title: Hippocampus, Male, P30, WT, replicate 3

status: Public on Dec 01 2025

first: Jacquelyn

last: Salzbank

department: Pediatrics

institute: Columbia University Irving Medical Center

description: Library name: HP.CM846.P30.M.WT

data_processing:
rRNA abundance was measured by mapping with Bowtie2.
Quality control was performed using Picard (v1.83) and RSeQC (v2.6.1).
Assembly: The reads were aligned with STAR (version 2.5.2a), and genes annotated in Gencode vM16 and quantified with featureCounts (v1.4.3-p1).
Supplementary files format and content: .csv file called "Processed_Counts_Matrix" includes raw counts for each sample

extract_protocol:
From each mouse the somatosensory cortex, the cerebellum and the hippocampus were collected. Tissues were homogenized in TRIzol Reagent (Thermo Fisher Scientific); total RNA was extracted with the RNeasy Mini Kit. (Qiagen, no. 74104). A total of 500 ng of RNA was used for sequencing.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library prep (Illumina, catalog number 20020595) in accordance with manufacturer recommendations, and using IDT for Illumina TruSeq DNA UD Indices (Illumina, catalog number 20022370) for adapters.

value: WT

tag: Sex


title: Hippocampus, Male, P30, WT, replicate 4

type: SRA

city: New York

state: NY

country: USA

description: Library name: HP.CM847.P30.M.WT

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

tag: tissue

value: Hippocampus

tag: genotype

value: Male

tag: age


title: Hippocampus, Male, P30, KO, replicate 4

description: Library name: HP.CM839.P30.M.KO

value: KO


title: Hippocampus, Male, P30, WT, replicate 2

description: Library name: HP.CM838.43472.M.WT


title: Hippocampus, Female, P15, WT, replicate 4

description: Library name: HP.1892.P15.F.WT

value: Female


title: Hippocampus, Female, P15, KO, replicate 4

description: Library name: HP.1891.P15.F.KO


title: Hippocampus, Male, P15, WT, replicate 4

description: Library name: HP.1547.P15.M.WT


title: Hippocampus, Female, P15, KO, replicate 3

description: Library name: HP.1546.P15.F.KO


title: Hippocampus, Female, P15, WT, replicate 3

description: Library name: HP.1544.P15.F.WT


title: Hippocampus, Female, P30, KO, replicate 4

description: Library name: HP.1467.P30.F.KO


title: Hippocampus, Male, P15, KO, replicate 4

description: Library name: HP.1540.P15.M.KO


title: Hippocampus, Male, P15, WT, replicate 3

description: Library name: HP.1542.P15.M.WT


title: Hippocampus, Male, P7, KO, replicate 3

description: Library name: HP.1414.P7.M.KO


title: Hippocampus, Female, P30, WT, replicate 4

description: Library name: HP.1466.P30.F.WT


title: Hippocampus, Male, P7, WT, replicate 4

description: Library name: HP.1380.P7.M.WT


title: Hippocampus, Female, P7, KO, replicate 5

description: Library name: HP.1381.P7.M.KO


title: Hippocampus, Female, P7, WT, replicate 4

description: Library name: HP.1410.P7.F.WT


title: Hippocampus, Male, P30, KO, replicate 3

description: Library name: HP.1341.P30.M.KO


title: Hippocampus, Female, P7, WT, replicate 3

description: Library name: HP.1336.43522.F.WT


title: Hippocampus, Male, P7, WT, replicate 3

description: Library name: HP.1370.43503.M.WT


title: Hippocampus, Male, P7, WT, replicate 2

description: Library name: HP.1330.P7.M.WT


title: Hippocampus, Male, P30, WT, replicate 1

description: Library name: HP.1265.P30.M.WT


title: Hippocampus, Male, P30, KO, replicate 2

description: Library name: HP.1266.P30.M.KO


title: Hippocampus, Female, P30, WT, replicate 3

description: Library name: HP.1263.P30.F.WT


title: Hippocampus, Female, P30, WT, replicate 2

description: Library name: HP.1262.P30.F.WT


title: Hippocampus, Female, P30, WT, replicate 1

description: Library name: HP.1258.P30.F.WT


title: Hippocampus, Male, P30, KO, replicate 1

description: Library name: HP.1255.P30.M.KO


title: Hippocampus, Female, P30, KO, replicate 2

description: Library name: HP.1257.P30.F.KO


title: Hippocampus, Male, P15, WT, replicate 2

description: Library name: HP.1233.P15.M.WT


title: Hippocampus, Male, P15, KO, replicate 3

description: Library name: HP.1231.P15.M.KO


title: Hippocampus, Female, P15, KO, replicate 2

description: Library name: HP.1225.P15.F.KO


title: Hippocampus, Male, P15, WT, replicate 1

description: Library name: HP.1220.P15.M.WT


title: Hippocampus, Female, P15, KO, replicate 1

description: Library name: HP.1215.P15.F.KO


title: Hippocampus, Male, P15, KO, replicate 1

description: Library name: HP.1210.P15.M.KO


title: Hippocampus, Male, P7, KO, replicate 1

description: Library name: HP.1185.P7.M.KO


title: Hippocampus, Female, P7, WT, replicate 2

description: Library name: HP.1196.P7.F.WT


title: Hippocampus, Female, P15, WT, replicate 1

description: Library name: HP.1212.P15.F.WT


title: Hippocampus, Female, P15, WT, replicate 2

description: Library name: HP.1221.P15.F.WT


title: Hippocampus, Female, P7, KO, replicate 2

description: Library name: HP.1183.P7.F.KO


title: Hippocampus, Male, P7, KO, replicate 2

description: Library name: HP.1191.P7.M.KO


title: Hippocampus, Female, P7, KO, replicate 3

description: Library name: HP.1193.P7.F.KO


title: Hippocampus, Female, P7, KO, replicate 1

description: Library name: HP.1170.P7.F.KO


title: Somatosensory Cortex, Male, P30, WT, replicate 4

description: Library name: S1.CM847.P30.M.WT

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: Somatosensory Cortex, Male, P30, WT, replicate 3

description: Library name: S1.CM846.P30.M.WT


title: Somatosensory Cortex, Female, P15, WT, replicate 4

description: Library name: S1.1892.P15.F.WT


title: Somatosensory Cortex, Female, P15, KO, replicate 3

description: Library name: S1.1891.P15.F.KO


title: Somatosensory Cortex, Female, P0, KO, replicate 4

description: Library name: S1.1742.P0.F.KO


title: Somatosensory Cortex, Female, P0, WT, replicate 3

description: Library name: S1.1734.P0.F.WT


title: Somatosensory Cortex, Male, P0, KO, replicate 2

description: Library name: S1.1702.P0.M.KO


title: Somatosensory Cortex, Female, P0, WT, replicate 2

description: Library name: S1.1653.P0.F.WT


title: Somatosensory Cortex, Female, P0, KO, replicate 1

description: Library name: S1.1621.P0.F.KO


title: Somatosensory Cortex, Male, P0, WT, replicate 1

description: Library name: S1.1620.P0.M.WT


title: Somatosensory Cortex, Male, P15, WT, replicate 3

description: Library name: S1.1542.P15.M.WT


title: Somatosensory Cortex, Male, P15, KO, replicate 4

description: Library name: S1.1540.P15.M.KO


title: Somatosensory Cortex, Female, P30, WT, replicate 4

description: Library name: S1.1466.P30.F.WT


title: Somatosensory Cortex, Female, P30, WT, replicate 3

description: Library name: S1.1465.P30.F.WT


title: Hippocampus, Female, P7, KO, replicate 4

description: Library name: HP.1344.43522.F.KO


title: Hippocampus, Female, P30, KO, replicate 1

description: Library name: HP.1254.P30.F.KO


title: Hippocampus, Female, P30, KO, replicate 3

description: Library name: HP.1264.P30.F.KO


title: Somatosensory Cortex, Male, P7, KO, replicate 3

description: Library name: S1.1414.P7.M.KO


title: Somatosensory Cortex, Female, P7, WT, replicate 4

description: Library name: S1.1410.P7.F.WT


status: Public on Dec 17 2025

city: Baltimore

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description:
Library name: D7_WT_Sham_Sp_3
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 3

data_processing:
Base calling was performed using CASAVA version 1.8.2 (Illumina, San Diego, CA).
The GENCODE mouse gene annotation (version M33) was used for alignment and quantification.
Gene-level quantification was performed using RSEM version 1.3.3 (PMID: 21816040).
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Tab-delimited text files containing Ensembl gene identifiers and gene/isoform expression values in TPM (transcripts per million).

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Following euthanasia 7 days and 6 weeks after SCI, mice were perfused with 50 mL of ice-cold normal saline. Total RNA was extracted from the spinal cord, lung, and spleen tissue with the miRNeasy Mini Kit (Qiagen, Cat# 74104).  In brief, approximately 600ul of QIAzol were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to Novogene Bioinformatics Technology Co., Ltd. (Sacramento, CA) for downstream sequencing assays.
Library preparations were carried out by Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp reads). mRNA was enriched through poly-A pulldown.

