title: Male 3mos Cortex NT 4 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_4.clusters.bed


title: Male 3mos Cortex NT 3 IP TDP43-eCLIPseq

status: Public on Jan 02 2025

type: SRA

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

country: USA

institute: UC Irvine

description: Male_TDP43eCLIPseq_3mos_CTX_NT_3.clusters.bed

library_source: other

data_processing:
*library strategy: eCLIP-seq
Illumina software used for basecalling
Fastq files were softtrimmed for adaptor sequence and low-quality sequenced dropped, then aligned to mm10
Peak calling was done by normalizing IP samples to input
Assembly: mm10
Supplementary files format and content: bed files containing IP reads normalized to input. Locations of input normalized read clusters (“peaks”) called using the CLIPper algorithm (https://github.com/YeoLab/clipper). The BED file contains the following tab-separated columns: Column 1: Chromosome Column 2: Start position Column 3: Stop position Column 4: -Log10(p-value) Column 5: Log2 fold enrichment in eCLIP vs. input Column 6: Strand (+ or -)

molecule: other

organism: Mus musculus

source_name: Brain

growth_protocol: All mice were housed on a 12/12-hr light/dark schedule with ad libitum access to food and water.

extract_protocol:
lysate was lysed in eCLIP-seq lysis buffer according to manufacturer protocol.
m6A-eCLIP seq (Eclipse Bioinnovation protocol v1.01R) & TDP43-eCLIP seq (Eclipse Bioinnovation protocol v2.01R) // based on Van Nostrand et al., 2016 Nature Methods

treatment_protocol: C57Bl/6 males were dosed at 5 weeks old with PBS control or ASO targeting TDP-43 at 500ug by Intracerebroventricular (ICV) bolus injection. Following 2 weeks post-dose, striatum were collected for downstream analysis.

tag: tissue

value: Brain

tag: cell type

value: Cortex

tag: genotype

value: Non-transgenic

tag: treatment

value: No Treatment


title: PBMCs, Korean cohort, B007_L002, H077

city: Singapore

first: Boxiang

last: Liu

address: 12 Science Drive 2, MD1 - Tahir Foundation Building, Level 5

country: Singapore

institute: National University of Singapore

description: Library name: KR_SGI_B007_L002_5GEX_H077

library_source: transcriptomic single cell

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction

value: blood

value: PBMCs


title: Male 3mos Cortex NT 2 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_2clusters.bed


title: PBMCs, Korean cohort, B007_L001, H083

description: Library name: KR_SGI_B007_L001_5GEX_H083


title: PBMCs, Korean cohort, B007_L001, H084

description: Library name: KR_SGI_B007_L001_5GEX_H084


title: PBMCs, Caucasian, B007_L001, LONZA3038306_2

description: Library name: KR_SGI_B007_L001_5GEX_LONZA3038306


title: PBMCs, Korean cohort, B007_L001, H080

description: Library name: KR_SGI_B007_L001_5GEX_H080


title: Male 3mos Cortex NT 1 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_1.clusters.bed


title: PBMCs, Korean cohort, B007_L001, H079

description: Library name: KR_SGI_B007_L001_5GEX_H079


title: PBMCs, Korean cohort, B007_L001, H081

description: Library name: KR_SGI_B007_L001_5GEX_H081


title: PBMCs, Korean cohort, B007_L001, H082

description: Library name: KR_SGI_B007_L001_5GEX_H082


title: Male 3mos Striatum R62 3 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_3.clusters.bed

value: Striatum


title: PBMCs, Korean cohort, B007_L001, H078

description: Library name: KR_SGI_B007_L001_5GEX_H078


title: PBMCs, Korean cohort, B007_L001, H076

description: Library name: KR_SGI_B007_L001_5GEX_H076


title: PBMCs, Korean cohort, B007_L001, H077

description: Library name: KR_SGI_B007_L001_5GEX_H077


title: Male 3mos Striatum R62 4 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_4.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H075

description: Library name: KR_SGI_B006_L002_5GEX_H075


title: Male 3mos Striatum NT 2 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_2.clusters.bed


