title: D-28_SN_scRNA-seq


title: 5354_cort

status: Public on Jan 02 2025

type: SRA

city: Cincinnati

first: Hyacinth

middle: Idu

last: Hyacinth

state: Ohi

address: 3230 Eden Avenue

department: Neurology

country: USA

institute: University of Cincinnati

library_source: transcriptomic

data_processing:
We used ToppFun and ToppCluster applications to perform functional enrichment analysis of differentially expressed genes (DEGs) in various groups. Genes differentially expressed in different comparisons were input into the ToppFun/ToppCluster for gene ontology (GO) and biological pathway annotation, with Benjamini and Hochberg’s correction for significance testing set at p value <0.05. To visualize the enriched biological processes and pathways, we used Cytoscape.v3.0.2 (for network representation) and Morpheus (https://software.broadinstitute.org/morpheus/; for heatmap representation) application.
Supplementary files format and content: comma delimited file containing read count.

molecule: total RNA

organism: Mus musculus

source_name: cort

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit for brain tissue. A total of 1.3ug of input RNA was used for the contruction of library
The raw sequencing reads were aligned to GRCm39 (mm39) using STAR. The number of reads that were aligned to each gene was obtained while mapping using the GENCODE gene annotation. Then we used edgeR to identify differentially expressed genes. For each genotype (“AA” or “SS”) in each tissue (Hippocampus, cortex), we included all samples in a model and compared the two “exposure” groups (RSD vs. No RSD) and then “treatment” groups (minocycline treatment vs. no minocycline treatment) in a pairwise fashion. We also compared across genotype; however, we ensured that only biologically meaningful comparisons were performed.
To isolate polyA RNA for library preparation, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with 500 ng good quality total RNA as input. The polyA RNA was enriched using SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Next, NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for library preparation under PCR cycle number of 9. After library QC and quantification via real-time qPCR (NEBNext Library Quant Kit, New England BioLabs), individually indexed libraries were proportionally pooled and sequenced using NextSeq 550 sequencer (Illumina, San Diego, CA) under the sequencing setting of single read 1x85 bp to generate about 25M reads.
Directional polyA RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core at the University of Cincinnati using established protocols as previously mentioned. To summarize, the quality of total RNA was QC analyzed by Bioanalyzer (Agilent, Santa Clara, CA).  After sequencing, fastq files for downstream data analysis were automatically generated via Illumina BaseSpace Sequence.

tag: treatment

value: No

tag: tissue

value: cort

tag: disease state

value: SS

tag: stress exposure

value: RSD


title: D-16_SN_scRNA-seq

city: Cambridge

first: Soumen

last: Khan

address: Babraham Hall

department: Epigenetics

country: United Kingdom

institute: Babraham Institute

data_processing:
Reads were trimmed using Trim Galore and aligned to the Mouse genome (GRCm38) using Hisat2 (v2.1.0) with deafult settings
Aligned reads were converted to BAM format using Samtools (v1.19.2). Unmapped, discordant and secondary alignments were filtered (bamtools view -F 0x256 -F 0x4 -F 0x8 )
Primary alignments were assigned to features of mouse oocyte transcriptome (Veselovska et al., 2015) using Seqmonk (v1.48.1) and raw counts were generated
Differentially expressed transcripts were identified using DESeq2
Assembly: GRCm38
Supplementary files format and content: Tab delimited file containing raw counts for all samples
Supplementary files format and content: Tab delimited file containing list of differentially expressed genes

molecule: polyA RNA

extract_protocol:
Fully-grown germinal vesicle (GV) oocytes were mechanically dissected from the ovaries of two 12-week-old C57Bl6/Babr mice in M2 medium (Sigma-Aldrich, M7167). After removing all cumulus cells, oocytes were placed in M2 with Hoechst (5µM, Abcam, 33343) and incubated for 10 minutes at room temperature. Oocytes were washed in PBS and NSN/SN stage was scored on a Zeiss LSM780 confocal microscope. Absence of a ring around the nucleolus was counted as “NSN”, a partial ring as “intermediate” and a full ring “SN”. After scoring, oocytes were frozen individually in 5μl RLT Plus buffer (Qiagen) and stored at -80°C until further use.
DNA and polyadenylated mRNA from individual oocytes were physically separated using poly-dT bound magnetic beads according to the G&T protocol published by Angermueller et al. 2016.  Bead-bound mRNA was transcribed into cDNA using SuperScript II (Invitrogen) and Template-Switching Oligo primers (TSO, Eurogentec), followed by amplification of cDNA with the 2x KAPA HiFi HotStart ReadyMix and ISPCR primers (Picelli et. al, 2013, Picelli et. al, 2014). Libraries were prepared from 100 to 400 pg of cDNA using the Nextera XT Kit (Illumina), per the manufacturer’s instructions but with one-fifth volumes.

tag: strain

tag: developmental stage

value: GV oocytes

tag: genotype

value: wildtype


title: D-27_SN_scRNA-seq


title: 5354_hip

source_name: hip

value: hip


title: C-21_SN_scRNA-seq


title: 9621_cort


title: C-17_SN_scRNA-seq


title: 9616_cort


title: 9621_hip


title: D-34_NSN_scBS_seq

library_source: genomic

data_processing:
First 6bp were trimmed from both 5' and 3' ends of raw reads using Trim Galore (v0.6.10) in single-end and non-directional mode
Trimmed files were aligned to the GRCm38 genome using Bismark (v0.23.1) followed by deduplication (deduplicate_bismark) and extraction of methylation calls (bismark_methylation_extractor) in single end mode. Bismark coverage files were generated using bismark2bedGraph
Libraries having a mapping efficiency <10%, fewer than 500,000 CpGs covered, or greater than 50% methylated CpGs were discarded
Assembly: GRCm38
Supplementary files format and content: Bismark coverage files

molecule: genomic DNA

extract_protocol:
Fully-grown germinal vesicle (GV) oocytes were mechanically dissected from the ovaries of two 12-week-old C57Bl6/Babr mice in M2 medium (Sigma-Aldrich, M7167). After removing all cumulus cells, oocytes were placed in M2 with Hoechst (5µM, Abcam, 33343) and incubated for 10 minutes at room temperature. Oocytes were washed in PBS and NSN/SN stage was scored on a Zeiss LSM780 confocal microscope. Absence of a ring around the nucleolus was counted as “NSN”, a partial ring as “intermediate” and a full ring “SN”. After scoring, oocytes were frozen individually in 5μl RLT Plus buffer (Qiagen) and stored at -80°C until further use.
Single-cell BS-seq (scBS-seq) libraries were prepared as previously described (Smallwood et al., 2014), with minor changes as described in (Castillo-Fernandez et.al, 2020)


title: C-19_SN_scRNA-seq


title: C-14_SN_scRNA-seq


title: C-20_SN_scRNA-seq


title: D-29_NSN_scBS_seq


title: 9616_hip


title: 9615_cort


title: D-23_NSN_scBS_seq


title: D-11_NSN_scBS_seq


title: D-17_NSN_scBS_seq


title: C-16_SN_scBS_seq


title: C-16_SN_scRNA-seq


title: D-10_SN_scRNA-seq


title: 9615_hip


title: C-18_SN_scBS_seq


title: 5400_cort


title: C-13_SN_scBS_seq


title: D-10_SN_scBS_seq


title: 5400_hip


title: D-21_SN_scBS_seq


title: D-12_SN_scBS_seq


title: 5391_cort


title: C-19_SN_scBS_seq


title: D-22_SN_scBS_seq


title: C-21_SN_scBS_seq


title: C-17_SN_scBS_seq


title: 5391_hip


title: 9890_cort

value: Yes


title: D-9_SN_scBS_seq


title: D-24_SN_scBS_seq


title: 9890_hip


title: D-13_SN_scBS_seq


title: 5801_cort


title: C-20_SN_scBS_seq


title: D-31_SN_scBS_seq


title: D-32_SN_scBS_seq


title: 5801_hip


title: 5875_cort


title: mdx 5dpi, scRNAseq

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were generated from raw sequencer output using the mkfastq command of cellranger 7.1.0
Cell-containing droplets were identified and quantified using the count command of cellranger 7.1.0
Transcripts were identified by alignment to the 10X Genomics mm10-2020 reference assembly
Assembly: mm10
Supplementary files format and content: HDF5 format files containing filtered feature-barcode matrices generated by 10X Cellranger (v7.1)

source_name: hindlimb muscle

extract_protocol:
Muscle stem cells were FACS (fluorescence-activated cell sorting) isolated based on a panel of negative selection for 7-AAD and a lineage cocktail (CD11b, CD45, CD31, Sca1) and postive selection for Integrin-α7 and GFP.
Libraries were generated according to manufacturer's instructions (single cell 3' v3 protocol, 10X Genomics)

value: hindlimb muscle

tag: cell type

value: muscle stem cell

value: 5 days post cardiotoxin


title: mdx no injury, scRNAseq

description: 10X Genomics

value: uninjured


title: C-9_SN_scBS_seq


title: 5875_hip


title: mdx_Myotube_2day_3

data_processing:
RNA-seq reads were mapped to transcripts from the GENCODE vM19 release using salmon v0.13.1
Data were loaded into R using the tximport library.
Gene/count matrix was filtered to retain only genes with five or more mapped reads in two or more samples.
Differential expression and principal component anaysis was assessed using DESeq2 .
Fold change was determined using lfcShrink, applying the apeglm method.
Assembly: GRCm38
Supplementary files format and content: Salmon transcript quantification (quant.sf) files (salmon v0.13.1)

growth_protocol: Primary myoblasts were isolated from hindlimb muscle by magnetic cell separation (MACS) based on lineage negative markers (CD31-, CD11b-, CD45-, SCA1-) and positive selection for α7-INTEGRIN. Myoblasts were cultured on collagen-coated dishes in Ham’s F10 medium (Wisent, 318-051-CL) supplemented with 20% FBS, 1% penicillin/streptomycin, and 5ng/mL of basic FGF. Myoblast differentiation was induced for 2days in Ham’sF10:DMEM1:1 supplemented with 5% horse serum, and 1% penicillin/streptomycin.

extract_protocol:
The RNA from in vivo derived MuSCs was isolated using Arcturus Picopure RNA extraction kit (Thermo Fisher). Total RNA from myoblasts and myotubes was extracted using the Nucleospin RNA II kit (Macherey-Nagel).
Library construction was performed with 20ng of input total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina - polyA mRNA workflow (New England Biolabs).

treatment_protocol: GFP+ (PAX7+) ITGA7+ and linage negative (CD31-, CD45-, SCA1-, CD11b-) MuSCs were FACS-isolated from resting and 3-day cardiotoxin injured hindlimb muscles.