value: Spleen

tag: strain

value: male

value: 19 to 22 months old

value: wild-type

tag: treatment

value: Sham

tag: collection time

value: 7 days after SCI

tag: replicate


title: Hippocampus, Male, P15, KO, replicate 2

description: Library name: HP.1223.P15.M.KO


title: Somatosensory Cortex, Female, P7, KO, replicate 5

description: Library name: S1.1381.P7.M.KO


title: Hippocampus, Female, P7, WT, replicate 1

description: Library name: HP.1181.P7.F.WT


title: Hippocampus, Male, P7, WT, replicate 1

description: Library name: HP.1171.P7.M.WT


title: Somatosensory Cortex, Male, P7, WT, replicate 3

description: Library name: S1.1370.P7.M.WT


title: Somatosensory Cortex, Male, P7, WT, replicate 4

description: Library name: S1.1380.P7.M.WT


title: Somatosensory Cortex, Female, P7, KO, replicate 4

description: Library name: S1.1344.P7.F.KO


title: Somatosensory Cortex, Male, P30, KO, replicate 3

description: Library name: S1.1341.P30.M.KO


title: Somatosensory Cortex, Male, P30, KO, replicate 4

description: Library name: S1.CM839.P30.M.KO


title: Somatosensory Cortex, Female, P0, WT, replicate 4

description: Library name: S1.1743.P0.F.WT


title: Somatosensory Cortex, Male, P30, WT, replicate 2

description: Library name: S1.CM838.P30.M.WT


title: Somatosensory Cortex, Male, P7, WT, replicate 2

description: Library name: S1.1330.P7.M.WT


title: Somatosensory Cortex, Female, P7, WT, replicate 3

description: Library name: S1.1336.P7.F.WT


title: Somatosensory Cortex, Male, P30, KO, replicate 2

description: Library name: S1.1266.P30.M.KO


title: Somatosensory Cortex, Male, P0, WT, replicate 4

description: Library name: S1.1741.P0.M.WT


title: Somatosensory Cortex, Male, P0, WT, replicate 3

description: Library name: S1.1713.P0.M.WT


title: Somatosensory Cortex, Female, P0, KO, replicate 3

description: Library name: S1.1733.P0.F.KO


title: Somatosensory Cortex, Male, P0, KO, replicate 4

description: Library name: S1.1712.P0.M.KO


title: Somatosensory Cortex, Male, P0, KO, replicate 3

description: Library name: S1.1704.P0.M.KO


title: Somatosensory Cortex, Male, P30, WT, replicate 1

description: Library name: S1.1265.P30.M.WT


title: Somatosensory Cortex, Male, P0, WT, replicate 2

description: Library name: S1.1700.P0.M.WT


title: Somatosensory Cortex, Female, P0, KO, replicate 2

description: Library name: S1.1654.P0.F.KO


title: Somatosensory Cortex, Female, P30, KO, replicate 3

description: Library name: S1.1264.P30.F.KO


title: Somatosensory Cortex, Male, P0, KO, replicate 1

description: Library name: S1.1650.P0.M.KO


title: Somatosensory Cortex, Female, P30, WT, replicate 1

description: Library name: S1.1258.P30.F.WT


title: Somatosensory Cortex, Female, P30, WT, replicate 2

description: Library name: S1.1262.P30.F.WT


title: Somatosensory Cortex, Male, P30, KO, replicate 1

description: Library name: S1.1255.P30.M.KO


title: Somatosensory Cortex, Female, P30, KO, replicate 2

description: Library name: S1.1257.P30.F.KO


title: Somatosensory Cortex, Female, P30, KO, replicate 1

description: Library name: S1.1254.P30.F.KO


title: Somatosensory Cortex, Male, P15, KO, replicate 3

description: Library name: S1.1231.P15.M.KO


title: Somatosensory Cortex, Male, P15, WT, replicate 2

description: Library name: S1.1233.P15.M.WT


title: Somatosensory Cortex, Female, P0, WT, replicate 1

description: Library name: S1.1614.P0.F.WT


title: Somatosensory Cortex, Female, P15, WT, replicate 2

description: Library name: S1.1221.P15.F.WT


title: Somatosensory Cortex, Male, P15, WT, replicate 4

description: Library name: S1.1547.P15.M.WT


title: Somatosensory Cortex, Female, P15, WT, replicate 3

description: Library name: S1.1544.P15.F.WT


title: Somatosensory Cortex, Female, P15, KO, replicate 2

description: Library name: S1.1546.P15.F.KO


title: Somatosensory Cortex, Male, P15, WT, replicate 1

description: Library name: S1.1220.P15.M.WT


title: Somatosensory Cortex, Female, P15, KO, replicate 1

description: Library name: S1.1215.P15.F.KO


title: Somatosensory Cortex, Female, P7, WT, replicate 2

description: Library name: S1.1196.P7.F.WT


title: Somatosensory Cortex, Male, P7, KO, replicate 2

description: Library name: S1.1191.P7.M.KO


title: Somatosensory Cortex, Male, P7, KO, replicate 1

description: Library name: S1.1185.P7.M.KO


title: Somatosensory Cortex, Female, P7, KO, replicate 3

description: Library name: S1.1193.P7.F.KO


title: Somatosensory Cortex, Male, P15, KO, replicate 1

description: Library name: S1.1210.P15.M.KO


title: Somatosensory Cortex, Male, P15, KO, replicate 2

description: Library name: S1.1223.P15.M.KO


title: Somatosensory Cortex, Female, P7, KO, replicate 2

description: Library name: S1.1183.P7.F.KO


title: Somatosensory Cortex, Female, P7, WT, replicate 1

description: Library name: S1.1181.P7.F.WT


title: Somatosensory Cortex, Female, P15, WT, replicate 1

description: Library name: S1.1212.P15.F.WT


title: Somatosensory Cortex, Male, P7, WT, replicate 1

description: Library name: S1.1171.P7.M.WT


title: Cerebellum, Male, P30, WT, replicate 4

description: Library name: CB.CM847.P30.M.WT

source_name: Cerebellum

value: Cerebellum


title: Cerebellum, Male, P30, WT, replicate 3

description: Library name: CB.CM846.P30.M.WT


title: Somatosensory Cortex, Female, P7, KO, replicate 1

description: Library name: S1.1170.P7.F.KO


title: Cerebellum, Male, P30, KO, replicate 4

description: Library name: CB.CM839.P30.M.KO


title: Cerebellum, Male, P30, WT, replicate 2

description: Library name: CB.CM838.P30.M.WT


title: Somatosensory Cortex, Female, P30, KO, replicate 4

description: Library name: S1.1467.P30.F.KO


title: Cerebellum, Female, P15, WT, replicate 5

description: Library name: CB.1892.P15.F.WT


title: Cerebellum, Female, P15, KO, replicate 4

description: Library name: CB.1891.P15.F.KO


title: Cerebellum, Female, P0, WT, replicate 3

description: Library name: CB.1734.P0.F.WT


title: Cerebellum, Male, P0, WT, replicate 4

description: Library name: CB.1741.P0.M.WT


title: Cerebellum, Female, P0, KO, replicate 4

description: Library name: CB.1742.P0.F.KO


title: Cerebellum, Female, P0, WT, replicate 4

description: Library name: CB.1743.P0.F.WT


title: Cerebellum, Female, P0, KO, replicate 3

description: Library name: CB.1733.P0.F.KO


title: Cerebellum, Male, P0, KO, replicate 3

description: Library name: CB.1704.P0.M.KO


title: Cerebellum, Male, P0, KO, replicate 4

description: Library name: CB.1712.P0.M.KO


title: Cerebellum, Male, P0, WT, replicate 3

description: Library name: CB.1713.P0.M.WT


title: Cerebellum, Male, P0, WT, replicate 2

description: Library name: CB.1700.P0.M.WT


title: Cerebellum, Female, P0, KO, replicate 2

description: Library name: CB.1654.P0.F.KO


title: Cerebellum, Male, P0, WT, replicate 1

description: Library name: CB.1620.P0.M.WT


title: Cerebellum, Female, P0, WT, replicate 2

description: Library name: CB.1653.P0.F.WT


title: Cerebellum, Female, P0, KO, replicate 1

description: Library name: CB.1621.P0.F.KO


title: Cerebellum, Male, P15, WT, replicate 4

description: Library name: CB.1547.P15.M.WT


title: Cerebellum, Female, P0, WT, replicate 1

description: Library name: CB.1614.P0.F.WT


title: Cerebellum, Male, P0, KO, replicate 2

description: Library name: CB.1702.P0.M.KO


title: Cerebellum, Male, P15, KO, replicate 4

description: Library name: CB.1540.P15.M.KO


title: Cerebellum, Female, P15, KO, replicate 3

description: Library name: CB.1546.P15.F.KO


title: Cerebellum, Female, P15, WT, replicate 4

description: Library name: CB.1544.P15.F.WT


title: Cerebellum, Female, P30, KO, replicate 4

description: Library name: CB.1467.P30.F.KO


title: Cerebellum, Female, P30, WT, replicate 4

description: Library name: CB.1466.P30.F.WT


title: Cerebellum, Male, P7, KO, replicate 3

description: Library name: CB.1414.P7.M.KO


title: Cerebellum, Female, P30, WT, replicate 3

description: Library name: CB.1465.P30.F.WT


title: Cerebellum, Female, P7, KO, replicate 4

description: Library name: CB.1381.P7.M.KO


title: Cerebellum, Male, P0, KO, replicate 1

description: Library name: CB.1650.P0.M.KO


title: Cerebellum, Male, P7, WT, replicate 3

description: Library name: CB.1370.P7.M.WT


title: Cerebellum, Male, P15, WT, replicate 3

description: Library name: CB.1542.P15.M.WT


title: Cerebellum, Male, P7, WT, replicate 4

description: Library name: CB.1380.P7.M.WT


title: Cerebellum, Male, P7, WT, replicate 2

description: Library name: CB.1330.P7.M.WT


title: Cerebellum, Male, P30, KO, replicate 3

description: Library name: CB.1341.P30.M.KO


title: Cerebellum, Female, P7, WT, replicate 2

description: Library name: CB.1336.P7.F.WT


title: Cerebellum, Female, P15, WT, replicate 3

description: Library name: CB.1344b.P15.F.WT


title: Cerebellum, Female, P7, WT, replicate 4

description: Library name: CB.1410.43525.F.WT


title: Cerebellum, Female, P30, WT, replicate 2

description: Library name: CB.1262.P30.F.WT


title: Cerebellum, Female, P30, KO, replicate 3

description: Library name: CB.1264.P30.F.KO


title: Cerebellum, Male, P30, WT, replicate 1

description: Library name: CB.1265.P30.M.WT


title: Cerebellum, Female, P30, KO, replicate 2

description: Library name: CB.1257.P30.F.KO


title: Cerebellum, Female, P30, WT, replicate 1

description: Library name: CB.1258.P30.F.WT


title: Cerebellum, Male, P15, WT, replicate 2

description: Library name: CB.1233.P15.M.WT


title: Cerebellum, Female, P30, KO, replicate 1

description: Library name: CB.1254.P30.F.KO


title: Cerebellum, Male, P15, KO, replicate 2

description: Library name: CB.1223.P15.M.KO


title: Cerebellum, Female, P15, KO, replicate 1

description: Library name: CB.1215.P15.F.KO


title: Cerebellum, Male, P15, WT, replicate 1

description: Library name: CB.1220.P15.M.WT


title: Cerebellum, Male, P15, KO, replicate 1

description: Library name: CB.1210.P15.M.KO


title: Cerebellum, Male, P7, KO, replicate 1

description: Library name: CB.1185.P7.M.KO


title: Cerebellum, Female, P7, KO, replicate 2

description: Library name: CB.1180.43523.F.KO


title: Cerebellum, Male, P7, WT, replicate 1

description: Library name: CB.1171.P7.M.WT


title: uninfected_10, run 2

city: Ann Arbor

first: Marc

last: Hershenson

state: Michigan

address: 1150 E. Medical Center Drive

institute: University of Michigan

description: Library name: 13215-JK-13

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCh38 (ENSEMBL 109)
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all samples.

