title: RiboTag IP-PV (Parvalbumin) | WT | male | S1 | Sample 42

description: Library name: 42-P2-WT-M-S1-IP


title: RiboTag IP-PV (Parvalbumin) | WT | female | S1 | Sample 41

status: Public on Mar 30 2026

type: SRA

city: Los Angeles

first: Anand

last: Suresh

state: CA

address: 650 CHARLES E YOUNG DR S, MED RECEIVING CHS, RM 76-200C

department: Neurology

country: USA

institute: University of California Los Angeles

description: Library name: 41-P1-WT-F-S1-IP

library_source: transcriptomic

data_processing:
Samples were checked for QC, demultiplexed reads were aligned using STAR aligner to the mouse genome (reference genome ID: mm10) and gene level quantification calculated by Salmon. Outliers were calculated by measuring connectivity between samples, using the WCGNA package and removing samples >2 SD from the mean for Bulk and IP samples. Genes with counts < 20 were excluded.All analysis was performed using R4.4.2.  Counts were VST transformed, Differential gene analysis was performed using limma-voom with FDR of 0.05
Assembly: Demultiplexed reads were aligned using STAR aligner to the mouse genome (reference genome ID: mm10)
Supplementary files format and content: 1CSV file includes raw counts for both cell-type

molecule: polyA RNA

organism: Mus musculus

source_name: Somatosensory Cortex (brain)

extract_protocol:
For each mRNA isolation experiment, mice were anaesthetized with isoflurane, followed by cardiac perfusion with ice cold choline ACSF containing 132 mM choline, 2.5 mM KCl, 1.25 mM NaH2PO4, 25 mM NaHCO3, 7 mM MgCl2, 0.5 mM CaCl2, and 8 mM D-glucose). Coronal sections (1.5 mm thick) containing S1 (A/P -0.5 to +1.82 mm, M/L 3.0 to 4.0 mm) and V1 (A/P +3.5 to 5.5 mm, M/L 1.5 to 3.0 mm) were collected using Stainless-Steel Brain Matrices (Zivic instruments) in chilled choline, from which S1 and V1 were dissected bilaterally. Samples were independently homogenized with a 2 mL Dounce homogenizer in 1 mL of supplemented homogenization buffer containing 1% w/v, HB-S: 1 mM DTT, protease inhibitors (1X), RNAsin (200 units/mL), cycloheximide (2 mg/l), and heparin (1 mg/mL). 100 μL of the homogenate was used for isolating bulk RNA from S1-V1. To isolate mRNA of HA-tagged Pvalb-Cre or Camk2a-Cre from non-HA tagged ribosomes, samples were incubated for 4 h with an anti-HA antibody (1:180, 5 μL in 900 μL of homogenate; 901513 Covance Anti-HA antibody), followed by overnight incubation with magnetic beads (Pierce Protein A/G Magnetic Beads 88802, 200 μL) at 4oC at 15 rpm centrifugation. The supernatant was washed 3 times with 800 μL of high-salt buffer (Tris 50 mM, KCl 300 mM, MgCl2 12 mM, 10% NP-40 (1%), DTT 1 mM, cycloheximide 100 μg/mL, dH2O), centrifuged at 15 rpm for 10 min at 4 oC. For RNA extraction, we used Zymo Research Direct-zol RNA Miniprep kit (R2051) for the homogenate (input), and the Zymo Research Direct-zol RNA Microprep kit (R2061) for the bead-antibody-protein sample (IP); RNA was eluted with DNAase/RNAse-free water. RNA Integrity Number (RIN) scores were used to evaluate the integrity of RNA through the ratio of 28S:18S ribosomal RNA (Agilent TapeStation 4200). We set a minimum RIN score of 7 for our samples.
RNA-seq libraries were prepared using Ovation® RNA-Seq System V2. Libraries were multiplexed for paired end 100 bp sequencing on NovaSeq S2, with a read depth of ~45 million reads on average.

tag: tissue

value: Somatosensory Cortex (brain)

tag: cell type

value: Pvalb

tag: genotype

value: WT

tag: batch

value: Batch 1


title: Muscle,sham control,rep1

city: Guangzhou

first: Xing

last: Fu

address: jinsui road NO.9

country: China

institute: Guangzhou Medical University

description: Library name: sample1

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)
1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5) .
The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: Aorta

extract_protocol:
RNA was harvested using TRIzol/chloroform/isoamyl alcohol. 1.0 ug of total RNA was used for the construction of sequencing lilbraries.
RNA libraries for RNA-seg were prepared using MGIEaSy mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: Aorta

tag: cell line

value: tissue

value: ApoE knock out

tag: treatment

value: sham control


title: 1Tgf_dDAVP_rep4

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description: Library name: sample_12

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 113). Transcripts per million (TPM) and expected counts were generated by RSEM. Computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Assembly: Ensemble release 113
Supplementary files format and content: TPM values in txt format

source_name: kidney

growth_protocol: Cells were cultured in DMEM/Ham’s F12 mediaum (DMEM/F12, Gibco) containing 5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin, and 2% fetal bovine serum which is referred to complete media at 37ºC.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Microprep kit (R2062, Zymo Research) following the manufacturer’s instructions.
First-strand and double-stranded cDNA was synthesized and amplified from 1 ng of total RNA using SMART-Seq® mRNA HT Kit (634796, TAKARA). Amplified cDNA were purified using AMPure XP beads (A63880, Beckman Coulter), and quantified using a Qubit dsDNA HS DNA assay kit (Q32851, Invitrogen). One nanogram of the synthesized cDNAs were fragmented and tagged with index primers (FC-131-1024, Nextera XT DNA library Preparation Kit, Illumina) for high-throughtput sequencing. Libraries were purified by AmPure XP beads, and quantified using a Qubit dsDNA HS DNA assay kit. Equal amounts of indexed libraries were pooled and sequenced on an Illumina platform.

treatment_protocol: To polarize the cells, cells were maintained on permeable membrane filters (3450, Corning) in complete medium for 4 days. Cells were then incubated in serum-free/hormone-deprived medium [containing 50 nM dexamethasone, 60 nM sodium selenite, and 5 μg/mL transferrin], referred to as simple medium, for another 24 hours. Cells were subsequently treated under four experimental conditions: vehicle-treated, 0.1 nM dDAVP (1-desamino-8-D-arginine-vasopressin, V1005, Sigma), 1 ng/mL TGF-β + 0.1 nM dDAVP, and 10 ng/mL TGF-β + 0.1 nM dDAVP in simple medium. dDAVP was applied to the basolateral side, whereas TGF-β was applied to both the apical and basolateral sides of polarized cells. After 24 hours, the medium was replaced with fresh simple medium containing the same treatments. Cells were harvested at the 48-h time point for sample preparation.

value: kidney

value: mpkCCD

value: mouse cortical collecting duct cell

value: 1 ng/mL TGF-b+dDAVP 0.1 nM, 48 hrs


title: Penn02_Bone_Rib_C_N

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

description:
Library name: Penn02_Bone_Rib_C_N
Control, RNAlater

library_source: genomic

data_processing:
The samples were mapped using Dragen. Percent total mapping against reference canine genome (CanFam4, GSD_1.0) is approximately 95% and uniquely mapped reads are above 60%. Library complexity (i.e., percentage of non-duplicate reads) was determined by measuring the percentage of unique fragments in the mapped reads using MarkDuplicate utility.
Percent duplicated reads are between 8% to 34%. Coverage statistics were also measured using Dragen.
The mapped sequencing depth coverage (after alignment and marking duplicates) was between 15x to 118x. Methylation calling was completed using Dragen. The mapping efficiency (number of sequences with a unique best alignment) against the reference genome is 83-91%. There are 42.39-83.64% cytosines methylated in the CpG context, 0.36-1.91% cytosines methylated in the CHG context, and about 0.35-2.27% cytosines methylated in the CHH context. The low levels of non-CpG methylation (CHG and CHH) were used as a proxy to estimate bisulfite conversion efficiency, which was approximately 98–99.6%.
Assembly: Canis lupus familiaris
Supplementary files format and content: tab-delimited text files include methylation percentage at each CpG site generated by using bismark values for each sample

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Normal Bone-Rib

extract_protocol:
DNA was isolated from tumor and normal tissues preserved in RNAlater using Qiagen Allprep DNA/RNA Mini Kit (Cat#80204). Qubit Fluorometer 2.0 with the Qubit dsDNA BR assay (ThermoFisher Scientific) and the TapeStation genomic DNA assay (Agilent Technologies) was used to assess the DNA quantity and quality.
Samples were sequenced on 8 NovaSeq 6000 S4 runs using EZ DNA Methylation-Gold Kit/Accel NGS Methyl-Seq DNA library preparation and paired-end sequencing.

value: Normal Bone-Rib

tag: Sex

value: Female


title: S_3 (Wild type, non-trained, female, muscle sample)

city: Madrid

first: Jose

middle: Luis

last: Cabrera

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Library name: S_3

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Adaptors from RNAseq were removed from reads and low quality reads filtered using the trimgalore v-0.6.6 and cutadapt v-1.18 software.
Trimmed reads were mapped and quantified on the transcriptome GRCm38 gene-build 91 using RSEM v-1.3.1 (calling STAR aligner).
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method, included in edgeR Bioconductor package).
Assembly: GRCm38 gene-build 91
Supplementary files format and content: Counts for mapped reads obtained with STAR v2.5.1 and RSEM v1.3.1

source_name: Muscle

extract_protocol:
RNA was extracted from mice tissues using the RNeasy® Mini Kit (Qiagen), following standard protocols
RNA libraries were produced using the NEBNext Ultra II Directional RNA kit (Illumina) and sequenced on a NextSeq 2000 (Illumina) platform.

value: Muscle


title: S_2 (Wild type, non-trained, female, muscle sample)

description: Library name: S_2


title: Penn02_Bone_Rib_A_N

description:
Library name: Penn02_Bone_Rib_A_N
Control, RNAlater


title: 1Tgf_dDAVP_rep3

description: Library name: sample_11


title: RiboTag IP-PV (Parvalbumin) | WT | male | V1 | Sample 39

description: Library name: 39-P26-WT-M-V1-IP

source_name: Visual Cortex (brain)

value: Visual Cortex (brain)


title: 10Tgf_dDAVP_rep1

description: Library name: sample_13

value: 10 ng/mL TGF-b+dDAVP 0.1 nM, 48 hrs


title: Penn01_Bone_Vertebrae_N

description:
Library name: Penn01_Bone_Vertebrae_N
Control, RNAlater

source_name: Normal Bone-Vertebrae

value: Normal Bone-Vertebrae


title: Penn01_Bone_Rib_N

description:
Library name: Penn01_Bone_Rib_N
Control, RNAlater


title: RiboTag IP-PV (Parvalbumin) | KO | male | V1 | Sample 38

description: Library name: 38-P25-KO-M-V1-IP

value: Pvalb

value: Fmr1 KO


title: S_1 (Wild type, non-trained, female, muscle sample)

description: Library name: S_1

value: WT


title: RiboTag IP-PV (Parvalbumin) | KO | male | V1 | Sample 37

description: Library name: 37-P24-KO-M-V1-IP

value: Batch 1


title: RiboTag IP-PV (Parvalbumin) | KO | female | V1 | Sample 36

description: Library name: 36-P23-KO-F-V1-IP


title: COTC021-2317-T

description:
Library name: COTC021-2317-T
primary OS, RNAlater

source_name: Untreated bone primary osteosarcoma

value: Untreated bone primary osteosarcoma

value: Male


title: 1Tgf_dDAVP_rep2

description: Library name: sample_10


title: 1Tgf_dDAVP_rep1

description: Library name: sample_9


title: TetRmit1_clr4H410L/C412Amyc_9me2

city: Waltham

first: Kaushik

last: Ragunathan

address: 415 South St

institute: Brandeis University

description: Library name: KR3920_TetRmit1_clr4H410L/C412Amyc_9me2

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by counts per million.
Assembly: custom
Supplementary files format and content: bwa