value: 2-day myotube


title: mdx_Myotube_2day_1


title: mdx_Myotube_2day_2


title: mdx_Myoblast_3

value: Primary myoblast


title: 9895_cort


title: mdx_Myoblast_2


title: 9895_hip


title: mdx_Myoblast_1


title: 5896_cort

value: AA


title: mdx_Activated_3dpi_MuSC_3

value: Activated muscle stem cell

value: 10 µM cardiotoxin intramuscular


title: 5896_hip


title: mdx_Freshly_Isolated_MuSC_2

value: Freshly isolated muscle stem cell


title: mdx_Freshly_Isolated_MuSC_3


title: mdx_Activated_3dpi_MuSC_2


title: mdx_Activated_3dpi_MuSC_1


title: 5648_cort

value: cort


title: D-18_SN_scBS_seq


title: WT_Myotube_2day_3


title: mdx_Freshly_Isolated_MuSC_1


title: WT_Myotube_2day_2


title: 5897_cort


title: WT_Myotube_2day_1


title: 5648_hip


title: WT_Myoblast_3


title: WT_Myoblast_2


title: WT_Myoblast_1


title: 5897_hip


title: WT_Activated_3dpi_MuSC_1


title: WT_Freshly_Isolated_MuSC_3


title: 5645_cort


title: WT_Activated_3dpi_MuSC_2


title: WT_Activated_3dpi_MuSC_3


title: WT_Freshly_Isolated_MuSC_1


title: T5

city: Nanning

first: Chunhong

last: Xue

address: 22 Shuangyong Road

department: Department of Histology and Embryology

country: China

institute: Guangxi Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

organism: Homo sapiens

source_name: glioma

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: glioma


title: T3


title: T4


title: 5646_hip

value: RSD


title: WT_Freshly_Isolated_MuSC_2


title: 9877_cort


title: T2


title: 5645_hip


title: 9877_hip


title: HSC_old_CD150_high_H3K27ac_rep2

city: Boston

first: Wenhao

last: Zhang

state: MA

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

description: CUT&RUN

data_processing:
For ATAC-seq and CUT&RUN datasets, sequencing adaptors and low-quality reads were removed by Trim Galore with parameter:  -q 20 --length 30 --paired. Then the clean reads were mapped to mouse reference genome (mm10) by bowtie2 (Version 2.5.1) with parameter: -N 1 -L 25 -X 2000 –no-discordant (ATAC-seq) and --no-mixed --no-discordant (CUT&RUN). After converting aligned SAM to BAM files using Samtools (Version 1.13), Picard (Version 2.26.4) was used for removing PCR duplications. Next, read counts were normalized by Reads Per Kilobase per Million mapped reads (RPKM) and converted to bigwig via bamCoverage (Version 3.5.1). The peaks were called by MACS2 (Version 2.2.7.1) with parameter ‘-t file -f BED -g mm -outdir OUTPUT -n NAME --nomodel –nolambda’ (ATAC-seq) and ‘-f BAMPE -g mm -B -q 0.01’ (CUT&RUN). The “norrowpeak” files were used for downstream analysis. The peaks that overlap in more than 60% of the replicate samples in each group were kept for feature counts and subsequent analysis using DiffBind (V3.0.15). The read counts for each peak were normalized using DESeq2 (V1.30.1). Peaks that differed significantly between groups were identified using DESeq2 with the following criteria: P-value < 0.05 and fold-change > 1.5 or < 0.67. Deeptools (Version 3.5.1) was used to visualize the read coverages at peak regions. Motif calling and peak annotation was performed with HOMER (V4.10) with all identified peaks as background.
mm10
bigwig format file with normalized CUT&RUN signal

source_name: Hematopoietic stem cells

extract_protocol: The sorted HSCs (2,000-5,000) were immediately used for CUT&RUN assay. The H3K4me3 (Cell Signaling Technology, # 9751S) and H3K27ac (EMD Millipore #07-360) CUT&RUN libraries were prepared. Briefly, the FACS-sorted HSCs were collected in a 1.5-ml tube containing 50 μl of wash buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, and 1× protease inhibitor cocktails (Sigma-Aldrich)]. The HSCs were then captured with BioMagPlus Concanavalin A (Polysciences) beads and incubated with a primary antibody overnight at 4°C in antibody incubation buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor cocktails (EDTA-free tablet, Roche), 2 mM EDTA, and 0.005% digitonin (Life Technologies)]. The H3K4me3 antibody (1:100) and H3K27ac antibody (1:100) were used. After unbound antibodies were washed away, protein A–MNase was added at a 1:200 ratio (500 ng/ml) and incubated for 3 hours at 4°C. After washing, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, incubated for 20 min at 4°C, and then stopped by adding 1/10 volume of 10× STOP buffer [1.7 M NaCl, 100 mM EDTA, 20 mM EGTA, RNase A (250 μg/ml; Invitrogen), and glycogen (250 μg/ml; Invitrogen)]. The protein-DNA complexes were released by incubating at 37°C for 10 min, followed by 16,000g centrifugation for 5 min at 4°C. The supernatant was transferred to a new Lo-bound tube, 1/100 volume of 10% SDS, and 1/80 volume of Proteinase K (25 mg/ml; Life technologies) were added and incubated at 55°C for at least 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol (25:24:1), followed by ethanol precipitation with glycogen, and then dissolved in water. Sequencing libraries were then prepared using the NEBNext Ultra II DNA library preparation kit for Illumina (New Engliand Biolabs) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina NextSeq 550 with pair-end 75-bp reads.

value: Hematopoietic stem cells


title: 5898_cort


title: C5

value: normal brain


title: HSC_old_CD150_high_H3K27ac_rep1

description: CUT&RUN


title: T1


title: 5898_hip

value: hip


title: C4


title: HSC_old_CD150_low_H3K27ac_rep3

description: CUT&RUN


title: HSC_old_CD150_low_H3K27ac_rep2

description: CUT&RUN


title: 9887_hip

value: Yes

value: SS

value: Ctrl


title: 9887_cort


title: 5646_cort


title: 9889_cort


title: HSC_old_CD150_high_H3K4me3_rep3

description: CUT&RUN


title: C1


title: 9889_hip


title: HSC_old_CD150_low_H3K27ac_rep1

description: CUT&RUN


title: Q150 HOMO 3880 mouse cortex RASL-seq

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description: 1 hemisphere was used to extract RNA

data_processing:
Illumina software used for basecalling
Fastq files were softtrimmed for adaptor sequence and low-quality sequenced dropped, then aligned to mm10
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw count data for each sample. '_s' is the short isoform and '_l' is the long isoform
Library strategy: RASL-seq

source_name: Brain

growth_protocol: Animals were housed at controlled temperature and humidity: 68–79 degrees F and humidity 30–70%

extract_protocol:
RNA was extracted using Trizol and total RN was used for the library construction.
RNA libraries were prepared using RASL-seq protocol from Hairi Li et al., 2012 [PMCID: PMC3325489]

treatment_protocol: no treatment

value: Brain

value: Cortex

value: No Treatment


title: HSC_old_CD150_high_H3K4me3_rep2

description: CUT&RUN


title: Q150 HOMO 3857 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 9888_cort


title: 9888_hip


title: HSC_old_CD150_high_H3K4me3_rep1

description: CUT&RUN


title: HSC_old_CD150_high_H3K27ac_rep3

description: CUT&RUN


title: HSC_old_CD150_low_H3K4me3_rep3

description: CUT&RUN


title: Q150 HOMO 8179 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Q150 HET 880 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 5844_hip

value: No


title: Q150 HET 876 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: C3


title: HSC_old_CD150_low_H3K4me3_rep2

description: CUT&RUN


title: 9836_cort

value: AA


title: LHCN-M2 cells, diff, RNA rep 4

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description:
ATS0270_RNA
diff_rep4_RNA

data_processing:
We processed MPRA data using a custom pipeline to quantify barcode counts within each sample (RNA, gDNA) separately while accounting for sequencing errors. We extracted 20-bp barcodes and 15-bp unique molecular identifiers (UMIs) with cutadapt and umitools, respectively. We used starcode-umi to cluster UMIs and correct for PCR amplification bias. We then clustered and counted barcodes using starcode with an edit distance of 0.
We matched individual barcodes to the barcode pairing dictionary. We retained all oligos with at least 10 unique barcodes. To normalize data and perform quantitative (activity) and allelic bias analysis, we used the R package mpra. For plotting purposes, we transformed counts to transcripts per million and plotted log2(RNA/DNA).
Assembly: Custom synthetic barcode sequences
Supplementary files format and content: File "tovar-nishino_library_barcode_pairing.txt" is a tab-delimited text file containing barcode-oligo pairings. File "tovar-nishino_diff_library_counts.txt" is a tab-delimited text file containing per-barcode counts for each sample.

extract_protocol:
We isolated RNA and gDNA from each replicate using the Qiagen AllPrep DNA/RNA mini kit.
After gDNA and RNA collection, we treated RNA with the TURBO DNA-free™ kit (Thermo Fisher Scientific, MA, USA) following the manufacturer’s instructions. We synthesized cDNA from the resulting cleaned RNA using the SuperScript™ III First-Strand Synthesis System (Thermo Fisher Scientific, MA, USA) with a GFP-specific primer containing a 15-bp UMI, and subsequently amplified cDNA via PCR. We attached sequencing adapters and a 13-bp UMI by PCR, then amplified libraries using P7 and P5 stubs. We added dual sequencing indexes to both cDNA and gDNA libraries in a final 6-cycle PCR reaction. We sequenced the resulting cDNA/gDNA libraries on an Illumina NovaSeq 6000 and received paired-end 150-bp reads.

tag: cell line

value: skeletal muscle myocytes


title: Q150 HET 873 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: C2


title: LHCN-M2 cells, diff, gDNA rep 3

description:
ATS0269_gDNA
diff_rep3_gDNA


title: Q150 HET 848 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 9836_hip


title: LHCN-M2 cells, diff, RNA rep 3

description:
ATS0269_RNA
diff_rep3_RNA


title: HSC_old_CD150_high_ATAC_rep2

description: ATAC-seq

data_processing:
For ATAC-seq and CUT&RUN datasets, sequencing adaptors and low-quality reads were removed by Trim Galore with parameter:  -q 20 --length 30 --paired. Then the clean reads were mapped to mouse reference genome (mm10) by bowtie2 (Version 2.5.1) with parameter: -N 1 -L 25 -X 2000 –no-discordant (ATAC-seq) and --no-mixed --no-discordant (CUT&RUN). After converting aligned SAM to BAM files using Samtools (Version 1.13), Picard (Version 2.26.4) was used for removing PCR duplications. Next, read counts were normalized by Reads Per Kilobase per Million mapped reads (RPKM) and converted to bigwig via bamCoverage (Version 3.5.1). The peaks were called by MACS2 (Version 2.2.7.1) with parameter ‘-t file -f BED -g mm -outdir OUTPUT -n NAME --nomodel –nolambda’ (ATAC-seq) and ‘-f BAMPE -g mm -B -q 0.01’ (CUT&RUN). The “norrowpeak” files were used for downstream analysis. The peaks that overlap in more than 60% of the replicate samples in each group were kept for feature counts and subsequent analysis using DiffBind (V3.0.15). The read counts for each peak were normalized using DESeq2 (V1.30.1). Peaks that differed significantly between groups were identified using DESeq2 with the following criteria: P-value < 0.05 and fold-change > 1.5 or < 0.67. Deeptools (Version 3.5.1) was used to visualize the read coverages at peak regions. Motif calling and peak annotation was performed with HOMER (V4.10) with all identified peaks as background.
mm10
bigwig format file with normalized ATAC-seq signal

extract_protocol: About 500 ~ 1000 cells were sorted by FACS to 10 µl tagmentation buffer (33 mM Tris–Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate, 16% Dimethylformamide, and 0.02% Digitonin). 0.5 µl Tn5-Adapter complex (Diagenode) was added after FACS sorting and incubated at 37°C for 30 min. Then, the tagmentation reaction was stopped by adding 10 µl stop buffer (100 mM Tris-HCl pH8.0, 100 mM NaCl, 0.4% SDS, 40 µg/ ml Proteinase K) and the samples were incubated at 55°C overnight to release the tagmentation fragments. SDS was then quenched by adding 5 µl 25% Tween-20 and incubated on ice for 10 min. Next, 25 µl samples were mixed with 30 µl NEBNext High- Fidelity 2X PCR Master Mix (NEB), 2.5 µl P5 primer (10 µM) and 2.5 µl P7 primer (10 µM) for PCR amplification. The PCR products were then purified with SPRI beads with 1:1.6 ratio (96 µl beads) before sequencing.