title: Male 3mos Striatum R62 2 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_2.clusters.bed


title: PBMCs, Caucasian, B006_L002, LONZA3038016

description: Library name: KR_SGI_B006_L002_5GEX_LONZA3038016


title: PBMCs, Korean cohort, B007_L001, H085

description: Library name: KR_SGI_B007_L001_5GEX_H085


title: PBMCs, Korean cohort, B006_L002, H074

description: Library name: KR_SGI_B006_L002_5GEX_H074


title: Male 3mos Striatum R62 1 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_1.clusters.bed


title: Male 3mos Cortex R62 3 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_3.clusters.bed


title: Male 3mos Cortex R62 4 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_4.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H071

description: Library name: KR_SGI_B006_L002_5GEX_H071


title: PBMCs, Korean cohort, B006_L002, H070

description: Library name: KR_SGI_B006_L002_5GEX_H070


title: PBMCs, Korean cohort, B006_L002, H072

description: Library name: KR_SGI_B006_L002_5GEX_H072


title: Male 3mos Striatum NT 4 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_4.clusters.bed


title: Male 3mos Cortex R62 2 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_2.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H069

description: Library name: KR_SGI_B006_L002_5GEX_H069


title: Male 3mos Striatum NT 1 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_1.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H073

description: Library name: KR_SGI_B006_L002_5GEX_H073


title: Male 3mos Cortex NT 4 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_4.clusters.bed


title: Male 3mos Cortex NT 3 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_3.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H066

description: Library name: KR_SGI_B006_L002_5GEX_H066


title: PBMCs, Korean cohort, B006_L002, H067

description: Library name: KR_SGI_B006_L002_5GEX_H067


title: PBMCs, Korean cohort, B006_L002, H068

description: Library name: KR_SGI_B006_L002_5GEX_H068


title: Male 3mos Cortex NT 1 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_1.clusters.bed


title: Male 3mos Striatum R62 4 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_4.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H064

description: Library name: KR_SGI_B006_L002_5GEX_H064


title: PBMCs, Korean cohort, B006_L002, H063

description: Library name: KR_SGI_B006_L002_5GEX_H063


title: Male 3mos Striatum NT 3 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_3.clusters.bed


title: Male 3mos Striatum R62 3 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_3.clusters.bed


title: Male 3mos Striatum R62 2 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_2.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H061

description: Library name: KR_SGI_B006_L002_5GEX_H061


title: Male 3mos Striatum R62 1 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_R62_1.clusters.bed


title: Male 3mos Striatum NT 4 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_4.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H062

description: Library name: KR_SGI_B006_L002_5GEX_H062


title: PBMCs, Caucasian, B006_L001, LONZA3038016

description: Library name: KR_SGI_B006_L001_5GEX_LONZA3038016


title: Male 3mos Striatum NT 3 input TDP43-eCLIPseq


title: PBMCs, Korean cohort, B006_L001, H075

description: Library name: KR_SGI_B006_L001_5GEX_H075


title: Male 3mos Striatum NT 2 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_2.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H072

description: Library name: KR_SGI_B006_L001_5GEX_H072


title: PBMCs, Korean cohort, B006_L001, H073

description: Library name: KR_SGI_B006_L001_5GEX_H073


title: Female 3mos Cortex R62 4 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_R62_4.clusters.bed


title: Male 3mos Cortex NT 2 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_NT_2.clusters.bed


title: Male 3mos Striatum NT 1 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_STR_NT_1.clusters.bed


title: Female 3mos Cortex R62 3 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_R62_3.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H071

description: Library name: KR_SGI_B006_L001_5GEX_H071


title: Male 3mos Cortex R62 1 input TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_1.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H074

description: Library name: KR_SGI_B006_L001_5GEX_H074


title: PBMCs, Korean cohort, B006_L001, H070

description: Library name: KR_SGI_B006_L001_5GEX_H070


title: Female 3mos Cortex R62 2 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_R62_2.clusters.bed