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: YEA, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

value: yeast


title: TetRmit1_clr4myc_9me2

description: Library name: KR3814_TetRmit1_clr4myc_9me2


title: Veh_dDAVP_rep4

description: Library name: sample_8

value: kidney

value: Vehicle+dDAVP 0.1 nM, 48 hrs


title: TetRmit1_clr4W31Gmyc_9me2

description: Library name: KR3808_TetRmit1_clr4W31Gmyc_9me2

value: TetR-mit1, ura4+-10xteto-ade6+, Clr4 W31G-myc


title: COTC022-2308-T

description:
Library name: COTC022-2308-T
primary OS, RNAlater


title: COTC021-2312-T

description:
Library name: COTC021-2312-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | WT | male | V1 | Sample 40

description: Library name: 40-P27-WT-M-V1-IP


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_6

description: Library name: KR3705_mat2p_ade6_mit1OE_epe1D_9me2


title: Veh_dDAVP_rep2

description: Library name: sample_6

value: mpkCCD

value: mouse cortical collecting duct cell


title: Veh_dDAVP_rep3

description: Library name: sample_7


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_6

description: Library name: KR3705_mat2p_ade6_mit1OE_epe1D_9me3


title: RiboTag IP-PV (Parvalbumin) | WT | male | V1 | Sample 34

description: Library name: 34-P21-WT-M-V1-IP


title: Veh_dDAVP_rep1

description: Library name: sample_5


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_5

description: Library name: KR3704_mat2p_ade6_mit1OE_epe1D_9me2


title: RiboTag IP-PV (Parvalbumin) | WT | male | V1 | Sample 35

description: Library name: 35-P22-WT-M-V1-IP


title: Veh_Con_rep4

description: Library name: sample_4

value: Vehicle+no dDAVP, 48 hrs


title: COTC022-1712-T

description:
Library name: COTC022-1712-T
primary OS, RNAlater


title: COTC022-2303-T

description:
Library name: COTC022-2303-T
primary OS, RNAlater

value: Female


title: RiboTag IP-PV (Parvalbumin) | WT | female | V1 | Sample 33

description: Library name: 33-P20-WT-F-V1-IP

value: Visual Cortex (brain)


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_4

description: Library name: KR3703_mat2p_ade6_mit1OE_epe1D_9me3


title: COTC022-1709-T

description:
Library name: COTC022-1709-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | KO | male | V1 | Sample 31

description: Library name: 31-P12-KO-M-V1-IP


title: COTC021-1703-T

description:
Library name: COTC021-1703-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | WT | female | V1 | Sample 32

description: Library name: 32-P18-WT-F-V1-IP


title: RiboTag IP-PV (Parvalbumin) | KO | female | V1 | Sample 30

description: Library name: 30-P11-KO-F-V1-IP


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_5

description: Library name: KR3704_mat2p_ade6_mit1OE_epe1D_9me3


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_4

description: Library name: KR3703_mat2p_ade6_mit1OE_epe1D_9me2


title: RiboTag IP-PV (Parvalbumin) | KO | female | V1 | Sample 29

description: Library name: 29-P10-KO-F-V1-IP


title: COTC022-1412-T

description:
Library name: COTC022-1412-T
primary OS, RNAlater


title: Veh_Con_rep1

description: Library name: sample_1


title: Veh_Con_rep2

description: Library name: sample_2


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_3

description: Library name: KR3702_mat2p_ade6_mit1OE_epe1D_9me3


title: RiboTag IP-PV (Parvalbumin) | KO | female | V1 | Sample 28

description: Library name: 28-P9-KO-F-V1-IP


title: Veh_Con_rep3

description: Library name: sample_3


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_3

description: Library name: KR3702_mat2p_ade6_mit1OE_epe1D_9me2


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep3_L006

city: Albuquerque

first: Steven

last: Bradfute

state: NM

address: 1 University of New Mexico

institute: University of New Mexico Health Sciences Center

description:
Library name: 9_MA8_SNHG15_KD_plus_TC83_24hpi_S9_L006
column name in Snhg15KD_counts.txt: ../star/ 9_MA8_SNHG15_KD_plus_TC83_24hpi_S9_L006

data_processing:
After checking the reads quality using FASTQC. STAR aligner used to generate genome indecies for alignment and to map the reads to the reference genome. The read counts were generated using Featurecount and DESeq2 was used to perform differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Tab seperated value (txt) file contains the raw counts for all the samples

source_name: Brain mixed primary mouse astrocytes

growth_protocol: Mouse C57 brain mixed primary astrocytes were grown in ABM Basal Medium supplemented with AGM SingleQuots and maintained at 37 °C  and 5% CO2 for 24 hours.

extract_protocol:
Total RNA extracted from experimental group and controls at 8, 16 and 24hpi using Direct-Zol RNA Microprep Kit following the manufacturer's protocol.
The total RNAs were sent to University of Colorado at Anchutz for library preperation and RNA sequencing. The libraries were prepared using Zymo-ribo free total RNA library kit.

treatment_protocol: At 24h post-seeding primary mouse astrocytes were transfected with eigther none-targeting siRNA or siRNA against Snhg15. At 24h post transfection the cells were incubated with VEEV TC-83 at MOI 5 for 1h. The medium changed to fresh medium and cells were maintained at 37C and 5% CO2 for 8h, 16h and 24h.

value: Brain mixed primary mouse astrocytes

value: Snhg15 KD cells infected with VEEV TC83 for 24h


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_2

description: Library name: KR3701_mat2p_ade6_mit1OE_epe1D_9me3


title: COTC021-1407-T

description:
Library name: COTC021-1407-T
primary OS, RNAlater


title: COTC022-1107-T

description:
Library name: COTC022-1107-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | KO | female | V1 | Sample 27

description: Library name: 27-P7-KO-F-V1-IP

value: Pvalb


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_2

description: Library name: KR3701_mat2p_ade6_mit1OE_epe1D_9me2


title: RiboTag IP-PV (Parvalbumin) | KO | male | V1 | Sample 26

description: Library name: 26-P6-KO-M-V1-IP

value: Fmr1 KO


title: COTC022-1023-T

description:
Library name: COTC022-1023-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | KO | male | V1 | Sample 25

description: Library name: 25-P5-KO-M-V1-IP


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep2_L006

description:
Library name: 29_MA7_SNHG15_KD_plus_TC83_24hpi_S29_L006
column name in Snhg15KD_counts.txt: ../star/ 29_MA7_SNHG15_KD_plus_TC83_24hpi_S29_L006


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep2_L005

description:
Library name: 29_MA7_SNHG15_KD_plus_TC83_24hpi_S29_L005
column name in Snhg15KD_counts.txt: ../star/ 29_MA7_SNHG15_KD_plus_TC83_24hpi_S29_L005


title: COTC022-1022-T

description:
Library name: COTC022-1022-T
primary OS, RNAlater


title: COTC021-1015-T

description:
Library name: COTC021-1015-T
primary OS, RNAlater


title: WT_mat2p_ade6_mit1OE_epe1D_9me3_1

description: Library name: KR3700_mat2p_ade6_mit1OE_epe1D_9me3


title: WT_mat2p_ade6_mit1OE_9me3

description: Library name: KR3697_mat2p_ade6_mit1OE_9me3


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep1_L005

description:
Library name: 19_MA6_SNHG15_KD_plus_TC83_24hpi_S19_L005
column name in Snhg15KD_counts.txt: ../star/ 19_MA6_SNHG15_KD_plus_TC83_24hpi_S19_L005


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep1_L006

description:
Library name: 19_MA6_SNHG15_KD_plus_TC83_24hpi_S19_L006
column name in Snhg15KD_counts.txt: ../star/ 19_MA6_SNHG15_KD_plus_TC83_24hpi_S19_L006


title: RiboTag IP-PV (Parvalbumin) | WT | male | V1 | Sample 22

description: Library name: 22-P2-WT-M-V1-IP

value: WT


title: COTC022-1012-T

description:
Library name: COTC022-1012-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_24hpi_biol_rep3_L005

description:
Library name: 9_MA8_SNHG15_KD_plus_TC83_24hpi_S9_L005
column name in Snhg15KD_counts.txt: ../star/ 9_MA8_SNHG15_KD_plus_TC83_24hpi_S9_L005


title: RiboTag IP-PV (Parvalbumin) | WT | female | V1 | Sample 23

description: Library name: 23-P3-WT-F-V1-IP

value: Batch 1


title: WT_mat2p_ade6_mit1OE_9me2

description: Library name: KR3697_mat2p_ade6_mit1OE_9me2


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep3_L006

description:
Library name: 8_MA8_sc_siRNA_plus_TC83_24hpi_S8_L006
column name in Snhg15KD_counts.txt: ../star/ 8_MA8_sc_siRNA_plus_TC83_24hpi_S8_L006

value: Cells transfected with none-targeting siRNA followed by VEEV TC83 infection for 24h


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep3_L005

description:
Library name: 8_MA8_sc_siRNA_plus_TC83_24hpi_S8_L005
column name in Snhg15KD_counts.txt: ../star/ 8_MA8_sc_siRNA_plus_TC83_24hpi_S8_L005


title: Epas1cko_ivpos

city: Chiba

first: Atsushi

last: Sasaki

state: Chiba

address: Chuo ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: Library name: Epas1cko_ivpos

library_source: transcriptomic single cell

data_processing:
FASTQ generation and alignment using Cell Ranger.
Filtering, normalization, and clustering using Seurat.
ssGSEA scoring using hypoxic Th2 signature genes derived from Fig.2.
Differential expression analysis between Epas1-sufficient and deficient TRM.
Assembly: Mus musculus mm10 (GRCm38).
Supplementary files format and content: Filtered gene-barcode matrices (h5 format)

source_name: lung

growth_protocol: Epas1^fl/fl and Epas1^fl/fl CD4-Cre mice were maintained under SPF conditions.

extract_protocol:
Lung CD4⁺ T cells were isolated via enzymatic digestion and FACS sorting. Tissue-resident CD4⁺ T cells were defined as i.v.– CD44^hi CD4⁺ cells.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium platform as described for Fig.1.

treatment_protocol: Mice were subjected to chronic HDM exposure for five weeks to induce lung inflammation.

