: 4-week PFC Akap11 WT Bulk RNA-seq Sample 4

value: WT


title: Single_nucleus_CTL_5

description: snRNA-seq

value: Euploid


title: 4-week PFC Akap11 -/- Bulk RNA-seq Sample 5


title: RNAseq Replicate 1 from HPGC before GPCR treatment

value: Human Peripheral Glial Cells


title: Single_nucleus_DS_1

description: snRNA-seq

value: Female


title: 4-week PFC Akap11 WT Bulk RNA-seq Sample 2


title: pATML1::GFP+CSLD5-csld5, rep2


title: csld5, rep3


title: MP6a1

description: Library name: Sample 1

value: Penis


title: csld5, rep2


title: 4-week PFC Akap11 -/- Bulk RNA-seq Sample 4

value: Prefrontal Cortex


title: Single_nucleus_CTL_4

description: snRNA-seq


title: Single_nucleus_CTL_3

description: snRNA-seq


title: Human primary chodroctes treated with cyproheptadine + IL-1β 5

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

description: Library name: 20idHOACHONDRnm54tyIL1BCYPR30UMrp5-3IL1BCYPR30UM

data_processing:
Raw BCL sequencing data was converted fastqs using bcl2fastq v2.19.0.
Samples were analyzed using nf-core/RNA-seq pipeline v1.4.2 (implemented on Nextflow v20.07.1)
Reads were trimmed for adapters using trimGalore! v0.6.4. Reads mapping to rRNA regions were removed using SortMeRNA v2.1b, and aligned to the huam reference genome (ENSEMBL build GRCh38) using STAR v2.6.1d. Gene-level assignment was then performed using featureCounts from subread package v2.0.1.
Differential expression analysis was performed separately using the DESeq2 R package v1.40.2
Assembly: Ensembl build GRCh38
Supplementary files format and content: tab-limited text file includes gene-level raw counts for each sample.

source_name: primary chondrocytes

extract_protocol:
Total RNA was isolated with Direct-zol RNA MicroPrep kit (Zymo Research).
Libraries for bulk RNAseq were prepared using an early access RNAseq library prep kit from Jumpcode Genomics. Basically, 20ng total RNA from each sample was reverse transcribed using random primers with partial P7 Illumina adapter sequence on the 5’ end. After RT, a partial P5 adapter sequence was ligated to the 3’ end of the cDNA molecule followed by PCR amplification with full length indexed Illumina adapter primers. PCR amplified library was treated with Jumpcode’s CRISPRclean reagent to cut library molecules containing rRNA sequences.

value: primary chondrocytes


title: csld5, rep1


title: col-0, rep2


title: 4-week PFC Akap11 -/- Bulk RNA-seq Sample 2


title: MP6a2

description: Library name: Sample 2


title: Human primary chodroctes treated with cyproheptadine + IL-1β 2

description: Library name: 17idHOACHONDRnm44tyIL1BCYPR30UMrp2-3IL1BCYPR30UM


title: 4-week PFC Akap11 +/- Bulk RNA-seq Sample 7


title: col-0, rep1


title: RNAseq Replicate 1 from AML patient UD5 at initial diagnosis

data_processing:
To perform transcripts counts we used Salmon.
Assembly: GRCh37
Supplementary files format and content: We provide a gene count table for AML samples. Each row reports a single gene and each column reports counts for a specific replicate sample.

source_name: Bone Marrow

extract_protocol:
RNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
RNAseq libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold.

