title: CD64+F4/80+ macrophages from CD64CRE Trem2 fl/fl mice rep 3

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq (version 4.0.0 and version 7.1.0)
Demultiplexed data was then processed using the Cell Ranger count pipeline (version 7.1.0).
Assembly: mm10
Supplementary files format and content: h5 file including raw gene count (output CellRanger)

value: CD64+F4/80+ macrophages

value: CD64CRE Trem2 fl/fl

value: 10x Genomics – v3.1


title: Live CD45+ liver cells post PBS rep 1, GEX

status: Public on Oct 30 2024

type: SRA

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq (version 4.0.0 and version 7.1.0)
Demultiplexed data was then processed using the Cell Ranger count pipeline (version 7.1.0).
Assembly: mm10
Supplementary files format and content: h5 file including raw gene count (output CellRanger)
Library strategy: CITEseq

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol: All Methods listed in De Ponti, Buijko et al. TREM2 expression delineates spatially restricted and ontogenically distinct hepatic macrophages populations required for tissue repair. Immunity. 2024.

tag: tissue

value: liver

tag: strain

tag: cell type

value: Live CD45+

tag: treatment

value: PBS

tag: type

value: CITEseq

tag: platform

value: 10x Genomics – v2

tag: library

value: mRNA

tag: nraddedabs


title: Live CD45+ liver cells post PBS rep 1, ADT

description: ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

value: ADT

tag: adt

value: IgG1_Rat_l, CD11a, Ly6C, CD43, CD5, CD62L, CD150, CLEC4F, CD86, CD62P, CD300LG, CD25, CD278, VSIG4, CD11b_mh, CD304, CD38, CD301b, CD44_mh, CD49d, CD274, CD127, CD117, CD15_mh, Siglec, CD102, Panendothelial, CD14, ERK1, CX3CR1, Ly6G, CD63, CD62E, Folate, Tim4, IgG2a_Rat_k, Integrin, CD195, CD192, CD69, CD106, IA_IE, CD19, NK1_1, CD357, FceRIa, CD54, CD4, CD134, CD206, CD223, CD24, MERTK, CD335, CD152, IgG1_Rat_k, CD16_CD32, CD8a, CD11c, KLRG1_mh, CD140a, XCR1, IgG_Hamster, CD68, CD23, CD49f, MAdCAM1, CD79b, CD207_mh, CD55, CD103, CD73, CD137, CD20, Ly6A_Ly6E, CD83, CD169, CD279, CD301a, CD197, CD366, IgG2c_Rat_k, CD64, CD135, CD370, CD21_CD35, Notch, CD122, CD309_A0554, CD93, CD183, IgG2a_Mouse_k, CD27_A0191, CD28, F4_80, IgG1_Mouse_k, CD8b, CD45R_B220, CD204, ESAM, CD200, CD196, CD115, IgG2b_Rat_k, P2RY12, IgG2b_Mouse_k, CD3e, TCRgd, CD71, CD172a, CD163, CD90, Ly6G_Ly6C, CD45_A0178, CD309_A0553, CD3, CD326, CD45, TCRg, CD29, TER119, TCRb8, TCRb, IgD, IRF4, CD41, RORg, IgG2a, CXCR4, CD146, CD45_A0157, H2Kb, TCRg3, TCRb5, CD36, CD90_A0075, TCRg2, CD49b, CD48, ReceptorD4, GABRB3, biotin, KCC2, CD201, IgM, CD200R, CD193, CD200R3, CD138, CD317, CD105, CD9, P2X7R, CD371, CD22, CD39, CD314, DR3, IL33Ra, Ly49H, Ly49D, CD185, CD278.1, TIGIT, CD80, CD49a, CD1d, CD226, CD34, TLR4, CD300c_d, JAML, CD272, PIRA_PIRB, CD26, DLL1, CD270, 4_1BB, ENPP1, CD2, Mac2, CD31, CD107a, CD124, CD95, Streptavidin_A0951, Streptavidin_A0952, Streptavidin_A0953, Streptavidin_A0954, Streptavidin_A0955, Ly6D, CD170

tag: adt added

value: IgG1_Rat_l, CD5, CD278, CD150, CD62P, CLEC4F, CD62L, CD86, VSIG4, CD11a, CD43, CD38, CD117, Ly6C, CD127, CD300LG, CD25, CD274, Tim4, MAdCAM1, CD195, CD304, CD301b, CD15_mh, Panendothelial, Siglec, ERK1, CD62E, CD63, IA_IE, CD102, CD192, CD106, CD357, CD69, Folate, CD19, CD14, NK1_1, CD4, CD335, Integrin, CD49d, CD134, CD223, FceRIa, MERTK, CD206, CD55, CD79b, CD44_mh, CD140a, Ly6G, CD8a, IgG1_Rat_k, Ly6A_Ly6E, IgG2a_Rat_k, CD370, CX3CR1, CD73, CD16_CD32, CD103, CD23, CD137, KLRG1_mh, CD68, CD207_mh, CD169, CD54, CD152, CD20, CD83, XCR1, CD21_CD35, CD11b_mh, CD197, IgG_Hamster, CD135, Notch, CD27_A0191, ESAM, CD183, CD366, IgG1_Mouse_k, CD122, CD45R_B220, IgG2c_Rat_k, CD309_A0554, CD93, CD8b, F4_80, CD11c, CD28, CD200, CD64, CD279, CD301a, CD24, CD204, CD49f, CD196, IgG2a_Mouse_k, IgG2b_Rat_k, CD115, IgG2b_Mouse_k, P2RY12, CD3e


title: Myeloid liver cells 24hrs post APAP, GEX

value: Myeloid

value: APAP 24h


title: CD64+F4/80+ macrophages from CD64CRE Trem2 fl/fl mice rep 2

library_source: transcriptomic single cell

value: single cell RNA-seq


title: CD64+F4/80+ macrophages from Trem2 fl/fl mice rep 4

value: Trem2 fl/fl


title: CD64+F4/80+ macrophages from Trem2 fl/fl mice rep 3


title: CD64+F4/80+ macrophages from CD64CRE Trem2 fl/fl mice rep 1


title: CD64+F4/80+ macrophages from Trem2 fl/fl mice rep 1


title: B10, mi, IS

status: Public on Oct 25 2024

city: Beijing

first: Lin

last: Ma

address: No. 2 Anzhen Rd District, Beijing, China

country: China

institute: Beijing Anzhen Hospital

data_processing:
The designated genome GRCh38 (ftp://ftp.ensembl.org/pub/release-101/fasta/ homo_ sapiens/) was adopted as a reference for sequence alignment and following testing. Considering the characteristics of the miRNA sequencing data, the Burrows–Wheeler alignment tool (https://sourceforge.net/ projects/bio-bwa/files/) was used to complete sequence alignment.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include differential expression tables.

organism: Homo sapiens

source_name: tumor tissue

extract_protocol:
Frozen plasma specimens were thawed at 26 °C, followed by stepwise centrifugation at 3,000 × g for 15 min to remove cell clumps. The supernatant was diluted 1:7 in phosphate-buffered saline (PBS), recentrifuged at 13,000 × g for 30 min, passed through a 0.22-μm filter for removal of oversized particles, and finally ultracentrifuged at 100,000 × g and 4 °C for 2 h for pelleting of the exosomes using a P50A72-986 rotor (CP100NX; Hitachi, Brea, CA, USA) . The pellet was dissolved in PBS and ultracentrifuged again as was done before, and re-suspended in 100 µL PBS. Exosomes were obtained by the SEC method described by Boing et al. with slight modifications. In brief, 1 mL of 0.8-μm-filtered plasma was diluted 1:1.5 in PBS, passed through Exosupur® columns (Echo Biotech, Beijing, China), and eluted with 0.01 mmol/L PBS. Eluate fractions (2 mL) were ultimately collected and further concentrated to 200 μL by 100 kDa molecular weight cut-off Amicon® Ultra spin filters according to the manufacturer’s instructions (Merck, Darmstadt, Germany). EVs were separated from tissues using a previously established protocol with slight modifications. Briefly, 200 mg tissue was cut into slice on dry ice and incubated with dissociation mixture from Miltenyi human tumor dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) for 10–5 min at RT, and passed through a 70-μm filter for removal of residual tissues. After spinning at 300 × g and 4 °C for 10 min, the supernatant was collected in a new tube and spun again at 2,000 × g and 4 °C for 10 min for depletion of cell debris. The supernatant was then centrifuged at 10,000 × g for 20 min at 4 °C, followed by filtration through a 0.22-μm filter to further remove cell debris. The cell-free suspension was ultracentrifuged at 150,000 × g and 4 °C for 2 h. Following UC, the pellet was dissolved in 1 mL PBS and processed similar to the procedure followed for isolation of plasma exosomes.
Ribosomal RNA, which accounts for approximately 90% of the total RNA, was depleted prior to library preparation. At least a total of 4.5 ng of RNA per sample was used for library sequencing using a SMARTer stranded total RNA-Seq Kit V2 (Takara Bio USA, Inc.) according to the manufacturer’s recommendations. Library quality was assessed using an Agilent Bioanalyzer 2100 and quantitative PCR, as well as clustering of the index-coded samples on the acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA). Finally, the Illumina NovaSeq 6000 platform was used for library and paired-end sequencing.

value: tumor tissue

tag: disease

value: CM with IS


title: B11, mi, IS


title: B8, mi, IS


title: B6, mi, IS


title: B7, mi, IS


title: B4, mi, non-IS

value: CM without IS


title: B5, mi, IS


title: B3, mi, non-IS


title: B1, mi, non-IS


title: A11, mi, IS

source_name: plasma

value: plasma


title: A10, mi, IS


title: A6, mi, IS


title: CD64+F4/80+ macrophages from CD64CRE Trem2 fl/fl mice rep4

value: liver

value: CD64+F4/80+ macrophages

value: CD64CRE Trem2 fl/fl

value: 10x Genomics – v3.1


title: A5, mi, IS


title: A4, mi, non-IS


title: A3, mi, non-IS


title: B7, lnc, IS

extract_protocol:
Frozen plasma specimens were thawed at 26 °C, followed by stepwise centrifugation at 3,000 × g for 15 min to remove cell clumps. The supernatant was diluted 1:7 in phosphate-buffered saline (PBS), recentrifuged at 13,000 × g for 30 min, passed through a 0.22-μm filter for removal of oversized particles, and finally ultracentrifuged at 100,000 × g and 4 °C for 2 h for pelleting of the exosomes using a P50A72-986 rotor (CP100NX; Hitachi, Brea, CA, USA) . The pellet was dissolved in PBS and ultracentrifuged again as was done before, and re-suspended in 100 µL PBS. Exosomes were obtained by the SEC method described by Boing et al. with slight modifications. In brief, 1 mL of 0.8-μm-filtered plasma was diluted 1:1.5 in PBS, passed through Exosupur® columns (Echo Biotech, Beijing, China), and eluted with 0.01 mmol/L PBS. Eluate fractions (2 mL) were ultimately collected and further concentrated to 200 μL by 100 kDa molecular weight cut-off Amicon® Ultra spin filters according to the manufacturer’s instructions (Merck, Darmstadt, Germany). EVs were separated from tissues using a previously established protocol with slight modifications. Briefly, 200 mg tissue was cut into slice on dry ice and incubated with dissociation mixture from Miltenyi human tumor dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) for 10–5 min at RT, and passed through a 70-μm filter for removal of residual tissues. After spinning at 300 × g and 4 °C for 10 min, the supernatant was collected in a new tube and spun again at 2,000 × g and 4 °C for 10 min for depletion of cell debris. The supernatant was then centrifuged at 10,000 × g for 20 min at 4 °C, followed by filtration through a 0.22-μm filter to further remove cell debris. The cell-free suspension was ultracentrifuged at 150,000 × g and 4 °C for 2 h. Following UC, the pellet was dissolved in 1 mL PBS and processed similar to the procedure followed for isolation of plasma exosomes.
Ribosomal RNA, which accounts for approximately 90% of the total RNA, was depleted prior to library preparation. At least a total of 4.5 ng of RNA per sample was used for library sequencing using a SMARTer stranded total RNA-Seq Kit V2 (Takara Bio USA, Inc.) according to the manufacturer’s recommendations. Library quality was assessed using an Agilent Bioanalyzer 2100 and quantitative PCR, as well as clustering of the index-coded samples on the acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA). Finally, the Illumina NovaSeq 6000 platform was used for library and paired-end sequencing.
lncRNA-seq