title: 9837_hip


title: Q150 Wildtype 3903 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA

value: Wildtype (Q7/Q7)


title: 9894_cort


title: LHCN-M2 cells, diff, gDNA rep 2

description:
ATS0268_gDNA
diff_rep2_gDNA


title: HSC_old_CD150_high_ATAC_rep1

description: ATAC-seq


title: 5844_cort


title: LHCN-M2 cells, diff, RNA rep 2

description:
ATS0268_RNA
diff_rep2_RNA


title: 9894_hip


title: Q150 Wildtype 3878 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Q150 Wildtype 861 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 5883_cort


title: HSC_old_CD150_low_ATAC_rep2

description: ATAC-seq


title: LHCN-M2 cells, diff, gDNA rep 1

description:
ATS0267_gDNA
diff_rep1_gDNA


title: HSC_old_CD150_low_H3K4me3_rep1

description: CUT&RUN


title: HSC_old_CD150_low_ATAC_rep3

description: ATAC-seq


title: HSC_old_CD150_low_ATAC_rep1

description: ATAC-seq


title: Q150 Wildtype 544 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Q150 Wildtype 811 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, diff, RNA rep 1

description:
ATS0267_RNA
diff_rep1_RNA


title: HSC_old_ATAC_rep3

description: ATAC-seq


title: 5800_cort


title: 5883_hip


title: HSC_old_CD150_high_ATAC_rep3

description: ATAC-seq


title: LHCN-M2 cells, diff, gDNA rep 4

description:
ATS0270_gDNA
diff_rep4_gDNA


title: Q150 HOMO 421 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, palmitate, RNA rep 4

description:
ATS0278_RNA
palmitate_rep4_RNA

data_processing:
We processed MPRA data using a custom pipeline to quantify barcode counts within each sample (RNA, gDNA) separately while accounting for sequencing errors. We extracted 20-bp barcodes and 15-bp unique molecular identifiers (UMIs) with cutadapt and umitools, respectively. We used starcode-umi to cluster UMIs and correct for PCR amplification bias. We then clustered and counted barcodes using starcode with an edit distance of 0.
We matched individual barcodes to the barcode pairing dictionary. We retained all oligos with at least 10 unique barcodes. To normalize data and perform quantitative (activity) and allelic bias analysis, we used the R package mpra. For plotting purposes, we transformed counts to transcripts per million and plotted log2(RNA/DNA).
Assembly: Custom synthetic barcode sequences
Supplementary files format and content: File "tovar-nishino_library_barcode_pairing.txt" is a tab-delimited text file containing barcode-oligo pairings. File "tovar-nishino_library_counts.txt" is a tab-delimited text file containing per-barcode counts for each sample.
Library strategy: MPRA


title: HSC_old_ATAC_rep2

description: ATAC-seq


title: 5800_hip


title: Q150 HOMO 403 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, palmitate, gDNA rep 3

description:
ATS0277_gDNA
palmitate_rep3_gDNA


title: HSC_old_ATAC_rep1

description: ATAC-seq


title: LHCN-M2 cells, palmitate, RNA rep 3

description:
ATS0277_RNA
palmitate_rep3_RNA


title: Q150 HOMO 35 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: HSC_young_ATAC_rep3

description: ATAC-seq


title: 9910_hip


title: 9910_cort


title: Q150 HOMO 34 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Q150 HET 420 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, palmitate, gDNA rep 4

description:
ATS0278_gDNA
palmitate_rep4_gDNA


title: LHCN-M2 cells, palmitate, RNA rep 2

description:
ATS0276_RNA
palmitate_rep2_RNA


title: HSC_young_ATAC_rep1

description: ATAC-seq


title: HSC_young_ATAC_rep2

description: ATAC-seq


title: 5797_hip


title: Q150 HET 78 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, palmitate, gDNA rep 2

description:
ATS0276_gDNA
palmitate_rep2_gDNA


title: LHCN-M2 cells, palmitate, RNA rep 1

description:
ATS0275_RNA
palmitate_rep1_RNA


title: Q150 HET 3 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, palmitate, gDNA rep 1

description:
ATS0275_gDNA
palmitate_rep1_gDNA


title: Q150 HET 2 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Blood_Unsorted_6M_TX_RRBS_rep3

data_processing:
Paired fastq files from RRBS seq were first merged and processed as a single file. Adaptors of all sequenced reads were trimmed by Trim Galore with parameters --illumina. Adaptor trimmed reads were mapped using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For base resolution 5mC level calculation, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC level for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on the CpG site.
mm10
Wig file containing CpG positions and methylation levels

source_name: Whole blood cells

extract_protocol: Genomic DNA of blood cells was extracted and incubated (~20 ng) at 50°C for 3 hours and 75°C for 30 min in a 5 μl lysis buffer [20 mM tris-EDTA (Sigma catalog # T9285-100ML), 20 mM KCl (Thermo Scientific, catalog # AM9640G), 0.3% Triton X-100 (Sigma catalog # 93443-100ML), and protease (1 mg/ml; Qiagen catalog # 19155)]. The lysed cells were then subject to Msp I digestion at 37°C for 3 hours and 80°C for 20 min. Following enzymatic digestion, end-repair mix [1 μl Klenow frag exo− (5 U/μl), 0.2 μl of 10× TangoBuf, and 0.8 μl of dNTP mix] was added and incubated at 37°C for 40 min and 75°C for 15 min. For adaptor ligation, the reaction was incubated at 16°C for 30 min, 4°C overnight, and 65°C for 20 min after adding the ligation mix [2.25 μl of H2O, 1 μl of T4 ligase (30 U/μl; Thermo Scientific, catalog # EL0013 ), 0.5 μl of 100 mM ATP (Thermo Scientific, catalog # R0441), and 0.75 μM methylated adaptor. Bisulfite conversion reaction was then performed by the EpiTect Bisulfite Kit (Qiagen catalog # 59104) following the manufacturer’s instructions. Adapter-tagged BS-DNA was then amplified by 16 cycles using Kapa HiFi Uracil+ ReadyMix (Kapa Biosystems, catalog # KK2801) with NEBNext Multiplex Oligos for Illumina (New England BioLabs catalog # E7500L).

value: Whole blood cells


title: 9810_cort

value: cort


title: 9810_hip


title: Blood_Unsorted_6M_TX_RRBS_rep2


title: Q150 Wildtype 404 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, AICAR, RNA rep 4

description:
ATS0274_RNA
aicar_rep4_RNA


title: Blood_Unsorted_6M_TX_RRBS_rep1


title: 9812_hip


title: LHCN-M2 cells, AICAR, gDNA rep 3

description:
ATS0273_gDNA
aicar_rep3_gDNA


title: Q150 Wildtype 80 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Blood_CD150L_6M_TX_RRBS_rep4


title: 5797_cort


title: 9813_cort


title: LHCN-M2 cells, AICAR, RNA rep 3

description:
ATS0273_RNA
aicar_rep3_RNA


title: 9813_hip


title: Blood_CD150L_6M_TX_RRBS_rep3


title: Q150 Wildtype 79 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, AICAR, gDNA rep 2

description:
ATS0272_gDNA
aicar_rep2_gDNA


title: Blood_Unsorted_6M_TX_RRBS_rep4


title: Q150 Wildtype 1 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Blood_CD150L_6M_TX_RRBS_rep2


title: LHCN-M2 cells, AICAR, gDNA rep 4

description:
ATS0274_gDNA
aicar_rep4_gDNA


title: LHCN-M2 cells, AICAR, RNA rep 2

description:
ATS0272_RNA
aicar_rep2_RNA


title: Blood_CD150L_6M_TX_RRBS_rep1


title: R6/2 HD 869 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 9878_hip


title: LHCN-M2 cells, AICAR, gDNA rep 1

description:
ATS0271_gDNA
aicar_rep1_gDNA


title: Blood_CD150H_6M_TX_RRBS_rep4


title: R6/2 HD 868 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 9812_cort


title: LHCN-M2 cells, AICAR, RNA rep 1

description:
ATS0271_RNA
aicar_rep1_RNA


title: 9852_hip


title: Blood_CD150H_6M_TX_RRBS_rep3


title: Q150 Wildtype 402 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: R6/2 HD 860 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: LHCN-M2 cells, undiff, gDNA rep 4

description:
ATS0266_gDNA
undiff_rep4_gDNA


title: Blood_CD150H_6M_TX_RRBS_rep2


title: 9853_cort


title: R6/2 Wildtype 6 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA

value: Wildtype


title: LHCN-M2 cells, undiff, RNA rep 4

description:
ATS0266_RNA
undiff_rep4_RNA


title: Blood_CD150H_6M_TX_RRBS_rep1


title: 9853_hip

value: RSD


title: 9878_cort


title: R6/2 Wildtype 4 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: Old_HSC_CD150H_RRBS_rep2

extract_protocol: FACS sorted HSCs were lysed at 50°C for 3 hours and 75°C for 30 min in a 5 μl lysis buffer [20 mM tris-EDTA (Sigma catalog # T9285-100ML), 20 mM KCl (Thermo Scientific, catalog # AM9640G), 0.3% Triton X-100 (Sigma catalog # 93443-100ML), and protease (1 mg/ml; Qiagen catalog # 19155)]. The lysed cells were then subject to Msp I digestion at 37°C for 3 hours and 80°C for 20 min. Following enzymatic digestion, end-repair mix [1 μl Klenow frag exo− (5 U/μl), 0.2 μl of 10× TangoBuf, and 0.8 μl of dNTP mix] was added and incubated at 37°C for 40 min and 75°C for 15 min. For adaptor ligation, the reaction was incubated at 16°C for 30 min, 4°C overnight, and 65°C for 20 min after adding the ligation mix [2.25 μl of H2O, 1 μl of T4 ligase (30 U/μl; Thermo Scientific, catalog # EL0013 ), 0.5 μl of 100 mM ATP (Thermo Scientific, catalog # R0441), and 0.75 μM methylated adaptor. Bisulfite conversion reaction was then performed by the EpiTect Bisulfite Kit (Qiagen catalog # 59104) following the manufacturer’s instructions. Adapter-tagged BS-DNA was then amplified by 16 cycles using Kapa HiFi Uracil+ ReadyMix (Kapa Biosystems, catalog # KK2801) with NEBNext Multiplex Oligos for Illumina (New England BioLabs catalog # E7500L).

value: Hematopoietic stem cells


title: LHCN-M2 cells, undiff, gDNA rep 3

description:
ATS0265_gDNA
undiff_rep3_gDNA


title: 5839_cort


title: LHCN-M2 cells, undiff, RNA rep 3

description:
ATS0265_RNA
undiff_rep3_RNA


title: 9852_cort


title: Old_HSC_CD150H_RRBS_rep1


title: R6/2 Wildtype 3 mouse cortex RASL-seq

description: 1 hemisphere was used to extract RNA


title: 5839_hip


title: LHCN-M2 cells, undiff, gDNA rep 2

description:
ATS0264_gDNA
undiff_rep2_gDNA


title: Old_HSC_CD150L_RRBS_rep1


title: KO+PBS 14days (7wk)