tag: disease

value: AML

value: Bone Marrow


title: MFe15

description: Library name: Sample 4

source_name: Forelimb

value: Forelimb


title: Human primary chodroctes treated with cyproheptadine + IL-1β 4

description: Library name: 19idHOACHONDRnm53tyIL1BCYPR30UMrp4-3IL1BCYPR30UM


title: Single_nucleus_CTL_2

description: snRNA-seq


title: col-0, rep3


title: Human primary chodroctes treated with cyproheptadine + IL-1β 3

description: Library name: 18idHOACHONDRnm52tyIL1BCYPR30UMrp3-3IL1BCYPR30UM


title: RNAseq Replicate 3 from AML patient UD5 after Relapse


title: RNAseq Replicate 2 from AML patient UD5 at initial diagnosis


title: Single_nucleus_CTL_1

description: snRNA-seq


title: Human primary chodroctes treated with cyproheptadine + IL-1β 1

description: Library name: 16idHOACHONDRnm43tyIL1BCYPR30UMrp1-3IL1BCYPR30UM


title: 4-week PFC Akap11 +/- Bulk RNA-seq Sample 5

source_name: Prefrontal Cortex


title: Human primary chodroctes treated with IL-1β 5

description: Library name: 15idHOACHONDRnm54tyIL1BDMSOrp5-1IL1BDMSO


title: 4-week PFC Akap11 +/- Bulk RNA-seq Sample 4


title: 4-week PFC Akap11 -/- Bulk RNA-seq Sample 1


title: Human primary chodroctes treated with IL-1β 3

description: Library name: 13idHOACHONDRnm52tyIL1BDMSOrp3-1IL1BDMSO


title: EXO1_KO_D16_R2

city: London

first: Simon

middle: J

last: Boulton

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Data was processed as followed (described in Hewitt et al, PMID:33333017):
"Raw data was trimmed by obtaining 20 bp after the first occurrence of “CACCG” in the read sequence.
Trimmed reads were then mapped with BWA (version 0.5.9-r16)(Li and Durbin, 2009) to a database of guide sequences for the human CRISPR Brunello lentiviral pooled library downloaded from Addgene (https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/) with the parameters “-l 20 -k 2 -n 2.” sgRNA counts were obtained after filtering the mapped reads for those that had zero mismatches, and mapped to the forward strand of the guide sequence.
The MAGeck ‘test’ command (version 0.5.7)(Li et al., 2014) was used to perform the sgRNA ranking analysis between the relevant conditions with parameters “–norm-method total–remove-zero both.”
Assembly: database of guide sequences for the human CRISPR Brunello lentiviral pooled library downloaded from Addgene (https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/)
Supplementary files format and content: Tab separated files counts per sgRNA, one file for each strand.
Library strategy: sgRNA amplicon-seq

source_name: blood cells

growth_protocol: eHAP iCas9 cells were grown in IMDM media + 10% Tet-free FBS + 1% penicillin/streptomycin. Knockout induction was achieved through Cas9 expression by addition of doxycycline.

extract_protocol:
At day 6 and day 16 cells were collected (60 million cells per sample) for genomic DNA preps with PureLink Genomic DNA Mini Kit (Invitrogen; 16 columns per sample).
200ug gDNA (to maintain representation) was used for PCRs with Ex Taq polymerase (TaKaRa) to prepare sgRNA libraries following Broad Institute’s protocol with P5 mix of oligos and barcoded P7 oligos. Libraries (354 nt product) were gel purified with QIAquick Gel Extraction Kit (QIAGEN), followed by MinElute PCR Purification kit (QIAGEN) for buffer exchange.

treatment_protocol: Doxycycline added to the transduced cells was at final concentration of 1µg/ml, and was kept on cells for 6 days (cells were passaged every 2 days).

value: blood cells

value: eHAP iCas9

value: myeloid cells (CML)

value: near diploid, derived from male CML patient

value: Cas9 expression with doxycycline to induce KO (4 days)