organism: Homo sapiens

source_name: nasal swab

extract_protocol:
Total RNA from nasal swab samples was prepared using Trizol extraction. RNA was purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
A TruSeq-based Takara kit was used during library preparation. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: nasal swab

tag: host viral_infection

value: uninfected

tag: library batch


title: uninfected_12, run 1

description: Library name: 13215-JK-8


title: uninfected_11, run 1

description: Library name: 13215-JK-7


title: RV (untyped)_4, run 1

description: Library name: 13215-JK-5

value: RV (untyped)


title: RV (untyped)_3, run 1

description: Library name: 13215-JK-4


title: uninfected_9, run 1

description: Library name: 11119-JK-46


title: RV (untyped)_1, run 1

description: Library name: 13215-JK-1


title: uninfected_6, run 2

description: Library name: 11119-JK-43


title: uninfected_5, run 2

description: Library name: 11119-JK-42


title: uninfected_4, run 2

description: Library name: 11119-JK-41


title: RSV_12, run 1

description: Library name: 11119-JK-40

value: RSV


title: RSV_10, run 1

description: Library name: 11119-JK-38


title: RVA_16, run 1

description: Library name: 11119-JK-35

value: RV-A


title: RVC_29, run 1

description: Library name: 11119-JK-34

value: RV-C


title: Cerebellum, Male, P30, KO, replicate 1

description: Library name: CB.1255.P30.M.KO

value: Male


title: Cerebellum, Female, P7, KO, replicate 1

description: Library name: CB.1170.P7.F.KO

value: KO


title: Cerebellum, Female, P7, WT, replicate 1

description: Library name: CB.1181.P7.F.WT

value: WT

value: Female


title: uninfected_1, run 3

description: Library name: 13215-JK-10


title: uninfected_9, run 2

description: Library name: 13215-JK-12


title: uninfected_2, run 3

description: Library name: 13215-JK-11


title: RVA_15, run 1

description: Library name: 11119-JK-30


title: RV (untyped)_5, run 1

description: Library name: 13215-JK-6


title: uninfected_8, run 1

description: Library name: 11119-JK-45


title: RVA_14, run 1

description: Library name: 11119-JK-28


title: RVC_24, run 1

description: Library name: 11119-JK-25


title: RVC_26, run 1

description: Library name: 11119-JK-29


title: RV (untyped)_2, run 1

description: Library name: 13215-JK-3


title: RVC_25, run 1

description: Library name: 11119-JK-27


title: RVA_13, run 1

description: Library name: 11119-JK-26


title: RVC_23, run 1

description: Library name: 11119-JK-24


title: uninfected_7, run 1

description: Library name: 11119-JK-44


title: RSV_11, run 1

description: Library name: 11119-JK-39


title: RVC_22, run 1

description: Library name: 11119-JK-23


title: RVC_21, run 1

description: Library name: 11119-JK-22


title: RVA_12, run 1

description: Library name: 11119-JK-21


title: RVC_20, run 1

description: Library name: 11119-JK-20


title: RVA_11, run 1

description: Library name: 11119-JK-19


title: RVA_10, run 1

description: Library name: 11119-JK-16


title: RVC_19, run 1

description: Library name: 11119-JK-14


title: RVA_9, run 1

description: Library name: 11119-JK-15


title: RVC_17, run 1

description: Library name: 11119-JK-12


title: RVC_18, run 1

description: Library name: 11119-JK-13


title: RVC_30, run 1

description: Library name: 11119-JK-36


title: RVC_15, run 1

description: Library name: 11119-JK-9


title: RVC_16, run 1

description: Library name: 11119-JK-10


title: RVA_8, run 1

description: Library name: 11119-JK-8


title: RVC_14, run 1

description: Library name: 11119-JK-7


title: RVC_12, run 1

description: Library name: 11119-JK-5


title: RVC_11, run 1

description: Library name: 11119-JK-4


title: RVC_10, run 1

description: Library name: 11119-JK-3


title: RVC_9, run 1

description: Library name: 11119-JK-2


title: RVC_8, run 1

description: Library name: 11119-JK-1


title: uninfected_3, run 2

description: Library name: 10455-JK-11


title: uninfected_2, run 2

description: Library name: 10455-JK-10


title: RSV_8, run 1

description: Library name: 10455-JK-8


title: RSV_7, run 1

description: Library name: 10455-JK-7


title: RSV_6, run 1

description: Library name: 10455-JK-6


title: RSV_5, run 1

description: Library name: 10455-JK-5


title: RSV_2, run 1

description: Library name: 10455-JK-2


title: RSV_3, run 1

description: Library name: 10455-JK-3


title: RSV_4, run 1

description: Library name: 10455-JK-4


title: RSV_1, run 1

description: Library name: 10455-JK-1


title: uninfected_6, run 1

description: Library name: 9400-JK-21


title: uninfected_4, run 1

description: Library name: 9400-JK-19


title: uninfected_3, run 1

description: Library name: 9400-JK-18


title: uninfected_5, run 1

description: Library name: 9400-JK-20


title: uninfected_1, run 1

description: Library name: 9400-JK-16


title: RVC_7, run 1

description: Library name: 9400-JK-15


title: RVC_6, run 1

description: Library name: 9400-JK-14


title: RVC_5, run 1

description: Library name: 9400-JK-13


title: RVC_4, run 1

description: Library name: 9400-JK-12


title: RVC_3, run 1

description: Library name: 9400-JK-11


title: RVA_7, run 1

description: Library name: 9400-JK-10


title: RVA_6, run 1

description: Library name: 9400-JK-9


title: RVA_5, run 1

description: Library name: 9400-JK-8


title: RVC_2, run 1

description: Library name: 9400-JK-7


title: RVC_1, run 1

description: Library name: 9400-JK-6


title: RVA_4, run 1

description: Library name: 9400-JK-4


title: RVA_3, run 1

description: Library name: 9400-JK-3


title: RVA_2, run 1

description: Library name: 9400-JK-2


title: RVA_1, run 1

description: Library name: 9400-JK-1


title: M. tuberculosis H37Rv pstA1 deletion mutant 60 min biological replicate 3

status: Public on Nov 27 2025

first: Venkata Anoushka Chinmayi

last: Gudipudi

address: 1550 Orleans Street

department: Medicine

institute: Johns Hopkins University School of Medicine

description:
Library name: pstA1del_60min_rep3
column name in raw_counts_all_samples.csv pstA1_RIF_60min_3

data_processing:
Raw reads were quality assessed using FastQC v0.12.1
Reads were aligned to M. tuberculosis H37Rv reference genome (GCF_000195955.2) using Bowtie2 v2.5.1
Gene counts were quantified using featureCounts (Subread v2.0.0)
Assembly: GCF_000195955.2 (ASM19595v2)
Supplementary files format and content: CSV file containing gene counts matrix with genes as rows and samples as columns

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis samples were cultured in 7H9 Middlebrook broth supplemented with 10% OADC enrichment, 0.2% glycerol and 0.05% Tween-80 at 37°C with shaking to mid-log phase (OD600 ~0.5).

extract_protocol:
Bacterial pellets (15 mL culture) were resuspended in TRIzol with 0.1 mm zirconia beads and lysed using a Precellys Evolution homogenizer (3 cycles, 30 seconds at 7,400 rpm). RNA was extracted with chloroform, precipitated with ethanol, and purified on RNeasy columns (Qiagen) with on-column DNase I digestion.
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection following manufacturer's protocols. Libraries were sequenced on Illumina NovaSeq X Plus platform (2×150 bp paired-end reads).

treatment_protocol: Bacterial RNA was extracted from mid-log phase cultures pre-rifampin treatment (0 minutes) and following exposure to sub-inhibitory rifampin (7.5 ng/ml, 1/4 MIC) for 30 or 60 minutes.

tag: cell type

value: Mycobacterium tuberculosis

value: pstA1 deletion mutant

value: rifampin 7.5 ng/ml 60 min


title: M. tuberculosis H37Rv pstA1 deletion mutant 60 min biological replicate 2

description:
Library name: pstA1del_60min_rep2
column name in raw_counts_all_samples.csv pstA1_RIF_60min_2


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 3

description:
Library name: pstA1del_30min_rep3
column name in raw_counts_all_samples.csv pstA1_RIF_30min_3

value: rifampin 7.5 ng/ml 30 min


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 2

description:
Library name: pstA1del_30min_rep2
column name in raw_counts_all_samples.csv pstA1_RIF_30min_2


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 1

description:
Library name: pstA1del_30min_rep1
column name in raw_counts_all_samples.csv pstA1_RIF_30min_1


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 3

description:
Library name: pstA1del_0min_rep3
column name in raw_counts_all_samples.csv pstA1_ctrl_3

value: untreated 0 min


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 2

description:
Library name: pstA1del_0min_rep2
column name in raw_counts_all_samples.csv pstA1_ctrl_2


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 1

description:
Library name: pstA1del_0min_rep1
column name in raw_counts_all_samples.csv pstA1_ctrl_1


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 3

description:
Library name: WT_60min_rep3
column name in raw_counts_all_samples.csv WT_RIF_60min_3

value: H37Rv wild-type


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 2

description:
Library name: WT_60min_rep2
column name in raw_counts_all_samples.csv WT_RIF_60min_2


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 3

description:
Library name: WT_30min_rep3
column name in raw_counts_all_samples.csv WT_RIF_30min_3


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 2

description:
Library name: WT_30min_rep2
column name in raw_counts_all_samples.csv WT_RIF_30min_2


title: RVC_13, run 1

description: Library name: 11119-JK-6


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 1

description:
Library name: WT_30min_rep1
column name in raw_counts_all_samples.csv WT_RIF_30min_1


title: Cerebellum, Female, P7, WT, replicate 3

description: Library name: CB.1374.P7.F.WT

value: Cerebellum


title: M. tuberculosis H37Rv wild-type untreated biological replicate 3

description:
Library name: WT_0min_rep3
column name in raw_counts_all_samples.csv WT_ctrl_3


title: uninfected_1, run 2

description: Library name: 10455-JK-9

value: nasal swab


title: M. tuberculosis H37Rv wild-type untreated biological replicate 2

description:
Library name: WT_0min_rep2
column name in raw_counts_all_samples.csv WT_ctrl_2


title: M. tuberculosis H37Rv wild-type untreated biological replicate 1

description:
Library name: WT_0min_rep1
column name in raw_counts_all_samples.csv WT_ctrl_1


title: Cerebellum, Male, P30, KO, replicate 2

description: Library name: CB.1266.P30.M.KO


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 1

description:
Library name: WT_60min_rep1
column name in raw_counts_all_samples.csv WT_RIF_60min_1


title: 9c_ERC_SVB

status: Public on Nov 14 2025

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: 9c_ERC_SVB

library_source: transcriptomic single cell

data_processing:
Sequenced chromium data was processed with 10x Genomics Cell Ranger
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and fastq.gz files

source_name: entorhinal cortex (ERC)

extract_protocol:
Entorhinal cortex was dissected from fresh frozen postmortem human tissue, 100 micron sections were obtained via cryo sectioning. Frozen cryosections were homogenized in chilled Nuclei EZ Lysis Buffer, then filtered and centrifuged to isolate nuclei. Pellets were washed in PBS containing 1% BSA and RNase Inhibitor, stained with propidium iodide, and passed through 35 μm strainers. Fluorescence-activated nuclear sorting (FANS) was performed on a MoFlo Legacy Cell Sorter to select whole, singlet, G0/G1 nuclei.
Library preparation for Chromium Next Gem Single Cell 3' v3.1 was completed according to the manufacturer’s protocol.