title: A1, mi, non-IS


title: B8, lnc, IS


title: B10, lnc, IS


title: CD64+F4/80+ macrophages from Trem2 fl/fl mice rep 2


title: B11, lnc, IS


title: B9, mi, IS


title: B9, lnc, IS


title: B6, lnc, IS


title: B5, lnc, IS


title: B3, lnc, non-IS


title: A8, lnc, IS


title: A9, mi, IS


title: A11, lnc, IS


title: A5, lnc, IS


title: A4, lnc, non-IS


title: A10, lnc, IS


title: A7, lnc, IS


title: A7, mi, IS


title: A1, lnc, non-IS


title: B1, lnc, non-IS


title: A9, lnc, IS


title: B4, lnc, non-IS


title: A8, mi, IS


title: BRAIN,HealthyControl,TC,3,biol rep 2

status: Public on Oct 24 2024

city: Abbiategrasso

first: Riccardo Rocco

last: Ferrari

address: Corso San Martino, 10

country: Italy

institute: Golgi Cenci Foundation

description:
HC3T2
All_libnorml_AD_TC.counts.txt

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: Brain tissue

extract_protocol:
Total RNA was isolated from brain tissue samples using Trizol® reagent. The specifications from the manufacturer were followed.
CORALL Total RNA-seq Library Prep Kit, using 500-ng total RNA. Qualities of sequencing libraries were assessed with 4200 TapeStation with the D1000 High-Sensitivity Kit. RNA processing has been carried out using Illumina NextSeq 550 Sequencing.

value: Brain tissue

tag: brain region

value: Temporal cortex

tag: Sex

value: M

tag: disease state

value: No dementia

tag: age


title: BRAIN,HealthyControl,SN,3,biol rep 2

description:
HC3S2
All_libnorml_AD_SN.counts.txt

value: Subtantia nigra


title: BRAIN,HealthyControl,CG,3,biol rep 2

description:
HC3C2
All_libnorml_AD_CG.counts.txt

value: Cingulate gyrus


title: BRAIN,HealthyControl,CG,2,biol rep 2

description:
HC2C2
All_libnorml_AD_CG.counts.txt

value: F


title: BRAIN,HealthyControl,HI,3,biol rep 2

description:
HC3H2
All_libnorml_AD_HI.counts.txt

value: Hippocampus


title: BRAIN,HealthyControl,PC,2,biol rep 2

description:
HC2P2
All_libnorml_AD_PC.counts.txt

value: Parietal cortex


title: BRAIN,HealthyControl,TC,1,biol rep 2

description:
HC1T2
All_libnorml_AD_TC.counts.txt


title: BRAIN,HealthyControl,TC,2,biol rep 2

description:
HC2T2
All_libnorml_AD_TC.counts.txt


title: BRAIN,HealthyControl,SN,1,biol rep 2

description:
HC1S2
All_libnorml_AD_SN.counts.txt


title: BRAIN,HealthyControl,CG,1,biol rep 2

description:
HC1C2
All_libnorml_AD_CG.counts.txt


title: BRAIN,HealthyControl,PC,1,biol rep 2

description:
HC1P2
All_libnorml_AD_PC.counts.txt


title: BRAIN,HealthyControl,SN,3,biol rep 1

description:
HC3S1
All_libnorml_AD_SN.counts.txt


title: A3, lnc, non-IS


title: BRAIN,HealthyControl,CG,3,biol rep 1

description:
HC3C1
All_libnorml_AD_CG.counts.txt


title: BRAIN,HealthyControl,CG,2,biol rep 1

description:
HC2C1
All_libnorml_AD_CG.counts.txt


title: BRAIN,HealthyControl,SN,2,biol rep 1

description:
HC2S1
All_libnorml_AD_SN.counts.txt


title: BRAIN,HealthyControl,SN,2,biol rep 2

description:
HC2S2
All_libnorml_AD_SN.counts.txt


title: BRAIN,HealthyControl,HI,1,biol rep 2

description:
HC1H2
All_libnorml_AD_HI.counts.txt


title: BRAIN,HealthyControl,TC,3,biol rep 1

description:
HC3T1
All_libnorml_AD_TC.counts.txt


title: BRAIN,HealthyControl,PC,3,biol rep 1

description:
HC3P1
All_libnorml_AD_PC.counts.txt


title: BRAIN,HealthyControl,HI,2,biol rep 2

description:
HC2H2
All_libnorml_AD_HI.counts.txt


title: BRAIN,HealthyControl,PC,3,biol rep 2

description:
HC3P2
All_libnorml_AD_PC.counts.txt


title: BRAIN,HealthyControl,PC,2,biol rep 1

description:
HC2P1
All_libnorml_AD_PC.counts.txt


title: BRAIN,HealthyControl,HI,2,biol rep 1

description:
HC2H1
All_libnorml_AD_HI.counts.txt


title: BRAIN,HealthyControl,CG,1,biol rep 1

description:
HC1C1
All_libnorml_AD_CG.counts.txt


title: BRAIN,HealthyControl,PC,1,biol rep 1

description:
HC1P1
All_libnorml_AD_PC.counts.txt


title: BRAIN,HealthyControl,TC,2,biol rep 1

description:
HC2T1
All_libnorml_AD_TC.counts.txt


title: BRAIN,HealthyControl,SN,1,biol rep 1

description:
HC1S1
All_libnorml_AD_SN.counts.txt


title: BRAIN,HealthyControl,HI,1,biol rep 1

description:
HC1H1
All_libnorml_AD_HI.counts.txt


title: BRAIN,HealthyControl,TC,1,biol rep 1

description:
HC1T1
All_libnorml_AD_TC.counts.txt


title: BRAIN,LBD,SN,6

description:
LBD6S
All_libnorml_LBD_SN.counts.txt

value: LBD


title: BRAIN,LBD,CG,6

description:
LBD6C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,TC,4

description:
LBD4T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,HI,3

description:
LBD3H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,LBD,TC,6

description:
LBD6T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,SN,2

description:
LBD2S
All_libnorml_LBD_SN.counts.txt


title: BRAIN,LBD,SN,5

description:
LBD5S
All_libnorml_LBD_SN.counts.txt


title: BRAIN,LBD,CG,5

description:
LBD5C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,CG,4

description:
LBD4C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,SN,4

description:
LBD4S
All_libnorml_LBD_SN.counts.txt


title: BRAIN,LBD,HI,6

description:
LBD6H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,LBD,CG,2

description:
LBD2C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,TC,2

description:
LBD2T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,HI,2

description:
LBD2H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,LBD,HI,5

description:
LBD5H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,LBD,PC,6

description:
LBD6P
All_libnorml_LBD_PC.counts.txt


title: BRAIN,LBD,SN,1

description:
LBD1S
All_libnorml_LBD_SN.counts.txt


title: BRAIN,LBD,TC,5

description:
LBD5T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,PC,4

description:
LBD4P
All_libnorml_LBD_PC.counts.txt


title: BRAIN,LBD,TC,1

description:
LBD1T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,CG,1

description:
LBD1C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,PC,2

description:
LBD2P
All_libnorml_LBD_PC.counts.txt


title: BRAIN,LBD,HI,4

description:
LBD4H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,LBD,SN,3

description:
LBD3S
All_libnorml_LBD_SN.counts.txt


title: BRAIN,LBD,TC,3

description:
LBD3T
All_libnorml_LBD_TC.counts.txt


title: BRAIN,LBD,CG,3

description:
LBD3C
All_libnorml_LBD_CG.counts.txt


title: BRAIN,LBD,PC,3

description:
LBD3P
All_libnorml_LBD_PC.counts.txt


title: BRAIN,LBD,HI,1

description:
LBD1H
All_libnorml_LBD_HI.counts.txt


title: BRAIN,AD,SN,6

description:
AD6S
All_libnorml_AD_SN.counts.txt

value: AD


title: BRAIN,AD,TC,6

description:
AD6T
All_libnorml_AD_TC.counts.txt


title: BRAIN,AD,HI,6

description:
AD6H
All_libnorml_AD_HI.counts.txt


title: BRAIN,AD,SN,5

description:
AD5S
All_libnorml_AD_SN.counts.txt


title: BRAIN,AD,PC,6

description:
AD6P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,CG,6

description:
AD6C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,PC,5

description:
AD5P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,HI,5

description:
AD5H
All_libnorml_AD_HI.counts.txt


title: BRAIN,AD,CG,5

description:
AD5C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,CG,4

description:
AD4C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,TC,4

description:
AD4T
All_libnorml_AD_TC.counts.txt


title: BRAIN,AD,HI,4

description:
AD4H
All_libnorml_AD_HI.counts.txt


title: BRAIN,AD,PC,3

description:
AD3P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,SN,4

description:
AD4S
All_libnorml_AD_SN.counts.txt


title: BRAIN,AD,PC,4

description:
AD4P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,SN,3

description:
AD3S
All_libnorml_AD_SN.counts.txt


title: BRAIN,AD,TC,3

description:
AD3T
All_libnorml_AD_TC.counts.txt


title: BRAIN,AD,HI,3

description:
AD3H
All_libnorml_AD_HI.counts.txt


title: BRAIN,AD,CG,2

description:
AD2C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,SN,2

description:
AD2S
All_libnorml_AD_SN.counts.txt


title: BRAIN,AD,SN,1

description:
AD1S
All_libnorml_AD_SN.counts.txt


title: BRAIN,AD,TC,5

description:
AD5T
All_libnorml_AD_TC.counts.txt


title: BRAIN,AD,TC,2

description:
AD2T
All_libnorml_AD_TC.counts.txt


title: BRAIN,AD,HI,2

description:
AD2H
All_libnorml_AD_HI.counts.txt


title: BRAIN,AD,PC,1

description:
AD1P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,PC,2

description:
AD2P
All_libnorml_AD_PC.counts.txt


title: BRAIN,AD,CG,1

description:
AD1C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,CG,3

description:
AD3C
All_libnorml_AD_CG.counts.txt


title: BRAIN,AD,HI,1

description:
AD1H
All_libnorml_AD_HI.counts.txt


title: G4R-81-FOXA1

status: Public on Oct 16 2024

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

country: USA

institute: UTHSC

library_source: genomic

data_processing:
Data was aligned using hg38 and STAR 2.0
Peak calling using MACS3 default settings
Assembly: hg38
Supplementary files format and content: bed files