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cornea

extract_protocol:
To ensure biological diversity, nuclei were initially isolated from snap frozen corneas of 5 mice per treatment group at 7 wks of age (WT,KO,PBS). Nuclei isolation protocol was adapted from 10x Genomics (Sample Preparation Demonstrated protocol, Rev D). Briefly, fresh corneas were dissected, minced, snap frozen in lysis buffer (Sucrose 0.32M, CaCl2 3mM, Mg(Ac)2 3mM, EDTA 0.1mM, Tris-HCL 10mM, DTT 1mM, Triton x100 0.1%, DEPC-treated water) and stored for further processing. Upon nuclei isolation, frozen sample were crushed using a pastel and combined into 15ml tube, with total volume of 5ml lysis buffer. Samples kept on ice for 15min with “vortexing” every 5 min. Sample were then transferred into ultracentrifuge tubes on ice (Beckman Coulter 355631), and 9ml of Sucrose solution (Sucrose 1.8M, Mg(Ac)2 3mM, Tris-HCL 10mM, DTT 1mM, DEPC-treated water) were carefully added to the bottom of the tube. Sample were spined 24,400 rpm for 2.5hr at 4°c. After spin, supernatant was removed, and 200ml of DEPC-based PBS was added for 20 min incubation on ice followed by resuspension. isolated nuclei solution was filtered twice using 10mm filter.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Cornea

value: whole cornea

value: KO

value: PBS for 14 days


title: 5837_cort

value: Yes


title: Old_HSC_CD150L_RRBS_rep2


title: LHCN-M2 cells, undiff, RNA rep 2

description:
ATS0264_RNA
undiff_rep2_RNA


title: KO 7wk

description: 10X genomics

value: untreated


title: 5837_hip

value: hip


title: 9876_cort


title: LHCN-M2 cells, undiff, gDNA rep 1

description:
ATS0263_gDNA
undiff_rep1_gDNA


title: Old_HSC_CD150L_14D_TX_scRNA

data_processing:
Paired reads from single-cell RNA seq were first aligned to mm10 reference genome with Cellranger --count (version 3.0.2) from 10X Genomics. Transcriptome annotation composed of protein coding genes was download and processed from Ensembl released-102. Single cells with feature numbers over 2000 and mitochondrial transcripts less than 5 percentage were filtered. Then, the remaining single cells were processed and analyzed with Seurat V4.
mm10
TSV files containing barcodes and features and MTX file containing matrix

extract_protocol: Single-cell RNA seq library is prepared with Chromium Next GEM Single Cell 3’ Reagent Kits V3.1 (Dual Index) from 10X Genomics according to manufacturer’s instruction. Briefly, single HSCs were sorted by FACS into PBS solution. Then microfluids was used to construct droplets containing single-cell, GEMs and reverse transcription reagents. 100 µl of droplets were incubated at 53°C for 45 minutes, then at 85°C for 5 min. Droplets were then released by Recovery Agent, cleaned up with Dynabeads MyOne SILANE and amplified by PCR for 12 cycles. The amplified cDNA was used for library construction according to the manufacturer’s instruction.


title: LHCN-M2 cells, undiff, RNA rep 1

description:
ATS0263_RNA
undiff_rep1_RNA


title: WT 7wk

description: 10X genomics

value: WT


title: Monocytes, HD 234, treated and untreated

city: Créteil

first: Mehdi

last: Khelfa

address: 5 Rue Gustave Eiffel

country: France

institute: Institut Mondor de Recherche Biomédicale

description: BD Rhapsody

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using SevenBridges (https://www.sevenbridges.com/) and SeqGeq software (https://www.bdbiosciences.com/en-fr/products/software/seqgeq-bioinformatics-software)
Assembly: hg38
Supplementary files format and content: comma-separated value files and matrix files

source_name: blood

extract_protocol:
PBMCs were isolated from buffy coats provided by EFS. Monocytes were purified by magnetic isolation from PBMCs with the Classical Monocyte Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) and stained with an anti CD14-PE antibody (Biolegend) for sorting on a BD FACSAria Fusion flow cytometer (BD Biosciences).
The library construction protocol was performed according to the manufacturer's instructions (BD Rhapsody Single-Cell Analysis System)

value: blood

value: leukocytes

value: monocytes

value: CD41a+ Evs


title: ChIPSeq_P7_Testis_Sox3_ChIPNexus_rep1

city: Salt Lake City

first: Bradley

middle: R.

last: Carins

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
ChIP-seq reads were aligned to the mouse reference genome (mm10) using the Novoalign (http://novocraf.com) with the parameters: -o SAM -r Random -H -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA including adapter sequence removal.
We removed PCR duplicates and all unmapped reads for fair comparison between all datasets using Picard MarkDuplicates (version 2.7.1)
Peak calling was performed using USeq8.9.6 packages and MACS (2.1.1) with the default parameters.
Peaks with -10log10(q-Value) (QValFDR) greater than 30 (q<0.001) for USeq and 20 (q<0.01) for MACS were included for downstream analyses.
bigWig files were generated using the USeq package and MACS2. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. only peaks from the merged files of two/three replicates overlapped with at least 50% of peaks from the union of biological replicates were considered for the merged replicates, using BEDTools intersect with parameters: -u -f 0.5.
Assembly: mm10
Supplementary files format and content: bigWig, peaks, narrowPeak (except for Input sample)

source_name: Mouse testis at P7

extract_protocol:
Tissues/THY1+ uSPGs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Branson sonifier (0.9 s on/0.1 s off x 7 cycles, average size 300-700 bp).
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina. 10 ng of DNA was used as starting material for input and ip samples. Libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were amplified using 7 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit

value: Mouse testis at P7

tag: chip antibody

value: SOX3 (SCBT, #sc-101155 and EMD Milipore, #AB5772)


title: ChIPSeq_P7_Testis_Sox3_ChIPNexus_rep2


title: Monocytes, HD 324, treated and untreated

description: BD Rhapsody


title: ChIPSeq_P7_Testis_Sox3_rep2


title: ChIPSeq_P7_Testis_Sox3_rep1


title: Monocytes, HD 190, treated and untreated

description: BD Rhapsody


title: Young_fresh_HSC_scRNA


title: Old_HSC_CD150L_4D_TX_RNA_rep3

data_processing:
Adaptor of all sequenced reads were first trimmed by Trim Galore with parameter --illumina --paried. Then the filtered reads were aligned to the mm10 reference genome by Hisat2 (version 2.0.0-b) with parameters --no-mixed --no-discordant --dta-cufflinks --no-unal. The aligned SAM files were then converted to BAM files with Samtools (version 1.14) for further analysis. Next, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene, with the main parameters set as: -f bam -s no -r pos. The reference genome was downloaded from the USCS Table Browser. To quantify gene expression, the read count for each gene was normalized using DESeq2 (V1.22.2). The differentially expressed genes from each group were filtered with following criteria: adjusted P-value < 0.05 and fold-change >2 or <0.5.
mm10
txt file containing gene names and FPKM values

extract_protocol: Bulk-RNA sequencing library is constructed based on Smart-seq2. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara catalog # 634890) was used and experiments were performed according to manufacturer’s instructions. Briefly, sorted HSCs were incubated in lysis buffer with RNase inhibitor on dry ice for 1 minutes, and then thawed at room temperature. First-Strand Buffer, SMART-Seq v4 Oligonucleotide, 3’ SMART-Seq CDS primer II and RNase inhibitor were added into the lysed cells and incubated at 72°C for 3 min before being put on ice. Incubating was performed after adding SMARTScribe II Reverse Transcriptase as following: 42°C for 90 minutes then 70°C for 10 minutes. Without purification, SeqAmp PCR Buffer, PCR Primer II A and SeqAmp DNA Polymerase were added for pre-amplification using thermal cycler for 12 cycles following the manufacturer’s instruction. The amplified cDNA was then purified by 1.8× volume of SPRIselect beads (Beckman Coulter catalog # B23318). Next, 200pg cDNA was used for library preparation with Nextera XT DNA Library Preparation Kit (Illumina catalog # FC-131-1024) according to manufacturer’s instruction.


title: RNAseq_KIT+_dSPG_Sox3_cKO_rep3

data_processing:
Novoalign
RNA-seq reads for each library were processed to Ensemble annotation NCBI38/mm10 using the Novoalign (http://novocraf.com), followed by trimming the adaptor sequence with the parameters: -o SAM -r All 50 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA.
Processed reads were mapped to the mouse mm10 genome using USeq8.9.6 packages, containing DESeq2 to generate FPKM value and analyze differential gene expression with the default parameter adding -x 50000000
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse KIT+ dSPG at P7

growth_protocol: Testes from three mice were pooled for each cell isolation experiment. Single cells were isolated from testes at P7 using 0.25% Trypsin digestion and resuspended in MACS separation buffer (Miltenyi Biotec). Harvested cells used to purify undifferentiated SPG and differentiating SPG using immunomagnetic cell sorting (IMCS) with anti-THY1/CD90.2 (Miltenyi Biotec) and anti-KIT/CD117 (Miltenyi Biotec) antibodies conjugated with magnetic microbeads.

extract_protocol:
Purified cells were lysed in Trizol and then were purified using Direct-zol RNA mini-prep kit, including DNase I treatment to remove genomic DNA (Zymo research). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold Kit following manufacturer's protocols.

value: Mouse KIT+ dSPG at P7

value: Sox3 cKO


title: Monocytes, HD 021, treated and untreated

description: BD Rhapsody


title: 5853_cort

data_processing:
We used ToppFun and ToppCluster applications to perform functional enrichment analysis of differentially expressed genes (DEGs) in various groups. Genes differentially expressed in different comparisons were input into the ToppFun/ToppCluster for gene ontology (GO) and biological pathway annotation, with Benjamini and Hochberg’s correction for significance testing set at p value <0.05. To visualize the enriched biological processes and pathways, we used Cytoscape.v3.0.2 (for network representation) and Morpheus (https://software.broadinstitute.org/morpheus/; for heatmap representation) application.
Supplementary files format and content: comma delimited file containing read count.

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit for brain tissue. A total of 1.3ug of input RNA was used for the contruction of library
The raw sequencing reads were aligned to GRCm39 (mm39) using STAR. The number of reads that were aligned to each gene was obtained while mapping using the GENCODE gene annotation. Then we used edgeR to identify differentially expressed genes. For each genotype (“AA” or “SS”) in each tissue (Hippocampus, cortex), we included all samples in a model and compared the two “exposure” groups (RSD vs. No RSD) and then “treatment” groups (minocycline treatment vs. no minocycline treatment) in a pairwise fashion. We also compared across genotype; however, we ensured that only biologically meaningful comparisons were performed.
To isolate polyA RNA for library preparation, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with 500 ng good quality total RNA as input. The polyA RNA was enriched using SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Next, NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for library preparation under PCR cycle number of 9. After library QC and quantification via real-time qPCR (NEBNext Library Quant Kit, New England BioLabs), individually indexed libraries were proportionally pooled and sequenced using NextSeq 550 sequencer (Illumina, San Diego, CA) under the sequencing setting of single read 1x85 bp to generate about 25M reads.
Directional polyA RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core at the University of Cincinnati using established protocols as previously mentioned. To summarize, the quality of total RNA was QC analyzed by Bioanalyzer (Agilent, Santa Clara, CA).  After sequencing, fastq files for downstream data analysis were automatically generated via Illumina BaseSpace Sequence.

value: cort

value: AA

value: RSD


title: Old_HSC_CD150L_4D_TX_RNA_rep2

value: Hematopoietic stem cells


title: Old_HSC_CD150H_14D_TX_scRNA


title: 5853_hip


title: Old_HSC_CD150L_4D_TX_RNA_rep1


title: 5838_cort


title: Resistant 1

city: Los Angeles

first: Krizia

last: Rohena Rivera

address: 8750 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality. FASTQ format described by four lines as described in the readme.txt.
"e" represents sequencing error rate, "Qphred" represents base quality values of Illunima, the Qphred=-10log10(e). Base Quality and Phred score relationship in illumina Casava 1.8 as in the readme.txt.
Assembly: Homo Sapiens hg19
Supplementary files format and content: FPKM.xls  Summary of gene expression level analysis

source_name: Bladder

growth_protocol: Cells were mantaine in  RPMI medium supplemented with 10%FBS

extract_protocol:
Total RNA was extracted with Qiagen Rneasy kit (Qiagen, Germantown, MA) according to the manufacturer’s instructions
Performed by Novogen, Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose.  NEB library: Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.  Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction
After library construction, diluting library to 1.5ng/ul with the preliminary quantitative result by Qubit2.0 and detecting the insert size by Agilent 2100. Q-PCR is used to accurately quantify the library effective concentration (> 2nM), in order to ensure the library quality

treatment_protocol: gemcitabine resistant cells were generated through acute treatment with gemcitabine

value: Bladder

value: Bladder Cancer

value: Gemcitabine Resistant

value: Untreated


title: 9876_hip

value: Yes

value: hip


title: Old_HSC_CD150H_4D_TX_RNA_rep3


title: 5838_hip


title: RNAseq_THY1+_uSPG_Sox3_WT_rep3

source_name: Mouse THY1+ uSPG at P7

value: Mouse THY1+ uSPG at P7

value: WT


title: Parental 1


title: 9851_cort


title: Old_fresh_HSC_scRNA


title: 9851_hip


title: RNAseq_KIT+_dSPG_Sox3_cKO_rep2


title: 5785_cort

value: No

value: SS

value: Ctrl


title: Old_HSC_CD150H_4D_TX_RNA_rep2


title: Old_HSC_CD150H_4D_TX_RNA_rep1


title: 5785_hip


title: RNAseq_THY1+_uSPG_Sox3_cKO_rep2


title: PN9

city: Wuhan

first: Yifei

last: Wang

address: Baofeng street

institute: Huazhong University of Science and Technology

description: SAMPLE 23

data_processing:
llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated.
Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtainthecleanreads.
The clean reads were mapped to the reference genome using HISAT2
Assembly: GRCh38.p13
Supplementary files format and content: FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count
Supplementary files format and content: PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples.