value: lung

value: CD44hi CD4+ T cell

value: Epas1 fl/fl, CD4-Cre

value: HDM, i.v. positive


title: COTC022-1006-T

description:
Library name: COTC022-1006-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma

value: Male


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep2_L006

description:
Library name: 28_MA7_sc_siRNA_plus_TC83_24hpi_S28_L006
column name in Snhg15KD_counts.txt: ../star/ 28_MA7_sc_siRNA_plus_TC83_24hpi_S28_L006


title: WT_mat2p_ade6_epe1D_9me2

description: Library name: KR3627_mat2p_ade6_epe1D_9me2

value: yeast


title: COTC021-1409-T

description:
Library name: COTC021-1409-T
primary OS, RNAlater


title: RiboTag IP-PV (Parvalbumin) | WT | female | V1 | Sample 21

description: Library name: 21-P1-WT-F-V1-IP


title: COTC021-1007-T

description:
Library name: COTC021-1007-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep2_L005

description:
Library name: 28_MA7_sc_siRNA_plus_TC83_24hpi_S28_L005
column name in Snhg15KD_counts.txt: ../star/ 28_MA7_sc_siRNA_plus_TC83_24hpi_S28_L005


title: WT_mat2p_ade6_mit1OE_epe1D_9me2_1

description: Library name: KR3700_mat2p_ade6_mit1OE_epe1D_9me2


title: RiboTag IP-PV (Parvalbumin) | WT | female | V1 | Sample 24

description: Library name: 24-P4-WT-F-V1-IP


title: WT_mat2p_ade6_epe1D_9me3

description: Library name: KR3627_mat2p_ade6_epe1D_9me3


title: WT_ivneg

description: Library name: WT_ivneg

value: Epas1 fl/fl

value: HDM, i.v. negative


title: TetRmit1_ccq1D_9me3

description: Library name: KR3453_ccq1_9me3

value: TetR-mit1, ccqD, ura4+-10xteto-ade6+


title: COTC022-0902-T

description:
Library name: COTC022-0902-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep1_L005

description:
Library name: 18_MA6_sc_siRNA_plus_TC83_24hpi_S18_L005
column name in Snhg15KD_counts.txt: ../star/ 18_MA6_sc_siRNA_plus_TC83_24hpi_S18_L005

value: Brain mixed primary mouse astrocytes


title: Epas1cko_ivneg

description: Library name: Epas1cko_ivneg


title: HDM_hypohi_2

description: Library name: HDM_hypohi_2

data_processing:
Raw base call files were converted to FASTQ using Cell Ranger mkfastq.
Reads were aligned to the mouse reference genome (mm10) using Cell Ranger count.
Gene-cell count matrices were generated and imported into Seurat.
Cells with low UMI counts or high mitochondrial gene percentages were filtered.
Data were normalized, scaled, and subjected to PCA and UMAP dimensional reduction.
Assembly: Mus musculus genome build mm10 (GRCm38).
Supplementary files format and content: Filtered gene-barcode matrices (h5 format), bigwig

growth_protocol: Wild-type C57BL/6 mice (6–8 weeks old) were maintained under specific pathogen-free conditions.

extract_protocol:
Lung tissues were harvested after perfusion. Single-cell suspensions were prepared by enzymatic digestion. Hypoxic cells were labeled in vivo using EF5 prior to sacrifice. Circulating and tissue-resident CD4⁺ T cells were distinguished by intravascular antibody labeling.
For scRNA-seq, FACS-sorted circulating (i.v.+) and tissue (i.v.–) CD44^hi CD4⁺ T cells were processed using the 10x Genomics Chromium platform. Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit according to the manufacturer’s instructions.

treatment_protocol: Mice were intranasally exposed to house dust mite (HDM) extract for five consecutive weeks to induce chronic airway inflammation and tertiary lymphoid structure (TLS) formation. Control mice received PBS.

value: wild-type

value: HDM, Hypoxyprobe hi


title: TetRmit1_ccq1D_9me2

description: Library name: KR3453_ccq1_9me2


title: HDM_hypohi_4

description: Library name: HDM_hypohi_4


title: WT_mat2p_ade6_9me3

description: Library name: KR3625_mat2p_ade6_9me3


title: COTC022-1004-T

description:
Library name: COTC022-1004-T
primary OS, RNAlater

value: Female


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep2_L006

description:
Library name: 26_MA7_SNHG15_KD_plus_TC83_16hpi_S26_L006
column name in Snhg15KD_counts.txt: ../star/ 26_MA7_SNHG15_KD_plus_TC83_16hpi_S26_L006

value: Snhg15 KD cells infected with VEEV TC83 for 16h


title: HDM_hypohi_3

description: Library name: HDM_hypohi_3


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep2_L005

description:
Library name: 26_MA7_SNHG15_KD_plus_TC83_16hpi_S26_L005
column name in Snhg15KD_counts.txt: ../star/ 26_MA7_SNHG15_KD_plus_TC83_16hpi_S26_L005


title: HDM_hypohi_1

description: Library name: HDM_hypohi_1


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_24hpi_biol_rep1_L006

description:
Library name: 18_MA6_sc_siRNA_plus_TC83_24hpi_S18_L006
column name in Snhg15KD_counts.txt: ../star/ 18_MA6_sc_siRNA_plus_TC83_24hpi_S18_L006


title: WT_ivpos

description: Library name: WT_ivpos


title: COTC022-1002-T

description:
Library name: COTC022-1002-T
primary OS, RNAlater


title: TetRclr4_9me3

description: Library name: KR3030_TetRclr4_9me3

value: TetR-clr4, ura4+-10xteto-ade6+


title: WT_mat2p_ade6_9me2

description: Library name: KR3625_mat2p_ade6_9me2


title: COTC021-1001-T

description:
Library name: COTC021-1001-T
primary OS, RNAlater


title: TetRclr4_9me2

description: Library name: KR3030_TetRclr4_9me2


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep1_L005

description:
Library name: 16_MA6_SNHG15_KD_plus_TC83_16hpi_S16_L005
column name in Snhg15KD_counts.txt: ../star/ 16_MA6_SNHG15_KD_plus_TC83_16hpi_S16_L005


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep1_L006

description:
Library name: 16_MA6_SNHG15_KD_plus_TC83_16hpi_S16_L006
column name in Snhg15KD_counts.txt: ../star/ 16_MA6_SNHG15_KD_plus_TC83_16hpi_S16_L006


title: COTC021-0723-T

description:
Library name: COTC021-0723-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep3_L005

description:
Library name: 6_MA8_SNHG15_KD_plus_TC83_16hpi_S6_L005
column name in Snhg15KD_counts.txt: ../star/ 6_MA8_SNHG15_KD_plus_TC83_16hpi_S6_L005


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_16hpi_biol_rep3_L006

description:
Library name: 6_MA8_SNHG15_KD_plus_TC83_16hpi_S6_L006
column name in Snhg15KD_counts.txt: ../star/ 6_MA8_SNHG15_KD_plus_TC83_16hpi_S6_L006


title: COTC021-0817-T

description:
Library name: COTC021-0817-T
primary OS, RNAlater


title: HDM_hypolo_3

description: Library name: HDM_hypolo_3

value: HDM, Hypoxyprobe lo


title: COTC021-0722-T

description:
Library name: COTC021-0722-T
primary OS, RNAlater


title: COTC021-0814-T

description:
Library name: COTC021-0814-T
primary OS, RNAlater


title: HDM_hypolo_1

description: Library name: HDM_hypolo_1

value: lung


title: COTC021-0809-T

description:
Library name: COTC021-0809-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep2_L006

description:
Library name: 25_MA7_sc_siRNA_plus_TC83_16hpi_S25_L006
column name in Snhg15KD_counts.txt: ../star/ 25_MA7_sc_siRNA_plus_TC83_16hpi_S25_L006

value: Cells transfected with none-targeting siRNA followed by VEEV TC83 infection for 16h


title: TetRmit1_9me3

description: Library name: KR3188_TetRmit1_9me3

value: TetR-mit1, ura4+-10xteto-ade6+


title: TetRmit1_clr4OE_9me2

description: Library name: KR3560_clr4OE_9me2

value: TetR-mit1, clr4OE, ura4+-10xteto-ade6+


title: WT_9me3

description: Library name: KR3013_WT_9me3


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep2_L005

description:
Library name: 25_MA7_sc_siRNA_plus_TC83_16hpi_S25_L005
column name in Snhg15KD_counts.txt: ../star/ 25_MA7_sc_siRNA_plus_TC83_16hpi_S25_L005


title: TetRmit1_FOA_9me2

description: Library name: KR3188F_TetRmit1_9me2


title: COTC022-0802-T

description:
Library name: COTC022-0802-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma


title: TetRmit1_K587A_9me3

description: Library name: KR3189_TetRmit1_K587A_9me3

value: TetR-mit1 K587A, ura4+-10xteto-ade6+


title: Control_hypolo_1

description: Library name: Control_hypolo_1

value: CD44hi CD4+ T cell

value: Control, Hypoxyprobe lo


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep3_L006

description:
Library name: 5_MA8_sc_siRNA_plus_TC83_16hpi_S5_L006
column name in Snhg15KD_counts.txt: ../star/ 5_MA8_sc_siRNA_plus_TC83_16hpi_S5_L006


title: TetRmit1_clr4OE_9me3

description: Library name: KR3560_clr4OE_9me3

value: yeast


title: HDM_hypolo_2

description: Library name: HDM_hypolo_2


title: HDM_hypolo_4

description: Library name: HDM_hypolo_4


title: TetRmit1_FOA_9me3

description: Library name: KR3188F_TetRmit1_9me3


title: COTC022-0642-T

description:
Library name: COTC022-0642-T
primary OS, RNAlater


title: COTC021-0631-T

description:
Library name: COTC021-0631-T
primary OS, RNAlater

value: Male


title: COTC021-0709-T

description:
Library name: COTC021-0709-T
primary OS, RNAlater


title: Control_hypolo_4

description: Library name: Control_hypolo_4


title: TetRmit1_clr4D_9me3

description: Library name: KR3186_TetRmit1_clr4D_9me3

value: TetR-mit1, clr4D, ura4+-10xteto-ade6+


title: TetRmit1_clr4D_9me2

description: Library name: KR3186_TetRmit1_clr4D_9me2


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep3_L005

description:
Library name: 5_MA8_sc_siRNA_plus_TC83_16hpi_S5_L005
column name in Snhg15KD_counts.txt: ../star/ 5_MA8_sc_siRNA_plus_TC83_16hpi_S5_L005

value: Brain mixed primary mouse astrocytes


title: COTC021-0621-T

description:
Library name: COTC021-0621-T
primary OS, RNAlater


title: TetRmit1_K587A_9me2

description: Library name: KR3189_TetRmit1_K587A_9me2


title: COTC021-0640-T

description:
Library name: COTC021-0640-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep1_L005

description:
Library name: 15_MA6_sc_siRNA_plus_TC83_16hpi_S15_L005
column name in Snhg15KD_counts.txt: ../star/ 15_MA6_sc_siRNA_plus_TC83_16hpi_S15_L005


title: Control_hypolo_3

description: Library name: Control_hypolo_3

value: wild-type


title: Control_ivpos

description: Library name: Control_ivpos

value: Control, i.v. positive


title: Control_hypolo_2

description: Library name: Control_hypolo_2


title: TetRmit1_9me2

description: Library name: KR3188_TetRmit1_9me2


title: WT_9me2

description: Library name: KR3013_WT_9me2


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep3_L006

description:
Library name: 3_MA8_SNHG15_KD_plus_TC83_8hpi_S3_L006
column name in Snhg15KD_counts.txt: ../star/ 3_MA8_SNHG15_KD_plus_TC83_8hpi_S3_L006

value: Snhg15 KD cells infected with VEEV TC83 for 8h


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_16hpi_biol_rep1_L006

description:
Library name: 15_MA6_sc_siRNA_plus_TC83_16hpi_S15_L006
column name in Snhg15KD_counts.txt: ../star/ 15_MA6_sc_siRNA_plus_TC83_16hpi_S15_L006


title: COTC022-0620-T

description:
Library name: COTC022-0620-T
primary OS, RNAlater

value: Female


title: HDM_ivpos

description: Library name: HDM_ivpos

value: HDM, i.v. positive


title: COTC022-0616-T

description:
Library name: COTC022-0616-T
primary OS, RNAlater


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep2_L005

description:
Library name: 23_MA7_SNHG15_KD_plus_TC83_8hpi_S23_L005
column name in Snhg15KD_counts.txt: ../star/ 23_MA7_SNHG15_KD_plus_TC83_8hpi_S23_L005


title: COTC022-0614-T

description:
Library name: COTC022-0614-T
primary OS, RNAlater


title: RNA_CE_VS_4

city: St. Louis

first: Gabor

last: Egervari

email: gabor@wustl.edu, egervarilab@gmail.com

state: MO

address: 4515 McKinley Ave, Couch Building

department: Genetics, Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

description: Library name: CE_VS_4

data_processing:
Base calling and demultiplexing: Base calls and demultiplexing were performed using Element Biosciences' bases2fastq software (CTX, dHPC; DSIL@CGSSB) or using Illumina's bcl2fastq software and a custom python demultiplexing program (vHPC, DS, VS; GTAC@MGI) allowing 1 mismatch in the indexing read.
Trimming: Adapters were trimmed from sequencing reads using Cutadapt 5.0 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Alignment: Trimmed reads were aligned to the Mus musculus GRCm39 reference genome assembly using STAR v2.7.10a with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --quantMode TranscriptomeSAM GeneCounts
Quantification: Counts were generated using featureCounts v2.0.6 and Mus_musculus.GRCm39.113.gtf. Gene counts were quantified with parameters -t exon -g gene_id -s 2 -p -B -C -O -M ; Transcript isoform counts were quantified with parameters -t exon -g transcript_id -s 2 -p -B -C -O -M
Assembly: GRCm39 (NCBI RefSeq GCF_000001635.27)
Supplementary files format and content: gene_counts.csv contains gene counts ; transcript_counts.csv contains transcript isoform counts

source_name: ventral striatum

growth_protocol: C57BL/6J male mice 8-10 weeks of age were housed on a 12h/12h light/dark cycle with food and water provided ad libitum.