molecule: genomic DNA

source_name: WHIM23 patient-derived xenograft

extract_protocol:
Proteins were immunoprecipitated and the DNA that is pulled down with the proteins are sequenced.
Illumina Truseq DNA

value: WHIM23 patient-derived xenograft

tag: cell line

value: WHIM23 PDX

value: breast cancer

tag: chip antibody

value: anti-FOXA1 (ab170933 from Abcam)

value: Enobosarm Resistant


title: G4R-737-ER

tag: tissue

value: anti-ER-alpha (sc8002 from Santa Cruz)


title: G4R-737-AR

value: anti-AR (PG21,  Millipore)


title: BRAIN,AD,TC,1

description:
AD1T
All_libnorml_AD_TC.counts.txt

value: Brain tissue

value: Temporal cortex


title: G4R-736-AR


title: G4R-737-FOXA1


title: G4R-736-FOXA1


title: G4R-Input

value: none (input)


title: G4-728-AR

value: Enobosarm


title: G4R-736-ER


title: G4R-81-ER


title: G4-728-FOXA1


title: G4-728-ER


title: BRAIN,LBD,PC,5

description:
LBD5P
All_libnorml_LBD_PC.counts.txt


title: G4-724-AR


title: G4-724-FOXA1


title: G4-724-ER


title: G4-723-AR


title: G4-723-ER


title: G4-723-FOXA1


title: G4-Input


title: G4R-81-AR


title: G2-720-FOXA1

value: DHT


title: G2-729-AR


title: G2-729-ER


title: G2-713-ER


title: G1-703-FOXA1

value: Vehicle


title: G2-729-FOXA1


title: G2-720-AR


title: G1-703-ER


title: G1-703-AR


title: G2-720-ER


title: G1-702-FOXA1


title: G2-713-AR


title: G1-702-AR


title: G1-701-FOXA1


title: G1-702-ER


title: G1-701-AR


title: G1-Input


title: G1-701-ER


title: SMC Donor6, Proliferative, DNA

status: Public on Oct 14 2024

city: Charlottesville

first: Nicolas

last: Barbera

state: Virginia

address: 1335 Lee Street

department: Department of Genome Sciences

institute: University of Virginia

description:
5F_ByAllele_dnaCounts.csv
5F_ByAllele_dnaAnnot.csv

data_processing:
Libraries were sequenced on NextSeq2000 instruments using a 40% PhiX spike-in and base called using the instrument's Real Time Analysis software.
Multiplexed paired end (PE) Illumina sequencing data was split based on sample index allowing up to zero substitutions in the barcode sequence.
The MPRAflow pipeline (Gordon et al, 2019) was used to process the MPRA data:
Consensus sequences were aligned to all designed oligo sequences using BWA MEM with parameters penalizing soft-clipping of alignment ends (-L 80). For RNA/DNA counts, sequences were matched against the designed barcode sequences
To normalize RNA and DNA for different sequencing depths in each sample, reads were divided the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Assembly: GRCh37
Supplementary files format and content: csv file containing count data for each CRS
Supplementary files format and content: csv file containing annotation data for count file

source_name: Ascending Aorta

growth_protocol: HCASMCs were cultured in either Lonza Complete SmBM media or FBS Free SmBM media on gelatin-coated dishes to an average of 10 million cells

extract_protocol:
Genomic DNA and RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen). 60ug RNA and reverse-transcribed using Superscript II. The cDNA and 12 ug genomic DNA were used for PCR. PCR products were size-selected with an agarose gel, purified with HighPrep PCR reagent (MagBio Genomics, cat. no. AC60050)
PCR library preparation was performed to add unique molecular identifiers (UMI) and Sample Index barcode sequences for four cycles. An additional amplification cycle was run for 30 cycles.

value: Ascending Aorta

value: Smooth Muscle Cell

value: female

value: Proliferative


title: SMC Donor2, Proliferative, DNA

value: male


title: SMC Donor4, Proliferative, DNA


title: SMC Donor5, Proliferative, DNA


title: SMC Donor3, Proliferative, DNA


title: SMC Donor1, Proliferative, DNA


title: SMC Donor6, Proliferative, RNA

description:
5F_ByAllele_rnaCounts.csv
5F_ByAllele_rnaAnnot.csv


title: G2-713-FOXA1

value: WHIM23 patient-derived xenograft

value: WHIM23 PDX


title: G2-Input

value: breast cancer


title: SMC Donor5, Proliferative, RNA


title: SMC Donor4, Proliferative, RNA


title: SMC Donor4, Quiescent, DNA

description:
NF_ByAllele_dnaCounts.csv
NF_ByAllele_dnaAnnot.csv

value: Quiescent


title: SMC Donor3, Quiescent, DNA


title: SMC Donor2, Proliferative, RNA


title: SMC Donor6, Quiescent, DNA


title: BRAIN,HealthyControl,HI,3,biol rep 1

description:
HC3H1
All_libnorml_AD_HI.counts.txt

value: Hippocampus

value: M

value: No dementia


title: SMC Donor5, Quiescent, DNA


title: SMC Donor1, Quiescent, DNA


title: SMC Donor5, Quiescent, RNA

description:
NF_ByAllele_rnaCounts.csv
NF_ByAllele_rnaAnnot.csv


title: SMC Donor3, Quiescent, RNA


title: SMC Donor4, Quiescent, RNA


title: SMC Donor1, Proliferative, RNA


title: SMC Donor6, Quiescent, RNA


title: SMC Donor3, Proliferative, RNA


title: SMC Donor1, Quiescent, RNA


title: SMC Donor2, Quiescent, DNA


title: mta, drought, GMUCT, replicate 3

status: Public on Oct 07 2024

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description:
Sequenced on NovaSeq X Plus
mta-DT3-GMUCT

data_processing:
Raw read quality was first diagnosed using FastQC.
Trim Galore! and Cutadapt was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Reads were aligned to the TAIR10 genome assembly using STAR (Dobin et al 2014).
M6A enriched regions were detected using the MACS2 callpeak algorithm (--nomodel, –extsize 50, -g 32542107, -q 1e-2) to identify regions with statistically significant enrichment in IP samples relative to input.
FeatureCounts (Liao et al 2014) was used for determine transcript abundance on gene-level features extracted from the TAIR10 annotation retrived from EnsemblPlants (Kersey et al 2016).
Bedtools (genomecov -bga -split -scale) was used to generate a bedGraph file from the BAM files. A per-million scaling factor was provided to the -scale flag, determined by 1,000,000/total fragments (total fragments = [samtools view -F 260 -c]/2). Then, bedGraphToBigWig (kentUtils) was used to generate bigWig files for visualizing read depth across TAIR10 features
Assembly: TAIR10
Supplementary files format and content: .narrowPeak: m6a enriched regions per strand as computed by MACS2 callpeak algoirthm (plus or minus), https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html
Supplementary files format and content: .counts: raw counts for genes (gene.counts) and non-coding RNAs (ncrna.counts) for each sample computed by FeatureCounts
Supplementary files format and content: .bigWig: files for visualizing read coverage (scaled to reads per million, RPM) in a genome browser (e.g. IGV) for each sample.

molecule: other

organism: Arabidopsis thaliana

source_name: Rosette

growth_protocol: Seeds of Arabidopsis thaliana (Col-0) and a post-embryonic mutant for MTA (mta ABI3:MTA) were planted in  pots (11 * 9 cm) filled with soil. The pots were kept at 4°C for 3 days for stratification and transferred to a growth chamber maintained under 8 h/16 h light/dark photocycle at 22/20 °C for 8 days, then transferred to a growth chamber under a12 h/12 h light/dark photocycle at 22/20°C for 9 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen); polysome was isolated as described by Govindan et al. (2022). Sucrose fractions with more than two ribosomes were pooled and used for polysome RNA isolation using TRIzol reagent.
M6A-RIP-seq: Approximately 1.5 µg of poly(A) RNA was chemically fragmented with the NEBNext Magnesium RNA Fragmentation Module (NEB). Fragmented poly(A) RNA was used for m6A-IP using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer’s instructions and 10% was kept, prior to IP, as the input control. Libraries from input (mRNA) and immunoprecipitated RNA (m6A-IP) were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).  Polysome-seq: Polysomes were isolated as previously described (Li et al., 2017; Govindan et al., 2022). Harvested leaf tissue was ground into a fine powder in liquid nitrogen. Approximately 1.25 mL of polysome extraction buffer (200 mM tris, pH 9.0, 200 mM KCl, 26 mM MgCl2, 25 mM EGTA, 100 μM 2-mercaptoethanol, 50 μg mL-1 cycloheximide, 50 μg mL-1 chloramphenicol, 1% Triton X-100, 1% Brij-35, 1% Tween-40, 1% IGEPAL CA-630, 2% polyoxyethylene 10 tridecyl ether, 1% deoxycholic acid) was added to the powdered tissue (500 mg) and mixed thoroughly and incubated on ice for 10 min with occasional mixing by inverting tubes. The mixture was spun for 2 min at 16,900 g (4°C). Approximately 600 μL of supernatant was layered onto the top of the sucrose density gradients (20–60% sucrose, w/v) and centrifuged for 120 min at 275,000 g in a Optima LE-80 centrifuge (Beckman, Brea, CA, USA). The optical density of the gradient fractions was measured by using a UA-5 detector and a Gradient Fractionator (model 640; ISCO, Lincoln, NE, USA) at 254 nm. Sucrose fractions with more than two ribosomes were pooled and used for polysome RNA isolation using TRIzol reagent. Approximately 8 μg of polysome RNA was used for mRNA purification and subsequently the RNA-seq library was constructed and sequenced using the KAPA Stranded mRNA-seq Kit (Illumina).  GMUCT: GMUCT libraries were constructed from 600 ng poly(A) RNA as previously described (Willmann et al., 2014).
RNA-seq, RIP-seq, Polysome-seq, OTHER: GMUCT

treatment_protocol: Seventeen days old seedlings were irrigated to soil capacity, then divided into two groups; one group was stopped watering and subjected to progressive drought stress for 12 days, whereas the other group continued to grow under regular watering. Rosette leaves from control and drought stress treatment were collected and frozen in liquid nitrogen, then stored at -80°C for RNA and polysome isolation.