value: entorhinal cortex (ERC)

tag: batch


title: uninfected_2, run 1

description: Library name: 9400-JK-17

value: uninfected


title: 8c_ERC_SVB

description: Library name: 8c_ERC_SVB


title: 7c_ERC_SVB

description: Library name: 7c_ERC_SVB


title: 5c_ERC_SVB

description: Library name: 5c_ERC_SVB


title: Cerebellum, Female, P15, WT, replicate 2

description: Library name: CB.1221.P15.F.WT


title: Cerebellum, Male, P15, KO, replicate 3

description: Library name: CB.1231.P15.M.KO


title: 6c_ERC_SVB

description: Library name: 6c_ERC_SVB


title: 4c_ERC_SVB

description: Library name: 4c_ERC_SVB


title: 3c_ERC_SVB

description: Library name: 3c_ERC_SVB


title: Cerebellum, Female, P15, KO, replicate 2

description: Library name: CB.1225.P15.F.KO


title: 31c_ERC_SVB

description: Library name: 31c_ERC_SVB


title: 30c_ERC_SVB

description: Library name: 30c_ERC_SVB


title: Cerebellum, Male, P7, KO, replicate 2

description: Library name: CB.1191.P7.M.KO


title: 28c_ERC_SVB

description: Library name: 28c_ERC_SVB


title: Cerebellum, Female, P15, WT, replicate 1

description: Library name: CB.1212.P15.F.WT


title: Cerebellum, Female, P7, KO, replicate 3

description: Library name: CB.1183.P7.F.KO


title: 27c_ERC_SVB

description: Library name: 27c_ERC_SVB


title: 2c_ERC_SVB

description: Library name: 2c_ERC_SVB


title: 25c_ERC_SVB

description: Library name: 25c_ERC_SVB


title: uninfected_13, run 1

description: Library name: 13215-JK-9


title: 29c_ERC_SVB

description: Library name: 29c_ERC_SVB


title: 22c_ERC_SVB

description: Library name: 22c_ERC_SVB


title: 19c_ERC_SVB

description: Library name: 19c_ERC_SVB


title: 21c_ERC_SVB

description: Library name: 21c_ERC_SVB


title: 18c_ERC_SVB

description: Library name: 18c_ERC_SVB


title: 24c_ERC_SVB

description: Library name: 24c_ERC_SVB


title: 26c_ERC_SVB

description: Library name: 26c_ERC_SVB


title: 15c_ERC_SVB

description: Library name: 15c_ERC_SVB


title: 20c_ERC_SVB

description: Library name: 20c_ERC_SVB


title: 12c_ERC_SVB

description: Library name: 12c_ERC_SVB


title: 14c_ERC_SVB

description: Library name: 14c_ERC_SVB


title: 11c_ERC_SVB

description: Library name: 11c_ERC_SVB


title: 10c_ERC_SVB

description: Library name: 10c_ERC_SVB


title: 13c_ERC_SVB

description: Library name: 13c_ERC_SVB


title: 23c_ERC_SVB

description: Library name: 23c_ERC_SVB


title: 1c_ERC_SVB

description: Library name: 1c_ERC_SVB


title: V13Y24-344_D1

description: Library name: V13Y24-344_D1

data_processing:
Raw seqencing data and images were processed with 10x genomics Space Ranger pipeling, generating FASTQ files
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg, barcodes.tsv.gz, detected_tissue_image.jpg, features.tsv.gz, matrix.mtx.gz, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions.csv files
Library strategy: Spatial Transcriptomics

extract_protocol:
Entorhinal cortex was dissected from fresh frozen postmortem human tissue, 10 micron sections were obtained via cryosectioning. Tissue sections were mounted on Visium gene Expression slides.
Spatial transcriptomics sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Reagent Kit and protocol.


title: 17c_ERC_SVB

description: Library name: 17c_ERC_SVB


title: V13Y24-344_C1

description: Library name: V13Y24-344_C1


title: 16c_ERC_SVB

description: Library name: 16c_ERC_SVB


title: uninfected_10, run 1

description: Library name: 11119-JK-47


title: V13Y24-344_A1

description: Library name: V13Y24-344_A1


title: V13Y24-344_B1

description: Library name: V13Y24-344_B1


title: V13Y24-343_A1

description: Library name: V13Y24-343_A1


title: V13Y24-342_D1

description: Library name: V13Y24-342_D1


title: V13Y24-343_D1

description: Library name: V13Y24-343_D1


title: V13Y24-343_C1

description: Library name: V13Y24-343_C1


title: V13Y24-342_C1

description: Library name: V13Y24-342_C1


title: V13Y24-342_A1

description: Library name: V13Y24-342_A1


title: V13Y24-340_D1

description: Library name: V13Y24-340_D1


title: V13Y24-343_B1

description: Library name: V13Y24-343_B1


title: V13Y24-342_B1

description: Library name: V13Y24-342_B1


title: V13B23-365_B1

description: Library name: V13B23-365_B1


title: V13B23-366_D1

description: Library name: V13B23-366_D1


title: V13B23-366_C1

description: Library name: V13B23-366_C1


title: V13Y24-340_A1

description: Library name: V13Y24-340_A1


title: V13Y24-340_B1

description: Library name: V13Y24-340_B1


title: V13B23-365_C1

description: Library name: V13B23-365_C1


title: V13Y24-340_C1

description: Library name: V13Y24-340_C1


title: V13B23-365_A1

description: Library name: V13B23-365_A1


title: V13B23-364_C1

description: Library name: V13B23-364_C1


title: V13B23-366_B1

description: Library name: V13B23-366_B1


title: V13B23-365_D1

description: Library name: V13B23-365_D1


title: V13B23-364_D1

description: Library name: V13B23-364_D1


title: RSV_9, run 1

description: Library name: 11119-JK-37

value: RSV


title: V13B23-364_B1

description: Library name: V13B23-364_B1


title: V13B23-364_A1

description: Library name: V13B23-364_A1


title: V13B23-363_D1

description: Library name: V13B23-363_D1


title: V13B23-363_B1

description: Library name: V13B23-363_B1


title: V13B23-363_C1

description: Library name: V13B23-363_C1


title: V13B23-363_A1

description: Library name: V13B23-363_A1


title: LP_input_rep1

status: Public on Oct 14 2025

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai Univ

description: Library name: LP_input_rep1

library_source: genomic

data_processing:
ChIP-seq; Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample. ChIP-seq data were mapped to the mouse genome bulid NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t -best -strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC genome browser (http://genome.ucsc.edu). ChIP peaks were identified with findPeaks.pl against a matched control sample using the setting “-P .1 -LP .1 -poisson .1 -style factor”. The identified peaks were annotated to genes with the annotatePeaks.pl command against the mm10 genomic build in the HOMER package. Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score <15, were considered for further analysis.
Assembly: mm10
Supplementary files format and content: txt files for IDR ChIP peaks

molecule: genomic DNA

source_name: Fetal liver

growth_protocol: Cas9-expressing lymphoid progenitor (Cas9-LP) cell lines were established from fetal liver progenitors of Ebf1-deficient;Rosa26-Cas9 knock-in mice as a previous report (Hirano et al eLife). Cas9-LPs were cultured in IMDM (Wako) with 10% fetal bovine serum (Sigma-Aldrich), penicillin-streptomycin-glutamine (Gibco), 50 uM b-mercaptoethanol (Sigma-Aldrich), 10 ng/ml mouse SCF (PeproTech), 10 ng/ml human Flt3L (PeproTech), 10 ng/ml human IL-7 (PeproTech) with mitomycin C (Wako) treated OP9.

extract_protocol:
Ten million of Cas9-LPs with or without Notch stimulation were fixed with 1 mg/ml disuccinimidyl glutarate (Thermo Scientific) in PBS for 30 min at room temperature followed by an additional 10 min with addition of formaldehyde up to 1 %. The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with cold PBS. Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl [pH 8.0], and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec sonication followed by 30 sec rest, with high power.
ChIP-seq libraries were constructed using NEBNext Ultra Ⅱ DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB) and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

treatment_protocol: Cas9-LPs were transduced with retroviral vectors encoding sgRNA-hNGFR. They were transferred onto OP9 or OP9-DLL4 for 3-5 days after infection, then CD25 and CD44 profiles on sgRNA+ retrovirus-infected cells were analyzed. For QuantSeq 3’ mRNA sequencing, Cas9-LPs were infected with sgRNA-hNGFR. Five days after sgRNA transduction, sgRNA-introduced hNGFR+CD45+ lymphoid progenitor cells were sorted on a BD FACSAria.

value: Fetal liver

tag: cell line

value: LP

tag: chip antibody

value: Cultured on OP9


title: Phase1_input_rep1

description: Library name: Phase1_input_rep1

value: Cultured on OP9-DLL4


title: D4_double-KO_rep3

status: Public on Oct 01 2025

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 24

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools (v1.13)
Reads were trimmed Trim Galore 3.4
Reads were mapped to the mouse  reference assembly (mm10) using STAR 2.7.10a
Reads were quantiﬁed using RSEM 1.3.1
Read count means, fold-change (FC) and p-adj were calculated with DEseq2 v1.34.0
Assembly: mm10
Supplementary files format and content: Tab-delimited .tsv matrix: rows contain gene symbols, columns contain all samples. The values are DESeq2 size-factor normalized counts (no log transform). The header is included.