source_name: PBMC

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: PBMC

value: PN


title: PN8

description: SAMPLE 22


title: RNAseq_KIT+_dSPG_Sox3_WT_rep2

value: Mouse KIT+ dSPG at P7


title: 9903_cort

value: cort


title: Resistant 2


title: PN7

description: SAMPLE 21


title: RNAseq_THY1+_uSPG_Sox3_cKO_rep3

value: Sox3 cKO


title: RNAseq_KIT+_dSPG_Sox3_WT_rep3


title: 9903_hip


title: Old_HSC_CD150_G4_RNA_mouse2

value: Hematopoietic stem cells


title: RNAseq_THY1+_uSPG_Sox3_WT_rep2


title: Old_HSC_CD150_G4_RNA_mouse1


title: PN6

description: SAMPLE 20


title: 5854_cort


title: RNAseq_KIT+_dSPG_Sox3_cKO_rep1


title: PN5

description: SAMPLE 19


title: Old_HSC_CD150_G3_RNA_mouse3


title: RNAseq_THY1+_uSPG_Sox3_cKO_rep1


title: PN4

description: SAMPLE 18


title: 9824_hip


title: Old_HSC_CD150_G3_RNA_mouse2


title: RNAseq_KIT+_dSPG_Sox3_WT_rep1


title: PN3

description: SAMPLE 17


title: RNAseq_THY1+_uSPG_Sox3_WT_rep1


title: 9848_cort


title: Old_HSC_CD150_G4_RNA_mouse3


title: PN2

description: SAMPLE 16


title: 9848_hip


title: Old_HSC_CD150_G3_RNA_mouse1


title: ChIPSeq_P7_THY1+_uSPG_H3K27me3_rep1

source_name: Mouse Thy1+ SSC


title: Old_HSC_CD150_G2_RNA_mouse3


title: PN1

description: SAMPLE 15


title: Old_HSC_CD150_G2_RNA_mouse2


title: Old_HSC_CD150_G2_RNA_mouse1


title: 9822_cort


title: 9822_hip


title: control7

description: SAMPLE 13

value: healthy control


title: ChIPSeq_P7_THY1+_uSPG_H3K4me3_rep1

value: H3K4me3 (Active Motif, #39159)


title: control8

description: SAMPLE 14


title: 5900_cort

value: AA


title: ChIPSeq_P7_THY1+_uSPG_Input_rep1


title: ChIPSeq_P7_THY1+_uSPG_H3K9me3_rep1

value: H3K9me3 (Active Motif, #39161)


title: control6

description: SAMPLE 12


title: 9824_cort


title: Old_HSC_CD150_G1_RNA_mouse2


title: 5900_hip


title: Old_HSC_CD150_G1_RNA_mouse1


title: 5899_cort


title: ChIPSeq_P7_Testis_ZBTB16_ChIPNexus_rep2

source_name: Mouse testis

value: Mouse testis at P7

tag: age


title: control4

description: SAMPLE 10


title: ChIPSeq_P7_Testis_SALL4_rep2

value: SALL4 (Abcam, #ab29112)

value: Sall4 (Abcam, #ab29112)


title: 5899_hip

value: hip


title: control3

description: SAMPLE 9


title: Old_fresh_HSC_RNA_rep3


title: Old_fresh_HSC_RNA_rep2


title: 9879_cort

value: No


title: control2

description: SAMPLE 8


title: ChIPSeq_P7_Testis_ZBTB16_goat_rep2


title: Old_HSC_CD150_G1_RNA_mouse3


title: Old_fresh_HSC_RNA_rep1


title: Young_fresh_HSC_RNA_rep3


title: control1

description: SAMPLE 7


title: BP6

description: SAMPLE 6

value: BP


title: ChIPSeq_P7_Testis_ZBTB16_rabbit_rep2


title: Young_fresh_HSC_RNA_rep2


title: ChIPSeq_P7_Testis_Input_rep2


title: 9879_hip

value: Ctrl


title: 9839_hip


title: BP5

description: SAMPLE 5

value: PBMC


title: ChIPSeq_P7_Testis_SALL4_ChIPNexus_rep1


title: 9839_cort


title: control5

description: SAMPLE 11


title: Young_fresh_HSC_RNA_rep1


title: ChIPSeq_P7_Testis_SALL4_ChIPNexus_rep2


title: 5845_cort


title: ChIPSeq_P7_Testis_ZBTB16_ChIPNexus_rep1


title: BP4

description: SAMPLE 4


title: 5845_hip


title: ChIPSeq_P7_Testis_SALL4_rep1


title: BP3

description: SAMPLE 3


title: ChIPSeq_P7_Testis_ZBTB16_goat_rep1


title: 9838_cort


title: RIPAb2

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

country: Spain

institute: Achucarro BCN

data_processing:
Alignment was carried out with STAR v2.7.1 (32) against Ensembl genome of Rattus norvegicus (BN7.2.toplevel ang gtf v105) and expression counts were obtained with htseq-count (-sreverse) (33). The count matrix was imported to R v4.2.2, where expression levels were normalised and further analysed with DESeq2 (34).
Assembly: Ensembl genome of Rattus norvegicus (BN7.2.toplevel ang gtf v105)
Supplementary files format and content: htseq-output count matrix

organism: Rattus norvegicus

source_name: Primary cultured oligodendrocytes

growth_protocol: Highly enriched OPCs were prepared from mixed glial cultures obtained from newborn (P0–P2) Sprague–Dawley rat forebrain cortices as previously described (27) with minor modifications (28). Briefly, forebrains were removed from the skulls and the cortices were enzymatically and mechanically digested. Then, tissue was plated in Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum. The mixed glial cells were grown in poly-D-lysine treated T75 flasks until they were confluent (8–10 days). Microglia were separated from the cultures by shaking the flasks on a rotary shaker. OPCs were isolated by additional shaking for 18 h (200 rpm, 37°C, 5% CO2). OPCs were seeded on to poly-D-lysine-coated coverslips and were maintained at 37°C and 5% CO2 for 3 days in a chemically defined maturation SATO medium.

extract_protocol:
In transfection assays, primary oligodendroglial cells were nucleofected with 20 µM siRNA pools (non-targeting siRNA, Dharmacon #D-001810-10-05; Mbp-targeting siRNA, Dharmacon #L-089810-02-0005) using AmaxaTM Basic NucleofectorTM kit (#VPI-1006, Lonza) for Primary Mammalian Glial cells following the manufacturer´s instructions.
RNA quantity and quality was assessed using Qubit RNA assay kit (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent RNA 6000 Pico Chips). Sequencing libraries were prepared using “SMARTer Stranded Total RNA-seq Kit v2 – Pico Input Mammalian” kit (Takara Bio USA, Cat. #634411). The protocol was started with 4-10 ng of total RNA. Paired-end readings were generated from all libraries using HiSeq200 sequencer following Illumina protocols. The base calls or BCL were converted into FASTQ files by utilizing Illumina Inc.’s package bcl2fastq and quality control analysis was performed (FastQC).

treatment_protocol: Oligomeric amyloid-β (Aβ1–42) was prepared as reported previously (29). Briefly, Aβ1–42 (Bachem, Germany) was initially dissolved in hexafluoroisopropanol (Sigma) to a concentration of 1 mM. For the aggregation protocol, the peptide was resuspended in dry dimethylsulfoxide (5 mM; Sigma). Hams F-12 (PromoCell) was added to adjust the final peptide concentration to 100 μM to obtain oligomers (4 °C for 24 h). In all experiments, Aβ refers to oligomeric amyloid-β unless otherwise stated.

value: Primary cultured oligodendrocytes

value: Amyloid-B


title: RIPAb4


title: 9838_hip


title: RIPC3

value: Control


title: ChIPSeq_P7_Testis_ZBTB16_rabbit_rep1


title: BP1

description: SAMPLE 1


title: RIPAb3


title: D37 MSNs from 50Q iPSCs with siTDP-43 Rep 3

description: 1 million cells were used to extract RNA

data_processing:
Illumina software used for basecalling
Fastq files were softtrimmed for adaptor sequence and low-quality sequenced dropped, then aligned to either mm10 or GRCh38 with STAR
gene counts were quantified using featureCounts and raw counts were used for normalization and differential stats using DESeq2
Assembly: mm10 or GRCh38
Supplementary files format and content: tab-delimited text file including raw count data for each sample.

growth_protocol: Cells are grown on Matrigel coated plates in tissue culture sterile conditions and passaged with nonenzymatic dissociation medium. Cells are fed with mTeSR1 (Stem cell technologies) every day, and passage at ~70% confluency. Small molecule-based Differentiation to MSNs were followed by Smith-Geater et al., 2020.

extract_protocol:
RNA was extracted using Trizol and 1ug of total RN was used for the library construction.
RNA libraries were prepared using the Truseq total RNA library prep kit following manufacturer's protocols.

treatment_protocol:
C57Bl/6 males were dosed at 5 weeks old with PBS control or ASO targeting TDP-43 at 500ug by Intracerebroventricular (ICV) bolus injection. Following 2 weeks post-dose, striatum were collected for downstream analysis.
Human TDP-43 and non-targeting control siRNA were obtained from (Accell SMARTPool, Horizondiscovery, cat# E-012394-00-0050), cells were treated with siRNA on day 23 and harvested at day 37.