value: Rosette

tag: ecotype

tag: genotype

value: mta

value: Drought


title: mta, unstressed, GMUCT, replicate 3

description:
Sequenced on NovaSeq X Plus
mta-CK3-GMUCT

tag: treatment

value: Unstressed


title: mta, drought, GMUCT, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-DT1-GMUCT


title: mta, unstressed, GMUCT, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-CK2-GMUCT


title: mta, unstressed, GMUCT, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-CK1-GMUCT


title: mta, drought, GMUCT, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-DT2-GMUCT


title: Col-0, drought, GMUCT, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-DT3-GMUCT

value: WT


title: Col-0, drought, GMUCT, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-DT2-GMUCT


title: Col-0, unstressed, GMUCT, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-CK3-GMUCT


title: Col-0, drought, GMUCT, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-DT1-GMUCT


title: SMC Donor2, Quiescent, RNA

value: Ascending Aorta

tag: cell type


title: Col-0, unstressed, GMUCT, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-CK1-GMUCT


title: Col-0, unstressed, GMUCT, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-CK2-GMUCT


title: mta, drought, polysomal RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
mta-DT3-PS


title: mta, unstressed, polysomal RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-CK1-PS


title: mta, unstressed, polysomal RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
mta-CK3-PS


title: mta, drought, polysomal RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-DT1-PS


title: mta, unstressed, polysomal RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-CK2-PS


title: Col-0, drought, polysomal RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-DT1-PS


title: Col-0, drought, polysomal RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-DT3-PS


title: mta, drought, polysomal RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-DT2-PS


title: Col-0, unstressed, polysomal RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-CK3-PS


title: mta, drought, m6a IP replicate 3

description:
Sequenced on NovaSeq X Plus
mta-DT3-m6A


title: Col-0, unstressed, polysomal RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-CK2-PS


title: Col-0, drought, m6A-IP, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-DT3-m6A


title: Col-0, drought, m6A-IP, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-DT1-m6A


title: mta, unstressed, m6a IP replicate 1

description:
Sequenced on NovaSeq X Plus
mta-CK1-m6A


title: Col-0, drought, m6A-IP, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-DT2-m6A


title: Col-0, unstressed, m6A-RIP, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-CK3-m6A


title: Col-0, unstressed, m6A-RIP, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-CK2-m6A


title: mta, drought, m6a IP replicate 1

description:
Sequenced on NovaSeq X Plus
mta-DT1-m6A


title: Col-0, unstressed, m6A-RIP, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-CK1-m6A


title: mta, drought, input RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
mta-DT3-input

molecule: polyA RNA


title: Col-0, drought, polysomal RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-DT2-PS


title: Col-0, unstressed, polysomal RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-CK1-PS


title: mta, drought, input RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-DT2-input


title: mta, drought, input RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-DT1-input


title: mta, unstressed, input RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
mta-CK3-input


title: mta, unstressed, input RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
mta-CK1-input


title: mta, drought, m6a IP replicate 2

description:
Sequenced on NovaSeq X Plus
mta-DT2-m6A


title: mta, unstressed, input RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
mta-CK2-input


title: Col-0, unstressed, input RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-CK3-input


title: Col-0, drought, input RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-DT1-input


title: mta, unstressed, m6a IP replicate 3

description:
Sequenced on NovaSeq X Plus
mta-CK3-m6A


title: Col-0, drought, input RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-DT2-input


title: Col-0, drought, input RNA, replicate 3

description:
Sequenced on NovaSeq X Plus
WT-DT3-input


title: CRSwNP_NP45

status: Public on Oct 03 2024

city: Jinan

first: Xinyu

last: Xie

address: Wenhua West Road

institute: Shandong University

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: hg38
Supplementary files format and content: Tab-separate values files and matrix files

source_name: nasal polyps

extract_protocol:
The nasal biopsies were washed in phosphate-buffered saline and were cut into approximately 0.5-mm3 pieces in RPMI-1640 medium supplemented with 1% penicillin/streptomycin, and then enzymatically digested with the Multi Tissue Dissociation Kit 2 according to the manufacturer’s instructions. The resultant cell suspension was sequentially filtered through cell strainers with pore sizes of 70 μm and 40 µm (BD).The samples were centrifuged at 300g for 10 minutes. Subsequent to the removal of the supernatant, the cells forming the pellet were reconstituted in red blood cell lysis buffer and subjected to a 2-minute incubation on ice to lyse the red blood cells. Following dual washes with PBS, the cellular pellets were re-suspended in PBS supplemented with 0.04% bovine serum albumin.
DNBelab C Series High-throughput Single-cell System (BGI-research) was utilized for scRNA-seq library preparation.

value: nasal polyps

tag: condition

value: chronic rhinosinusitis and nasal polyps


title: Col-0, unstressed, input RNA, replicate 1

description:
Sequenced on NovaSeq X Plus
WT-CK1-input


title: mta, unstressed, m6a IP replicate 2

description:
Sequenced on NovaSeq X Plus
mta-CK2-m6A


title: CRSwNP_NP38


title: Col-0, unstressed, input RNA, replicate 2

description:
Sequenced on NovaSeq X Plus
WT-CK2-input


title: CRSwNP_MT25

source_name: middle turbinate

value: middle turbinate


title: CRSwNP_MT21


title: CRSwNP_MT26


title: CRSwNP_IT19

source_name: inferior turbinate

value: inferior turbinate


title: CRSwNP_NP35


title: CRSwNP_IT13


title: HC_IT02

value: healthy


title: HC_IT01


title: BRAIN,LBD,PC,1

description:
LBD1P
All_libnorml_LBD_PC.counts.txt

value: Brain tissue

value: Parietal cortex

value: LBD


title: RNAseq_SC_10_4

status: Public on Oct 02 2024

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

description: 50bp SE

data_processing:
RNAseq reads were pre-processed and mapped to the genome using STAR aligner. Read counts were obtained using ht-seeq count
RRBS analysis was done using Bisulfite Analysis Tool (BAT). Reads were trimmed using Trimmomatic and reads aligned to the killifish genome. We used BAT modules to call methylation levels and DMRs.
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011125445.2/
Assembly: GCF_011125445.2 and GCF_011125445.2_MU-UCD_Fhet_4.1_genomic.gtf
Supplementary files format and content: RNAseq read counts (txt files)
Supplementary files format and content: RRBS calls

organism: Fundulus heteroclitus

source_name: Liver

growth_protocol: Fish were maintained in ambient seawater (32 parts per thousand salinity). These fish are the offspring of the adult fish obtained from New Bedford Harbor (New Bedford, MA) and Scorton Creek (Sandwich, MA). Adult fish were spawned in the laboratory by In vitro fertilization and raised following established protocols (Karchner et al., 2022). Embryos were reared in the lab for six months prior to conducting the experiments.

extract_protocol:
Total RNA and DNA were isolated using ZR-Duet DNA/RNA Mini Prep kit (Zymo Research, California). RNA and DNA were checked for quality using Bioanalyzer and Tape station respectively.
Gene expression libraries were prepared usiig Illumina External HiSeq2500 High Output SE 50 were sequenced; DNA methylation was conducted using Reduced Representation Bisulfite Sequencing. Library preparations were done using Premium RRBS kit (Diagenode) and sequenced using Illumina Hi-Seq 4000 PE 50bp reads

treatment_protocol: Six month old juvenile killifish (Fundulus heteroclitus) were exposed to two levels of hypoxia (5% and 10% oxygen) for 6 hours. A control group was maintained under ambient oxygen conditions (Normoxia). At the end of exposure, liver tissue was dissected and used for gene expression and DNA methylation profiling.

value: Liver

value: Scorton Creek

value: 10% hypoxia


title: RNAseq_NBH_C_2

description: 50bp SE

value: New Bedford Harbor

value: Control


title: RNAseq_NBH_C_3

description: 50bp SE


title: RNAseq_SC_C_3

description: 50bp SE


title: RNAseq_SC_C_4

description: 50bp SE


title: RNAseq_SC_C_2

description: 50bp SE


title: RNAseq_NBH_C_1

description: 50bp SE


title: RNAseq_SC_10_5

description: 50bp SE


title: RNAseq_NBH_10_4

description: 50bp SE


title: RNAseq_SC_10_3

description: 50bp SE


title: RNAseq_SC_C_1

description: 50bp SE


title: RNAseq_NBH_10_5

description: 50bp SE


title: CRSwNP_NP37


title: RNAseq_NBH_C_4

description: 50bp SE


title: RNAseq_SC_C_5

description: 50bp SE


title: RNAseq_NBH_C_5

description: 50bp SE


title: RNAseq_SC_10_1

description: 50bp SE


title: RNAseq_SC_10_2

description: 50bp SE


title: RNAseq_SC_5_5

description: 50bp SE

value: 5% hypoxia


title: RNAseq_NBH_10_1

description: 50bp SE


title: RNAseq_SC_5_3

description: 50bp SE


title: RNAseq_SC_5_2

description: 50bp SE


title: RNAseq_SC_5_1

description: 50bp SE


title: RNAseq_SC_5_4

description: 50bp SE


title: RNAseq_NBH_5_5

description: 50bp SE


title: RNAseq_NBH_5_4

description: 50bp SE


title: RNAseq_NBH_10_2

description: 50bp SE


title: RNAseq_NBH_10_3

description: 50bp SE


title: RNAseq_NBH_5_1

description: 50bp SE


title: RRBS_SC_C_4

description: 50bp PE


title: RRBS_NBH_C_5

description: 50bp PE


title: RRBS_NBH_C_2

description: 50bp PE


title: RRBS_SC_C_3

description: 50bp PE


title: RRBS_NBH_C_4

description: 50bp PE


title: RRBS_SC_10_3

description: 50bp PE


title: RRBS_NBH_C_1

description: 50bp PE


title: RRBS_SC_10_4

description: 50bp PE


title: RRBS_SC_10_1

description: 50bp PE


title: A6, lnc, IS

value: plasma

value: CM with IS


title: RRBS_SC_C_2

description: 50bp PE


title: RNAseq_NBH_5_2

description: 50bp SE


title: RRBS_NBH_C_3

description: 50bp PE


title: RRBS_NBH_10_1

description: 50bp PE


title: RRBS_NBH_5_3

description: 50bp PE


title: RRBS_SC_5_2

description: 50bp PE


title: RRBS_NBH_10_3

description: 50bp PE


title: RRBS_SC_5_4

description: 50bp PE


title: RRBS_SC_10_2

description: 50bp PE


title: RRBS_SC_5_3

description: 50bp PE


title: RRBS_SC_C_1

description: 50bp PE


title: RNAseq_NBH_5_3

description: 50bp SE


title: RRBS_NBH_5_2

description: 50bp PE


title: RRBS_NBH_5_1

description: 50bp PE


title: luminal PBeYFP, 2w, mouse 2, plate 2

status: Public on Sep 24 2024

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Data were analyzed using the Seurat package v.4.0. 6. Cell QC filtering was done using the following thresholds: nCount > 500, nCount < 40000, nFeature > 300 percent.mito < 20, log10GenesPerUMI > 0.8 percent.spike_in < 30.
AddModuleScore from the Seurat package was used for inferring the activity of gene-sets of interest.
Assembly: mm10
Supplementary files format and content: Raw and filtered Seurat RDS objects

source_name: prostate

extract_protocol:
Whole mouse prostates were harvested and digested to single cell solution as previously described (10, 46) using 5mg/mL collagenase in advanced DMEM (+/+/+) for 1 hour of shaking at 37 degrees Celsius. This was followed by medium washes and 15-minute incubation with TrypLE at 37 degrees Celsius then the digest solution was passed through a 70uM filter. Cells treated with DAPI for live/dead stain were sorted at the Department of BioMedical Research FACs Core facilities in a solution of PBS with 0.2% fetal bovine serum. Protocols for sorting single eYFP+ cells into wells of 384-well SORT-Seq plates were conducted under the recommendations of Single Cell Discoveries (https://www.scdiscoveries.com/). eYFP positive control prostates were used to adjust A488 gating settings for each sort. Two animals and three 96-well plates were collected as single cells for each group, centrifuged at 4 degrees Celsius, snap-frozen on dry ice, and then stored at -80 degrees Celsius until transport to sequencing facilities
The SORT-seq protocol (a partially robotized method based on the CEL-Seq2 protocol) was used to generate libraries for scRNA-Seq

treatment_protocol: The luminal model eYFP+ selected cells were collected from male prostates with a Probasin (PB) -Cre (PB-Cre) recombinase system. Basal cells were labeled in vivo using a tamoxifen-inducible cytokeratin 5 (Krt5)- specific Cre recombinase system paired with a Rosa26eYFP reporter gene. Cre activation occurs by 8 weeks of age, and eYFP+ cells were collected with FACs two weeks later for both models.