title: RNAseq Replicate 2 from AML patient UD5 after Relapse


title: 4-week PFC Akap11 +/- Bulk RNA-seq Sample 2

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: EXO1_KO_D16_R1


title: 12-week HP Akap11 WT Bulk RNA-seq Sample 4

source_name: Hippocampus

value: Hippocampus


title: RNAseq Replicate 1 from AML patient UD5 after Relapse


title: 12-week HP Akap11 WT Bulk RNA-seq Sample 5


title: EXO1_KO_D16_R3


title: Human primary chodroctes treated with IL-1β 2

description: Library name: 12idHOACHONDRnm44tyIL1BDMSOrp2-1IL1BDMSO


title: RNAseq Replicate 3 from AML patient UD10 at initial diagnosis


title: WT_D16_R2


title: Human primary chodroctes treated with IL-1β 1

description: Library name: 11idHOACHONDRnm43tyIL1BDMSOrp1-1IL1BDMSO


title: RNAseq Replicate 3 from AML patient UD10 after Relapse


title: RNAseq Replicate 2 from AML patient UD10 at initial diagnosis


title: WT_D16_R1


title: EXO1_KO_D6_R2


title: 12-week HP Akap11 WT Bulk RNA-seq Sample 1


title: 12-week HP Akap11 WT Bulk RNA-seq Sample 3


title: Human primary chodroctes treated with cyproheptadine 5

description: Library name: 10idHOACHONDRnm53tyCYPR30UMrp5-2CYPR30UM


title: EXO1_KO_D6_R1


title: RNAseq Replicate 1 from AML patient UD10 at initial diagnosis


title: Human primary chodroctes treated with IL-1β 4

description: Library name: 14idHOACHONDRnm53tyIL1BDMSOrp4-1IL1BDMSO


title: 12-week HP Akap11 WT Bulk RNA-seq Sample 2


title: EXO1_KO_D6_R3


title: 4-week PFC Akap11 +/- Bulk RNA-seq Sample 1


title: Human primary chodroctes treated with cyproheptadine 3

description: Library name: 08idHOACHONDRnm49tyCYPR30UMrp3-2CYPR30UM


title: RNAseq Replicate 1 from AML patient UD10 after Relapse


title: WT_D6_R3


title: 12-week HP Akap11 -/- Bulk RNA-seq Sample 5


title: RNAseq Replicate 2 from AML patient UD10 after Relapse


title: Human primary chodroctes treated with cyproheptadine 2

description: Library name: 07idHOACHONDRnm44tyCYPR30UMrp2-2CYPR30UM


title: Human primary chodroctes treated with cyproheptadine 1

description: Library name: 06idHOACHONDRnm43tyCYPR30UMrp1-2CYPR30UM


title: WT_D16_R3


title: Human primary chodroctes treated with DMSO (Control) 5

description: Library name: 05idHOACHONDRnm53tyDMSOCTRLrp5-0DMSOCTRL


title: WT_D6_R2


title: 12-week HP Akap11 -/- Bulk RNA-seq Sample 3


title: Human primary chodroctes treated with cyproheptadine 4

description: Library name: 09idHOACHONDRnm50tyCYPR30UMrp4-2CYPR30UM


title: RNAseq Replicate 2 from AML patient AML2 at initial diagnosis


title: WT_D6_R1


title: RNAseq Replicate 3 from AML patient AML2 at initial diagnosis


title: Human primary chodroctes treated with DMSO (Control) 4

description: Library name: 04idHOACHONDRnm50tyDMSOCTRLrp4-0DMSOCTRL


title: 12-week HP Akap11 -/- Bulk RNA-seq Sample 2


title: RNAseq Replicate 1 from AML patient AML2 at initial diagnosis


title: 12-week HP Akap11 -/- Bulk RNA-seq Sample 1


title: GF adipose tissue of 2 apple-shaped and 2 pear-shaped subjects

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
EIF3_EIF4_library
Libraries prepared from ADSCs isolated from GF adipose tissue of 4 apple-shaped and 4 pear-shaped subjects. Pear shaped subjects: 16, 44, 28 and 36 Apple shaped subjects: 19, 37, 23 and 27.

data_processing:
Fastq files were processed using the CogentAP pipeline (v1.0). Briefly, reads were trimmed with cutadapt and aligned to the GRCh37 reference genome using STAR aligner. Gene counts were created using Subread.
Assembly: GRCh37
Supplementary files format and content: Processed files include raw read count values for genes for each sample.

source_name: GF adipose tissue

growth_protocol: Cells were cultured in aMEM supplemented with 2.5% FBS, FGF and EGF.