extract_protocol:
Total RNA was extracted using TRIzol-chloroform and the RNeasy Mini Kit (Qiagen 74104) with on-column RNase-free DNase (Qiagen 79254) treatment according to manufacturer protocols. Total RNA quality was assessed using the High Sensitivity RNA ScreenTape Assay on a TapeStation 4200 system (Agilent 5067-5579, 5067-5580).
mRNA was isolated from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490). Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB E7770) [CTX, dHPC] or the NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760) [vHPC, DS, VS] in coordination with compatible NEBNext Multiplex Oligos (NEB E7335, E7500, E7710 [CTX, dHPC]; NEB E6440 [vHPC, DS, VS]) and HighPrep PCR beads (MagBio AC-60050). Library quality was assessed using the DNA ScreenTape Assay on a TapeStation 4200 System (Agilent 5067-5602, 5067-5582). Libraries were quantified using the NEBNext Library Quant Kit (NEB E7630) on an Applied Biosystems QuantStudio 5 Real-Time PCR system, and the concentration of amplifiable templates in each library was calculated using the NEBioCalculator qPCR Library Quantification Web Tool. Libraries were then pooled in equal concentrations and submitted for sequencing.

treatment_protocol: Each mouse was administered a daily dose of 2 g/kg ethanol (20% ethanol in saline solution) or equivalent volume saline (vehicle control) via i.p. injection for 1 day (acute) or 10 days (chronic). Mice were sacrificed 4 hours after the final injection.

value: ventral striatum

tag: paradigm

value: chronic

value: ethanol

tag: condition

value: chronic ethanol

tag: group

tag: mouse

value: male

tag: strain


title: COTC022-0615-T

description:
Library name: COTC022-0615-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma


title: RNA_CE_VS_6

description: Library name: CE_VS_6


title: HDM_ivneg

description: Library name: HDM_ivneg

value: lung

value: CD44hi CD4+ T cell

value: HDM, i.v. negative


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep1_L005

description:
Library name: 13_MA6_SNHG15_KD_plus_TC83_8hpi_S13_L005
column name in Snhg15KD_counts.txt: ../star/ 13_MA6_SNHG15_KD_plus_TC83_8hpi_S13_L005


title: COTC022-0613-T

description:
Library name: COTC022-0613-T
primary OS, RNAlater

value: Male


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep1_L006

description:
Library name: 13_MA6_SNHG15_KD_plus_TC83_8hpi_S13_L006
column name in Snhg15KD_counts.txt: ../star/ 13_MA6_SNHG15_KD_plus_TC83_8hpi_S13_L006


title: RNA_CE_VS_1

description: Library name: CE_VS_1


title: COTC021-0515-T

description:
Library name: COTC021-0515-T
primary OS, RNAlater


title: HSapiens_exp3_chip2_CRISPR

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Library name: HSapiens_exp3_chip2_CRISPR_lib

library_source: other

data_processing:
Per batch and library type, the experimental workflow yielded up to 128 FASTQ files due to the different combinations of 10x and flow cell lanes as well as the paired-end setup. All FASTQ data were processed using Cell Ranger (10x Genomics, v7.0.0). Reads of the GEX libraries were aligned to the hg38 and macFas6 reference genomes extended by the sequence of the dCas9 insert, while reads of the CRISPR libraries were aligned to a custom reference containig the gRNA protospacer sequences.
We demultiplexed the reads by species using cellsnp-lite (v1.2.2) and vireo (v0.2.3), based on a list of single nucleotide polymorphisms (SNPs) derived from bulk RNA-seq data of the wild-type cell lines.
We assigned perturbations to the cells based on the gRNA calls.  We only kept cells that contained a single dominant gRNA (i.e., all other detected gRNAs in the cell contributed <10% of gRNA UMIs and <1000 UMIs combined) and with >10 UMIs supporting the dominant gRNA. To generate the subset of data presented in this repository, we filtered the FASTQ files, count matrices, and gRNA calls to include only POU5F1-perturbed and control cells.
Assembly: GRCh38/hg38 GENCODE release 32 and Macaca fascicularis 6.0/macFas6 ENSEMBL release 105, both extended by the sequence of the dCas9 insert
Supplementary files format and content: Hierarchical data format 5 (h5)  files - filtered count matrices output by Cell Ranger
Supplementary files format and content: Comma-separated values (csv) files - gRNA calls per cell output by Cell Ranger

molecule: other

organism: Homo sapiens

growth_protocol: For standard maintenance, iPSCs were grown in geltrex-coated 12-wells in StemFit Basic03. Medium was changed every other day.

extract_protocol:
To quantify mRNA and gRNAs of the cells, cells were dissociated to single cells using Accumax, washed and stored in PBS +0.04 % Bsa. Human and cynomolgus cells were pooled to equal cell numbers per cell line, then the single cell suspension was loaded on a 10x Genomics Chromium Controller for GEM generation. RT and cDNA amplification were conducted according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening; USER GUIDE: CG000510 Rev B).
We performed three CRISPRi screens in total, using one 10x chip in the first two and three 10x chips in the third experiment (5 batches in total). Per 10x chip and lane, two libraries were generated: a gene expression library and a CRISPR library (identified as GEX and CRISPR lib in the sample names). For details see the manufacturer’s protocol.

treatment_protocol: To conduct single-cell CRISPRi screens, iPSCs were seeded as single-cells in geltrex-coated wells. Cells were transduced with lentiviral gRNA libraries (MOI 0.1). Transduced cells were selected with puromycin, then they were expanded for 5 days, while also inducing KRAB-dCas9 expression by adding doxycycline to the SF03 medium.

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus

tag: library type

value: 10x Genomics 5' CRISPR Guide Capture


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep3_L005

description:
Library name: 3_MA8_SNHG15_KD_plus_TC83_8hpi_S3_L005
column name in Snhg15KD_counts.txt: ../star/ 3_MA8_SNHG15_KD_plus_TC83_8hpi_S3_L005

value: Brain mixed primary mouse astrocytes


title: Control_ivneg

description: Library name: Control_ivneg

value: wild-type

value: Control, i.v. negative


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep3_L006

description:
Library name: 2_MA8_sc_siRNA_plus_TC83_8hpi_S2_L006
column name in Snhg15KD_counts.txt: ../star/ 2_MA8_sc_siRNA_plus_TC83_8hpi_S2_L006

value: Cells transfected with none-targeting siRNA followed by VEEV TC83 infection for 8h


title: HSapiens_exp3_chip3_GEX

description: Library name: HSapiens_exp3_chip3_GEX_lib

value: 10x Genomics 5' Gene Expression


title: Primary_Mouse_astrocytes_Treated _with_si_siRNA_against_Snhg15_plus_TC83_8hpi_biol_rep2_L006

description:
Library name: 23_MA7_SNHG15_KD_plus_TC83_8hpi_S23_L006
column name in Snhg15KD_counts.txt: ../star/ 23_MA7_SNHG15_KD_plus_TC83_8hpi_S23_L006

value: Snhg15 KD cells infected with VEEV TC83 for 8h


title: HSapiens_exp3_chip3_CRISPR

description: Library name: HSapiens_exp3_chip3_CRISPR_lib


title: HSapiens_exp3_chip2_GEX

description: Library name: HSapiens_exp3_chip2_GEX_lib


title: COTC022-0512-T

description:
Library name: COTC022-0512-T
primary OS, RNAlater

value: Female


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep3_L005

description:
Library name: 2_MA8_sc_siRNA_plus_TC83_8hpi_S2_L005
column name in Snhg15KD_counts.txt: ../star/ 2_MA8_sc_siRNA_plus_TC83_8hpi_S2_L005


title: COTC022-0602-T

description:
Library name: COTC022-0602-T
primary OS, RNAlater


title: RNA_CP_VS_6

description: Library name: CP_VS_6

value: ventral striatum

value: chronic

value: saline

value: chronic saline


title: COTC021-0335-T

description:
Library name: COTC021-0335-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma


title: HSapiens_exp3_chip1_CRISPR

description: Library name: HSapiens_exp3_chip1_CRISPR_lib


title: RNA_CE_DS_6

description: Library name: CE_DS_6

source_name: dorsal striatum

value: dorsal striatum

value: ethanol

value: chronic ethanol

value: male


title: RNA_CP_VS_3

description: Library name: CP_VS_3


title: COTC021-0327-T

description:
Library name: COTC021-0327-T
primary OS, RNAlater

value: Male


title: COTC021-0314-T

description:
Library name: COTC021-0314-T
primary OS, RNAlater


title: HSapiens_exp3_chip1_GEX

description: Library name: HSapiens_exp3_chip1_GEX_lib

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep2_L005

description:
Library name: 22_MA7_sc_siRNA_plus_TC83_8hpi_S22_L005
column name in Snhg15KD_counts.txt: ../star/ 22_MA7_sc_siRNA_plus_TC83_8hpi_S22_L005

value: Brain mixed primary mouse astrocytes


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep1_L006

description:
Library name: 12_MA6_sc_siRNA_plus_TC83_8hpi_S12_L006
column name in Snhg15KD_counts.txt: ../star/ 12_MA6_sc_siRNA_plus_TC83_8hpi_S12_L006

value: Cells transfected with none-targeting siRNA followed by VEEV TC83 infection for 8h


title: RNA_CP_VS_5

description: Library name: CP_VS_5


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep2_L006

description:
Library name: 22_MA7_sc_siRNA_plus_TC83_8hpi_S22_L006
column name in Snhg15KD_counts.txt: ../star/ 22_MA7_sc_siRNA_plus_TC83_8hpi_S22_L006


title: HSapiens_exp2_chip1_CRISPR

description: Library name: HSapiens_exp2_chip1_CRISPR_lib

value: 10x Genomics 5' CRISPR Guide Capture


title: HSapiens_exp2_chip1_GEX

description: Library name: HSapiens_exp2_chip1_GEX_lib

value: 10x Genomics 5' Gene Expression


title: RNA_CE_DS_5

description: Library name: CE_DS_5


title: Megf10_9mo_NeuN_sorted

city: Saint Louis

first: Khai

last: Nguyen

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: Sample6

data_processing:
Raw sequencing data was processed using CellRanger v8 or v9
Assembly: GRChm39 with Clec7a recombinant sequence added
Supplementary files format and content: cell x gene matrix, h5ad file