source_name: Double-KO differentiated cells

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation Kit (NZYTech, MB13402), according to the protocol provided by the manufacturer. Libraries were prepared with the RNA sample preparation kit (Truseq stranded mRNA Library).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

value: Double-KO differentiated cells

value: Differentiated cells

value: Double-KO

value: 4-OHT treated


title: LP_input_rep2

description: Library name: LP_input_rep2


title: D4_double-KO_rep1

description: Library name: Sample 22


title: D4_double-KO_rep2

description: Library name: Sample 23


title: D4_Mll2-KO_rep1

description: Library name: Sample 19

source_name: Mll2-KO differentiated cells

value: Mll2-KO differentiated cells


title: D4_Mll2-KO_rep2

description: Library name: Sample 20


title: D4_Mll1-KO_rep2

description: Library name: Sample 17

source_name: Mll1-KO differentiated cells

value: Mll1-KO differentiated cells

value: Untreated


title: D4_Mll1-KO_rep1

description: Library name: Sample 16


title: D4_WT_rep3

description: Library name: Sample 15

source_name: WT differentiated cells

value: WT differentiated cells

value: WT


title: D4_WT_rep2

description: Library name: Sample 14


title: D4_WT_rep1

description: Library name: Sample 13


title: D4_Mll1-KO_rep3

description: Library name: Sample 18


title: D0_double-KO_rep2

description: Library name: Sample 11

source_name: Double-KO mESC

value: Double-KO mESC

value: mESC


title: D0_double-KO_rep3

description: Library name: Sample 12


title: D0_double-KO_rep1

description: Library name: Sample 10


title: D0_Mll2-KO_rep3

description: Library name: Sample 9

source_name: Mll2-KO mESC

value: Mll2-KO mESC


title: D0_Mll2-KO_rep1

description: Library name: Sample 7


title: RVC_28, run 1

description: Library name: 11119-JK-32

value: nasal swab

value: RV-C


title: RVC_27, run 1

description: Library name: 11119-JK-31


title: D0_Mll1-KO_rep1

description: Library name: Sample 4

source_name: Mll1-KO mESC

value: Mll1-KO mESC


title: D0_WT_rep1

description: Library name: Sample 1

source_name: WT mESC

value: WT mESC


title: D0_Mll1-KO_rep3

description: Library name: Sample 6


title: D0_WT_rep3

description: Library name: Sample 3


title: D4_double-KO_H3K4me3_repB

description: Library name: Sample 81

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimgalore(v0.6.7).
Reads were mapped to the mm10 reference genome with STAR v2.6.1d (--outSAMtype BAM Unsorted --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --readFilesCommand zcat).
Duplicate reads were marked with picard tool (3.1.1)
Bigwig files were generated with deepTools v3.5.1 using bamCoverage (--normalizeUsing 'RPGC').
Assembly: mm10

extract_protocol:
Approximately 10 million and 40 million cells were used for histone PTMs and COMPASS subunits ChIPs, respectively.  For histone modification ChIP assays, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature (RT) before being quenched with 0.125 M glycine for another 10 minutes, while for COMPASS subunits ChIP assays cells were double crosslinked with ChIP cross-link Gold (Diagenode, C01019027) and 1% formaldehyde according to the manufactor’s instructions. Chromatin was isolated through sequential incubation with three distinct lysis buffers: LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin sonication was carried out in LB3 using an EpiShearTM sonicator (Active Motif; 4-5 minutes, 20 seconds ON and 30 seconds OFF at 25% amplitude). The sheared chromatin was then incubated O/N at 4 °C with either 5 or 10 μg of antibody for histone PTMs or COMPASS subunits respectively.
DNA libraries were prepared using the TruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

value: H3K3me3 antibdy (Active Motif, 39159)


title: D4_double-KO_H3K27me3_repB

description: Library name: Sample 85

value: Double-KO differentiated cells

value: H3K27me3 antibody (Active Motif, 39155)


title: D4_double-KO_H3K27me3_repA

description: Library name: Sample 84

value: Differentiated cells

value: Double-KO


title: D4_double-KO_H3K27ac_repA

description: Library name: Sample 82

value: H3K27ac antibody (Active Motif, 39133)


title: D4_double-KO_H3K27ac_repB

description: Library name: Sample 83


title: D4_double-KO_H3K4me2_repA

description: Library name: Sample 78

value: H3K4me2 antibody (Active Motif, 39141)


title: D4_WT_H3K27me3_repB

description: Library name: Sample 76


title: D4_double-KO_input

description: Library name: Sample 77


title: D4_WT_H3K27ac_repB

description: Library name: Sample 74


title: D4_WT_H3K27ac_repA

description: Library name: Sample 73


title: D4_WT_H3K4me3_repB

description: Library name: Sample 72


title: D4_WT_RBBP5_repB

description: Library name: Sample 68

value: RBBP5 antibody (Diagenode, C15410342)


title: D4_WT_MLL2_repB

description: Library name: Sample 66

value: WT differentiated cells

value: GFP antibody (Invitrogen, A11122)


title: D4_WT_H3K4me2_repB

description: Library name: Sample 70

value: WT


title: D0_double-KO_RING1B_repA

description: Library name: Sample 62

value: Double-KO mESC

value: mESC

value: RING1B antibody (Cell Signalling, 5694)


title: D4_WT_input

description: Library name: Sample 64


title: D4_WT_MLL2_repA

description: Library name: Sample 65


title: D0_double-KO_RING1B_repB

description: Library name: Sample 63


title: D0_double-KO_H3K9me3_repA

description: Library name: Sample 60

value: H3K9me3 antibody (Active Motif, 61014)


title: D0_double-KO_H3K27me3_repB

description: Library name: Sample 59


title: D0_double-KO_H3K27ac_repB

description: Library name: Sample 57


title: D0_double-KO_H3K27me3_repA

description: Library name: Sample 58


title: D0_double-KO_H3K27ac_repA

description: Library name: Sample 56


title: D0_double-KO_H3K4me3_repB

description: Library name: Sample 55


title: D0_double-KO_H3K4me2_repA

description: Library name: Sample 52


title: D0_double-KO_H3K4me2_repB

description: Library name: Sample 53


title: D0_double-KO_H3K4me1_repA

description: Library name: Sample 50

value: H3K4me1 antibody (Active Motif, 39297)


title: D0_double-KO_RBBP5_repA

description: Library name: Sample 48


title: D0_double-KO_input_histmod_RBBP5

description: Library name: Sample 47


title: D0_Mll2-KO_H3K27ac_repA

description: Library name: Sample 43

value: Mll2-KO mESC


title: D0_Mll2-KO_H3K4me3_repB

description: Library name: Sample 42

value: H3K3me3 antibdy (Active Motif, 39159)


title: D0_Mll2-KO_H3K4me2_repB

description: Library name: Sample 40


title: Phase1_input_rep2

description: Library name: Phase1_input_rep2

value: Fetal liver

value: Cultured on OP9-DLL4


title: D0_Mll2-KO_H3K4me1_repA

description: Library name: Sample 37


title: D0_Mll2-KO_MLL1_repB

description: Library name: Sample 36

value: MLL1 antibody (Active Motif, 61295)


title: D0_Mll2-KO_MLL1_repA

description: Library name: Sample 35


title: D0_Mll2-KO_input_histmod_MLL1

description: Library name: Sample 34


title: D0_Mll1-KO_H3K27me3_repB

description: Library name: Sample 33

value: Mll1-KO mESC

value: H3K27me3 antibody (Active Motif, 39155)


title: D0_Mll1-KO_H3K27ac_repA

description: Library name: Sample 30

value: H3K27ac antibody (Active Motif, 39133)


title: D4_WT_H3K27me3_repA

description: Library name: Sample 75

value: Differentiated cells


title: D4_WT_H3K4me3_repA

description: Library name: Sample 71

value: WT differentiated cells


title: D0_Mll1-KO_H3K4me3_repA

description: Library name: Sample 28


title: D0_Mll1-KO_H3K4me2_repB

description: Library name: Sample 27

value: H3K4me2 antibody (Active Motif, 39141)


title: D0_Mll1-KO_H3K4me2_repA

description: Library name: Sample 26


title: D0_Mll1-KO_H3K4me1_repB

description: Library name: Sample 25


title: D0_Mll1-KO_input_histmod

description: Library name: Sample 23


title: D0_double-KO_RBBP5_repB

description: Library name: Sample 49

value: Double-KO

value: RBBP5 antibody (Diagenode, C15410342)


title: D0_WT_RING1B_repB

description: Library name: Sample 22

value: WT mESC

value: mESC

value: WT


title: D0_Mll2-KO_H3K27me3_repA

description: Library name: Sample 45


title: Mouse, ske, E76R, rep 2

status: Public on Mar 02 2026

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
Library name: Mouse_ske_E76R_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R2

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

source_name: Quadriceps

growth_protocol: Mice were housed five per cage and maintained under controlled temperature (22.5 °C) and a 12 h light/dark cycle, with food and water provided ad libitum.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: Quadriceps

value: Whole tissue

value: H2B E76R


title: Mouse, ske, WT, rep 1

description:
Library name: Mouse_ske_WT_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske1_WT

value: H2B WT


title: D0_Mll2-KO_H3K27ac_repB

description: Library name: Sample 44

value: Mll2-KO mESC


title: D0_Mll2-KO_H3K4me3_repA

description: Library name: Sample 41

value: H3K3me3 antibdy (Active Motif, 39159)


title: D0_WT_H3K9me3_repA

description: Library name: Sample 19

value: H3K9me3 antibody (Active Motif, 61014)


title: D0_WT_H3K9me3_repB

description: Library name: Sample 20


title: D0_WT_H3K27me3_repB

description: Library name: Sample 18

value: H3K27me3 antibody (Active Motif, 39155)


title: D0_WT_H3K27me3_repA

description: Library name: Sample 17


title: D0_WT_H3K27ac_repA

description: Library name: Sample 15

value: H3K27ac antibody (Active Motif, 39133)


title: D0_WT_H3K4me3_repA

description: Library name: Sample 13


title: D0_WT_H3K4me2_repA

description: Library name: Sample 11


title: D0_WT_H3K4me1_repB

description: Library name: Sample 10

value: H3K4me1 antibody (Active Motif, 39297)


title: D0_WT_H3K4me1_repA

description: Library name: Sample 9


title: D0_WT_RBBP5_repB

description: Library name: Sample 5


title: D0_WT_MLL1_repA

description: Library name: Sample 6

value: MLL1 antibody (Active Motif, 61295)


title: D0_WT_RBBP5_repA

description: Library name: Sample 4


title: D0_WT_MLL2_repA

description: Library name: Sample 2

value: GFP antibody (Invitrogen, A11122)


title: D0_WT_MLL2_repB

description: Library name: Sample 3


title: D0_WT_input_MLL2_RBBP5_MLL1

description: Library name: Sample 1


title: Rep 1. Input Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

status: Public on Sep 26 2025

city: Santa Cruz

first: Ali

middle: S

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

description: Library name: ChIP_input_rep1

data_processing:
ChIP-seq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using Bowtie2, to the mouse mm10 genome. MACS2 was used for peak calling, and only peaks with a q-value > 13 were used for analysis. ChIPSeeker was used to classify peaks based on Gencode VM23 gene annotation
Assembly: mm10
Supplementary files format and content: MACS2 call peak output (q-value >10) in BED format for EV and E2F1 samples

growth_protocol: NIH/3T3 cells were grown in DMEM supplemented with 10% heat-inactivated fetal bovine serum (HIFBS) and 1x penicillin+streptomycin (P/S). For maintaining cultures, cells were split using 0.25% Trypsin + 0.5mM EDTA every 3-4 days at a subcultivation ratio of 1/10. Cells were grown in a humified incubator at 37degC and 5%CO2

extract_protocol:
RNA was extracted following the Zymo RNA microprep kit.
RNA libraries were prepared by Novogene inc using polyA selection and paired-end sequencing and sequenced on the Illumina NovaSeq 6000 (150bp reads)

treatment_protocol: Cells were serum starved (DMEM, 0.25% HIFBS, 1x P/S) for 48 hours. Following this, cells were treated with 500ng/ml doxycycline or 10% HIFBS for up to 24 hours

value: Dox-inducible EV

value: Doxycycline 12 hr


title: Rep 2. Input Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_input_rep2


title: Rep 2.Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_EV_rep2


title: D4_Mll2-KO_rep3

description: Library name: Sample 21

value: Mll2-KO differentiated cells

value: Differentiated cells

value: 4-OHT treated


title: D0_WT_H3K4me3_repB

description: Library name: Sample 14

value: WT mESC

value: mESC

value: WT


title: Rep 2.Dox-inducible E2F1 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_E2F1_rep2