title: PBMCs, Korean cohort, B006_L002, H065

description: Library name: KR_SGI_B006_L002_5GEX_H065


title: PBMCs, Korean cohort, B006_L001, H069

description: Library name: KR_SGI_B006_L001_5GEX_H069


title: Female 3mos Cortex R62 1 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_R62_1.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H066

description: Library name: KR_SGI_B006_L001_5GEX_H066


title: PBMCs, Korean cohort, B006_L001, H068

description: Library name: KR_SGI_B006_L001_5GEX_H068


title: Female 3mos Cortex NT 4 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_NT_4.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H067

description: Library name: KR_SGI_B006_L001_5GEX_H067


title: Female 3mos Cortex NT 3 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_NT_3.clusters.bed


title: Female 3mos Cortex R62 4 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_R62_4.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H064

description: Library name: KR_SGI_B006_L001_5GEX_H064


title: Female 3mos Cortex R62 3 input m6A-eCLIPseq


title: Female 3mos Cortex NT 2 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_NT_2.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H062

description: Library name: KR_SGI_B006_L001_5GEX_H062


title: Female 3mos Cortex R62 1 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B006_L001, H065

description: Library name: KR_SGI_B006_L001_5GEX_H065


title: Female 3mos Cortex NT 1 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_NT_1.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H060

description: Library name: KR_SGI_B005_L002_5GEX_H060


title: Female 3mos Cortex R62 2 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B006_L001, H061

description: Library name: KR_SGI_B006_L001_5GEX_H061


title: PBMCs, Caucasian, B005_L002, LONZA3038306_2

description: Library name: KR_SGI_B005_L002_5GEX_LONZA3038306


title: Female 3mos Cortex NT 4 input m6A-eCLIPseq


title: Female 3mos Striatum R62 4 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_4.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H057

description: Library name: KR_SGI_B005_L002_5GEX_H057


title: Female 3mos Cortex NT 3 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L002, H059

description: Library name: KR_SGI_B005_L002_5GEX_H059


title: PBMCs, Korean cohort, B005_L002, H055

description: Library name: KR_SGI_B005_L002_5GEX_H055


title: Female 3mos Cortex NT 1 input m6A-eCLIPseq


title: Female 3mos Striatum R62 2 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_2.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H058

description: Library name: KR_SGI_B005_L002_5GEX_H058


title: PBMCs, Korean cohort, B005_L002, H054

description: Library name: KR_SGI_B005_L002_5GEX_H054


title: Female 3mos Striatum R62 1 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_1.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H053

description: Library name: KR_SGI_B005_L002_5GEX_H053


title: PBMCs, Korean cohort, B005_L002, H056

description: Library name: KR_SGI_B005_L002_5GEX_H056


title: Female 3mos Striatum R62 3 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_3.clusters.bed


title: Female 3mos Striatum NT 1 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_NT_1.clusters.bed


title: PBMCs, Korean cohort, B006_L001, H063

description: Library name: KR_SGI_B006_L001_5GEX_H063


title: PBMCs, Korean cohort, B005_L002, H052

description: Library name: KR_SGI_B005_L002_5GEX_H052


title: Female 3mos Striatum NT 2 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_NT_2.clusters.bed


title: Female 3mos Striatum NT 4 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_NT_4.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H051

description: Library name: KR_SGI_B005_L002_5GEX_H051


title: Female 3mos Striatum NT 3 IP m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_NT_3.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H050

description: Library name: KR_SGI_B005_L002_5GEX_H050


title: Female 3mos Striatum R62 3 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L002, H049

description: Library name: KR_SGI_B005_L002_5GEX_H049


title: Female 3mos Striatum R62 4 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_4.clusters.bed


title: Female 3mos Cortex NT 2 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_CTX_NT_2.clusters.bed


title: PBMCs, Korean cohort, B005_L002, H048

description: Library name: KR_SGI_B005_L002_5GEX_H048


title: PBMCs, Korean cohort, B005_L002, H047

description: Library name: KR_SGI_B005_L002_5GEX_H047


title: Female 3mos Striatum R62 2 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_2.clusters.bed


title: Female 3mos Striatum NT 1 input m6A-eCLIPseq


title: Female 3mos Striatum R62 1 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_R62_1.clusters.bed