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Brains from perfused mice were harvested and flash frozen. Nuclei were isolated from 4-5 randomly selected brains. NeuN- or NeuN- Olig2- nuclei were isolated by FACS.
Library was prepared using 10X Chromium Single-Cell 3' v3 and v4 kit (NeuN- samples) or 10X Chromium Single-Cell 5' v2 kit (NeuN- Olig2- samples) according to manufacturer instructions.

value: Brain

value: NeuN- sorted nuclei

tag: age


title: RNA_CE_DS_4

description: Library name: CE_DS_4

value: chronic


title: COTC021-0305-T

description:
Library name: COTC021-0305-T
primary OS, RNAlater


title: COTC021-0309-T

description:
Library name: COTC021-0309-T
primary OS, RNAlater


title: MOLM14 cells, ATRA+DOX, DoxATRA3

city: Montpellier

first: Catherine

last: Teyssier

address: 208, rue des apothicaires

country: France

description:
Library name: Sample12
Column name in_raw_counts_All_samples.txt: DoxATRA3

data_processing:
Galaxy platform (usegalaxy.fr)
Quality control of raw FASTQ files was performed using FastQC to assess read quality, adapter content, and sequence duplication levels.
Gene-level read counts were obtained using HTSeq-count in union mode, with the data specified as stranded, a minimum alignment quality of 10, and counting reads at the exon level. Reads mapping to multiple genomic locations or overlapping multiple genes were excluded from downstream analysis.
Assembly: Reads were aligned to the human reference genome GRCh38.105 using STAR aligner with default parameters.
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text files includes normalized count for all samples

source_name: blood

growth_protocol: MOLM14 cells were maintained in Minimum Essential Medium-α supplemented with 10% Tetracyline-free fetal bovine serum and antibiotics in humidified atmosphere  with 5% CO2 at 37°C

extract_protocol:
RNA was extracted from cells using the Quick RNATM Miniprep kit (Zymo Research)
RNA sequencing was performed by GENEWIZ (Azenta Life Sciences, Germany) using their standard protocols for library preparation and paired-end sequencing on an Illumina® NovaSeq™ platform

treatment_protocol: Doxycycline was used to induce the expression of shRIP140 at  50ng/mL and replaced every other day. ATRA was used a concentration of 1µM for 48h

value: blood

value: acute myeloid leukemia

value: ATRA+DOX


title: T24_H3K18la_IP

first: Dongqing

last: Li

address: South Shatai road

department: Department of Urology

institute: Southern medical university

description: Library name: S1

data_processing:
In the ChIP-seq analysis of transcription factors with both Input and IP, we use the Input as the background, employ Macs2 to call peaks on the IP, and use the narrow peak mode for peak calling.
By using Homer to search for motifs earlier, we can identify the relationships between the motifs and the corresponding peaks. Subsequently, by combining the peak annotations with associated genes, we can locate the genes corresponding to the motifs, thereby establishing a correspondence between motifs, peaks, and genes.
Assembly: Homo_sapiens.GRCh38.101
Supplementary files format and content: T24_H3K18la_IP.bw  ,T24_H3K18la_Input.bw

source_name: bladder

extract_protocol:
The extraction was performed according to the ChIP-seq protocol of LC-BIO, as follows. T24 bladder cancer cells (≥1 × 10⁷) were crosslinked with 1% formaldehyde for 15 min at room temperature, and the reaction was quenched. Cell nuclei were isolated using lysis buffer, and chromatin was sheared by sonication to obtain fragments ranging from 200 to 600 bp, with sonication conditions optimized to ensure efficient fragmentation. After centrifugation, the soluble chromatin was collected and incubated overnight at 4°C with H3K18la antibody. Protein A/G magnetic beads were then added and incubated for an additional 3 h to capture the antibody‑protein‑DNA complexes. The beads were sequentially washed with low‑salt, high‑salt, and LiCl‑containing buffers to remove non‑specific binding. Following elution, crosslinking was reversed by incubation at 65°C overnight. Proteins were digested with proteinase K, and the enriched DNA fragments were purified using phenol‑chloroform extraction or spin‑column purification, yielding purified DNA suitable for subsequent library construction.
The steps for constructing a DNA library are as follows: 1. Perform terminal repair on the DNA extracted from the IP, adding an A base. 2. Processing of DNA for repair, addition of A, and sequencing adapters. 3. Use magnetic beads to recover small fragments and perform PCR amplification to generate a library for sequencing. 4. Use agarose gel electrophoresis to inspect the library constructed. 5. Use Qubit 2.0 to perform a quantitative analysis of the library to determine if the library concentration is suitable for analysis. 6. Once the quality control of the library has been completed, the different libraries are loaded onto the Illumina sequencing instruments based on their effective concentration and the required data volume for the target analysis.

value: bladder

value: Wildtype

value: Logarithmic-phase bladder cancer (BCa) T24 cells were seeded into culture flasks and incubated for 48 hours.


title: T24_H3K18la_Input

description: Library name: S2

value: Logarithmic-phase bladder cancer (BCa) T24 cells were seeded into culture flasks and incubated for 49 hours.


title: GFP_9mo_NeuN_sorted

description: Library name: Sample5


title: RNA_CE_DS_1

description: Library name: CE_DS_1

value: dorsal striatum

value: ethanol

value: chronic ethanol

value: male


title: RNA_CP_DS_6

description: Library name: CP_DS_6

value: saline

value: chronic saline


title: Dectin1_9mo_NeuN_sorted

description: Library name: Sample4


title: COTC022-0304-T

description:
Library name: COTC022-0304-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma

value: Male


title: COTC021-0301-T

description:
Library name: COTC021-0301-T
primary OS, RNAlater


title: COTC021-0311-T

description:
Library name: COTC021-0311-T
primary OS, RNAlater

value: Female


title: Primary_Mouse_astrocytes_Treated _with_none-targeting_siRNA_plus_TC83_8hpi_biol_rep1_L005

description:
Library name: 12_MA6_sc_siRNA_plus_TC83_8hpi_S12_L005
column name in Snhg15KD_counts.txt: ../star/ 12_MA6_sc_siRNA_plus_TC83_8hpi_S12_L005

value: Brain mixed primary mouse astrocytes

value: Cells transfected with none-targeting siRNA followed by VEEV TC83 infection for 8h


title: RNA_CP_DS_3

description: Library name: CP_DS_3

value: chronic


title: COTC022-0220-T

description:
Library name: COTC022-0220-T
primary OS, RNAlater


title: MOLM14 cells, DOX, Dox1

description:
Library name: Sample7
Column name in_raw_counts_All_samples.txt: Dox1

value: blood

value: acute myeloid leukemia

value: DOX


title: MOLM14 cells, ATRA+DOX, DoxATRA1

description:
Library name: Sample10
Column name in_raw_counts_All_samples.txt: DoxATRA1

value: ATRA+DOX


title: RNA_CP_DS_2

description: Library name: CP_DS_2


title: Megf10_5mo_NeuN_sorted

description: Library name: Sample3

value: Brain

value: NeuN- sorted nuclei


title: CHART_Xist_WT_rep1

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

description:
Xist-CHART_WT.500bp_1kb-smooth_sub-input.bw
Xist-CHART_WT.genome1.500bp_1kb-smooth_sub-input.bw
Xist-CHART_WT.genome2.500bp_1kb-smooth_sub-input.bw
Xist-CHART_WT.unassigned.500bp_1kb-smooth_sub-input.bw

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 500 bp, 1kb smoothing and normalized by INPUT.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized CHART-seq read counts using a bin size of 500 bp, 1kb smoothing.
Library strategy: CHART-seq

source_name: TTF

extract_protocol:
25M cells were resuspended in 1XPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The formaldehyde was quenched with addition of 0.125M glycine, washed three times with PBS-0.05% tween-20, and cell pellets were snap freeze in liquid nitrogen. Cell pellets were thawed on ice with 1ml sucrose buffer (10mM HEPES pH7.5, 0.3M sucrose, 1% Triton X-100, 100mM potassium acetate, 0.1mM EGTA, supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1XProtease Inhibitor Cocktail (11873580001, Sigma), 10U/mL SUPERaseIN RNase Inhibitor (AM2694, Thermo Fisher Scientific) freshly), resuspended and rotated for 10min at 4C. then cells were dounced 20 times with dounce homogenizer (357544, Wheaton) in 3ml sucrose buffer. The cells were layered on a cushion of 7.5ml glycerol buffer (10mM HEPES pH7.5, 25% glycerol, 1mM EDTA, 0.1mM EGTA, 100mM potassium acetate, freshly supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X PIC, and 5U/mL SUPERaseIN) and centrifugated for 10min in 4C at 1500g. pellets were resuspended in 3ml 1X PBS and 3ml of 6% formaldehyde in 1X PBS (3% formaldehyde final) was added for second fixation, that was carried in rotated for 30 minutes at room temperature. Next, the cells were centrifugated at 1000g for 5min in 4C, and washed 3 times with cold PBS-0.05% tween-20. The pellets were resuspended in 1ml nuclear extraction buffer (50mM HEPES pH 7.5, 250mM NaCl, 0.1mM EGTA, 0.5%N-lauroylsarcosine, 0.1% sodium deoxycholate, 5mM DTT, 10U/mL SUPERaseIN), rotated 10 minutes at 4C, spinned-down at 400g for 5 minutes at 4C and nuclei were resuspended in sonication buffer (50mM HEPES pH 7.5, 75mM NaCl, 0.1mM EGTA, 0.5%N-lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS, 5mM DTT, 10U/mL SUPERaseIN). The lysate was divided to two Covaris microtubes, with 130μl in each and sonication was preformed with Covaris E220 sonicator at power: 140W, duty factor: 10%, cycles per burst: 200 for 5 minutes at 4C. Chromatin was pooled, cleared by centrifugation at full speed for 20 minutes at 4C, supernatant was taken to new tube, and volume was adjusted to 390μl. The lysate was pre-cleared with addition of 640μl 2X hybridization buffer (50mM Tris-HCl pH 7.0, 750mM NaCl, 1% SDS, 1mM EDTA, 15% formamide, 1mM DTT, 1mM PMSF, 1X PIC, and 100U/mL SUPERaseIN) and 60μl of washed Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen) in rotation at room temperature for 1 hour. Then, supernatant was divided to two tubes for probe hybridization, each reaction with 520μl. 1% was kept frozen for input. Each tube received 3.6μl from a 10μM mix of 10 Xist probes and hybridization was performed at room temperature in rotation overnight. Next, 120μl of washed beads were added for each reaction and the tubes were incubated in rotation at 37C for 1 hour. Then beads were washed once with 1X hybridization buffer (33% sonication buffer, 67% 2X hybridization buffer) for 10 min, 5 times with 2% SDS buffer (10mM HEPES pH 7.6, 250mM NaCl, 2% SDS, 2mM EDTA, 2mM EGTA, and 1mM DTT) for 5 min and twice with 0.5% NP40 buffer (10mM HEPES pH7.6, 250mM NaCl, 0.5% NP-40, 3mM MgCl2, and 10mM DTT) for 5min, at 37C. Beads were resuspended with 180μl of 0.5% NP40 buffer and 20μl RNase H (5U/μl, NEB) for 20 minutes in room temperature to elute the DNA twice. Input DNA was also resuspended with 0.5% NP40 buffer to 400μl. Eluted DNA was spined down at full speed for 1 min to pellet residual beads, 10μl RNase A (12091-021,Thermo Fisher Scientific) was added to the supernatant, and DNA was incubated for 1h at 37C in rotation. Next, DNA was treated with 10μl of Proteinase K (20mg/ml), SDS to 1% final, and EDTA to 10mM final concentration and the samples were incubated at 55°C for 1 hour. To reverse crosslinking the DNA, NaCl was added to 300mM and the samples were incubated at 65°C overnight. DNA was extracted with phenol-chloroform extraction. Xist pulldown was validated by qPCR with primers around Xist-promoter and compared to primers of Gapdh promoter. To proceed for sequencing, DNA was diluted to 130µl in TE and sonicated in Covaris microtubes at power: 140W, duty factor: 10%, cycles per burst: 200 for 2min at 4C. DNA was cleaned up with 1.8X ampure XP beads (A63881, Beckman Coulter).
Sequencing libraries were prepared with NEBNext® Ultra II DNA Library Prep Kit for Illumina (#E7645S)