extract_protocol:
Cells were harvest at 80% confluency using trypsin.
Selected cell were subjected to first-strand cDNA synthesis initiated by oligo dT primer (SMART-Seq ICELL8 CDS), followed by template switching with template switching oligo (SMART-Seq ICELL8 oligonucleotide) for 2nd strand cDNA synthesis, prior to unbiased amplification of full-length cDNA. Synthesized full-length cDNA was tagmented by TDE1 (Illumina Tagment DNA enzyme) and amplified using forward (i5) and reverse (i7) indexing primers. Each single cell/nucleus was indexed by a unique combination of 1 of 72 forward and 1 of 72 reverse indexing primers allowing for downstream identification. Collected cDNA was purified twice using a 1:1 proportion of AMPure XP beads (Beckman, A63880), further amplified according to manufacturer’s instructions and purified again at a 1:1 proportion of AMPure XP beads. The resultant sequencing-ready cDNA librairy was assessed for concentration by fluorometer (Qubit) and quality by electrophoresis (Agilent Bioanalyzer high sensitivity DNA chips) respectively. Librairies were sequenced with Illumina HiSeq X

value: GF adipose tissue

value: ADSCs

tag: individuals


title: 12-week HP Akap11 +/- Bulk RNA-seq Sample 5

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Akap11 mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

tag: genotype


title: ABD adipose tissue of 2 apple-shaped and 2 pear-shaped subjects

description:
EIF1_EIF2_library
Libraries prepared from ADSCs isolated from ABD adipose tissue of 4 apple-shaped and 4 pear-shaped subjects. Pear shaped subjects: 16, 44, 28 and 36 Apple shaped subjects: 19, 37, 23 and 27.

source_name: ABD adipose tissue

value: ABD adipose tissue


title: RNAseq Replicate 2 from AML patient AML2 after Relapse


title: Human primary chodroctes treated with DMSO (Control) 2

description: Library name: 02idHOACHONDRnm44tyDMSOCTRLrp2-0DMSOCTRL


title: RNAseq Replicate 3 from AML patient AML2 after Relapse


title: 12-week HP Akap11 -/- Bulk RNA-seq Sample 4


title: Human primary chodroctes treated with DMSO (Control) 3

description: Library name: 03idHOACHONDRnm49tyDMSOCTRLrp3-0DMSOCTRL


title: neuron_edited

first: Xiaonan

last: Guan

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

data_processing:
Trim Galore was used to remove adaptor and low-quality reads.
The high-quality reads were mapped to human GRCh38 version genome using Bowtie2 with default parameters.
To match sequencing depth, 7 million reads were randomly sampled from each library. Peaks were called by MACS2.
For dCas9-Tet1 with sgRNA-3 sample, input and dCas9-Tet1 with scrambled sgRNA were used as control separately to call peaks. Then the overlapped peaks were defined as binding sites for dCas9-Tet1 with sgRNA-3.  (dC-T_11+3_chip is the dCas9-Tet1 with sgRNA-3 sample; dC-T_11+3_input is the input sample; dC-T_11+sc_chip is the dCas9-Tet1 with scrambled sgRNA sample.)
Assembly: human GRCh38 version genome
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Neuron derived from hESC

extract_protocol:
Briefly, cells were cross-linked by 1% formaldehyde in the medium for 10 min in room temperature, and then quenched by adding 0.125 M Glycine for 5 min. Collected cells were washed with PBS twice, and then re-suspended in 3.5 ml of sonication buffer. Sonication was performed for 10 cycles with 0.5 min pulse on and 1 min rest, and 24 watts in ice-water mixture. Then cell lysate was spun down with 14,000 x rpm for 10 min at 4 °C. 50 ul of supernatant was saved as input for gDNA. 10 ul of anti-Cas9 antibody (Active Motif) was added and incubate overnight at 4 °C. 50 ul protein G dynabeads was added into antibody-cell lysate mixture and incubate overnight at 4 °C. Then beads were washed with sonication buffer, sonication buffer with high salt (500 mM NaCl), LiCl wash buffer, and TE buffer. Bound protein-DNA complex was eluted from beads by incubation in a 65 °C oven for 15 min, and then reverse cross-linked under 65 °C over-night. The bound DNA was purified with Qiagen QIAquick PCR Purification Kit, and then subject to sequencing.
NEBNext® Ultra™ II DNA Library Prep Kit was used