value: Dox-inducible E2F1


title: Rep 1.Dox-inducible EV 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_EV_rep1


title: D0_WT_H3K27ac_repB

description: Library name: Sample 16


title: Rep 1.Dox-inducible E2F1 3T3 cells, ChIP-Seq measured at t=12hr dox induction after starvation

description: Library name: ChIP_E2F1_rep1


title: D0_WT_H3K4me2_repB

description: Library name: Sample 12

value: H3K4me2 antibody (Active Motif, 39141)


title: D0_Mll1-KO_rep2

description: Library name: Sample 5

value: Mll1-KO mESC

value: Untreated


title: D0_Mll2-KO_rep2

description: Library name: Sample 8

value: Mll2-KO mESC


title: D0_WT_input_histmod_1

description: Library name: Sample 8


title: D4_double-KO_H3K4me2_repB

description: Library name: Sample 79

value: Double-KO differentiated cells

value: Double-KO


title: D0_WT_rep2

description: Library name: Sample 2


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_12hr_rep2

data_processing:
ATAC-seq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using Bowtie2, to the mouse mm10 genome. Reads flagged as PCR duplicates were removed using RmDup, and reads in ENCODE blacklisted regions were removed (mm10.blacklist.v2). MACS2 was used for peak calling, peaks with q value > 50 were used for later analysis. Pooled replicate MACS2 analysis used to combine data from biological replicate experiments. HOMER was used for differential peak signal and motif calling.
Assembly: mm10
Supplementary files format and content: BED files of MACS2 call peak output

extract_protocol:
ATAC sample were prepared according the ActiveMotif ATAC-Seq kit.
ATAC-Seq libraries were prepared according to the ActiveMotif ATAC-Seq kit.

value: 10% Serum 12 hr


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_6hr_rep2

value: 10% Serum 6 hr


title: D4_double-KO_H3K4me3_repA

description: Library name: Sample 80

value: H3K3me3 antibdy (Active Motif, 39159)


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_2hr_rep1

value: Dox-inducible EV

value: 10% Serum 2 hr


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_12hr_rep1


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_2hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: ATAC_EV_serum_6hr_rep1


title: D0_WT_MLL1_repB

description: Library name: Sample 7

value: MLL1 antibody (Active Motif, 61295)


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_EV_dox_12hr_rep2

value: Doxycycline 12 hr


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_EV_dox_2hr_rep2

value: Doxycycline 2 hr


title: Rep 2. Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_EV_dox_0hr_rep2

value: Doxycycline 0 hr


title: Rep 2.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_EV_dox_6hr_rep2

value: Doxycycline 6 hr


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_EV_dox_2hr_rep1


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_EV_dox_12hr_rep1


title: D4_WT_RBBP5_repA

description: Library name: Sample 67

value: WT differentiated cells

value: Differentiated cells

value: WT

value: RBBP5 antibody (Diagenode, C15410342)


title: Rep 2. Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_E2F1_dox_0hr_rep2

value: Dox-inducible E2F1


title: Rep 1.Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_EV_dox_6hr_rep1


title: Rep 1. Dox-inducible EV 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_EV_dox_0hr_rep1


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_12hr_rep1


title: D4_WT_H3K4me2_repA

description: Library name: Sample 69

value: H3K4me2 antibody (Active Motif, 39141)


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_6hr_rep1


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=6hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_6hr_rep2


title: D0_double-KO_H3K9me3_repB

description: Library name: Sample 61

value: Double-KO mESC

value: mESC

value: Double-KO

value: H3K9me3 antibody (Active Motif, 61014)


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_2hr_rep2


title: Rep 2.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=12hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_12hr_rep2


title: Rep 1.Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=2hr dox induction after starvation

description: Library name: ATAC_E2F1_dox_2hr_rep1


title: D0_double-KO_H3K4me3_repA

description: Library name: Sample 54

value: H3K3me3 antibdy (Active Motif, 39159)


title: Rep 1. Dox-inducible E2F1 3T3 cells, ATAC-Seq measured at t=0 after starvation

description: Library name: ATAC_E2F1_dox_0hr_rep1


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_6hr_rep2

data_processing:
RNAseq FASTQ files were inspected with FastQC. Low quality reads were removed using Trimmomatic, removing adapter/index sequences, quality filtering (sliding window 4:20) and retaining only reads of 50bp or longer. Data was aligned using HISAT2, unstranded, to the mouse mm10 genome. Featurecounts was used for counting, with Gencode VM23 gene annotation. Count norrmalization and differential gene expression was calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: Normalized counts .csv file with all samples;  .txt for each pairwise comparison against control (time point 0 hr) of differential gene expression

value: Dox-inducible EV

value: 10% Serum 6 hr


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_2hr_rep2

value: 10% Serum 2 hr


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_12hr_rep1

value: 10% Serum 12 hr


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_12hr_rep2


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_6hr_rep1


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_EV_dox_6hr_rep1


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_EV_dox_12hr_rep1

value: Doxycycline 12 hr


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_EV_dox_12hr_rep2


title: Rep 1. Dox-inducible EV 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_EV_dox_0hr_rep1

value: Doxycycline 0 hr


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_EV_dox_2hr_rep1

value: Doxycycline 2 hr


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_EV_dox_2hr_rep2


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_E2F1_dox_12hr_rep2


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_E2F1_dox_6hr_rep2

value: Doxycycline 6 hr


title: Rep 1.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=2hr 10% serum addition after starvation

description: Library name: RNA_EV_serum_2hr_rep1


title: Rep 2.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_E2F1_dox_2hr_rep2


title: Rep 2. Dox-inducible EV 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_EV_dox_0hr_rep2


title: Rep 2. Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_E2F1_dox_0hr_rep2


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=12hr dox induction after starvation

description: Library name: RNA_E2F1_dox_12hr_rep1


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_E2F1_dox_6hr_rep1


title: Rep 1.Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=2hr dox induction after starvation

description: Library name: RNA_E2F1_dox_2hr_rep1


title: AML980

status: Public on Sep 25 2025

type: genomic

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Illumina iScan System with default settings

data_processing: R package minfi ((version 1.50.0)

label: Cy3 and Cy5

source_name: AML PDX model

label_protocol: Standard Illumina protocol

growth_protocol: PDX cells were amplified in NSG mice and reisolated from bone marrow

extract_protocol: DNA was extracted using the standard protocol recommended for the Illumina Infiniumm MethylationEPIC BeadChip array

treatment_protocol: mice were not treated

tag: mutations panel

value: DNMT3A, TET2, NPM1, FLT3-TKD, ASXL1, FLT3-ITD

tag: cytogenetics / fusions / cnas

value: PDX cells not analyzed. Primary patient cells:CN

tag: disease status

value: ID

tag: age group

value: older adults

value: patient derived xenograft cells

tag: disease

value: acute myeloid leukemia


title: AML955

value: DNMT3A, NPM1, WT1

value: CN / no fusions detected / del(13q)

value: adults (unspecified)

tag: tissue


title: AML896

value: DNMT3A, IDH2, FLT3-ITD, NPM1, ASXL2

value: adults


title: AML842

value: NPM1, FLT3-ITD, DCLK1, DNMT3A

value: PDX cells not analyzed. Primary patient cells:complex, including +8

value: young adults


title: AML579

value: DNMT3A, IDH1, NPM1, FLT3-ITD

value: CN / no fusions detected / del(7q), del(11p)

value: R


title: AML372

value: TP53, KRAS

value: complex, including 5q13 Del, ETV6-Del, -7, -17 / no fusions detected /del(5q), -7, amp(8q), del(10q), del(11q), del(12p), del(13q), del(14q) del(15p), del(16q), del(17p), del(20p)


title: AML788

value: DNMT3A, NPM1, FLT3-ITD

value: PDX cells not analyzed. Primary patient cells:CN

value: ID


title: AML640

value: IDH1, NPM1, FLT3-ITD

value: t(11;15)(p1?1;q?22) / no fusions detected / no CNAs detected

value: older adults

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML959

value: NPM1, FLT3-ITD, DNMT3A, TET2

value: no cytogenetics / del(2q)

value: adults (unspecified)


title: AML393

value: BCOR, KRAS

value: adults


title: AML491

value: DNMT3A, BCOR, NRAS, KRAS, ETV6, PTPN11, RUNX1

value: del7q (7q21.13 q36.3) / no fusions detected / amp(2q), amp(4q), amp(6q), del(7q), del(10q)


title: AML661

value: DNMT3A, BCOR, NRAS, ETV6, PTPN11, RUNX1, JAK1, EZH2

value: del7q (7q21.13 q36.3) / no fusions detected / del(7q)

value: R


title: AML573

value: DNMT3A, IDH2, FLT3-ITD, WT1

value: CN / no fusions detected / no CNAs detected


title: AML664

value: no cytogenetics / KMT2A::MLLT3 / del(2q), +21

value: pediatric


title: AML602

value: DNMT3A, TET2, NPM1, FLT3-ITD, CEBPA, JAK3

value: no cytogenetics / t(4;12) / del(3q), del(11p)


title: AML981

value: DNMT3A, TET2, NPM1, FLT3-ITD, FLT3-TKD, WT1, ASXL1

value: 46,XY,t(16;17)(q24;p12) / no fusions detected / no CNAs detected

value: older adults

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML388

value: KRAS

value: t(6;11)(q27;q23) / KMT2A::AFDN / no CNAs detected

value: ID


title: AML538

value: DNMT3A, IDH1

value: no cytogenetics / BCR::ABL1; KMT2A-PTD / amp(2q), amp(4q), amp(5q), amp(13q), amp(18q)

value: adults (unspecified)


title: AML346

value: cKIT

value: interstitial 5q Del, interstitial 13q Del / CBFA2T3::GLIS2 (inv16) / del(5q), del(13q), amp(13q) -> follows after the deletion

value: R


title: AML358

value: pediatric


title: AML356

value: KRAS, U2AF1

value: no cytogenetics / KMT2A::MLLT3 / del(1p), amp(2q), amp(3q), amp(6p), +8, del(10p),amp(11q), amp(19q)


title: 16-20 h embryo, ft-GFP[C], Replicate 3, NovaSeq X Plus (ChIP)

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 3 (ChIP)

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.33 with default settings.  ChIP-seq reads were algined to dm6 genome using Burrows-Wheeler Aligner v0.7.16a with default settings. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequnced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format using HOMER 4.11.1.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <= 0.01 and were annotated with ChIPseeker and motifs identified with HOMER v4.11.1.
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, bed

organism: Drosophila melanogaster

source_name: 16-20 h embryo

growth_protocol: Drosophila were reared at 25C on standard fly food.  Embryos were collected and aged at 25C on grape juice agar plates.