tag: chart probe

value: Xist

value: TTF

value: WT


title: MOLM14 cells, ATRA, 0DoxATRA3

description:
Library name: Sample6
Column name in_raw_counts_All_samples.txt: ATRA3

value: ATRA


title: COTC022-0227-T

description:
Library name: COTC022-0227-T
primary OS, RNAlater


title: COTC021-0215-T

description:
Library name: COTC021-0215-T
primary OS, RNAlater


title: GFP_5mo_NeuN_sorted

description: Library name: Sample2


title: MOLM14 cells, ATRA, 0DoxATRA2

description:
Library name: Sample5
Column name in_raw_counts_All_samples.txt: ATRA2


title: RNA_CE_vHPC_4

description: Library name: CE_vHPC_4

source_name: ventral hippocampus

value: ventral hippocampus

value: ethanol

value: chronic ethanol

value: male


title: COTC022-0214-T

description:
Library name: COTC022-0214-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma

value: Male


title: COTC021-0209-T

description:
Library name: COTC021-0209-T
primary OS, RNAlater

value: Female


title: RNA_CP_vHPC_6

description: Library name: CP_vHPC_6

value: chronic

value: saline

value: chronic saline


title: CHART_Xist_S7KO_rep2

description:
Xist-CHART_TTF-S7KO-c9.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c9.genome1.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c9.genome2.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c9.unassigned.500bp_1kb-smooth_sub-input.bw


title: MOLM14 cells, DOX, Dox3

description:
Library name: Sample9
Column name in_raw_counts_All_samples.txt: Dox3

value: blood

value: acute myeloid leukemia

value: DOX


title: COTC022-0212-T

description:
Library name: COTC022-0212-T
primary OS, RNAlater


title: MOLM14 cells, ATRA+DOX, DoxATRA2

description:
Library name: Sample11
Column name in_raw_counts_All_samples.txt: DoxATRA2

value: ATRA+DOX


title: INPUT_WT_rep1

value: Xist

value: TTF


title: RNA_CP_vHPC_3

description: Library name: CP_vHPC_3


title: CHART_Xist_S7KO_rep1

description:
Xist-CHART_TTF-S7KO-c5.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c5.genome1.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c5.genome2.500bp_1kb-smooth_sub-input.bw
Xist-CHART_TTF-S7KO-c5.unassigned.500bp_1kb-smooth_sub-input.bw


title: MOLM14 cells, DOX, Dox2

description:
Library name: Sample8
Column name in_raw_counts_All_samples.txt: Dox2


title: Dectin1_5mo_NeuN_sorted

description: Library name: Sample1

value: Brain

value: NeuN- sorted nuclei


title: MOLM14 cells, ATRA, 0DoxATRA1

description:
Library name: Sample4
Column name in_raw_counts_All_samples.txt: ATRA1

value: ATRA


title: RNA_CE_vHPC_5

description: Library name: CE_vHPC_5

value: ventral hippocampus

value: ethanol

value: chronic ethanol


title: MOLM14 cells, untreated, 0dox2

description:
Library name: Sample2
Column name in_raw_counts_All_samples.txt: 0Dox2

value: untreated


title: MOLM14 cells, untreated, 0dox3

description:
Library name: Sample3
Column name in_raw_counts_All_samples.txt: 0Dox3


title: RNA_CE_vHPC_6

description: Library name: CE_vHPC_6

value: male


title: RNA_CP_vHPC_2

description: Library name: CP_vHPC_2

value: chronic


title: INPUT_S7KO_rep2

value: Female


title: COTC021-0207-T

description:
Library name: COTC021-0207-T
primary OS, RNAlater

value: Untreated bone primary osteosarcoma

value: Male


title: INPUT_S7KO_rep1


title: RNA_AE_VS_5

description: Library name: AE_VS_5

value: ventral striatum

value: acute

value: acute ethanol


title: COTC022-0102-T

description:
Library name: COTC022-0102-T
primary OS, RNAlater


title: MOLM14 cells, untreated, 0dox1

description:
Library name: Sample1
Column name in_raw_counts_All_samples.txt: 0Dox1

value: blood

value: acute myeloid leukemia


title: G4chipseq(TTtAGGG)22

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

description: Library name: G4chipseq(TTtAGGG)22

data_processing:
Reads were aligned to the Neurospora crassa OR74A genome using Bowtie2 (v2.4.4).
Genome-wide signal tracks were generated and normalized using RPKM (Reads Per Kilobase per Million mapped reads).
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: bigwig

organism: Neurospora crassa

source_name: fungal tissue

growth_protocol: Neurospora crassa strains were cultured in liquid Vogel’s minimal medium with 1.5% sucrose at 32°C with shaking at 200 rpm overnight.

extract_protocol:
Fixed cells were lysed using a Branson Sonifier 450 in lysis buffer supplemented with 1 X Halt Protease Inhibitor Cocktail (Thermo Scientific). Chromatin was sheared using a Bioruptor (Diagenode). Immunoprecipitation was performed using anti-H3K27me2/3 antibody (Active motif 39536) or anti-G4 antibody (Sigma-Aldrich MABE917). DNA was purified using Minelute columns (Qiagen).
ChIP DNA was subjected to end-repair, adaptor ligation, and PCR amplification using NEBNext Ultra II DNA Library Prep Kit. Libraries were size-selected using AMPure XP beads and sequenced using Illumina NextSeq 500 with either single-end or paired-end reads.

treatment_protocol: Cells were cross-linked with 0.5% formaldehyde for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 10 minutes and then washed with 1 X PBS. No other treatments were applied.

value: fungal tissue

value: hyphae

value: csr1::(TTtAGGG)22; mus52::bar+

tag: antibody


title: RNA_AE_VS_3

description: Library name: AE_VS_3


title: RNA_AE_VS_2

description: Library name: AE_VS_2


title: adult zebrafish heart, healthy,#1

city: Berlin

first: Janita

last: Mintcheva

address: Robert-Rössle-Str. 10

institute: Max-Delbrück Center for Molecular Medicine

description:
Library name: Hr42
10X Genomics

data_processing:
Demultiplexing and mapping was performed using CellRanger v4.0.0
Assembly: Danio rerio genome GRCz11, release 92 with RFP gene added
Supplementary files format and content: tab separates values filex and matrix files

organism: Danio rerio

source_name: heart

extract_protocol:
Zebrafish hearts were dissociated in HBSS supplemented with Pluronic-F68 and liberase (Roche). A detailed protocol can be found in the source publication.
Libraries were constructed following manufacturers instructions of the 10X Genomics 3' GEX NextGEM v3.1 protocol.

value: heart


title: COTC022-0202-T

description:
Library name: COTC022-0202-T
primary OS, RNAlater


title: sgRNA after CRISPR screening

city: jinan

first: Mengmeng

last: Wang

address: wenhuaxilu

institute: shandong university of pharm

description: Library name: sample 2

data_processing:
Based on the characteristics of Illumina sequencing, for data generated from paired-end sequencing, we require the average Q30 proportion to be above 80% and the average error rate to be below 0.1%. The raw sequencing reads obtained contain reads with adapters and low-quality reads. To ensure the quality of downstream bioinformatics analysis, stringent filtering is applied to the raw reads to obtain clean reads. All subsequent analyses are performed using these clean reads. The data processing steps are as follows: (1) Remove read pairs containing adapter sequences; (2) Discard a read pair if the proportion of N bases (indicating undetermined base information) in either single-end read exceeds 10%; (3) Discard a read pair if the number of low-quality bases (with a Phred quality score below 5) in either single-end read exceeds 50% of the read's length.
Assembly: hg38
Supplementary files format and content: A zip file containing inter-group comparisons of sgRNA read enrichment.
Library strategy: CRISPR Screen

source_name: A549 cells

extract_protocol:
H460 cells were infected with a focused sgRNA library designed to target genes involved in phospholipid metabolism, with 4 sgRNAs per gene. At 48 hours post-infection, cells were enriched for transduced populations via selection with 2 μg/mL puromycin for 72 hours. PD-L1low cells, low 10% of the population, were enriched via two fluorescence-activated cell sorting (FACS) rounds on days 7 and 15 following library transduction. For the first sort, at least 2 × 107 cells were obtained with trypsin, stained on ice for 15 minutes using an APC anti-human PD-L1 antibody, and washed with PBS. Cells exhibiting low PD-L1 expression were isolated using a BD Influx flow cytometer. Genomic DNA (gDNA) was isolated from sorted and unselected populations of mutagenized cells on day 15 by Genomic DNA Purification Kit and sent to Novogene for sequencing.
After end repair and A-tailing of the DNA template, adapters were ligated to both ends of the fragments. No PCR amplification was performed during the process, resulting in the preparation of a PCR-free library. After library construction, the library was first quantified using Qubit 2.0 for a preliminary assessment. The insert size was then checked with the Agilent 2100 system. Upon confirming that the insert size met expectations, the effective concentration of the library (3 nM) was accurately quantified via qPCR to ensure library quality.

value: A549 cells

value: human lung adenocarcinoma cells


title: adult zebrafish heart, injured, 1dpci #3

description:
Library name: Hr41
10X Genomics

value: cryoinjury


title: G4chipseq(TTAGcG)20

description: Library name: G4chipseq(TTAGcG)20

value: csr1::(TTAGcG)20; mus52::bar+


title: RNA_AP_VS_4

description: Library name: AP_VS_4

value: saline

value: acute saline

value: male


title: G4chipseq(TTAGGG)11

description: Library name: G4chipseq(TTAGGG)11

value: csr1::(TTAGGG)11; mus52::bar+


title: RNA_AP_VS_2

description: Library name: AP_VS_2

value: ventral striatum


title: adult zebrafish heart, injured, 6hpci #3

description:
Library name: Hr40
10X Genomics

value: AB


title: sgRNA before CRISPR screening

description: Library name: sample 1


title: VOA-10841-Replicate 2

city: Melbourne

first: Kathleen

last: Pishas

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 41
Column name in raw_counts_All_Samples.csv: 41-VOA-10841-Rep-2_S79

data_processing:
Libraries were indexed for multiplex sequencing, and RNA sequencing was performed using the Illumina NovaSeq X10 platform, generating 100 bp paired-end reads. A sequencing depth of 50 million reads per sample was targeted to ensure comprehensive transcriptome coverage. Raw sequencing data were processed using a Python-based RNA-seq analysis framework. Quality control and adapter trimming were conducted with Trimmomatic, followed by alignment to the human reference genome (hg38) using STAR.
Assembly: Normalization of gene expression was performed using counts per million (CPM), and differential expression analysis was conducted with DESeq2, implemented within Python.
Supplementary files format and content: CSV files include gene-level raw counts for each sample.