value: prostate

value: luminal

value: PBeYFP

tag: time

value: 2 weeks


title: basal CK5eYFP, 2w, mouse 2, plate 2

value: basal


title: RRBS_SC_5_1

description: 50bp PE


title: basal CK5eYFP, 2w, mouse 1, plate 2


title: RRBS_NBH_10_2

description: 50bp PE


title: luminal PBeYFP, 2w, mouse 1, plate 1


title: basal CK5eYFP, 2w, mouse 2, plate 1


title: Mouse cortex, KO, E15.5, Rep3

status: Public on Sep 18 2024

first: Liang-Yu

last: Ni

state: Beijing

address: Peking university Health Science center

institute: Peking University

description:
Mouse RNA-Seq.csv
KO_3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg38 & mm38
Supplementary files format and content: Read counts in .csv files

source_name: Mouse, Cortex, Emx1-Cre; CDYLloxp/loxp

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8-2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length).

value: Mouse, Cortex, Emx1-Cre; CDYLloxp/loxp

value: whole cortex

value: Emx3-Cre; CDYLloxp/loxp


title: basal CK5eYFP, 2w, mouse 1, plate 1


title: Mouse cortex, KO, E15.5, Rep2

description:
Mouse RNA-Seq.csv
KO_2

value: Emx2-Cre; CDYLloxp/loxp


title: Mouse cortex, WT, E15.5, Rep2

description:
Mouse RNA-Seq.csv
WT_2

source_name: Mouse, Cortex, CDYLloxp/loxp

value: Mouse, Cortex, CDYLloxp/loxp

value: CDYLloxp/loxp


title: Mouse cortex, WT, E15.5, Rep1

description:
Mouse RNA-Seq.csv
WT_1


title: Organoid, CDYL KO, Day80, Rep3

description:
Human RNA-Seq.csv
KO_D80_3

source_name: Organoid, CDYL KO

value: Organoid, CDYL KO

value: Cortical organoids

value: CDYL-/-


title: Organoid, Control, Day80, Rep2

description:
Human RNA-Seq.csv
H9_D80_2

source_name: Organoid, Control

value: Organoid, Control

value: CDYL+/+


title: Organoid, Control, Day80, Rep3

description:
Human RNA-Seq.csv
H9_D80_3


title: Organoid, CDYL KO, Day80, Rep1

description:
Human RNA-Seq.csv
KO_D80_1


title: Organoid, Control, Day80, Rep1

description:
Human RNA-Seq.csv
H9_D80_1


title: Organoid, CDYL KO, Day80, Rep2

description:
Human RNA-Seq.csv
KO_D80_2


title: Organoid, CDYL KO, Day30, Rep2

description:
Human RNA-Seq.csv
KO_D30_2


title: Organoid, CDYL KO, Day30, Rep1

description:
Human RNA-Seq.csv
KO_D30_1


title: Organoid, Control, Day30, Rep2

description:
Human RNA-Seq.csv
H9_D30_2


title: Organoid, Control, Day30, Rep3

description:
Human RNA-Seq.csv
H9_D30_3


title: Organoid, Control, Day30,Rep1

description:
Human RNA-Seq.csv
H9_D30_1


title: luminal PBeYFP, 2w, mouse 1, plate 2


title: P1 Het, male, replicate 2, snRNAseq

status: Public on Aug 12 2024

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

data_processing:
The demultiplexing, barcode processing, trimming, alignment, and gene counting was done using the ScaleBio ScaleRna Single-cell RNA Nextflow workflow v1.4.0 (https://github.com/ScaleBio/ScaleRna)
DoubletFinder v2.0.3 was used to remove doublets and Seurat v4.3.0 was used to process the feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
Supplementary files format and content: H5ad containing cell by feature matrix, metadata, and embeddings

source_name: Brain

extract_protocol:
For E14 and P1 samples, forebrain tissue from mice were dissected and flash frozen in liquid nitrogen. The brain tissues were Dounce homogenized in ice-cold homogenization buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1mM DTT, 1X cOmplete EDTA-free Protease Inhibitor (Roche 4693132001), and 0.2U/ul RNasin Inhibitor (Promega N2515) using a 2ml KIMBLE KONTES Dounce Tissue Grinder (DWK 885300-002) with 15 strokes with the “A” large clearance pestle, followed by 15 strokes of the “B” small clearance pestle. The homogenate was transferred to a 15 ml centrifuge tube. Walls of the homogenizer tubes were washed with 1ml of homogenization buffer and combined with the homogenate in the 15ml tube. The nuclei were pelleted by centrifugation in a swinging bucket rotor (Eppendorf S-4-104) at 500x g for 5 mins at 4°C. The supernatant was aspirated and discarded. The pellets were washed twice with 1ml nuclei wash buffer (DPBS, 1% BSA, and 0.2U/ul RNase inhibitor), filtered through a 40um Flowmi cell strainer (Millipore Sigma BAH136800040), and manually counted using a hemocytometer with Trypan Blue or propidium iodide (Biotium 40017).  For P21 samples, the pellets after the first centrifugation were resuspended in 1ml homogenization buffer. Density gradient centrifugation was performed to purify the nuclei from cellular debris and myelin generated during tissue dissociation. A 50% iodixanol-PBS working solution was prepared by diluting the stock solution of 60% w/v Optiprep (Millipore Sigma Aldrich D1556) with DPBS (ThermoFisher 14190136). A 35% iodixanol solution was made by diluting the 50% iodixanol with DPBS. To make the 25% Iodixanol layer, 1ml 50% iodixanol was added to 1ml of the homogenate containing the nuclei and debris. This was carefully layered on top of 2ml 35% iodixanol in a clear polycarbonate tube (Beckman Coulter 355672) and centrifuged using an Allegra 64R (Beckman Coulter 367586) at 10,000x g for 30 min at 4°C in a S0410 swinging bucket rotor (Beckman Coulter 364660) with no braking. After the centrifugation, myelin and cellular debris remaining at the top of the 25% iodixanol layer was aspirated and discarded. The purified nuclei at the interface of the 25% and 35% iodixanol layers was collected using a P1000 pipette and transferred to a clean 15ml centrifuge tube. The volume was brought up to 6 ml with nuclei wash and resuspension buffer and pelleted by centrifuging at 500x g for 5 min at 4°C. The supernatant was carefully removed, washed once with nuclei wash buffer to ensure removal of carryover ioxidanol, filtered through a 40um Flowmi cell strainer, and manually counted using a hemocytometer with Trypan Blue or propidium iodide.
The libraries were made according to manufacturer's instructions for Scale Biosciences' Single Cell RNA Kit.

value: Brain

tag: region

value: Forebrain

value: Male

value: Het

tag: strain

value: MYT1L S710fsX


title: P1 Het, male, replicate 3, snRNAseq


title: luminal PBeYFP, 2w, mouse 2, plate 1

value: prostate

value: luminal

value: PBeYFP

value: 2 weeks


title: P1 Het, female, replicate 1, snRNAseq

value: Female


title: P1 WT, female, replicate 3, snRNAseq

value: WT


title: P1 WT, female, replicate 2, snRNAseq


title: P1 WT, female, replicate 1, snRNAseq


title: Mouse cortex, KO, E15.5, Rep1

description:
Mouse RNA-Seq.csv
KO_1

value: Mouse, Cortex, Emx1-Cre; CDYLloxp/loxp

value: whole cortex

value: Emx1-Cre; CDYLloxp/loxp


title: Organoid, CDYL KO, Day30, Rep3

description:
Human RNA-Seq.csv
KO_D30_3

value: Organoid, CDYL KO

value: Cortical organoids

value: CDYL-/-


title: P1 Het, male, replicate 1, snRNAseq

value: Brain


title: P1 WT, male, replicate 1, snRNAseq

value: Forebrain


title: P1 WT, male, replicate 4, snRNAseq

value: Male


title: Mouse cortex, WT, E15.5, Rep3

description:
Mouse RNA-Seq.csv
WT_3

value: Mouse, Cortex, CDYLloxp/loxp

value: CDYLloxp/loxp


title: cortex,Olig1/2,E15.5, scRNA-seq

status: Public on Aug 10 2024

city: SHANGHAI

first: YU

last: TIAN

state: SHANGHAI

address: 131 DONGAN ROAD

institute: FUDAN UNIVERSITY

description: 10x Genomics

data_processing:
scRNA-seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
CUT&Tag: Basecells were performed using bcl2fastq v2.17 for Novaseq outut
Assembly: mm10 (scRNA-seq); mm39 (Cut&Tag)
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: bigWig

source_name: Cortex

extract_protocol:
ScRNA-seq were performed on FACS sorted tdT+ cells from the P1 Olig1/2f/f;IS-reporter mice cortex which were electroporated of pCAG-Cre plasmid at E15.5.Emx1-CRE;Olig1/2f/f mice cortex were dissected out at P7 and immediately submerged in fresh ice-cold Hanks balanced salt solution. The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit according to the manufacturer’s instructions.
The CUT&Tag assay was conducted on FACS-sorted GFP+ cells, using the cortex dissected from hGFAP-GFP at P1
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 or Illumina Hiseq4000.
CUT&Tag liabraries were prepared using the Vazyme#TD901 complemented with TruePrep® Index Kit V2 for Illumina  10 ng of DNA was used as starting material for CUT&Tag simples.Liabraries were amplified using 18 cycles on the thermocycler.

value: Cortex


title: P1 WT, male, replicate 2, snRNAseq

value: MYT1L S710fsX


title: P1 WT, male, replicate 3, snRNAseq


title: C1-C4flxflx;CRE_rep3_fb

status: Public on Aug 07 2024

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
50-bp paired-end raw sequence reads using lcdb-wf v1.9rc [github.com/lcdb/lcdb-wf]. Adapters were trimmed, along with light quality trimming, using cutadapt v3.4 with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 --minimum-length = 25”
Trimmed reads were provided to Salmon v1.10.1 for quantification. The Salmon index was built from a transcriptome fasta file created by using the GENCODE vM18 basic annotation and the GENCODE vM18 genome fasta file, using the gffread package.