tag: cell line

value: Neuron derived from hESC

value: human neuron cells

value: neurons derived from dCas9-Tet1 methylation edited RTT hESCs

tag: chip antibody

value: anti-CTCF antibody


title: 12-week HP Akap11 +/- Bulk RNA-seq Sample 4

tag: tissue


title: Human primary chodroctes treated with DMSO (Control) 1

description: Library name: 01idHOACHONDRnm43tyDMSOCTRLrp1-0DMSOCTRL

value: primary chondrocytes


title: RNAseq Replicate 1 from AML patient AML2 after Relapse

value: AML


title: D1_Johnson (Bladder Cancer)

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

description: Library name: D1_Johnson

data_processing:
Image alignment, UMI counting and spatial mapping were performed using 10x Genomics Loupe Browser and Space Ranger (version 3.1.0) pipeline. Quality-control metrics were reviewed to exclude low-quality bins prior to downstream analyses.
Supplementary files format and content: D1_Johnson.tar.gz
Library strategy: Spatial Transcriptomics

source_name: Bladder

extract_protocol: Archival FFPE tissue blocks from muscle-invasive bladder cancer patients treated at The Houston Methodist Hospital were obtained under IRB protocol PRO00037670 (?Molecular analysis of archived cancer tissues?). FFPE tissue sections were processed using the 10x Genomics Visium HD Spatial Gene Expression platform according to the manufacturer?s protocol (Visium HD Spatial Gene Expression Reagent Kits for FFPE, CG000663). Briefly, 5 µm-thick FFPE sections were mounted onto Visium HD slides and baked at 60°C for 1 hour. Following deparaffinization and heat-induced epitope retrieval, tissue sections were hybridized with probe sets targeting the human transcriptome and subjected to reverse transcription to capture spatial barcodes and unique molecular identifiers (UMIs). .Slides were then permeabilized at 37 °C for 30 minutes to release the barcoded cDNA fragments, which were collected and amplified to generate sequencing libraries. Whole-transcriptome libraries were sequenced on an Illumina platform to a target depth of approximately 200?300 million reads per capture area.

value: Bladder


title: 12-week HP Akap11 +/- Bulk RNA-seq Sample 3

first: Ally

last: Nicolella

address: 75 Ames St

institute: Broad Institute


title: synovial fibroblasts, RA109_aPD-L1

city: TOKYO

first: HITOSHI

last: TOYODA

address: 1-5-8 Hatanodai

institute: SHOWA UNIVERCITY

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Transcriptome sequencing (100 bp paired-end sequencing) was performed on a NovaSeq 6000 (Illumina Inc.).
Adapter sequences and low-quality bases in pairedend reads were removed with fastp (version 0.22.0).
Filtered paired-end reads were mapped to the human reference genome (GRCh38) by HISAT2 (version 2.2.1) and expression levels were quantified by StringTie (version 2.1.7).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes Counts values for each Sample

source_name: synovial tissue

growth_protocol: RA synovial tissues (STs) were obtained from patients undergoing arthroplasty or synovectomy. Fresh STs were minced and digested in a tissue enzyme digestion solution. RA-FLS were maintained in RPMI 1640 medium with L-glutamine, phenol red, and sodium pyruvate (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific Life Technologies Japan, Tokyo, Japan) and 100 U/mL penicillin-streptomycin (FUJIFILM Wako Pure Chemical Corporation) at 37°C in an atmosphere containing 5% CO2. Cells were seeded into 6-well plates (BD Biosciences, Bedford, MA, USA) at a density of 1 × 105cells per well and maintained in complete medium.

extract_protocol:
Total RNA extracted from RAFLS was isolated from the cells using RNeasy Mini Kit (QIAGEN Inc., CA USA)
Sequencing libraries were prepared from poly-A selected RNA of each sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc., CA, USA).