value: 50Q iPSCs

value: Medium Spiny Neurons

value: TDP-43 siRNA


title: 10638_hip

value: Yes

value: RSD


title: D37 MSNs from 50Q iPSCs with siTDP-43 Rep 2


title: 10633_cort

source_name: cort

value: cort

value: AA


title: RIPC2


title: ChIPSeq_P7_Testis_Input_rep1

value: Mouse testis at P7


title: RNAseq_KIT+_dSPG_Zbtb16_Null_rep3

source_name: spermatogoniall stem cells

value: Mouse KIT+ dSPG at P7

value: Zbtb16 null


title: RNAseq_THY1+_uSPG_Zbtb16_Null_rep3

value: Mouse THY1+ uSPG at P7


title: D37 MSNs from 50Q iPSCs with siTDP-43 Rep 1


title: 10638_cort


title: RNAseq_KIT+_dSPG_Zbtb16_WT_rep3

value: WT


title: IgG_4

value: Amyloid-B/Control (pool)


title: D37 MSNs from 50Q iPSCs with siSCR Rep 3

value: Scramble siRNA


title: 7037_cort


title: IgG_3

value: Primary cultured oligodendrocytes


title: 10633_hip

source_name: hip

value: hip


title: RNAseq_THY1+_uSPG_Zbtb16_WT_rep3


title: BP2

description: SAMPLE 2

value: PBMC

value: BP


title: D37 MSNs from 50Q iPSCs with siSCR Rep 2

value: 50Q iPSCs

value: Medium Spiny Neurons


title: 7037_hip

value: Yes


title: D37 MSNs from 50Q iPSCs with siSCR Rep 1


title: IgG_2


title: RNAseq_KIT+_dSPG_Zbtb16_Null_rep2


title: InputAb3

value: Amyloid-B


title: RIPC4

value: Control


title: 7078_cort

value: cort

value: SS

value: RSD


title: RNAseq_THY1+_uSPG_Zbtb16_Null_rep2

value: Zbtb16 null


title: InputAb2


title: 7078_hip


title: D37 MSNs from 18Q iPSCs with siTDP-43 Rep 3

value: 18Q iPSCs

value: TDP-43 siRNA


title: RNAseq_KIT+_dSPG_Zbtb16_WT_rep2

value: Mouse KIT+ dSPG at P7

value: WT


title: D37 MSNs from 18Q iPSCs with siTDP-43 Rep 2


title: 7076_cort


title: 7076_hip


title: InputAb4

value: Primary cultured oligodendrocytes


title: RNAseq_KIT+_dSPG_Zbtb16_Null_rep1


title: InputC3


title: RNAseq_THY1+_uSPG_Zbtb16_WT_rep2

value: Mouse THY1+ uSPG at P7


title: RNAseq_THY1+_uSPGs_Zbtb16_Null_rep1


title: D37 MSNs from 18Q iPSCs with siTDP-43 Rep 1


title: 7121_cort

value: Ctrl


title: D37 MSNs from 18Q iPSCs with siSCR Rep 3

value: Scramble siRNA


title: 7121_hip

value: hip


title: D37 MSNs from 18Q iPSCs with siSCR Rep 2

value: Medium Spiny Neurons


title: RNAseq_KIT+_dSPG_Zbtb16_WT_rep1


title: InputC4


title: D37 MSNs from 18Q iPSCs with siSCR Rep 1


title: Rat_5 [SP402BD4]

first: wenzhong

last: xiao

state: ma

address: 38 sidney st, suite 161

institute: massachusetts general hospital

data_processing:
Sequencing quality was assessed additionally using FASTQC (v0.11.9). Transcriptome annotations of each species were downloaded from Ensembl (https://www.ensembl.org, v90). For each sample, firstly, reads were aligned to human genome hg38 using STAR in the established bulk-RNA sequencing workflow of Bcbio (v1.2.1).  Secondly, the abundance of the annotated genes of the species was estimated from the RNA-seq reads as Transcripts per Million (TPM) using Sailfish. Thirdly, to compare the gene expression between species, the abundance of the genes in each species was then translated to that of the corresponding human orthologues. Here, only genes in a non-human species that had known orthologous human genes (Ensembl v90) were considered in further analysis. When m genes in a non-human species had n orthologous genes in human (m>=0, n>=1), the abundance of each of the human orthologues is assumed to be the sum of the abundance of the m genes divided by n.
Assembly: hg38 Ensembl v90
Supplementary files format and content: TPM matrix

extract_protocol:
After incubation, blood in TruCulture tubes was separated according to the manufacturer’s instructions with additional centrifugation at 800 ×g for 10 minutes.  Supernatants were saved and frozen at −80 °C for cytokine analysis.  The cell pellets were lysed using red blood cell lysis solution for 10 min followed by centrifugation at 2,000 ×g for 3 minutes, and remaining white blood cells were lysed in Qiazol and frozen at −80 °C until library construction (Qiagen).
RNA isolated from white blood cells (Qiazol, Qiagen) was quality controlled using A260/A280 ratio, 28S/18S rRNA ratio, and an RNA integrity summary score (Agilent RIN). Total RNA samples (250ngs, RIN>=7.0) were enriched for mRNA, fragmented, and converted into indexed cDNA libraries according to Illumina TruSeq Stranded mRNA protocol and quantity controlled using Agilent TapeStation. Samples were sequenced to at least 25M of 2 x 50bp paired-end reads and assessed using in-house QA/QC metric (Q2Solutions Expression Analysis).

treatment_protocol: Blood was collected into heparin tubes using meticulous pyrogen-free conditions. TruCulture tubes (Myriad RBM) containing either cell culture media only (“control”) or cell culture media plus 10 ng, 100 ng, or 1 μg/mL E. coli0113 US national reference strain LPS were prepared in advance, stored at -20 °C or below, and thawed at room temperature immediately prior to use. 1 mL blood was added to each tube and samples were incubated for 2, 6 and 24 h at 37 °C with 5% CO2.

value: blood

tag: subject

value: NC

tag: time

tag: timeunit

value: Hour

tag: dose

tag: doseunit

value: ng/mL

tag: group

value: R (resilient)


title: 7108_cort

tag: treatment

value: Yes

value: cort

value: SS


title: InputC2

value: Control


title: LNCAP-ER DOX_positive_3

first: Keisuke

last: Shigeta

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: prostate

growth_protocol: LNCaP AND DU-145 cells were maintained in Gibco RPMI 1640 Media containing 10% heat inactivated FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: enzalutamide and docetazel were continuously treated for creating resistant cell lines

tag: tissue

value: prostate

value: LNCaP

value: prostate cancer

value: enzalutamide resistant


title: Rat_5 [SP162FA3]


title: Baboon_4 [SPACB1CC]

organism: Papio anubis


title: 7108_hip

tag: disease state

value: Ctrl


title: LNCAP-ER DOX_positive_2


title: 10639_cort

value: AA

tag: stress exposure


title: Rat_5 [SPD94610]

value: LPS


title: Baboon_4 [SPCF36E0]


title: Rat_5 [SP992D75]


title: 10639_hip

value: hip


title: Baboon_4 [SP37632E]

value: blood


title: LNCAP-ER DOX_negative_3


title: LNCAP-ER DOX_negative_2


title: Baboon_4 [SP9D9065]


title: Rat_5 [SPEB6119]


title: WT, replicate 2, scRNAseq

city: La Jolla

first: Yun Sok

last: Lee

address: 9500 Gilman Dr MC0673

department: Medicine

institute: University of California San Diego

description: 10x Genomics

data_processing:
Alignment and gene quantification were made using Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequences were aligned to reference mm10-2020-A provided by 10X Genomics
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Cells were extracted per recommendations of the 10X genomics single cell 3' v3 kit
Libraries were constructed per recommendations of the 10X genomics single cell 3' v3 kit

value: sorted CD45+ live leukocytes

value: Liver

tag: strain

value: around 8months


title: WT, replicate 1, scRNAseq

description: 10x Genomics


title: Rat_5 [SP323462]

value: Hour

value: ng/mL

value: R (resilient)


title: Rat_5 [SPD7ADF7]


title: KO, replicate 2, scRNAseq

description: 10x Genomics


title: Rat_5 [SP506BBC]


title: KO, replicate 1, scRNAseq

description: 10x Genomics


title: Baboon_4 [SP3020F1]


title: RNAseq_THY1+_uSPG_Zbtb16_WT_rep1

value: Mouse THY1+ uSPG at P7

value: WT


title: Baboon_4 [SP23AE91]


title: Rat_5 [SP77DC86]


title: LNCaP shMUC1-C OE-1

value: prostate


title: LNCAP-ER DOX_positive_1

value: LNCaP


title: LNCaP shMUC1-C OE-3

value: prostate cancer


title: Baboon_4 [SPE84560]


title: LNCaP shMUC1-C OE-2


title: Baboon_4 [SP27BCE8]


title: Rat_5 [SP946F23]


title: 3T3-L1 cells, sgAcad8, guide 1, rep2

first: Christian

middle: M

last: Metallo

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology Laboratory

institute: Salk Institute for Biological Studies

description: Library: mRNA stranded; Roughly 25M reads/sample

data_processing:
Kallisto for quantification / Sleuth for analysis
Quantified with Kallisto with sequence-based bias correction and 100 bootstraps
Pseudoalign reads to GrCM38.96/mm10 using Kallisto
Convert transcripts to genes in sleuth using ensembl biomart package
Perform pairwise Wald test in sleuth
Assembly: mm10 (Mus_musculus.GRCm38.96)
Supplementary files format and content: tab-delimited tsv files include RPKM values for each Sample; xlsx files contain transcript ID, gene ID, significance, effect size (b), and gene rank obtained via Wald test

extract_protocol:
Trizol per manufacterer's instructions
RNA libraries for RNA-seq were prepared by the IGM Genomics Core using mRNA stranded Library Prep Kit following the manufacturer's protocols.

value: pre-adipocyte fibroblast cell line

value: Acad8 knockdown

value: fully differentiated adipocytes

value: Day 8 of differentiation


title: Baboon_4 [SP6C4E25]

value: LPS


title: LNCAP-ER DOX_negative_1

value: enzalutamide resistant


title: LNCaP-2

value: wild-type


title: LNCaP-3


title: Rat_5 [SPC3D415]

value: blood


title: 3T3-L1 cells, sgBckdha, guide 1, rep3

value: Bckdha knockdown


title: Baboon_4 [SPA58F3A]

value: Hour


title: LNCaP-1


title: Rat_4 [SP70D462]

value: NC

value: ng/mL


title: Baboon_4 [SP167BEE]

value: R (resilient)


title: 3T3-L1 cells, sgBckdha, guide 1, rep2


title: Rat_4 [SP981B44]


title: DU145DR DOX_positive3


title: Baboon_4 [SP1814D0]


title: Rat_4 [SPC1FAC2]


title: 3T3-L1 cells, sgControl, rep3

value: WT


title: 3T3-L1 cells, sgBckdha, guide 1, rep1


title: 3T3-L1 cells, sgAcad8, guide 1, rep3


title: DU145DR DOX_positive2

value: prostate


title: Rat_5 [SP15A0D8]


title: Baboon_3 [SPE0B2D6]


title: DU145DR DOX_positive1


title: 3T3-L1 cells, sgAcad8, guide 1, rep1


title: Baboon_3 [SP8FE594]


title: DU145DR DOX_negative3

value: DTX resistant


title: 3T3-L1 cells, sgControl, rep2


title: Rat_4 [SPB56193]


title: Baboon_3 [SPF35B53]


title: DU145DR DOX_negative2

value: prostate cancer


title: Rat_4 [SP4E2DBC]


title: 3T3-L1 cells, sgControl, rep1

value: pre-adipocyte fibroblast cell line


title: 511US116

city: Guelph

first: Isabelle

last: Aicklen

address: 50 Stone Road East

institute: University of Guelph

data_processing:
fastp was used to trim adapters and remove low quality reads.
Indexing and read alignment for the reference genome alignment was completed using STAR. Annotation and gene ontology was completed using blastp, the Amaranthus hybridus reference genome was aligned to the UniProt Swiss-Prot database and the most appropriate match was selected based on lowest E-value.
Indexing and read alignment for the de novo transcriptome alignment was completed using Bowtie 2. SAM files were converted to BAM files using samtools, read summarization was quantified using featureCounts. Annotation of the transcriptome was done using TransDecoder. Protein sequences were aligned to UniProt Swiss-Prot database using blastp, GO terms were added using InterProScan.
Assembly: Reference sequence (Amaranthus hybridus) and assembled de novo transcriptome.
Supplementary files format and content: Comma delimited file contains raw counts for each sample.

organism: Amaranthus powellii

source_name: Leaf tissue from 4th true leaf sampled when plants were 8 to 10 cm tall

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit by Zymo Research. Libraries were generated using 250 ng of total RNA.
Enrichment of mRNA and library preparation were performed using Illumina Stranded mRNA Prep kit (Illumina) following manufacturer's instructions. A single sample of RNA extracted from susceptible tissue was used for PacBio sequencing. cDNA libraries were prepared using Pacific Biosciences Preparing Iso-Seq libraries using SMRTbell prep kit 3.0 protocol.

value: Untreated


title: Baboon_3 [SP8A7EDE]


title: Rat_4 [SP73473B]


title: 511US14

value: Leaf tissue from 4th true leaf sampled when plants were 8 to 10 cm tall


title: Baboon_3 [SP1671AE]


title: Rat_4 [SP4921B5]


title: DU145DR DOX_negative1


title: Rat_4 [SP4E8C3B]


title: Baboon_3 [SP21E9F9]


title: lymphoblastic leukemia t cells, shBCAT-329 Etoposide rep 3

city: Padova

first: Erich

last: Piovan

address: via Gattamelata 64

department: Surgery, Oncology and Gastroenterology

country: Italy

institute: University of Padova

data_processing:
reads were trimmed for adapter sequences using trimgalore
trimmed reads were mapped to the genome using the STAR algorithm with default settings
The number of fragments overlapping genes were counted using featureCountsin Subread software packages
differential analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: T cell lymphoblastic leukemia

growth_protocol: CCRF-CEM shCTRL and CCRF-CEM shBCAT1 (#223 and #329) were plated in 24-well plates in triplicate at a celllular density of 0.5 million cells/well prior to treatment.