Assembly: mm10
Supplementary files format and content: Salmon output directory as compressed tar

source_name: E 11.5 forebrain

extract_protocol:
RNA was isolated using trizol reagent
Libraries were prepared using TruSeq Stranded mRNA prep kit with PolyA purification and sequenced on Novaseq6000

value: E 11.5 forebrain

value: mut

tag: embryo

value: female


title: C1-C4flxflx_rep3_fb

value: wt


title: C1-C4flxflx;CRE_rep2_fb


title: C1-C4flxflx_rep2_fb


title: C1-C4flxflx;CRE_rep4_mb

source_name: E11.5 midbrain

value: E11.5 midbrain

value: male


title: C1-C4flxflx;CRE_rep3_mb


title: C1-C4flxflx;CRE_rep2_mb


title: C1-C4flxflx_rep1_fb


title: C1-C4flxflx;CRE_rep1_mb


title: C1-C4flxflx;CRE_rep1_fb


title: C1-C4flxflx_rep3_mb


title: P1 WT, male, replicate 5, snRNAseq

value: WT


title: C1-C4flxflx_rep2_mb


title: C1-C4flxflx_rep1_mb


title: E4.5_C5-C6_HOM_SC_234

data_processing:
50-bp paired-end raw sequence reads using lcdb-wf v1.9rc [github.com/lcdb/lcdb-wf]. Adapters were trimmed, along with light quality trimming, using cutadapt v3.4 with parameters “-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -q 20 --minimum-length = 25”
Trimmed reads were provided to Salmon v1.10.1 for quantification. The Salmon index was built from a transcriptome fasta file created by using the GENCODE vM18 basic annotation and the GENCODE vM18 genome fasta file, using the gffread package.
multimapping reads by default.
Assembly: mm10
Supplementary files format and content: Salmon output directory as compressed tar

source_name: E4.5 Blastocyst

extract_protocol:
RNA was isolated from each embryo using Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher, 61012) as previously described (Huffman et al., 2012).
Library preparation was done as described earlier (Trombetta et al., 2014) using Nextera XT DNA Library Prep Kit (Illumina, #FC-131-1024). Briefly, in a 384 well plate, 1 µl of cDNA, 2µl of Tagment DNA Buffer and 1µl of Amplicon Tagment Mix was mixed in ice and tagmentation was done in a thermocycler at 55°C for 10 mins. Reaction was neutralized with 1 µl of Neutralize Tagment Buffer, incubated at room temperature for 5 mins and transferred to ice. Amplification PCR was set up with 3µl of Nextera PCR Mastermix and 2µl of each adaptor from Illumina DNA/RNA UD Indexes Set A (Illumina, #20027213) per sample. Tagmented DNA was incubated at 72°C for 3 mins, 95°C for 30 secs and 12 cycles of 95°C for 10 secs, 55°C for 30 secs, 72°C for 1 min and a final extension at 72°C for 5 mins. Library DNA was purified with 0.9X SPRI and quality was assessed using D1000 Screen Tape assay (Agilent, #5067-5585) before sequencing.

treatment_protocol: Blastocysts at E4.5 were flushed out of the uterine horns from super-ovulated females using M2 media and transferred into 50 µl of pre-warmed lysis buffer (100mM Tris-HCl pH-7.5, 500mM LiCl, 10mM EDTA pH-8, 1%LiDS, 5mM DTT) in DNA low binding PCR tubes. Lysed embryos were stored in -20C and processed within a few weeks.

value: E4.5 Blastocyst

value: hom

tag: mod


title: E4.5_C5-C6_WT_SC_235


title: E4.5_C5-C6_HOM_SC_233


title: E4.5_C5-C6_WT_SC_232

data_processing:
50-bp paired-end raw sequence reads using lcdb-wf v1.9rc [github.com/lcdb/lcdb-wf]. Adapters were trimmed, along with light quality trimming, using cutadapt v3.4 with parameters “-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -q 20 --minimum-length = 25”
Trimmed reads were provided to Salmon v1.10.1 for quantification. The Salmon index was built from a transcriptome fasta file created by using the GENCODE vM18 basic annotation and the GENCODE vM18 genome fasta file, using the gffread package.

Assembly: mm10
Supplementary files format and content: Salmon output directory as compressed tar


title: E4.5_C5-C6_WT_SC_231


title: E4.5_C5-C6_WT_SC_230


title: E4.5_C5-C6_HOM_SC_229


title: E4.5_C7-C10_HOM_SC_228


title: C1-C4flxflx;CRE_rep4_fb


title: E4.5_C7-C10_WT_SC_227


title: E4.5_C7-C10_WT_SC_225


title: E4.5_C7-C10_HOM_SC_222


title: E4.5_C7-C10_WT_SC_221


title: E4.5_C7-C10_WT_SC_223


title: 2203_BA46

status: Public on Jul 22 2024

city: Cambridge

first: Sudeshna

last: Das

address: 65 Landsdowne St

department: Neurology

institute: MGH

data_processing:
Raw reads were processed using Cell Ranger 3.0.0 (10X Genomics) with default settings, pre-mRNA package and aligned to the human GRCh38 genome.
Assembly: GRCH38
Supplementary files format and content: matrix.mtx and tab separated files

extract_protocol:
Nuclei were isolated and sorted following published procedures18. Briefly, 30-40 forty-μm-thick cryostat sections were lysed in a sucrose lysis buffer (10 mM Tris-HCl pH 8.0, 320 mM sucrose, 5 mM CaCl2, 3 μM Mg(Ac)2, 0.1 mM EDTA, 1 mM DTT, and 0.1% Triton X-100). The resulting lysates were filtered through a 70 μm-pore cell strainer and nuclei were purified from filtrates by ultracentrifugation (107,000xg for 1.5 h at 4oC) through a sucrose cushion (10 mM Tris-HCl pH 8.0, 1.8 M sucrose, 3 μM Mg(Ac)2, 0.1 mM EDTA, and 1 mM DTT). Supernatants were removed and pellets were resuspended in 2% BSA/PBS containing RNase inhibitor (0.2 U/μL, Roche). To enrich astrocyte nuclei, we followed a strategy of depletion of neurons and oligodendrocytes. Nuclei were labeled with AlexaFluor647- conjugated mouse monoclonal anti-NeuN antibody (clone 1B7, Novus Biologicals, NBP1-92693AF647) and PE-conjugated mouse monoclonal anti-OLIG2 antibody (clone 211F1.1, EMD Millipore, MABN50A4). After washes, nuclei were stained with Sytox blue (Thermo Fisher) and sorted on a BD FACSAria Fusion. For each sample, we collected SytoxposNeuNposOLIG2neg and SytoxposNeuNnegOLIG2neg.
Single-nucleus cDNA libraries were constructed using the Chromium Single Cell 3‘ Reagents Kit V3 following the manufacturer’s instructions (10x Genomics). Samples were pooled and sequenced targeting at least 30K reads per cell on a Illumina NovaSeq 6000. Separation of NeuNposOLIG2neg and NeuNnegOLIG2neg into unique libraries allowed for increased number of reads and detected genes in non-neuronal cells as compared to published studies containing non-enriched nuclei
snRNA-seq

tag: assay type

value: RNA-Seq

tag: avgspotlen

tag: bases

tag: biomaterial provider

value: Hyman lab\, MADRC Brain Bank

tag: bioproject

tag: bytes

tag: center name

value: ABBVIE

tag: consent

value: public

tag: datastore filetype

tag: datastore provider

tag: datastore region

tag: isolate

tag: librarysource

value: TRANSCRIPTOMIC SINGLE CELL

tag: platform

value: ILLUMINA

tag: releasedate

tag: create date

tag: version

tag: sra study


title: 2203_V1

tag: tissue

tag: age

tag: Sex

tag: assay type

tag: avgspotlen


title: 1906_EC

source_name: EC

value: EC

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: center name


title: 1906_V2

tag: consent

tag: datastore filetype

tag: datastore provider

tag: datastore region

tag: isolate


title: E4.5_C5-C6_HOM_SC_236

tag: genotype

tag: mod

tag: embryo


title: 2259_V2

tag: tissue

tag: age

tag: librarysource

tag: platform

tag: releasedate

tag: create date

tag: version

tag: sra study


title: 1906_BA20

tag: Sex

tag: assay type

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: center name


title: E4.5_C7-C10_HOM_SC_224

tag: genotype

tag: mod

tag: embryo


title: 2259_V1

tag: tissue

tag: age

tag: consent

tag: datastore filetype

tag: datastore provider

tag: datastore region

tag: isolate

tag: librarysource


title: 2259_BA20

tag: Sex

tag: assay type

tag: avgspotlen

tag: platform

tag: releasedate

tag: create date

tag: version

tag: sra study


title: 2259_BA46

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: center name


title: 2259_EC

tag: tissue

tag: age

tag: consent

tag: datastore filetype

tag: datastore provider


title: 2097_BA46

tag: Sex

tag: assay type

tag: datastore region

tag: isolate

tag: librarysource


title: 2097_EC

tag: avgspotlen

tag: platform

tag: releasedate

tag: create date

tag: version


title: 2097_BA20

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: sra study


title: 2097_V2

tag: tissue

tag: age

tag: center name

tag: consent

tag: datastore filetype


title: 1845_V1

tag: Sex

tag: assay type

tag: datastore provider

tag: datastore region

tag: isolate


title: 1837_V1

tag: avgspotlen

tag: librarysource

tag: platform

tag: releasedate

tag: create date


title: 1837_V2

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: version


title: 2057_BA46

tag: tissue

tag: age

tag: center name

tag: consent

tag: sra study


title: 1906_BA46

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: datastore region


title: 1837_BA46

tag: avgspotlen

tag: isolate

tag: librarysource

tag: platform

tag: releasedate


title: 1872_V2

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: create date


title: 1872_V1

tag: tissue

tag: age

tag: center name

tag: consent

tag: version


title: 2068_V1

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 1872_BA20

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: platform


title: 1872_BA46

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: releasedate


title: 1628_BA46

tag: tissue

tag: age

tag: center name

tag: consent

tag: create date


title: 1628_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 1628_V2

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: sra study


title: 1628_EC

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: platform


title: 1628_V1

tag: tissue

tag: age

tag: center name

tag: consent

tag: releasedate


title: 2219_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 2219_V1

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: version


title: 2057_V1

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: sra study


title: 2097_V1

tag: tissue

tag: age

tag: center name

tag: consent

tag: platform


title: 2219_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 2219_EC

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: create date


title: 2169_EC

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: version


title: 2169_V2

tag: tissue

tag: age

tag: center name

tag: consent

tag: sra study


title: 2219_BA46

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: platform


title: 2169_V1

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: releasedate


title: 2169_BA46

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: create date


title: 2232_BA20

tag: tissue

tag: age

tag: center name

tag: consent

tag: version


title: 2232_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 2169_BA20

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: platform


title: 2068_BA20

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: releasedate


title: 2232_BA46

tag: tissue

tag: age

tag: center name

tag: consent

tag: create date


title: 1703_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 1821_V2

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: sra study


title: 1703_BA20

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: platform


title: 1845_BA46

tag: tissue

tag: age

tag: center name

tag: consent

tag: releasedate


title: 1872_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 1703_V1

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: version


title: 1845_V2

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: sra study


title: 2019_BA20

tag: tissue

tag: age

tag: center name

tag: consent

tag: platform


title: 1907_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 2019_EC

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: create date


title: 2019_V1

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: version


title: 2019_V2

tag: tissue

tag: age

tag: center name

tag: consent

tag: sra study


title: 2068_BA46

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: platform


title: 2019_BA46

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: releasedate


title: 1854_V1

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: create date


title: 1854_EC

tag: tissue

tag: age

tag: center name

tag: consent

tag: version


title: 1854_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 1854_BA46

tag: avgspotlen

tag: datastore region

tag: isolate

tag: librarysource

tag: platform


title: 1907_BA20

tag: bases

tag: biomaterial provider

tag: bioproject

tag: bytes

tag: releasedate


title: 2233_V2

tag: tissue

tag: age

tag: center name

tag: consent

tag: create date


title: 1854_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: E4.5_C7-C10_HOM_SC_226