treatment_protocol: After overnight serum starvation (0.1% BSA in RPMI medium), RA-FLSs were stimulated with TNF-a (R&D Systems, Minneapolis, MN, USA)(1, 10, 50 ng/ml), then RA-FLSs were stimulated with αPD-L1 ab (BioXCell) or Ctrl IgG (Rat, Sigma-Aldrich) at 100 μg/ml for 24 h.

tag: individual

value: synovial tissue

value: primary culture

value: synovial fibroblasts

value: female

tag: treatment

value: anti-PD-L1 antibody (100 µg/ml)


title: hNP-Mock

data_processing:
4C-seq samples were processed using fourfold.
Assembly: hg19
Supplementary files format and content: wig files
Library strategy: 4C

extract_protocol:
neuronal cultures were dissociated using Accutase and 5 million cells were resuspended in 5 mL 10% FBS in PBS. 5 mL of 4% formaldehyde in 10% FBS in PBS was added and cells were crosslinked for 10 minutes. Glycine was added to a final concentration of 0.125M and cells were centrifuged at 300 rcf for 5 minutes. Cells were washed twice with PBS, then snap frozen and stored at -80 C.
To amplify 4C libraries, PCR amplification was performed with 16 x 50 μL PCR reactions using Roche Expand Long Template polymerase (Roche 11759060001). Reaction conditions are as follows: 11.2 μL Roche Expand Long Template Polymerase, 80 μL of 10 X Roche Buffer 1, 16 μL of 10 mM dNTPs (Promega PAU1515), 112 μL of 10 M forward primer, 112 μL of 10 M reverse primer, 200 ng 4C template DNA, and H2O until 800 μL total. Reactions were mixed and then distributed into 16 x 50 μL reactions for amplification. Cycling conditions were: 2 minutes at 94 C, 10 seconds at 94 C, 1 minute at 63 C, 30 seconds at 68 C, repeat steps 2-4 but decrease annealing temperature by one degree, until 53 C is reached at which point the reaction is cycled an additional 15 times at 53 C, after 25 total cycles are performed the reaction is held for 5 minutes at 68 C and then 4 C. Libraries were cleaned-up using a Roche High Pure PCR purification kit (Roche 11732676001) using 4 columns per library. Purified 4C-seq libraries were resuspended in 120 μL of 10 mM Tris-HCl pH 7.5.

value: Mock

tag: cell type

value: Neurons derived from Rest syndrome like hESCs (RTT hESCs)


title: Heart_II_hires

description: Library name: Heart_II_hires

data_processing:
ST by 10x Genomics Visium The tissue slides were permeabilized at 37 °C for 6 min, and polyadenylated mRNA was captured by oligonucleotides bound to the slides. Reverse transcription, second-strand synthesis, complementary DNA (cDNA) amplification and library preparation proceeded using the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics, 1000520) according to the manufacturer’s protocol. After evaluation by real-time PCR, cDNA amplification included 13-14 cycles. Indexed libraries were pooled equimolarly and sequenced on a NovaSeq X Plus instrument in a PE28/150 run (Illumina). An average of 26, 011 paired reads were generated per spot and the median genes per spot were 2,277. Tissues were stained with H&E, and slides were scanned on a Pannoramic MIDI scanner (3DHISTECH) using a ×20, 0.8-NA objective.
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol: FFPE heart failure tissue samples were collected using standard-of-care procedures. Tissue sections (10 μm) obtained from the FFPE tissues were mounted on Visium spatial gene expression slides (10x Genomics, 1000520). The samples were processed as described in the manufacturer’s protocols.

value: Heart


title: 12-week HP Akap11 +/- Bulk RNA-seq Sample 2

value: Hippocampus


title: hNP-dC-T

value: dC-T

value: Neurons derived from dCas9-Tet1 methylation edited RTT hESCs


title: STKO_DMXAA2

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA of STING-KO Primary islet treated with DMXAA

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: Primary islet

growth_protocol: Primary islet isolation from mice was performed as previously described with slight modification47. Briefly, freshly prepared collagenase P solution (0.75 mg/mL) was injected into the pancreas via the ampulla of vater to make the pancreas fully inflated. The perfused pancreas was digested at 37 ℃ water bath and shake at 60 rpm for 20~30 min, islets were handpicked under a stereoscopic microscope. Islets were recovered in complete RPMI1640 medium overnight and ready for the following experiments the next day.