extract_protocol:
Embryos were collected for 4 hrs, aged for 16 hrs at 25C, and dechorionated in 50% bleach.  Eye-brain complexes were dissected from 3rd instar larvae in ice-cold PBS.  Tissues were crosslinked in 2 mM EGS for 45 min, followed by paraformaldehyde for 15 min, quenched, washed, flash frozen in liquid nitrogen and stored at -80C until use.  50 ml settled embryos or 100 eye-brain complexes were used per sample.  Crosslinked tissues were homogenized by douncing, followed by nuclear lysis and sonication of the genomic DNA using a Bioruptor or Qsonica Q700 sonicator.  Fragmented chromatin was incubated with anti-GFP or anti-FLAG antibodies and precipitated using MagnaChIP A+G beads or Dynabeads G.
ChIP-seq libraries were prepared from 10 ng DNA.  DNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends.  Size selection was performed with AMPure beads to limit the fragment size to 150-700 bp.  Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: 16-20 h embryo

tag: genotype

value: Ft-GFP[C]

value: a-GFP (ab290)


title: 16-20 h embryo, ft-GFP[C], Replicate 2, NovaSeq X Plus (Input)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 2 (Input)


title: 16-20 h embryo, ft-GFP[C], Replicate 2, NovaSeq X Plus (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 2 (ChIP)


title: L3 eye-brain, w[1118], Replicate 2, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, w[1118], Replicate 2 (input)

source_name: L3 eye-brain complex

value: L3 eye-brain complex

value: a-FLAG (M2, Sigma F1804)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 3, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 3 (input)

value: ubi-Gal4; UAS-FtICD-FLAG


title: L3 eye-brain, w[1118], Replicate 2, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, w[1118], Replicate 2 (ChIP)


title: L3 eye-brain, w[1118], Replicate 1, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, w[1118], Replicate 1 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 3, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 3 (ChIP)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 2, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 2 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 5, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 5 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 2, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 2 (ChIP)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 1, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 1 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 1, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 1 (ChIP)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 4, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 4 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 4, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 4 (ChIP)


title: 16-20 h embryo, w[1118], Replicate 3, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 3 (Input)


title: 16-20 h embryo, w[1118], Replicate 2, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 2 (Input)


title: 16-20 h embryo, w[1118], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, w[1118], Replicate 1 (ChIP)


title: 16-20 h embryo, ubi>FtICD-FLAG, Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ubi_FtICD-FLAG, Replicate 1 (Input)


title: 16-20 h embryo, ubi>FtICD-FLAG, Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ubi_FtICD-FLAG, Replicate 1 (ChIP)


title: 16-20 h embryo, ft-GFP[int], Replicate 3, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 3 (Input)

value: Ft-GFP[int]


title: 16-20 h embryo, ft-GFP[int], Replicate 3, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 3 (ChIP)


title: 16-20 h embryo, ft-GFP[int], Replicate 2, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 2 (Input)


title: 16-20 h embryo, w[1118], Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 1 (Input)


title: 16-20 h embryo, ft-GFP[int], Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 1 (Input)


title: 16-20 h embryo, ft-GFP[C], Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 1 (Input)


title: 16-20 h embryo, ft-GFP[C], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 1 (ChIP)


title: AML959

status: Public on Sep 18 2025

description: Library name: AML959

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
Reads were mapped to a concatenated genome of human and mouse (hg38, mm10).
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Supplementary files format and content: cell (columns) and gene (rows) -wise read counts

extract_protocol:
prime-seq (Janjic et al., 2022)
Library was constructed using the prime-seq protocol

value: NPM1, FLT3-ITD, DNMT3A, TET2

value: no cytogenetics / del(2q)

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML663

description: Library name: AML663

value: FLT3-ITD, WT1

value: CN / no fusions detected / no CNAs detected


title: AML538

description: Library name: AML538

value: DNMT3A, IDH1

value: no cytogenetics / BCR::ABL1; KMT2A-PTD / amp(2q), amp(4q), amp(5q), amp(13q), amp(18q)

value: R

value: adults (unspecified)


title: AML491

description: Library name: AML491

value: DNMT3A, BCOR, NRAS, KRAS, ETV6, PTPN11, RUNX1

value: del7q (7q21.13 q36.3) / no fusions detected / amp(2q), amp(4q), amp(6q), del(7q), del(10q)

value: adults


title: AML810

description: Library name: AML810

value: FLT3-ITD, DCLK1, NPM1, DNMT3A

value: PDX cells not analyzed. Primary patient cells:+8

value: ID

value: young adults


title: AML980

description: Library name: AML980

value: DNMT3A, TET2, NPM1, FLT3-TKD, ASXL1, FLT3-ITD

value: PDX cells not analyzed. Primary patient cells:CN

value: older adults


title: AML573

description: Library name: AML573

value: DNMT3A, IDH2, FLT3-ITD, WT1, MLL-PTD

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML640

description: Library name: AML640

value: IDH1, NPM1, FLT3-ITD

value: t(11;15)(p1?1;q?22) / no fusions detected / no CNAs detected


title: AML388

description: Library name: AML388

value: KRAS

value: t(6;11)(q27;q23) / KMT2A::AFDN / no CNAs detected


title: AML896

description: Library name: AML896

value: DNMT3A, IDH2, FLT3-ITD, NPM1, ASXL2


title: AML602

description: Library name: AML602

value: DNMT3A, TET2, NPM1, FLT3-ITD, CEBPA, JAK3

value: no cytogenetics / t(4;12) / del(3q), del(11p)


title: UNCseq1757 ROI1 ARID1A Positive_Mutated

status: Public on Apr 22 2026

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Department of Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

description: Library name: UNCseq1757 ROI1 ARID1A Pos

data_processing:
The .dcc files generated by the NanoString GeoMx Digital Spatial Profiler represent ROI digital counts derived from spatially resolved transcriptomic profiling.
The Hs_R_NGS_WTA_v1.0.pkc file is the probe annotation (PKC) file for the GeoMx Human RNA Whole Transcriptome Atlas (NGS-based) panel, used to map probe-level counts in .dcc files to gene targets and associated control probes during downstream processing.
Assembly: FASTQ files process into DCC files by geomxngspipline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC file format
Library strategy: Spatial Transcriptomics

source_name: Endometrium

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

value: ARID1A Mutated

value: total RNA


title: AML579

description: Library name: AML579

value: DNMT3A, IDH1, NPM1, FLT3-ITD

value: CN / no fusions detected / del(7q), del(11p)

value: R

value: adults


title: AML358

description: Library name: AML358

value: pediatric


title: AML788

description: Library name: AML788

value: DNMT3A, NPM1, FLT3-ITD

value: PDX cells not analyzed. Primary patient cells:CN

value: ID

value: patient derived xenograft cells


title: 16-20 h embryo, ft-GFP[int], Replicate 2, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 2 (ChIP)

value: 16-20 h embryo

value: Ft-GFP[int]

value: a-GFP (ab290)


title: UNCseq1804 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI3 ARID1A Neg


title: AML356

description: Library name: AML356

value: KRAS, U2AF1

value: no cytogenetics / KMT2A::MLLT3 / del(1p), amp(2q), amp(3q), amp(6p), +8, del(10p),amp(11q), amp(19q)

value: acute myeloid leukemia


title: 16-20 h embryo, ft-GFP[int], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 1 (ChIP)


title: AML415

description: Library name: AML415

value: FLT3-ITD, NPM1, DNMT3A, IDH1

value: PDX:no cytogenetics; primary patient cells:CN / del(15q)

value: older adults


title: AML664

description: Library name: AML664

value: no cytogenetics / KMT2A::MLLT3 / del(2q), +21


title: AML979

description: Library name: AML979

value: DNMT3A, NPM1, FLT3-ITD, IDH2, WT1


title: AML981

description: Library name: AML981

value: DNMT3A, TET2, NPM1, FLT3-ITD, FLT3-TKD, WT1, ASXL1

value: 46,XY,t(16;17)(q24;p12) / no fusions detected / no CNAs detected

value: R


title: AML661

description: Library name: AML661

value: DNMT3A, BCOR, NRAS, ETV6, PTPN11, RUNX1, JAK1, EZH2

value: del7q (7q21.13 q36.3) / no fusions detected / del(7q)

value: adults


title: AML393

description: Library name: AML393

value: BCOR, KRAS

value: patient derived xenograft cells


title: AML955

description: Library name: AML955

value: DNMT3A, NPM1, WT1

value: CN / no fusions detected / del(13q)

value: adults (unspecified)


title: Br8667_Nac-PI+NeuN+

status: Public on Sep 10 2025

description: Library name: 20c_Nac_SVB

data_processing:
FASTQ and image data files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and fastq.gz files

source_name: nucleus accumbens

extract_protocol:
Nucleus accumbens samples were dissected from fresh frozen postmortem human brain tissue. 100 micron coronal sections were obtained by cryosectioning (about 70-100 mg of tissue). Nuclei were isolated by homogenizing tissue in Nuclei EZ Lysis Buffer, followed by filtration through a mesh strainer, and three washes. Nuclei pellets from each donor were divided into two groups, one stained with propidium iodide (PI), to select all nuclei, and the other stained with both PI and anti- NeuN antibody, to select only the neuronal nuclei. Fluorescent-activated nuclear sorting (FANS) was performed to obtain PI+ nuclei and PI+NeuN+ nuclei for each donor.
Libraries were prepared using the Chromium Next GEM Single cell 3' v3.1 (dual-index) kit according to manufacturer's instructions (CG000315, revision E, 10x Genomics)

value: nucleus accumbens

value: PI+NeuN+


title: AML346

description: Library name: AML346

value: cKIT

value: interstitial 5q Del, interstitial 13q Del / CBFA2T3::GLIS2 (inv16) / del(5q), del(13q), amp(13q) -> follows after the deletion

value: pediatric

value: acute myeloid leukemia


title: Br6522_Nac-PI+NeuN+

description: Library name: 18c_Nac_SVB


title: Br8667_Nac-PI+

description: Library name: 19c_Nac_SVB

value: PI+


title: Br6522_Nac-PI+

description: Library name: 17c_Nac_SVB


title: Br6471_Nac-PI+NeuN+

description: Library name: 16c_Nac_SVB


title: Br6471_Nac-PI+

description: Library name: 15c_Nac_SVB


title: Br6432_Nac-PI+NeuN+

description: Library name: 14c_NAc_SVB


title: Br3942_Nac-PI+

description: Library name: 11c_NAc_SVB


title: Br6432_Nac-PI+

description: Library name: 13c_NAc_SVB


title: Br3942_Nac-PI+NeuN+

description: Library name: 12c_NAc_SVB


title: Br2743_Nac-PI+NeuN+

description: Library name: 10c_NAc_SVB


title: UNCseq0585 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI4 ARID1A Neg

value: Endometrium

value: ARID1A Mutated

value: total RNA


title: Br2743_Nac-PI+

description: Library name: 9c_NAc_SVB


title: Br6423_Nac-PI+NeuN+

description: Library name: 8c_NAc_SVB


title: Br6423_Nac-PI+

description: Library name: 7c_NAc_SVB


title: Rep 2.Dox-inducible EV 3T3 cells, RNA-Seq measured at t=6hr dox induction after starvation