growth_protocol: Duplicate independent samples of LGSOC cell lines were grown for 72 hours (reaching 70–80%) with cell pellets collected. Cell lines were maintained in a 1:1 mixture of M199 and MCDB105 media (Sigma-Aldrich) supplemented with 10% HyClone FBS and 1% Penicillin-Streptomycin (Sigma-Aldrich). Cells were cultured at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol, which included on-column DNase treatment to remove residual genomic DNA. 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by the Molecular Genomics Core (Peter MacCallum Cancer Centre, Australia) using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs), incorporating rRNA depletion to enhance the detection of low-abundance transcripts.

treatment_protocol: Cell media only.

value: Low Grade Serous Ovarian

value: NRAS (Q61K)


title: K27chipseqTRF-1-LexADBD, rep2

description: Library name: K27chipseqTRF-1-LexADBD, rep2

value: TRF-1-LexADBD; csr-1::;lexAO(2x)


title: adult zebrafish heart, injured, 6hpci #2

description:
Library name: Hr38
10X Genomics


title: G4chipseq(TTgGGG)11

description: Library name: G4chipseq(TTgGGG)11

value: fungal tissue

value: csr1::(TTgGGG)11; mus52::bar+


title: adult zebrafish heart, injured, 1dpci #2

description:
Library name: Hr39
10X Genomics


title: RNA_AE_DS_5

description: Library name: AE_DS_5

value: dorsal striatum

value: acute

value: ethanol

value: acute ethanol


title: RNA_AP_VS_6

description: Library name: AP_VS_6


title: K27chipseq(TTtAGGG)22, rep2

description: Library name: K27chipseq(TTtAGGG)22, rep2

value: hyphae

value: csr1::(TTtAGGG)22; mus52::bar+


title: VOA-10841-Replicate 3

description:
Library name: Sample 42
Column name in raw_counts_All_Samples.csv: 42-VOA-10841-Rep-3_S80


title: SLC58-Replicate 2

description:
Library name: Sample 38
Column name in raw_counts_All_Samples.csv: 38-SLC58-Rep-2_S78

value: USP9X Mutant


title: SLC58-Replicate 1

description:
Library name: Sample 37
Column name in raw_counts_All_Samples.csv: 37-SLC58-Rep-1_S77


title: K27chipseq(TTtAGGG)22, rep1

description: Library name: K27chipseq(TTtAGGG)22, rep1


title: RNA_AE_DS_3

description: Library name: AE_DS_3


title: adult zebrafish heart, injured, 6hpci #1

description:
Library name: Hr36
10X Genomics

value: heart

value: cryoinjury


title: RNA_AP_DS_6

description: Library name: AP_DS_6

value: saline

value: acute saline

value: male


title: bulk SLAM-seq of spleen with 200mM of 4sU IP injected (6h labeling in total), fish 2

description:
Library name: SLAM-seq 200mM IP, fish 2, spleen
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

data_processing:
demultiplexing performed with bcl2fastq, mapping performed with STAR v2.7.8a (SLAM-seq time course) or STAR v2.7.3 (remaining samples)
Assembly: Danio rerio genome version GRCz11, release 92 for SLAM-seq time course; Danio rerio GRCz11, release 95 for remaining samples.
Supplementary files format and content: tab delimited text files containing nucleotide counts and SLAM specific nucleotide conversion counts for SLAM-seq analysis.

source_name: spleen

extract_protocol:
zebrafish hearts were homogenised and RNA extracted with TRIzol.
Thiol modification with iodoacetamide, followed by library construction based on a modified CEL-seq protocol. Detailed instructions can be found in the source publication.

value: spleen

value: AB


title: iOvCa241-Replicate 1

description:
Library name: Sample 34
Column name in raw_counts_All_Samples.csv: 34-iOvCa241-Rep-1_S75

value: Low Grade Serous Ovarian

value: KRAS (G12D)


title: K27chipseq(TTgGGG)11, rep1

description: Library name: K27chipseq(TTgGGG)11, rep1

value: fungal tissue

value: csr1::(TTgGGG)11; mus52::bar+


title: RNA_AE_DS_4

description: Library name: AE_DS_4

value: dorsal striatum

value: acute


title: bulk SLAM-seq of spleen with 200mM of 4sU IP injected (6h labeling in total), fish 3

description:
Library name: SLAM-seq 200mM IP, fish 3, spleen
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: RNA_AP_DS_4

description: Library name: AP_DS_4


title: iOvCa241-Replicate 2

description:
Library name: Sample 35
Column name in raw_counts_All_Samples.csv: 35-iOvCa241-Rep-2_S76


title: adult zebrafish heart, injured, 1dpci #1

description:
Library name: Hr37
10X Genomics


title: K27chipseq(TTAGGG)11, rep2

description: Library name: K27chipseq(TTAGGG)11, rep2

value: csr1::(TTAGGG)11; mus52::bar+


title: bulk SLAM-seq of spleen with 200mM of 4sU IP injected (6h labeling in total), fish 1

description:
Library name: SLAM-seq 200mM IP, fish 1, spleen
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: VOA-6406-Replicate 2

description:
Library name: Sample 32
Column name in raw_counts_All_Samples.csv: 32-VOA-6406-Rep-2_S74

value: NRAS (Q61R)


title: RNA_AP_DS_2

description: Library name: AP_DS_2


title: VOA-3448-Replicate 3

description:
Library name: Sample 30
Column name in raw_counts_All_Samples.csv: 30-VOA-3448-Rep-3_S72

value: MAPK Wildtype


title: RNA_AE_vHPC_3

description: Library name: AE_vHPC_3

value: ventral hippocampus

value: ethanol

value: acute ethanol


title: VOA-3448-Replicate 2

description:
Library name: Sample 29
Column name in raw_counts_All_Samples.csv: 29-VOA-3448-Rep-2_S70


title: VOA-6406-Replicate 1

description:
Library name: Sample 31
Column name in raw_counts_All_Samples.csv: 31-VOA-6406-Rep-1_S73


title: K27chipseq(TTgGGG)11, rep2

description: Library name: K27chipseq(TTgGGG)11,rep2

value: hyphae


title: K27chipseq(TTAGcG)20, rep2

description: Library name: K27chipseq(TTAGcG)20, rep2

value: csr1::(TTAGcG)20; mus52::bar+


title: K27chipseq(TTAGGG)11, rep1

description: Library name: K27chipseq(TTAGGG)11, rep1


title: bulk SLAM-seq of liver with 200mM of 4sU IP injected (6h labeling in total), fish 3

description:
Library name: SLAM-seq 200mM IP, fish 3, liver
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

source_name: liver

value: liver


title: RNA_AE_vHPC_5

description: Library name: AE_vHPC_5

value: male


title: bulk SLAM-seq of liver with 200mM of 4sU IP injected (6h labeling in total), fish 2

description:
Library name: SLAM-seq 200mM IP, fish 2, liver
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: AB


title: K27chipseq WT, rep1

description: Library name: K27chipseq WT, rep1

value: WT


title: RNA_AE_vHPC_4

description: Library name: AE_vHPC_4


title: RNA_AP_vHPC_4

description: Library name: AP_vHPC_4

value: saline

value: acute saline


title: K27chipseq WT2, rep2

description: Library name: K27chipseq WT, rep2

value: fungal tissue


title: VOA-4627-Replicate 2

description:
Library name: Sample 23
Column name in raw_counts_All_Samples.csv: 23-VOA-4627-Rep-2_S67

value: Low Grade Serous Ovarian


title: hic_csr1

description: Library name: csr1_tel17_NcHiC

data_processing:
Reads were aligned to the Neurospora crassa OR74A genome using Bowtie2 (v2.4.4). Hi-C matrices were generated and ICE-normalized using rfy_hic2 software (https://github.com/rafysta/rfy_hic2).
Processed HiC data were converted to juicer format using the pre command of JUICER program (version 1.22.01)
Assembly: neurospora crassa genome (OR74A)
Supplementary files format and content: Juicer format

growth_protocol: Neurospora crassa cells were cultured in liquid Vogel’s minimal medium with 1.5% sucrose at 25°C with shaking at 200 rpm. Cultures were started by inoculating 2.5 × 10^8 conidia into 50 mL medium and incubated for 16 hours before fixation.

extract_protocol:
In situ Hi-C was conducted as described in Tanizawa 2017 with some modifications.  The fixed cells were disrupted with a Mini-Beadbeater-16 (BioSpec Products) and glass beads (Sigma, G8772) in the presence of lysis buffer [50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1x Complete (Roche, 11836170001), and 1 mM PMSF].  The cells were washed twice with 1x PBS and once with 1.11x NEBuffer 3.1 (New England Biolabs).  Nuclei were permeabilized in 1.11x NEBuffer 3.1 containing 0.1% sodium dodecyl sulfate (SDS) at 62°C for 10 minutes.  The SDS reaction was quenched with 1% Triton X-100 at 37°C for 15 minutes.  Genomic DNA within the permeabilized nuclei was digested with 0.1 U/µL DpnII (New England Biolabs, R0543) at 37°C overnight.  The restriction enzyme was heat-inactivated at 62°C for 20 minutes.  DNA fragment cohesive ends were blunted with 0.13 U/µL Klenow fragment (New England Biolabs, M0210) at 37°C for 45 minutes in the presence of 50 µM biotin-14-dATP (Jena Bioscience, NU-835-BIO14) to label DNA fragment ends with biotin.  The resulting blunt-ended DNA fragments were subjected to proximity ligation using 4.17 U/µL T4 DNA ligase (New England Biolabs, M0202) at room temperature for 4 hours.  DNA was treated by 0.5 mg/mL proteinase K (Invitrogen, 25530049) in the presence of 0.5% SDS at 65°C for 4 hours, followed by phenol:chloroform:isoamyl alcohol (Sigma, P2069) extraction and ethanol precipitation.
The purified DNA was fragmented by sonication with a Bioruptor UCD-200 (Diagenode) and subsequently purified with a 1:1 volume ratio of AMPure XP (Beckman Coulter, A63881) magnetic beads.  Biotin-labeled DNA fragments were captured using Dynabeads MyOne Streptavidin T1 magnetic beads (Invitrogen, 65601) at 25°C for 15 minutes.  While immobilized on the beads, DNA end-repair was performed with 0.5 U/µL T4 polynucleotide kinase (New England Biolabs, M0201), 0.12 U/µL T4 DNA polymerase (New England Biolabs, M0203), and 0.05 U/µL Klenow fragment (New England Biolabs, M0210) at 25°C for 30 minutes.  This step was followed by dA tailing with 0.5 mM dATP and 0.25 U/µL 3'→5' exo- Klenow fragment (New England Biolabs, M0212) at 37°C for 30 minutes.  The resultant dA-tailed DNA was ligated to NEBNext Adaptor for Illumina (New England Biolabs) using the NEBNext Ultra II Ligation Module (New England Biolabs, E7595) in combination with USER Enzyme (New England Biolabs).  Next-generation sequencing libraries were amplified with four cycles of PCR using NEBNext Ultra II Q5 Master Mix (New England Biolabs, M0544) and NEBNext Multiplex Oligos for Illumina (New England Biolabs).  Post-amplification, libraries were purified with a 0.9:1 volume ratio of AMPure XP beads (Beckman Coulter, A63881).  Where applicable, libraries were multiplexed prior to sequencing on an Illumina NextSeq 500 platform.

treatment_protocol: Cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes. Cross-linking was quenched with 125 mM Tris-HCl (pH 8.0) for 10 minutes. No additional treatments were applied.