title: Female 3mos Striatum NT 4 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L002, H046

description: Library name: KR_SGI_B005_L002_5GEX_H046


title: Female 3mos Striatum NT 3 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L001, H060

description: Library name: KR_SGI_B005_L001_5GEX_H060


title: PBMCs, Korean cohort, B005_L001, H059

description: Library name: KR_SGI_B005_L001_5GEX_H059


title: PBMCs, Caucasian, B005_L001, LONZA3038306_2

description: Library name: KR_SGI_B005_L001_5GEX_LONZA3038306


title: R440_CD4

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description:
Library name: R440
mapped to HG38

library_source: transcriptomic

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Assembly: HG38
Supplementary files format and content: matrix with ENS number and samples in each one column

molecule: total RNA

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells,

extract_protocol:
Total RNA purification (Norgen, Ontario, Canada)
RNA-seq

treatment_protocol: culture activated with anti-CD3, 48h

value: Primary activated CD4 cells from PBMC

tag: cell line

value: Primary cells


title: R441_CD4

description:
Library name: R441
mapped to HG38


title: Male 3mos Cortex R62 4 IP m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L001, H057

description: Library name: KR_SGI_B005_L001_5GEX_H057


title: Female 3mos Striatum NT 2 input m6A-eCLIPseq

description: Female_m6Aseq_3mos_STR_NT_2.clusters.bed


title: R438_CD4

description:
Library name: R438
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H058

description: Library name: KR_SGI_B005_L001_5GEX_H058


title: R439_CD4

description:
Library name: R439
mapped to HG38


title: Male 3mos Cortex R62 3 IP m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L001, H056

description: Library name: KR_SGI_B005_L001_5GEX_H056


title: R436_CD4

description:
Library name: R436
mapped to HG38


title: R437_CD4

description:
Library name: R437
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H054

description: Library name: KR_SGI_B005_L001_5GEX_H054


title: R435_CD4

description:
Library name: R435
mapped to HG38


title: Male 3mos Cortex R62 2 IP m6A-eCLIPseq


title: R434_CD4

description:
Library name: R434
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H053

description: Library name: KR_SGI_B005_L001_5GEX_H053


title: R431_CD4

description:
Library name: R431
mapped to HG38


title: R430_CD4

description:
Library name: R430
mapped to HG38


title: R442_CD4

description:
Library name: R442
mapped to HG38


title: Male 3mos Cortex R62 1 IP m6A-eCLIPseq


title: R428_CD4

description:
Library name: R428
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H051

description: Library name: KR_SGI_B005_L001_5GEX_H051


title: R429_CD4

description:
Library name: R429
mapped to HG38


title: Male 3mos Cortex NT 3 IP m6A-eCLIPseq


title: Male 3mos Cortex NT 2 IP m6A-eCLIPseq


title: Male 3mos Cortex NT 1 IP m6A-eCLIPseq


title: R427_CD4

description:
Library name: R427
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H049

description: Library name: KR_SGI_B005_L001_5GEX_H049


title: PBMCs, Korean cohort, B005_L001, H052

description: Library name: KR_SGI_B005_L001_5GEX_H052


title: Male 3mos Cortex R62 4 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L001, H048

description: Library name: KR_SGI_B005_L001_5GEX_H048


title: R421_CD4

description:
Library name: R421
mapped to HG38


title: R423_CD4

description:
Library name: R423
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H050

description: Library name: KR_SGI_B005_L001_5GEX_H050


title: R422_CD4

description:
Library name: R422
mapped to HG38


title: Male 3mos Cortex R62 3 input m6A-eCLIPseq


title: R433_CD4

description:
Library name: R433
mapped to HG38


title: R432_CD4

description:
Library name: R432
mapped to HG38


title: R420_CD4

description:
Library name: R420
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H047