tag: genotype

tag: mod

tag: embryo


title: 2233_BA46

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: isolate

tag: librarysource

tag: platform

tag: sra study


title: 2233_BA20

tag: tissue

tag: age

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: releasedate

tag: create date


title: 2233_V1

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 2112_V2

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: isolate


title: 1886_V2

tag: tissue

tag: age

tag: librarysource

tag: platform

tag: sra study


title: 1886_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: releasedate


title: 2232_V1

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 1886_V1

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: version


title: 2068_EC

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: platform


title: 1845_EC

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: sra study


title: 1669_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 1669_BA20

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: create date


title: 2068_V2

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: version


title: 1845_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: platform


title: 2203_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 2122_EC

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: releasedate


title: 1669_V1

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: create date


title: 2122_BA46

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: version


title: 1636_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: platform


title: 2122_V1

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: sra study


title: 2122_V2

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: releasedate


title: 2122_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: create date


title: 1636_BA46

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 1636_EC

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: platform


title: 1636_V1

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: sra study


title: 2203_V2

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: releasedate


title: 1636_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 1821_V1

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: version


title: 2233_EC

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: platform


title: 2015_BA46

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: sra study


title: 2015_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 2015_V1

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: create date


title: 1907_V1

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: version


title: 2015_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: platform


title: 2015_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 2225_BA20

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: releasedate


title: 2225_V1

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: create date


title: 2225_V2

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: version


title: 2225_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: platform


title: 2112_BA46

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: sra study


title: 2225_BA46

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: releasedate


title: 2112_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: create date


title: 2112_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 1907_BA46

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: platform


title: 2223_V1

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: sra study


title: 2191_V2

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: releasedate


title: 2223_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 1821_BA20

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: version


title: 2223_BA20

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: platform


title: 2191_V1

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: sra study


title: 2191_BA46

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 2191_EC

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: create date


title: 1926_BA46

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: version


title: 2057_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: platform


title: 2223_V2

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 1926_BA20

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: releasedate


title: 2191_BA20

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: create date


title: 2112_V1

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: version


title: 1926_V1

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: platform


title: 1926_V2

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: sra study


title: 2132_BA46

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: releasedate


title: 2132_BA20

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: create date


title: 2132_V1

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: version


title: 1926_EC

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: platform


title: 2132_V2

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: sra study


title: 2132_EC

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: releasedate


title: 2018_EC

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: create date


title: 2018_V2

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: version


title: 2057_V2

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: platform


title: 2018_V1

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: sra study


title: 2018_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: releasedate


title: 2223_BA46

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: create date


title: 2021_V2

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: version


title: 2018_BA46

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: platform


title: 2021_BA20

tag: Sex

tag: assay type

tag: datastore filetype

tag: datastore provider

tag: sra study


title: 2021_EC

tag: avgspotlen

tag: bases

tag: biomaterial provider

tag: datastore region

tag: releasedate


title: 2021_BA46

tag: tissue

tag: age

tag: isolate

tag: librarysource

tag: create date


title: 1906_V1

tag: bioproject

tag: bytes

tag: center name

tag: consent

tag: version


title: True leave 2

status: Public on Jul 08 2024

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The integration of the replicates and the processing of the data was generated in Seurat.
Assembly: Glycine_max_v2.1.52 From: http://ftp.ensemblgenomes.org/pub/plants/release-52/gtf/; http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/glycine_max/

organism: Glycine max

source_name: leaf

extract_protocol:
Tissues were chopped and passed through a 30µm cell strainer. The filtered nuclei were purified by cell sorting using FACSAria II™ cell sorter (BD Biosciences). An average of 80-100,000 nuclei were collected for each sample, centrifuged, and re-suspended in phosphate buffered saline-bovine serum albumin 0.5%-RNA-inhibitor solution.
Libraries were performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10x Genomics).

value: leaf

tag: strain

value: Merr. Cultivar 'Williams 82'

value: TBD


title: True leave 1

description: 10x Genomics


title: SAM 2

description: 10x Genomics

source_name: apical meristem

value: apical meristem


title: Trifoliate_leaf1, replicate 1, sNucRNAseq

description: 10x Genomics


title: Flower bud 1

description: 10x Genomics

source_name: Flower

value: Flower

value: 10 days


title: SAM 1

description: 10x Genomics


title: Green Pod 2

description: 10x Genomics

source_name: Pod

value: Pod


title: Seed heart 3

description: 10x Genomics

source_name: seed

value: seed

value: early stage


title: Green Pod 1

description: 10x Genomics


title: Seed early cotyledon 1

description: 10x Genomics


title: Seed mid-maturation 2

description: 10x Genomics

value: mid-stage


title: Daphnia_D16

status: Public on Jul 05 2024

city: Los Angeles

first: Matteo

last: Pellegrini

state: LA

address: 610 Charles E. Young Drive

institute: University of California, Los Angeles

description: bisulfite whole genome sequencing

data_processing:
The denatured BS-converted cfDNA was subject to the adaptase, extension, and ligation reaction.
The DNA underwent primer extension (98C for 1 minute; 70C for 2 minutes; 65C for 5 minutes; 4C hold) using oligos containing random UMI at the location of the i5 barcode.
The extension using a UMI-containing primer allows the tagging of each individual molecule in order to be able to remove PCR duplicates and correctly estimate DNA methylation levels.
Following exonuclease I treatment and subsequent purification, the libraries were then amplified using a universal custom P5 primer and i7-barcoded P7 primers (initial denaturation: 98C for 30 seconds; 10 cycles of: 98C for 10 seconds, 60C for 30 seconds, 68C for 60 seconds; final extension: 68C for 5 minutes; 4C hold).
The resulting single-indexed libraries were then purified, quantified using the Qubit HS-dsDNA assay, the quality checked using the D1000-HS assay (Agilent - TapeStation 4200).
Assembly: BioProject ID: PRJNA624896
Supplementary files format and content: a zipped tab separated text format describing the methylation status of observed cyotsines

organism: Daphnia magna

source_name: whole animal

growth_protocol: A heat-tolerant clone of D. magna, IL-MI-8, was originally acquired from the Ebert Lab at the University of Basel, Switzerland. This clone was sourced from a pond in Jerusalem, Israel, as part of Ebert Lab stock collection. To ensure synchronized cohorts, neonates born within a two day window were separated from their mothers. Sex was determined at 8-9 day old animals. Female individuals were exclusively used in all experiments conducted in this study. All mothers received adequate nutrition and were cultured under identical conditions at 25°C within an incubator. All cultures, including mother cultures, neonate cultures, and tank cultures, were maintained in ADaM water. Animals were exposed to a light cycle consisting of 16 hours of light followed by 8 hours of darkness. Animals were fed a daily suspension of the green alga Scenedesmus obliquus at a concentration of 10^5 cells/ml (adjusted for population density, with one animal per 20 ml). Every sixth day, the water was replaced, and offspring were manually removed until animals were transferred to the culture platform. The operational protocols for the culture platform are akin to those described in previously published protocols.

extract_protocol:
Approximately 30-50 ng of purified genomic DNA in 50 µl has been subject to sonication using the Bioruptor Pico (Diagenode) for 15 cycles of (30 ON; 90 OFF). Fragmentation patterns have been checked with the D1000HS Assay (Agilent Technologies) on a 4200 TapeStation. The volume of the fragmented DNA has been reduced to 20 µl using a Vacufuge (Eppendorf), then subject to bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research).
The libraries have been prepared using the Accel-NGS Methyl kit (Swift Biosciences - now xGen Methyl-Seq Library Prep - IDT) according to the manufacturer’s recommendations except a major modification.

value: whole animal

tag: genotype

value: WT


title: Seed heart 2

description: 10x Genomics


title: Seed early cotyledon 2

description: 10x Genomics


title: Daphnia_D15

description: bisulfite whole genome sequencing


title: Flower bud 2

description: 10x Genomics


title: Seed mid-maturation 1

description: 10x Genomics


title: Daphnia_D14

description: bisulfite whole genome sequencing


title: Daphnia_D10

description: bisulfite whole genome sequencing


title: Daphnia_D12

description: bisulfite whole genome sequencing


title: Seed heart 1

description: 10x Genomics


title: Daphnia_D13

description: bisulfite whole genome sequencing


title: 2021_V1

tag: Sex

value: female

tag: assay type

value: RNA-Seq

tag: avgspotlen

value: Hyman lab\, MADRC Brain Bank

value: ABBVIE

tag: datastore filetype

tag: datastore provider

tag: platform

tag: sra study


title: Daphnia_D7

description: bisulfite whole genome sequencing

tag: tissue

tag: age


title: Daphnia_D6

description: bisulfite whole genome sequencing


title: Daphnia_D5

description: bisulfite whole genome sequencing


title: Daphnia_D4

description: bisulfite whole genome sequencing


title: Daphnia_D3

description: bisulfite whole genome sequencing


title: Daphnia_D2

description: bisulfite whole genome sequencing


title: Daphnia_S2

description: bisulfite whole genome sequencing


title: Daphnia_D1

description: bisulfite whole genome sequencing


title: Daphnia_S1

description: bisulfite whole genome sequencing


title: C&R,Zf5,Gaf,Rep1

status: Public on Apr 15 2024

city: philadelphia

first: Mustafa

last: Mir

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia

data_processing:
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20
Library strategy: Cut and Run

organism: Drosophila melanogaster

extract_protocol:
Embryos were staged to NC12-NC13 and were placed and briefly dried on a double-sided tape . Using a sterile 18 gauge metal needle, embryos were popped into pools of the wash buffer previously described in Panday, A. 2022. Extracted contents were quickly moved in the wash buffer into a 1.5ul tube and temporarily stored at room temperature while samples were collected. Nuclei were collected by slow centrifugation at room temperature at 1500 RCF for 10 minutes.
Cut & Run libraries were made using NEBNext Ultra II NGS library kit and size selected using AMPure XP beads using manufacturer’s protocols.

value: mNG-ZF5 GLC

tag: antibody

value: GAF


title: C&R,WT,Gaf,Rep2

value: sfGFP-ZLD


title: P21 Het, female, replicate 2, snRNAseq

status: Public on Apr 10 2024

description: Scale Biosciences; instrument model: Illumina NovaSeq X

data_processing:
The demultiplexing, barcode processing, trimming, alignment, and gene counting was done using the ScaleBio ScaleRna Single-cell RNA Nextflow workflow v1.4.0 (https://github.com/ScaleBio/ScaleRna)
Seurat v4.3.0 was used to analyze the feature-barcode matrices, DoubletFinder v2.0.3 was used to remove doublets, DESeq2 v1.38.3 was used for pseudobulk differential gene analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
For P21 samples, cortices from mice were dissected and flash frozen in liquid nitrogen. The tissue was dissociated by dounce homogenization and a gradient centrifugation step using 25:35 Iodixanol and centrifuged at 10,000 xg for 30 min at 4C was performed to purify the nuclei from cellular debris and myelin generated during tissue dissociation. The nuclei were carefully collected from the interface, filtered through a 40um filter, washed with Nuclei Wash Buffer (DPBS, 1% BSA, and 0.1U/ul RNase Inhibitor), and 500k-2.5M nuclei were fixed using the ScaleBio Sample Fixation Kit. The nuclei were stored at -80C until all samples have been collected and fixed. 3 replicates each of male and female MYT1L WT and Het mice were included in this experiment. Libraries were made using the Scale Biosciences Single Cell RNA Kit.
The libraries were made according to manufacturer's instructions for Scale Biosciences' Single Cell RNA Kit.