extract_protocol:
Total RNA of multiple tissues were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

treatment_protocol: Primary islets were isolated from 25~30 weeks WT and Sting-/- mice and cultured with 1640 medium with 10% FBS. Then the islets were incubated with DMSO or DMXAA (50 μg/mL) for 3 hours.

value: Primary islet

value: STING KO

tag: agent

value: DMXAA


title: synovial fibroblasts, RA108_aPD-L1


title: HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep4

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with RPKM values for every gene and every sample

source_name: peripheral blood

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: i'NKT cells are isolated from peripheral blood mononuclear cells stimed by aGalcer(200μg/ml)/ IL-2(50UI) for 7 days

value: peripheral blood

tag: disease state

value: HCC

value: i'NKT cells

value: aGalcer/IL-2 treated


title: synovial fibroblasts, RA109_NS

value: synovial tissue

value: primary culture

value: Ctrl IgG (100 µg/ml)


title: synovial fibroblasts, RA108_NS

value: synovial fibroblasts

value: female


title: 12-week HP Akap11 +/- Bulk RNA-seq Sample 1

tag: age


title: HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep3


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 6

value: WT


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 5


title: STKO_DMXAA1


title: STKO_DMSO2

description: expressed RNA of STING-KO Primary islet treated with DMSO

value: DMSO


title: LNCaP, siPCCA, 3

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 100 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCh38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: prostate

extract_protocol:
RNA was extracted from cells using the Ambion PureLink RNA Mini Kit (Life Technologies) according to the manufacturer's instructions and treated with DNase I (amplification grade, Sigma-Aldrich).
RNA libraries were prepared for sequencing using  Illumina stranded mRNA library preparation kit

value: prostate

value: LNCaP

value: adenocarcinoma

value: PCCA knock down


title: HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep2


title: neuron_mock

value: Neuron derived from hESC

value: human neuron cells

value: neurons derived from Rest syndrome like hESCs(RTT hESCs)

value: anti-CTCF antibody


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 4

value: Hippocampus


title: HCC, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep1

value: peripheral blood

value: HCC

value: i'NKT cells

value: aGalcer/IL-2 treated


title: STKO_DMSO1

value: Primary islet

value: STING KO


title: LNCaP, siPCCA, 2


title: CHB, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep3

value: CHB


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 3

value: WT


title: WT_DMXAA2

description: expressed RNA of WT Primary islet treated with DMXAA

value: wildtype

value: DMXAA


title: LNCaP, siControl, 3

value: prostate

value: LNCaP

value: adenocarcinoma


title: WT_DMXAA1


title: WT_DMSO2

description: expressed RNA of WT Primary islet treated with DMSO

value: DMSO


title: LNCaP, siControl, 2


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 1


title: CHB, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep2


title: 4-week HP Akap11 -/- Bulk RNA-seq Sample 5


title: CHB, peripheral blood, aGalcer/IL-2 treated, i'NKT cells, biol rep1


title: WT_DMSO1


title: LNCaP, siControl, 1


title: 4-week HP Akap11 -/- Bulk RNA-seq Sample 4


title: HD, aGalcer/IL-2 treated, i'NKT cells, biol rep2

value: HD


title: HD, aGalcer/IL-2 treated, i'NKT cells, biol rep3


title: ZR_3

data_processing:
Raw data were trimmed, aligned to sgRNA sequences from the Brunello library (https://www.nature.com/articles/s41467-018-07901-8), and counted using the built-in count function of MaGeCK (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0554-4). The MaGeCK test command was used to compare sgRNA counts between indicated experimental conditions and to generate sgRNA ranking analyses.
Assembly: sgRNA sequences from the Brunello library (https://www.nature.com/articles/s41467-018-07901-8)
Supplementary files format and content: Tab separated counts per sgRNA per sample.
Library strategy: sgRNA amplicon-seq

extract_protocol:
At day 10 cells were collected (60 million cells per sample) for genomic DNA preps with PureLink Genomic DNA Mini Kit (Invitrogen; 16 columns per sample).
200ug gDNA (to maintain representation) was used for PCRs with Ex Taq polymerase (TaKaRa) to prepare sgRNA libraries following Broad Institute’s protocol with P5 mix of oligos and barcoded P7 oligos. Libraries (354 nt product) were gel purified with QIAquick Gel Extraction Kit (QIAGEN), followed by MinElute PCR Purification kit (QIAGEN) for buffer exchange.