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

treatment_protocol: CCRF-CEM shCTRL and CCRF-CEM shBCAT1 (#223 and #329) were treated in triplicate with etoposide (1 uM) or vehicle (DMSO) for 24h.

value: T cell lymphoblastic leukemia

value: Etoposide


title: Baboon_3 [SPC12796]

value: LPS


title: 511US12


title: lymphoblastic leukemia t cells, shBCAT-329 Etoposide rep 2


title: lymphoblastic leukemia t cells, shBCAT-329 Etoposide rep 1


title: 501US118


title: Rat_4 [SPE830F7]


title: Rat_4 [SP923584]


title: lymphoblastic leukemia t cells, shBCAT-329 DMSO, rep 3

value: DMSO


title: Baboon_3 [SP0EA95F]

value: blood


title: 501US18


title: Rat_4 [SP91EF90]


title: 501US13


title: Baboon_3 [SP6CA56A]


title: lymphoblastic leukemia t cells, shBCAT-329 DMSO, rep 2


title: Rat_4 [SP8D7519]


title: Baboon_3 [SP877017]


title: Rat_3 [SPCECAFD]


title: 511TS16

value: MCPA herbicide


title: Baboon_3 [SPB32E70]

value: Hour


title: 511TS13


title: Rat_3 [SP232F3D]

value: NC


title: Baboon_2 [SP0A32E2]

value: ng/mL


title: Rat_3 [SPA56ECD]

value: R (resilient)


title: lymphoblastic leukemia t cells, shBCAT-223 Etoposide rep 1


title: 501TS110


title: Baboon_2 [SP2F59CB]


title: Rat_3 [SP4D1C94]


title: Baboon_3 [SPB4E257]


title: lymphoblastic leukemia t cells, shBCAT-223 Etoposide rep 2


title: 501TS14


title: 501TS11


title: Baboon_2 [SP285D7C]


title: Rat_3 [SP3344EF]


title: lymphoblastic leukemia t cells, shBCAT-223 DMSO, rep 3


title: Baboon_2 [SPFC39B9]


title: Rat_3 [SPA3D599]


title: IgG_LACE-seq of E14.5 NPCs

city: Beijing

first: Haoyang

last: Yu

state: Beijing

address: 9 Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

description: Library name: IgG_LACEseq_E14.5

data_processing:
Adapter trimming: Cutadapt was used to remove adapter sequences (for LACE-seq, scRNA-seq, and RNA-seq as needed). Alignment: LACE-seq reads were first mapped to mouse pre‐rRNA (Bowtie) to remove rRNA, then aligned to mm10 allowing up to two mismatches (Bowtie). RNA‐seq reads were mapped to mm10 using HISAT2 (default parameters). scRNA‐seq data were processed with the 10x Genomics pipeline (cellranger) or equivalent for barcode demultiplexing and mm10 alignment. Peak calling (LACE-seq): Piranha (parameters: -s -b 20 -p 0.01) identified enrichment peaks; IgG background signals were removed. Differential expression (RNA-seq): DESeq2 was used to compare WT vs. cKO. Single-cell analysis (scRNA-seq): Clustering, cell-type identification, and differential expression were performed using standard pipelines (e.g., Seurat).
Assembly: All alignments used mm10
Supplementary files format and content: LACE‐seq: The processed files include bigWig (.bw) tracks, representing per-base coverage of captured RNAs after immunoprecipitation. RNA‐seq: Count matrices (.txt/.csv) derived from aligned reads are provided, containing gene-level read counts for each sample. scRNA‐seq: Three files—matrix.mtx, barcodes.tsv, and features.tsv—are included. matrix.mtx holds the raw or filtered gene expression matrix in Matrix Market format, barcodes.tsv lists unique cell barcodes, features.tsv (or genes.tsv) lists gene identifiers or features.

extract_protocol:
LACE-seq: RNA immunoprecipitation (IP) was performed using anti‐Syncrip or mouse IgG; captured RNA was fragmented by MNase, then dephosphorylated and adapter‐ligated. RNA-seq: Total RNA was extracted using TRIzol (Invitrogen) from cultured NPCs. scRNA-seq: Single-cell suspensions were generated from dissected dorsal cortex, with no separate “extraction” step beyond cell dissociation.
LACE‐seq: After reverse transcription, the first‐strand cDNA was barcoded and linearly amplified prior to high‐throughput sequencing. RNA‐seq: Libraries were prepared with NEBNext Ultra RNA Library Prep (paired-end, 2×150 bp). scRNA‐seq: Single‐cell libraries were generated using the 10x Genomics Chromium Single Cell 3′ Kit (v3.1), capturing ~6000 cells per channel.

value: primary cells

value: Neural progenitor cells


title: Baboon_2 [SP4A6387]


title: lymphoblastic leukemia t cells, shBCAT-329 DMSO, rep 1


title: Rat_3 [SPE70385]


title: lymphoblastic leukemia t cells, shBCAT-223 DMSO, rep 1


title: 511TS112


title: Baboon_2 [SP39827C]


title: lymphoblastic leukemia t cells, shBCAT-223 Etoposide rep 3


title: Rat_3 [SPCF2DA5]


title: lymphoblastic leukemia t cells, shCTRL Etoposide, rep 3

value: shCTRL


title: SYNCRIP_LACE-seq of E14.5 NPCs (Rep1)

description: Library name: SYNCRIP_LACEseq_E14.5_Rep1


title: Baboon_2 [SP29EA91]


title: lymphoblastic leukemia t cells, shCTRL Etoposide, rep 2


title: Rat_3 [SP92FC34]


title: Baboon_2 [SP65813D]


title: lymphoblastic leukemia t cells, shCTRL Etoposide, rep 1


title: B16F10 Pros1-deficient (BdP) cells treated with cisplatin, replicate 3

city: Birmingham

first: Nestor

last: Prieto-Dominguez

state: AL

department: Microbiology

institute: The University of Alabama at Birmingham (UAB)

description:
Library name: D3_BdPC
gene_fpkm.csv; D3_BdPC

data_processing:
Original data files from Illumina NovaSeq X Plus were transformed to sequenced reads by CASAVA base recognition and stored in FASTQ (fq) format files.
Raw data was processed using Novogene-specific scripts to remove both adapter and low-quality reads from raw data. Q20, Q30, and GC content were calculated to ensure data quality.
Paired-end clean reads were aligned to the reference genome using Hisat2 v.2.0.5 as the mapping tool.
FeatureCounts v.1.5.0-p3 software was used to count the number of reads mapped to each gene. FPKM was then calculated based on the number of reads counted and the length of each gene.
Assembly: GRCm38/mm10 genome was used as the reference genome sequence for read alignment
Supplementary files format and content: .csv file includes the fpkm counts obtained from each sample separated in different columns (data added in description column).

growth_protocol: B16F10 and BdP cells were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS) and 1% Penicillin-Streptomycin at 37C. When confluent, 1*10^5 B16F10 or BdP cells were implanted subcutaneously into the right flank of C57BL/6J 8-week mice of both sexes. Treatment started when tumors were palpable (8 days after implantation).

extract_protocol:
End-stage tumors were disaggregated, lysed and mRNA was collected using the RNeasy Plus Mini-Kit  from Quiagen. RNA quality was assayed with the Bioanalyzer 2100 system (Agilent Technologies)
RNA-seq libraries were generated using the NEBNext UltraTM RNA Library Prep Kit for the Illumina system (New England Biolabs) following the manufacturer's recommendations.

treatment_protocol: Tumors were treated with two rounds (days 1-3 and 7-9 of the experiment) of PBS (ip, once daily for 3 days) or cisplatin (5mgkg, ip, once daily for 3 days)

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

tag: cell genotype

value: Pros1 knockdown

value: Cisplatin, 5mg/kg, ip, once daily for three days, two rounds

tag: tumor stage

value: end stage tumor


title: Rat_3 [SP332A72]

city: Cambridge


title: Rat_3 [SP2AC576]


title: lymphoblastic leukemia t cells, shBCAT-223 DMSO, rep 2

tag: cell type

value: T cell lymphoblastic leukemia

tag: genotype


title: Baboon_2 [SPEF9D44]

value: LPS


title: Baboon_2 [SP9A3A8A]


title: lymphoblastic leukemia t cells, shCTRL DMSO, rep 3

value: DMSO


title: Rat_3 [SP3151D0]

value: blood


title: lymphoblastic leukemia t cells, shCTRL DMSO, rep 2


title: B16F10 Pros1-deficient (BdP) cells treated with cisplatin, replicate 1

description:
Library name: D1_BdPC
gene_fpkm.csv; D1_BdPC

tag: cell line


title: B16F10 Pros1-deficient (BdP) cells treated with cisplatin, replicate 2

description:
Library name: D2_BdPC
gene_fpkm.csv; D2_BdPC


title: Baboon_2 [SP559206]

tag: subject


title: B16F10 Pros1-deficient (BdP) cells treated with PBS, replicate 4

description:
Library name: C4_BdPV
gene_fpkm.csv; C4_BdPV

value: PBS, ip, once daily for three days, two rounds


title: Baboon_2 [SPB84E74]

tag: time

value: Hour


title: Rat_2 [SP6180E6]

value: NC

tag: timeunit


title: Rat_2 [SP3C30F8]

tag: dose

value: ng/mL


title: SYNCRIP_LACE-seq of E14.5 NPCs (Rep2)

description: Library name: SYNCRIP_LACEseq_E14.5_Rep2


title: B16F10 Pros1-deficient (BdP) cells treated with PBS, replicate 3

description:
Library name: C3_BdPV
gene_fpkm.csv; C3_BdPV


title: lymphoblastic leukemia t cells, shCTRL DMSO, rep 1


title: Rat_2 [SPBA15B1]

tag: doseunit

value: R (resilient)


title: UV285 Aqueous BCR

city: Aurora

last: Concepcion

state: Colorado

institute: University of Colorado Denver Anschutz Medical

description: 10x Genomics

data_processing:
"We processed the raw FASTQ sequencing files using CellRanger with alignment to the 10x Genomics human reference genome (refdata-gex-GRCh38-2020-A).  We imported the count matrices into Seurat and  used the Immcantation suite of R packages to observe the mutations in BCRs and TCRs.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scBCR-seq

source_name: Peripheral blood

extract_protocol:
We sampled 100-200 ul of the inflamed anterior chamber fluid using a 25- to 30-gauge needle. We pelleted cells by centrifugation (400 x g, 5 min) to remove the aqueous fluid and cryopreserved cells in fetal bovine serum containing 10% DMSO.
We used the 10x Genomics 5'v2 gene expression kit according to the manufacturer's protocol.