value: Brain

tag: region

value: Cortex

value: Female

value: Het

value: MYT1L S710fsX


title: P21 Het, male, replicate 1, snRNAseq

value: Male


title: P21 Het, male, replicate 2, snRNAseq


title: Daphnia_D11

description: bisulfite whole genome sequencing


title: P21 Het, male, replicate 3, snRNAseq


title: P21 Het, female, replicate 3, snRNAseq


title: P21 WT, female, replicate 3, snRNAseq


title: Daphnia_D8

description: bisulfite whole genome sequencing


title: P21 WT, male, replicate 2, snRNAseq


title: P21 WT, male, replicate 3, snRNAseq


title: E14 KO, replicate 2, run 2,snRNAseq

description: Scale Biosciences

data_processing:
The demultiplexing, barcode processing, trimming, alignment, and gene counting was done using the ScaleBio ScaleRna Single-cell RNA Nextflow workflow v1.4.0 (https://github.com/ScaleBio/ScaleRna)
Seurat v4.3.0 was used to analyze the feature-barcode matrices, DoubletFinder v2.0.3 was used to remove doublets, DESeq2 v1.38.3 was used for pseudobulk differential gene analysis. Monocle v1.3.1, Python 3.9.18, velocyto v0.17.17, scanpy v1.12.0, scvelo v0.3.1, and cellrank v2.0.2 were used for trajectory analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
For E14 samples, the forebrains were dissected and flash frozen in liquid nitrogen. The tissue was dissociated by dounce homogenization, filtered through a 40um filter, and washed twice with Nuclei Wash Buffer (DPBS, 1% BSA, and 0.2U/ul RNase Inhibitor). The nuclei were counted and 500k-2.5M nuclei were fixed using the ScaleBio Sample Fixation Kit. The nuclei were stored at -80C until all samples have been collected and fixed.
The libraries were made according to manufacturer's instructions for Scale Biosciences' Single Cell RNA Kit.

value: Forebrain

value: KO


title: P21 WT, female, replicate 2, snRNAseq


title: E14 KO, replicate 3, run 2,snRNAseq

description: Scale Biosciences


title: P21 WT, male, replicate 1, snRNAseq


title: Daphnia_D9

description: bisulfite whole genome sequencing

value: whole animal


title: E14 KO, replicate 1, run 2,snRNAseq

description: Scale Biosciences


title: E14 Het, replicate 2, run 2,snRNAseq

description: Scale Biosciences


title: E14 WT, replicate 3, run 2,snRNAseq

description: Scale Biosciences

value: WT


title: E14 Het, replicate 3, run 2,snRNAseq

description: Scale Biosciences


title: E14 KO, replicate 3, run 1, snRNAseq

description: Scale Biosciences


title: E14 KO, replicate 2, run 1, snRNAseq

description: Scale Biosciences


title: E14 KO, replicate 1, run 1, snRNAseq

description: Scale Biosciences


title: E14 Het, replicate 3, run 1, snRNAseq

description: Scale Biosciences


title: E14 Het, replicate 1, run 2,snRNAseq

description: Scale Biosciences


title: P21 Het, female, replicate 1, snRNAseq


title: P21 WT, female, replicate 1, snRNAseq


title: E14 Het, replicate 1, run 1, snRNAseq

description: Scale Biosciences


title: E14 WT, replicate 2, run 2,snRNAseq

description: Scale Biosciences


title: E14 WT, replicate 3, run 1, snRNAseq

description: Scale Biosciences


title: E14 WT, replicate 1, run 2, snRNAseq

description: Scale Biosciences


title: GCG-Ab, 5

status: Public on Mar 30 2024

city: Nashville

first: Wenbiao

last: Chen

address: 743 Robinson Research Building

department: MPB

institute: Vanderbilt Univ School of Medicine

data_processing:
~72-137 million uniquely mapped reads were acquired per sample. Reads mapping to ribosomal and mitochondrial genome were removed before performing alignment using Bowtie2 (v2.5.1)
Alignment was performed using STAR (v2.7.3a) aligner(Dobin et al., 2013 ). The paired-end reads were aligned to the reference Mouse genome downloaded from Ensembl database (genome-build GRCm38.p6; genome-version GRCm38; genome-build-accession NCBI: GCA_000001635.8).
GTF file was downloaded from the following website (ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz).
The raw read counts were estimated using HTSeq (v0.11.2). Only reads mapping unambiguously to a single gene are counted, whereas reads aligned to multiple positions or overlapping with more than one gene are discarded
Assembly: mm10
Supplementary files format and content: tab limited text files contains raw counts per sample

source_name: pancreas

growth_protocol: All mice were housed and bred at Vanderbilt animal facility. All mice were maintained on standard rodent chow under 12-hour light/ 12-hour dark cycle.

extract_protocol:
To purify acinar cells, the mouse pancreas was digested by collagenase and acini were picked up by hand. Total RNA was extracted from acinar cells using an RNAqueous RNA isolation kit (Ambion, Austin, TX)
Takara SMART-Seq v4 Ultra low Input RNA kit - single cell

treatment_protocol: To interrupt glucagon signaling, C57BL/J6 mice were intraperitoneally injected with 10mg/kg of monoclonal antibody targeting the glucagon receptor (GCGR-Ab) or IgG once a week for 2, 4 or 8 weeks

value: pancreas

tag: cell type

value: acinar cells

tag: treatment

value: GCG-Ab


title: E14 WT, replicate 1, run 1, snRNAseq

description: Scale Biosciences


title: GCG-Ab, 4


title: GCG-Ab, 2


title: GCG-Ab, 3


title: GCG-Ab, 1


title: IgG, 3

value: IgG


title: IgG, 4


title: IgG, 2


title: IgG, 1


title: ENDSEQ-VABL-HP_STI1

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
END-seq reads were aligned to the mouse (mm10) genome using Bowtie (version 1.1.2) with the options–best–all –strata –l 50. 3 mismatches were allowed while keepinng the best strata for tags with multiple alignments (-n 3 –k 1).
MACS 1.4.3 was used for peak calling of H.pylori-infected data, with default parameters (p value cutoff for peak detection = 1x10E-5;–keep-dup = auto). Uninfected cells were used as control, keeping > 10-fold-enriched peaks.
For genome browser tracks visualization, aligned bed files were converted into bedgraph using bedtools genomecov, following by bedGraphToBigWig to make a bigwig file. Values were normalized to reads per million. Visualization of genomic profiles was done by the Integrative Genomic Viewer (IGV) browser.
Assembly: mm10
Supplementary files format and content: bigwig file
Library strategy: END-seq

source_name: vAbl cell line

growth_protocol: RAG1-/- preB vAbl cells - generously contributed by Dr. Andre Nussenzweig, National Cancer Institute, NIH -were cultured in RPMI supplemented with 15% FBS (Gibco), penicillin streptomycin, L-Glutamine and Sodium Pyruvate (Gibco) at 37 °C.

extract_protocol:
single-cell suspensions of vAbl cells (40 million cells for STI-treated and 20 million cells for untreated), were washed with PBS, and resuspended in cell suspension buffer (Bio-Rad), embedded in agarose, and transferred into plug molds (Bio-Rad). Plugs were allowed to solidify at 4°C and were then incubated with Proteinase K solution (Puregene, QIAGEN) for 1 hr at 50°C and then for ON at 37°C, followed by consecutive washes in a wash buffer containing 10 mM Tris-HCl (pH 8.0) and 50 mM EDTA (Wash Buffer) and then in a TE Buffer containing (10 mM Tris (pH 8.0) and 1 mM EDTA). Washed plugs were subsequently treated with RNaseA (Puregene, QIAGEN), washed again in Wash Buffer, and stored at 4°C (up to 2-4 days).
Blunting, A-tailing, and ligation to END-seq hairpin adaptor 1 were done at 37°C, 4°C respectively. DNA recovered from melted plugs was sheared to a length between 150 and 200 bp by sonication (Covaris), and biotinylated DNA fragments were purified using streptavidin beads (MyOne C1, Invitrogen). Following streptavidin capture, the newly generated ends were end repaired using T4 DNA polymerase (15 U), Klenow fragment (5 U), and T4 polynucleotide kinase (15 U); A-tailed with Klenow exo-fragment (15 U); and finally ligated to END-seq hairpin adaptor 2 using the NEB Quick ligation kit. After the second adaptor ligation, libraries were prepared by first digesting the hairpins on both adapters with USER enzyme (NEB) and PCR amplified for 16 cycles using TruSeq index adapters. PCR reactions were run on a 2% agarose gel and a smear of 200-400bp was cut and gel purified using MACHEREY-NAGEL extraction Kit (740609.50S).  Quantification of the library was performed by KAPA Library Quantification Kit for Illumina Platforms (Roche) and using dsDNA HS Assay Kit and QUBIT (Molecular Probes, Life Technologies) and qualification was done using the Agilent HS DNA Kit and Bioanalyzer 2100.  10nM of each library was pooled together and was diluted to 4nM according to NextSeq manufacturer’s instructions. 1.7pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced by Illumina NextSeq 500 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

tag: cell line

value: vAbl cell line

value: pre-B

value: H.pylori infection+STI


title: liver, 20CBD, long-term,5

status: Public on Mar 16 2024

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: liver

extract_protocol:
Tissues were collected and immediately submerged in stayRNA™ (A&A Biotechnology) reagent. After 24 of cooling (4C), tissues were frozen at -80C until the time of RNA isolation. For RNA isolation, tissue scrapes (15-30 mg) were homogenized and used for RNA isolation with AllPrep DNA/RNA (Qiagen) kit. Following isolation, RNA was controlled for quality with the TapeStation4150 system and quantified.
Libraries were prepared using CORALL mRNA-Seq V2 (Lexogen) following standard protocol.
RNA-Seq, stranded

treatment_protocol: The experiment was conducted on C57BL/6J laboratory mice strain (n=48), divided into subgroups receiving CBD at doses of 0.2, 10, or 20 mg/kg of body weight, and a control group receiving placebo, administered for 2 (short-term) or 28 (long-term) days. CBD was administered once a day via intraperitoneal injection. RNA-Seq analysis of the liver was conducted to identify alternations in mouse transcriptomes induced by CBD treatment in those organs.

value: liver

value: 20CBD, long-term


title: liver, 20CBD, long-term,4


title: liver, 20CBD, long-term,6


title: liver, 20CBD, long-term,3


title: liver, 20CBD, long-term,2


title: E14 Het, replicate 2, run 1, snRNAseq

description: Scale Biosciences

value: Brain


title: liver, 20CBD, long-term,1


title: liver, 10CBD, long-term,6

value: 10CBD, long-term


title: liver, 10CBD, long-term,5


title: liver, 10CBD, long-term,1


title: liver, 10CBD, long-term,2


title: E14 WT, replicate 2, run 1, snRNAseq

description: Scale Biosciences

value: MYT1L S710fsX


title: liver, 0.2CBD, long-term,6

value: 0.2CBD, long-term


title: liver, 0.2CBD, long-term,3


title: liver, 0.2CBD, long-term,2


title: liver, 0.2CBD, long-term,4