title: bulk SLAM-seq of liver with 200mM of 4sU IP injected (6h labeling in total), fish 1

description:
Library name: SLAM-seq 200mM IP, fish 1, liver
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of heart with 200mM of 4sU IP injected (6h labeling in total), fish 2

description:
Library name: SLAM-seq 200mM IP, fish 2, heart
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: heart


title: VOA-4627-Replicate 1

description:
Library name: Sample 22
Column name in raw_counts_All_Samples.csv: 22-VOA-4627-Rep-1_S66


title: K27chipseq(TTAGcG)20, rep1

description: Library name: K27chipseq(TTAGcG)20, rep1


title: RNA_AP_vHPC_2

description: Library name: AP_vHPC_2

value: acute


title: RNA_AP_vHPC_6

description: Library name: AP_vHPC_6


title: bulk SLAM-seq of heart with 200mM of 4sU IP injected (6h labeling in total), fish 3

description:
Library name: SLAM-seq 200mM IP, fish 3, heart
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: HUF-Replicate 2

description:
Library name: Sample 26
Column name in raw_counts_All_Samples.csv: 26-HUF-Rep-2_S69

source_name: HUF

value: HUF

value: Primary uterine fibroblast


title: HUF-Replicate 1

description:
Library name: Sample 25
Column name in raw_counts_All_Samples.csv: 25-HUF-Rep-1_S68


title: bulk SLAM-seq of brain with 200mM of 4sU IP injected (6h labeling in total), fish 3

description:
Library name: SLAM-seq 200mM IP, fish 3, brain
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

source_name: brain

value: brain


title: RHI166_hg38

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Reads were aligned to reference genome (hg38) using STAR.
Transcript abundances were quantified using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing TPM and FPKM values for each sample

source_name: 33-day old forebrain organoid

extract_protocol:
RNA was extracted from three to five 33-day-old brain organoids per line using DirectZol RNA miniprep Plus kit (Zymo Research, R2051) as per manufacturer’s recommendations.
Library preparation (Illumina RiboZero, human) and sequencing (Illumina HiSeq4000) was performed at the Next-Generation Sequencing Platform (NGSP), Genome Institute of Singapore (GIS), A*STAR, Singapore.

tag: gender

value: F

tag: diagnosis

value: case


title: hic_WT

description: Library name: Nc3753_HiC

tag: tissue

tag: cell type

value: hyphae


title: Nodal Knockout, d10.5, 2

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

description:
Library name: Sample 4
10X Genomics

data_processing:
Droplet libraries were processed using Cell Ranger multi pipeline. Sequencing reads were aligned to the mm10 mouse reference genome, and transcript counts were quantified for each annotated gene within every cell.
Assembly: mm10
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features.

source_name: myometrium, decidua, placenta

growth_protocol: 8-12 week old Nodal loxP/loxP and Nodal Δ/Δ female mice were mated with wild-type CD1 males overnight. The presence of a copulatory plug the following morning indicated day 0.5 of pregnancy

extract_protocol:
Single cells were isolated from implantation sites (myometrium, decidua and placenta) of Nodal loxP/loxP and Nodal Δ/Δ female mice on day 10.5 of pregnancy by Liberase enzymatic digestion (25 ug/0.1 g of tissue, incubation at 37 C for 45 minutes with agitation). Blood cells were removed by ACK lysis. Single cells were stained with anti-mouse CD45-APC (30 minutes at 4 C) before incubation with anti-APC magnetic beads (15 minutes at 4 C) and MACS enrichment (AutoMACs Pro, Miltenyi Biotec). Cells were fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics) according to manufacter's protocol.
Probe hybridization was performed on approximately 500,000 cells/sample using the Chromium Fixed RNA Mouse Transcriptome Kit (10X Genomics) following manufacter's protocol. 18,000 cells were encapsulated for a target library of 10,000 cells/sample (Chromium iX, 10X Genomics).

value: myometrium, decidua, placenta

value: leukocyte

tag: developmental stage

value: gestational day 10.5

value: female

tag: genotype

value: Nodal delta/delta


title: bulk SLAM-seq of brain with 200mM of 4sU IP injected (6h labeling in total), fish 2

description:
Library name: SLAM-seq 200mM IP, fish 2, brain
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: AB


title: RHI165_hg38

tag: cell line

value: M

value: control


title: mouse skin single cell Transcriptome-3

city: Shanghai

first: Shenbin

address: 131 Dongan road

department: Fudan University

institute: MOE Frontiers Center for Brain Science

description:
Library name: RHS sympathetic
Sympathetic ganglia cells from RHS- and MC903-treated mice

data_processing:
For skin CD45 cell: scRNA-seq data were analyzed in R v3.6.0 using Seurat v5.1.0, or batched analysis was performed using the Seaborn Python package; For sympathetic ganglia: All downstream single-cell analyses were performed using Cell Ranger and Seurat (37). Briefly, for each gene and each cell barcode (filtered by Cell Ranger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat: A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Cell Ranger reanalyzes feature barcode matrices produced by Cell Ranger count or Ranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using Cell Ranger default parameter settings. The Seurat package was used to normalize data, dimensionality reduction, clustering, and differential expressions. The Seurat alignment method of canonical correlation analysis (CCA) (38) was used to integrate the datasets. For clustering, highly variable genes were selected, and the principal components based on those genes were used to build a graph segmented with a resolution of 0.6. Based on the filtered gene expression matrix by Seurat, differential expression analysis was carried out between samples using the edge R package to obtain zone-specific marker genes. Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P-values less than 0.05 were considered significantly enriched by the marker gene. KEGG (39) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism, and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high throughput experimental technologies. We used the cluster Profiler R package to test the statistical enrichment of marker genes in KEGG pathways. Reactome pathway-based analysis of marker genes was implemented by the ReactomePA R package. We identified TH+ noradrenergic sympathetic neurons based on Snap25, Tubb3, Th, and Dbh expression but negative for Chat transcripts. We then visualized the gene expression of each cluster in R v3.6.0 using Seurat v5.1.0.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Sympathetic ganglia

extract_protocol:
For scRNA-seq of skin CD45+ cells, the tissues from EtOH- and MC903-treated mice were surgically removed and digested as described above (see the procedure of “flow cytometry”). After digestion, the samples were sieved through a 40 µM cell strainer and centrifuged at 300 g for 10 minutes. The obtained cell pellet was resuspended in 90 μL MACS buffer (supplemented with 0.5% bovine serum albumin (9048-46-8, Vetec) and 2 mM EDTA (60-00-4, Sigma-Aldrich) and 10 μL CD45 Microbeads (130-052-301, Miltenyi Biotec) per 107 cells, and the cells were incubated for 15 minutes at 4°C in the refrigerator. CD45+ cells were subsequently sorted as described above. Single cells were stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). For sNucRNA-seq of sympathetic neurons, sympathetic ganglia (SCG, STG, T2-T4, CG) were dissected from thirty MC903-challenged mice and placed in the cold (4°C) artificial cerebrospinal fluid (ACSF) solution (in mM: 125 NaCl, 3 KCl, 20 NaHCO3, 1.25 NaH2PO4, 2 MgCl2, 20 D-glucose, 2 CaCl2, 0.0001 tetrodotoxin, 0.02 6,7-dinitroquinoxaline-2,3-dione, 0.05 DL-2-amino-5-phosphonovaleric acid), continually bubbled with 95%O2 and 5%CO2. Harvested tissue was homogenized at 4°C in a buffer containing 0.3% IGEPAL CA-630 and a protease inhibitor cocktail (ab65621, Abcam), and the following components (in mM): 250 sucrose, 25 KCl, 20 NaHCO3, 1.25 NaH2PO4, 5 MgCl2, 20 Tricine-KOH, 0.15 spermine, 0.5 spermidine, and 1 dithiothreitol. Samples were filtered through 70 mM strainers, diluted with iodixanol to a final concentration of 25%, and layered on an iodixanol gradient (30% and 40% iodixanol containing 0.04% BSA and RNasin (Promega N2611, 64 units/mL). The samples were centrifuged at 10,000 g for 20 minutes at 4°C, and the nuclei were collected from the 30-40% iodixanol interface.
The BD Rhapsody system was used to capture transcriptomic information of the single cells. Single-cell capture was achieved by randomly distributing a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation to ensure a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcode capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow, which included random priming and extension (RPE), RPE amplification PCR, and WTA index PCR.

value: Sympathetic ganglia

value: neuron


title: bulk SLAM-seq of heart with 200mM of 4sU IP injected (6h labeling in total), fish 1

description:
Library name: SLAM-seq 200mM IP, fish 1, heart
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: heart


title: Nodal Knockout, d10.5, 1

description:
Library name: Sample 3
10X Genomics

tag: Sex


title: RHI164_hg38


title: Nodal Control, d10.5, 2

description:
Library name: Sample 2
10X Genomics

value: Nodal loxP/loxP


title: AOCS2-Replicate 2

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.csv: 17-AOCS2-Rep-2_S63

value: Low Grade Serous Ovarian

value: MAPK Wildtype


title: VOA-4698-Replicate 2

description:
Library name: Sample 20
Column name in raw_counts_All_Samples.csv: 20-VOA-4698-Rep-2_S65


title: VOA-4698-Replicate 1

description:
Library name: Sample 19
Column name in raw_counts_All_Samples.csv: 19-VOA-4698-Rep-1_S64


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 3

city: Bethesda

first: Ian

middle: L

last: Morgan

address: 50 Center Dr.

institute: National Heart Lung and Blood Institute

description: Library name: neg_sc_Mt_gyrase_Del_CTD_cip_rep3

data_processing:
Trimmomatic to trim adapters from reads
BWA-MEM to align the reads to the reference sequence
SAMtools to index the reads
Pysam to extract reads, count enzyme-cleaved DNA ends, and normalize counts by spikein reads
Assembly: pBR322_plus_spikes.fa
Supplementary files format and content: TXT file with number and location of enzyme-cleaved DNA ends from forward and reverse reads

organism: Synthetic plasmid

source_name: Synthetic plasmid

growth_protocol: Supercoiled pBR322 DNA was treated with  M. tuberculosis gyrase CTD deletion mutant.

extract_protocol:
Qiagen PCR Clean-up Kit
SHAN-seq

value: Synthetic plasmid

tag: treatment

value: 100 uM ciprofloxacin

tag: sample group


title: RHI163_hg38


title: bulk SLAM-seq of heart with 200mM of 4sU IT injected, 6hps sham injured (7h labeling in total), sample 2

description:
Library name: SLAM-seq 200mM IT, 6hps, sample 2
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: AOCS2-Replicate 1

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.csv: 16-AOCS2-Rep-1_S62


title: bulk SLAM-seq of brain with 200mM of 4sU IP injected (6h labeling in total), fish 1

description:
Library name: SLAM-seq 200mM IP, fish 1, brain
organs with same "fish number" are from same fish. nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: brain


title: Nodal Control, d10.5, 1

description:
Library name: Sample 1
10X Genomics

value: myometrium, decidua, placenta


title: RHI162_hg38

value: case


title: bulk SLAM-seq of heart with 200mM of 4sU IT injected, 6hps sham injured (7h labeling in total), sample 1

description:
Library name: SLAM-seq 200mM IT, 6hps, sample 1
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of heart with 200mM of 4sU IT injected, 6hpci cryoinjured (7h labeling in total), sample 2

description:
Library name: SLAM-seq 200mM IT, 6hpci, sample 2
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: RHI160_hg38


title: VOA-1056-Replicate 2

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.csv: 14-VOA-1056-Rep-2_S61

value: NRAS (Q61R)


title: RHI161_hg38