value: Peripheral blood


title: UV286 Blood BCR

description: 10x Genomics


title: Baboon_1 [SPD2E7BB]

source_name: blood

tag: group


title: B16F10 Pros1-deficient (BdP) cells treated with PBS, replicate 2

description:
Library name: C2_BdPV
gene_fpkm.csv; C2_BdPV

tag: treatment


title: B16F10 Pros1-deficient (BdP) cells treated with cisplatin, replicate 4

description:
Library name: D4_BdPC
gene_fpkm.csv; D4_BdPC


title: Baboon_1 [SPA889A9]

tag: tissue


title: Baboon_1 [SPA0C6C1]


title: B16F10 wild-type cells treated with cisplatin, replicate 4

description:
Library name: B4_B16C
gene_fpkm.csv; B4_B16C

value: wild-type


title: Baboon_1 [SP9C8E22]


title: UV215-004 Blood BCR

description: 10x Genomics


title: UV284 Aqueous BCR

description: 10x Genomics

source_name: Ocular Aqueous fluid

value: Ocular Aqueous fluid


title: Rat_2 [SPBC037E]


title: B16F10 wild-type cells treated with cisplatin, replicate 3

description:
Library name: B3_B16C
gene_fpkm.csv; B3_B16C

value: C57bl/6J, 8-week old, both sexes.


title: Rat_2 [SPA4F851]


title: Baboon_1 [SP75C242]


title: Baboon_1 [SP4F7682]


title: UV215-003 Blood BCR

description: 10x Genomics


title: Rat_2 [SP03F3BE]


title: B16F10 wild-type cells treated with cisplatin, replicate 1

description:
Library name: B1_B16C
gene_fpkm.csv; B1_B16C

value: Melanoma murine cells


title: B16F10 wild-type cells treated with cisplatin, replicate 2

description:
Library name: B2_B16C
gene_fpkm.csv; B2_B16C


title: UV215-003 Aqueous BCR

description: 10x Genomics


title: Baboon_1 [SPFC9C03]


title: Rat_2 [SP33D6FB]


title: B16F10 wild-type cells treated with PBS, replicate 4

description:
Library name: A4_B16V
gene_fpkm.csv; A4_B16V


title: Baboon_1 [SPFB4C41]


title: Rat_2 [SP262B9B]


title: B16F10 wild-type cells treated with PBS, replicate 3

description:
Library name: A3_B16V
gene_fpkm.csv; A3_B16V


title: UV284 Blood BCR

description: 10x Genomics


title: Rat_2 [SPE56360]


title: B16F10 Pros1-deficient (BdP) cells treated with PBS, replicate 1

description:
Library name: C1_BdPV
gene_fpkm.csv; C1_BdPV

value: Pros1 knockdown


title: UV143 Blood BCR

description: 10x Genomics


title: Baboon_1 [SP4ABC93]


title: UV215-004 Aqueous BCR

description: 10x Genomics


title: B16F10 wild-type cells treated with PBS, replicate 2

description:
Library name: A2_B16V
gene_fpkm.csv; A2_B16V


title: UV143 Aqueous BCR

description: 10x Genomics


title: Baboon_1 [SP0CA59F]


title: Rat_2 [SP9B25A8]


title: B16F10 wild-type cells treated with PBS, replicate 1

description:
Library name: A1_B16V
gene_fpkm.csv; A1_B16V


title: Baboon_1 [SP03EF74]


title: UV132 Blood BCR

description: 10x Genomics


title: brain, Cd8-cre+, rep1

city: St. Louis

first: Robyn

last: Klein

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

description: 10X Genomics

data_processing:
Gene couting and aggregation were made using the Cell ranger-7.2.0.
Cell count matrix was analyzed in Partek Flow software v12.0.2 suite with the standard pipeline for scRNA-seq analyses to conduct QA/QC filtering, align and normalize reads, identify cell clusters, generate lists of DEGs and conduct GSEA.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Forebrain

extract_protocol:
Mice were anesthetized and sacrificed by cardiac perfusion with ice-cold dPBS (Gibco). Brains were aseptically dissected, minced and enzymatically digested in HBSS containing 0.05% collagenase D (Sigma), 0.1 μg/mL TLCK trypsin inhibitor (Sigma), 10 μg/mL DNase I (Sigma), and 10 mM HEPES (Gibco) at 37°C for 1h with shaking. Tissues were then pushed through a 70 μm strainer and centrifuged at 500× g for 10 min. Brain cell pellets were resuspended in 37% isotonic Percoll (Cytiva, cat. no. 17089101) and centrifuged at 1200× g for 30 min to remove myelin debris. Cells were washed in PBS. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, cat. no. 130-090-101). Live cells were diluted to 1000 cells/µL with ice-cold 0.04% BSA in PBS.
Samples were sent to Genome Access Technology Center at the McDonnell Genome Institute for library preparation using 10x Genomics Chromium Single Cell 5' Reagent Kits and sequencing.

value: Forebrain

value: Immune cells


title: UV132 Aqueous BCR

description: 10x Genomics


title: rbr1-4_Rep2

city: Shanghai

first: Lei

last: Li

address: Xinjiangwancheng

institute: Fudan University

data_processing:
For data analysis, adapter trimming was performed using TrimGalore. Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR aligner, bigwig files were generated using the bamCoverage function in DeepTools (Ramírez et al., 2014). Kallisto was used to estimate transcript abundance and read counts for all transcripts in TAIR10. Differential gene expression analysis between Col-0 and rbr1-4 was performed using DESeq2 with default settings. Differentially expressed genes were classified with a false-discovery rate (FDR)-adjusted P < 0.05 and an absolute shrunken log2-transformed fold change of > 1 or < -1.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: mature pollen

extract_protocol:
Total RNA was extracted from mature pollen of Col-0 and rbr1-4 by Trizol (Ambion, 15596-026).
1 µg DNase I-digested total RNA was treated with a Ribo Zero kit (Epicenter) to obtain a ribosomal RNA-depleted RNA (ribo- RNA). Then ribo- RNA was used for library preparation with the Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N15031048).

value: mature pollen


title: brain, cre-, rep2

description: 10X Genomics

value: cre-


title: Rat_2 [SP3F88AF]

value: LPS


title: UV165 Blood BCR

description: 10x Genomics


title: UV229 Aqueous BCR

description: 10x Genomics


title: UV229 Blood BCR

description: 10x Genomics


title: Col-0_Rep2


title: Rat_2 [SPA73914]

value: blood


title: SS amp1lamp1

city: Riverside

first: Ye

last: Xu

address: 900 University Ave

institute: University of California, Riverside

data_processing:
The MethylC-seq raw reads were mapped and converted to every cytosine according to description previously (Li et al., 2016, DOI: 10.1093/nar)
The methylation level of reads mapped to specific genomic loci (SUC:SUL locus, endogenous SUL locus, IR-71 locus and At5g22960 locus) were calculated according to  methods described previously (Li et al., 2016, DOI: 10.1093/nar).
Assembly: TAIR10

source_name: SUCSUL amp1lamp1 transgenic line

growth_protocol: 16 hr light and 8 hr dark at 22 ˚C on 1/2 MS medium

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) and sonicated as described previously (Li et al., 2016, DOI: 10.1093/nar)
The sonicated DNA fragments were purified and ligated with methylated adapters from the TruSeq DNA Sample Preparation Kit (Illumina) at 16°C overnight. Less than 400 ng ligated product was used for bisulfite conversion using the Methyl- Code Kit (Invitrogen) according to the manufacturer’s guidelines.

tag: ecotype

tag: transgene

value: 13-d-old seedling


title: Col-0_Rep1


title: Baboon_1 [SPBC5A0E]

value: Hour


title: rbr1-4_Rep1


title: brain, cre-, rep1

description: 10X Genomics


title: Transduced lung organoids

city: toronto

first: Haibo

last: Zhang

state: ontario

address: 209 victoria st

department: Anesthesia

institute: Unityhealth Toronto

description: Library name: sample 1

data_processing:
All analyses and plotting were performed using the R package Seurat version 4.0.5.   The cell ranger output (10X; https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for the naive and the transduced cells datasets were read in and assessed for quality. We evaluated mitochondrial RNA content, number of unique features (genes) and total counts of detected RNA molecules and selected a basic filter (nFeature_RNA > 200 & nFeature_RNA < 8000 & percent.mt < 30 & nCount_RNA >= 300) which would retain most of the cells but exclude those which would be likely to be broken or doublets. The cells available for downstream analysis were 5382 for the naive experiment, and 1036 for the transduced (from 8117 and 3019 for naive and transduced, respectively).  Each dataset was normalized in Seurat using the SCTransform function, which has been shown to improve common downstream analytical tasks. At this point, the two datasets were integrated using the standard SCT integration workflow (SelectIntegrationFeatures with nFeatures = 3000, PrepSCTIntegration, FindIntegrationAnchors, IntegrateData) to allow a more straightforward comparison.
Assembly: The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v2.11 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: tab-separated values files and matrix files

source_name: induced-pluripotent stem cells

extract_protocol:
Human iPSCs-derived lung organoids were chemically dissociated into single cells using dispase (5 units, Cat. No. CACB354235, VWR, PA, USA) for 5 minutes at 37°C and cell viability percentage was estimated using Trypan Blue (Cat. No T8154, Sigma-Aldrich, MO, USA) staining and 5000 live cells were collected and resuspended with human iPSCs-derived lung organoids maturation media and collected into an Eppendorf tube and placed on ice. The live lung single-cell suspension was proceeded with the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics, product code 1000075) using a 10x Genomics Chromium Controller.
library was performed according to manufacturer's instrcution (single cell 3' v2 protocol, 10X Genomics)

treatment_protocol: Lentiviral vector transduction

value: induced-pluripotent stem cells

value: iPSC-derived lung organoids

value: lentiviral vector transduced


title: HMEC, IFNy, LPS, STATTIC, rep3

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
After quality control, adapter trimming, and quality filtering with fastp (v.0.22.0), fastq files were mapped to the Homo sapiens GRCh38/hg38 genome using STAR version 2.6.1d
Read counts were generated using FeatureCounts v1.6.2 with default parameters
Counts normalization and DEG analysis were performed using the edgeR (v.3.30.3) package in R version 3.6.3
Assembly: GRCh38/hg38 genome build (release-100)
Supplementary files format and content: text file (csv) with raw counts for each sample

source_name: skin

growth_protocol: HMEC cell line (https://pubmed.ncbi.nlm.nih.gov/1361507/) was cultured in MCDB complete medium supplemented with 10% FBS (10500-064, TFS), 1:100 L-glutamine (X0550, BioWest) and 1:100 antibiotic/antimycotic solution (A5955, Sigma-Aldrich), hydrocortisone (H0888, MERCK) and EGF (324831, MERCK) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated with GeneMATRIX Universal RNA Purification Kit (E3598, EURx) following the manufacturer's protocol.
RNA-seq libraries were prepared in three biological replicates from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

treatment_protocol:
Cells were seeded on the 6-well plates in MCDB complete medium. After around 24-28 h when they reached around 70% confluency, the medium was changed, and cells were kept in 1% FBS MCDB starving medium
After at least 8h of starvation they were pre-treated with ALEKSIN compound (10μM, ZINC9547778, MolPort-004-931-223; supplier: IBS (STOCK6S-36352)) for 24h or STATTIC (10μM, 19983-44-9, Sigma) for 8h. In order to mimic inflammation in the cell culture environment HMECs were stimulated with IFNγ (10 ng/ml, IF002, MERCK) for 8h and LPS (1µg/ml, L4391, Sigma-Aldrich)  for 4h before RNA was isolated.

value: skin

value: primary endothelial cells

value: WT

value: IFNgamma (8h, 10 ng/ml), LPS (4h, 1microg/ml ) in the presence of 10microM STATTIC (8h)


title: Naïve lung organoids

description: Library name: sample 2


title: HMEC, IFNy, LPS, STATTIC, rep2