description: Library name: RNA_EV_dox_6hr_rep2

value: Dox-inducible EV

value: Doxycycline 6 hr


title: Br2720_Nac-PI+NeuN+

description: Library name: 6c_NAc_SVB


title: Br8492_Nac-PI+NeuN+

description: Library name: 4c_NAc_SVB


title: AML372

description: Library name: AML372

value: TP53, KRAS

value: complex, including 5q13 Del, ETV6-Del, -7, -17 / no fusions detected /del(5q), -7, amp(8q), del(10q), del(11q), del(12p), del(13q), del(14q) del(15p), del(16q), del(17p), del(20p)

value: R

value: adults


title: Br2720_Nac-PI+

description: Library name: 5c_NAc_SVB


title: Br8492_Nac-PI+

description: Library name: 3c_NAc_SVB


title: Br8325_Nac-PI+NeuN+

description: Library name: 2c_NAc_SVB


title: Br8325_Nac-PI+

description: Library name: 1c_NAc_SVB


title: Hs_Br8667_V13M13-362-C1

description: Library name: 79v_NAc_SVB

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: fastq.gz, matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz, aligned_fiducials.jpg, scalefactors_json.json, detected_tissue_image.jpg, tissue_positions_list.csv, hires_image.png, lowres_image.png, tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

extract_protocol:
Nucleus accumbens samples were dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

tag: subject status

value: neurotypical control postmortem human brain donor

tag: sample group


title: Rep 1. Dox-inducible E2F1 3T3 cells, RNA-Seq measured at t=0 after starvation

description: Library name: RNA_E2F1_dox_0hr_rep1

value: Dox-inducible E2F1

tag: treatment

value: Doxycycline 0 hr


title: Hs_Br8667_V13M13-362-B1

description: Library name: 78v_NAc_SVB

value: nucleus accumbens


title: Hs_Br3942_V13M06-379-D1

description: Library name: 76v_NAc_SVB


title: Hs_Br3942_V13M06-379-B1

description: Library name: 74v_NAc_SVB


title: Hs_Br3942_V13M06-379-C1

description: Library name: 75v_NAc_SVB


title: AML979

value: DNMT3A, NPM1, FLT3-ITD, IDH2, WT1

value: older adults

value: patient derived xenograft cells


title: Hs_Br2743-Left_V13M06-378-D1

description: Library name: 64v_NAc_SVB


title: Hs_Br3942_V13M06-379-A1

description: Library name: 73v_NAc_SVB


title: Hs_Br2743-Left_V13M06-378-B1

description: Library name: 62v_NAc_SVB


title: Hs_Br2743-Left_V13M06-378-C1

description: Library name: 63v_NAc_SVB


title: Hs_Br2743-Left_V13M06-378-A1

description: Library name: 61v_NAc_SVB


title: AML663

value: FLT3-ITD, WT1

value: CN / no fusions detected / no CNAs detected

value: pediatric

value: acute myeloid leukemia


title: AML415

value: FLT3-ITD, NPM1, DNMT3A, IDH1

value: PDX:no cytogenetics; primary patient cells:CN / del(15q)


title: Hs_Br6471-Left_V13M06-377-C1

description: Library name: 59v_NAc_SVB


title: Hs_Br6471-Left_V13M06-377-D1

description: Library name: 60v_NAc_SVB


title: Hs_Br6471-Left_V13M06-377-B1

description: Library name: 58v_NAc_SVB


title: Hs_Br6432_V11D01-384-D1

description: Library name: 56v_NAc_SVB


title: Hs_Br6432_V11D01-384-C1

description: Library name: 55v_NAc_SVB


title: Hs_Br6432_V11D01-384-A1

description: Library name: 53v_NAc_SVB


title: Hs_Br6471-Left_V13M06-377-A1

description: Library name: 57v_NAc_SVB


title: AML669

value: KRAS (subclonal)

value: no cytogenetics / KMT2A::MLLT3 / del(12q)


title: Hs_Br8325_V13M06-376-C1

description: Library name: 51v_Nac_SVB


title: Hs_Br8325_V13M06-376-A1

description: Library name: 49v_Nac_SVB


title: Hs_Br8325_V13M06-376-B1

description: Library name: 50v_Nac_SVB


title: Hs_Br6423_V13F06-313-D1

description: Library name: 48v_Nac_SVB


title: Hs_Br8325_V13F06-313-C1

description: Library name: 47v_Nac_SVB


title: Hs_Br8325_V13M06-376-D1

description: Library name: 52v_Nac_SVB


title: Hs_Br6432_V11D01-384-B1

description: Library name: 54v_NAc_SVB


title: 16-20 h embryo, ft-GFP[C], Replicate 3, NovaSeq X Plus (Input)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 3 (Input)

value: 16-20 h embryo

value: Ft-GFP[C]

value: a-GFP (ab290)


title: Hs_Br6423_V13F06-313-A1

description: Library name: 45v_Nac_SVB

value: neurotypical control postmortem human brain donor


title: Hs_Br6522_V12-D07-333-D1

description: Library name: 44v_NAc_SVB


title: Hs_Br6423_V13F06-313-B1

description: Library name: 46v_Nac_SVB


title: Hs_Br6522_V12-D07-333-C1

description: Library name: 43v_NAc_SVB


title: Hs_Br6522_V12-D07-333-B1

description: Library name: 42v_NAc_SVB


title: Hs_Br6522_V12-D07-333-A1

description: Library name: 41v_NAc_SVB


title: Hs_Br8492_V12D07-078-D1

description: Library name: 40v_NAc_SVB


title: Hs_Br8492_V12D07-078-C1

description: Library name: 39v_NAc_SVB


title: Hs_Br8492_V12D07-078-B1

description: Library name: 38v_NAc_SVB


title: Hs_Br8492_V12D07-078-A1

description: Library name: 37v_NAc_SVB


title: Hs_Br2720_V12D07-074-C1

description: Library name: Nac_2720_35V_SVB


title: Hs_Br2720_V12D07-074-D1

description: Library name: Nac_2720_36V_SVB


title: Hs_Br2720_V12D07-074-B1

description: Library name: Nac_2720_34V_SVB


title: Hs_Br2720_V12D07-074-A1

description: Library name: Nac_2720_33V_SVB


title: L3 eye-brain, w[1118], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, w[1118], Replicate 1 (ChIP)

value: L3 eye-brain complex

value: a-FLAG (M2, Sigma F1804)


title: Br8492_VSPG (ST)

status: Public on Sep 02 2025

description: Library name: Br8492_VSPG

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: spatial transcriptomics

source_name: brain (dACC)

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (dACC)


title: Br2743_VSPG (ST)

description: Library name: Br2743_VSPG


title: Br3942_VSPG (ST)

description: Library name: Br3942_VSPG


title: Br6423_VSPG (ST)

description: Library name: Br6423_VSPG


title: SK-N-AS, sgDIORA1, CRISPRi, replicate 1

status: Public on Sep 08 2025

city: Solna

first: Tilen

last: Trselic

address: Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

description: Library name: P34306_1001

data_processing:
SKNAS and SKNSH CRISPRi: Samples were sequenced on NovaSeqXPlus (NovaSeqXSeries Control Software 1.2.2.48004) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using '10B' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Output FastQ files are transferred securely to UPPMAX, where a number of standardised bioinformatics quality control checks are performed to ensure that data meets our guarantee of data quality and quantity before delivery. Basecalling and demultiplexing was performed using Illumina bcl2fastq (v2.20) software. Sequence data quality was assessed using FastQC (v0.11.8). Adapter trimming was performed using BBDuk (part of BBMap package v38.41). Reads were aligned to Ensembl GRCh38 reference genome using STAR (v2.6.1d). Gene counts were estimated using featureCounts (v1.5.1). SKNASH siRNA: Samples were sequenced on NovaSeqXPlus. Original image data file from high-throughput sequencing platforms  is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality. Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Assembly: Ensembl GRCh38
Supplementary files format and content: 3 tab-delimited files with raw counts for all samples - one for each knockdown, i.e. SKNSH and SKNAS CRISPRi, SKNSH siRNA

source_name: SK-N-AS

growth_protocol: Cells were grown in corresponding complete media as suggested by ATCC.

extract_protocol:
Cells were either lysed directly in RLT buffer (Qiagen) and subjected to RNA extraction using TRIzol Reagent (Invitrogen), followed by RNA cleanup with the RNeasy Mini Kit (Qiagen), using the cleanup protocol provided by the manufacturer.
SKNSH and SKNAS CRISPRi: Sequencing libraries were generated using the Illumina Stranded mRNA Prep kit. SKNSH siRNA: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: SK-N-AS

value: DIORA1 knockdown (sgRNA)


title: Br8667_V12Y31-080_B1 (ST)

description: Library name: Br8667_V12Y31-080_B1


title: Br8492_V12N28-334_B1 (ST)

description: Library name: Br8492_V12N28-334_B1


title: Br8325_V12Y31-080_C1 (ST)

description: Library name: Br8325_V12Y31-080_C1


title: Br6522_V12N28-332_D1 (ST)

description: Library name: Br6522_V12N28-332_D1


title: Br6522_V12N28-331_D1 (ST)

description: Library name: Br6522_V12N28-331_D1


title: Br6471_V12N28-332_C1 (ST)

description: Library name: Br6471_V12N28-332_C1


title: Br6471_V12N28-331_C1 (ST)

description: Library name: Br6471_V12N28-331_C1


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 5, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 5 (ChIP)

value: ubi-Gal4; UAS-FtICD-FLAG


title: Br6432_V12N28-332_B1 (ST)

description: Library name: Br6432_V12N28-332_B1


title: Br6432_V12J03-002_B1 (ST)

description: Library name: Br6432_V12J03-002_B1


title: Br6423_V12N28-334_D1 (ST)

description: Library name: Br6423_V12N28-334_D1


title: Br3942_V12N28-334_A1 (ST)

description: Library name: Br3942_V12N28-334_A1


title: Br2720_V12N28-332_A1 (ST)

description: Library name: Br2720_V12N28-332_A1


title: Br2743_V12N28-334_C1 (ST)

description: Library name: Br2743_V12N28-334_C1


title: Br2720_V12J03-002_A1 (ST)

description: Library name: Br2720_V12J03-002_A1


title: Br8492-9c_dACC (snRNA-seq)

description: Library name: 9c_dACC

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of dACC from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.


title: Br8325-8c_dACC (snRNA-seq)

description: Library name: 8c_dACC


title: Br2720_V12N28-331_A1 (ST)

description: Library name: Br2720_V12N28-331_A1


title: Br6423-7c_dACC (snRNA-seq)

description: Library name: 7c_dACC


title: Br3942-6c_dACC (snRNA-seq)

description: Library name: 6c_dACC