treatment_protocol: Doxycycline added to the transduced cells was at final concentration of 1µg/ml, and was kept on cells for 10 days (cells were passaged every 2-3 days).

value: blood cells

value: eHAP iCas9

value: myeloid cells (CML)

value: near diploid, derived from male CML patient

value: Cas9 expression with doxycycline to induce KO (4 days)


title: Kidney_day25_scATAC

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: Uniklinik RWTH Aachen

description:
Library name: Sample 8
10X multiome

library_source: genomic single cell

data_processing:
The Cell Ranger ARC Software Suite (version 1.0.1) was used for processing sequencing information and single cell barcodes.
scATAC-seq fragments for each timepoint was merged, then macs2(version 2.2.7.1) was used to do peakcalling.
Seurat (version 3.2.3) was used to process snRNA-seq data and ArchR(version 1.0.2) was used to process snATAC-seq data
hg38
barcodes: barcodes present in input data
Assembly: fragments: a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay and positions are 0-based. The columns are defined as following: chrom, chromStart, chromEnd, barcode and duplicateCount.
Supplementary files format and content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary files format and content: features: a bed file contains the gene expression.

source_name: Kidney organoid

extract_protocol: All protocols to generate 10X Single Cell Multiome ATAC + Gene Expression, including sample prep, library prep, instrument and sequencing settings, are available here: https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expre

value: Kidney organoid

value: Day 25


title: 4-week HP Akap11 -/- Bulk RNA-seq Sample 3

city: Cambridge

value: Hippocampus


title: ZR_2


title: Kidney_day25_scRNA

description:
Library name: Sample 7
10X multiome


title: 4-week HP Akap11 -/- Bulk RNA-seq Sample 2


title: LNCaP, siPCCA, 1

value: PCCA knock down


title: 4-week HP Akap11 WT Bulk RNA-seq Sample 2

value: WT


title: HD, aGalcer/IL-2 treated, i'NKT cells, biol rep1

value: peripheral blood

value: i'NKT cells

value: aGalcer/IL-2 treated


title: DNA sequencing from AML patient UD5 after Relapse

data_processing:
Sequencing reads were basecalled with Guppy and aligned to the GRCh37 reference genome version with minimap2. Methylation calling has been performed with Nanopolish.
Assembly: GRCh37
Supplementary files format and content: We provide tables reporting methylation frequency and entropy for each sample. Each file contains 6 columns indicating respectively: chromosome, position, methylation entropy, number of reads supporting methylation entropy value, methylaiton frequency,  number of reads supporting methylation frequency value

extract_protocol:
AML: DNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
AML: DNA library preparation was performed with Sequencing Kit SQK-LSK109.

value: Bone Marrow


title: 4-week HP Akap11 -/- Bulk RNA-seq Sample 1


title: DNA sequencing from AML patient UD5 at initial diagnosis


title: Kidney_day19_scATAC

description:
Library name: Sample 6
10X multiome

value: Day 19


title: 4-week HP Akap11 +/- Bulk RNA-seq Sample 7


title: Kidney_day19_scRNA

description:
Library name: Sample 5
10X multiome


title: ZR_1


title: FG_3


title: FG_1


title: Kidney_day12_scRNA

description:
Library name: Sample 3
10X multiome

value: Day 12


title: DNA sequencing from AML patient UD10 at initial diagnosis


title: 4-week HP Akap11 +/- Bulk RNA-seq Sample 5


title: Kidney_day12_scATAC

description:
Library name: Sample 4
10X multiome


title: 4-week HP Akap11 +/- Bulk RNA-seq Sample 4