description: Library name: KR_SGI_B005_L001_5GEX_H047


title: Male 3mos Cortex R62 2 input m6A-eCLIPseq


title: R419_CD4

description:
Library name: R419
mapped to HG38


title: Male 3mos Cortex NT 4 IP m6A-eCLIPseq


title: R418_CD4

description:
Library name: R418
mapped to HG38


title: R426_CD4

description:
Library name: R426
mapped to HG38


title: R417_CD4

description:
Library name: R417
mapped to HG38


title: R424_CD4

description:
Library name: R424
mapped to HG38


title: R416_CD4

description:
Library name: R416
mapped to HG38


title: Male 3mos Cortex R62 1 input m6A-eCLIPseq


title: PBMCs, Caucasian, B004_L002, LONZA3038097

description: Library name: KR_SGI_B004_L002_5GEX_LONZA3038097


title: R415_CD4

description:
Library name: R415
mapped to HG38


title: Male 3mos Cortex NT 4 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B005_L001, H046

description: Library name: KR_SGI_B005_L001_5GEX_H046


title: Male 3mos Cortex NT 3 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L002, H045

description: Library name: KR_SGI_B004_L002_5GEX_H045


title: Male 3mos Cortex NT 2 input m6A-eCLIPseq


title: R410_CD4

description:
Library name: R410
mapped to HG38


title: R411_CD4

description:
Library name: R411
mapped to HG38


title: R412_CD4

description:
Library name: R412
mapped to HG38


title: R413_CD4

description:
Library name: R413
mapped to HG38


title: PBMCs, Korean cohort, B005_L001, H055

description: Library name: KR_SGI_B005_L001_5GEX_H055


title: Male 3mos Cortex NT 1 input m6A-eCLIPseq


title: R409_CD4

description:
Library name: R409
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H043

description: Library name: KR_SGI_B004_L002_5GEX_H043


title: R408_CD4

description:
Library name: R408
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H042

description: Library name: KR_SGI_B004_L002_5GEX_H042


title: R405_CD4

description:
Library name: R405
mapped to HG38


title: Male 3mos Striatum R62 4 IP m6A-eCLIPseq


title: R407_CD4

description:
Library name: R407
mapped to HG38


title: R406_CD4

description:
Library name: R406
mapped to HG38


title: Male 3mos Striatum R62 3 IP m6A-eCLIPseq


title: Male 3mos Striatum R62 2 IP m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L002, H040

description: Library name: KR_SGI_B004_L002_5GEX_H040


title: R404_CD4

description:
Library name: R404
mapped to HG38


title: R402_CD4

description:
Library name: R402
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H041

description: Library name: KR_SGI_B004_L002_5GEX_H041


title: PBMCs, Korean cohort, B004_L002, H039

description: Library name: KR_SGI_B004_L002_5GEX_H039


title: Male 3mos Striatum R62 1 IP m6A-eCLIPseq


title: R403_CD4

description:
Library name: R403
mapped to HG38


title: R401_CD4

description:
Library name: R401
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H038

description: Library name: KR_SGI_B004_L002_5GEX_H038


title: R398_CD4

description:
Library name: R398
mapped to HG38


title: R399_CD4

description:
Library name: R399
mapped to HG38


title: Male 3mos Striatum NT 4 IP m6A-eCLIPseq


title: R414_CD4

description:
Library name: R414
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H037

description: Library name: KR_SGI_B004_L002_5GEX_H037


title: Male 3mos Striatum NT 3 IP m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L002, H044

description: Library name: KR_SGI_B004_L002_5GEX_H044


title: PBMCs, Korean cohort, B004_L002, H036

description: Library name: KR_SGI_B004_L002_5GEX_H036


title: R395_CD4

description:
Library name: R395
mapped to HG38


title: Male 3mos Striatum NT 2 IP m6A-eCLIPseq


title: R396_CD4

description:
Library name: R396
mapped to HG38


title: R394_CD4

description:
Library name: R394
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H034

description: Library name: KR_SGI_B004_L002_5GEX_H034


title: R392_CD4

description:
Library name: R392
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H035

description: Library name: KR_SGI_B004_L002_5GEX_H035


title: Male 3mos Striatum R62 3 input m6A-eCLIPseq


title: R393_CD4

description:
Library name: R393
mapped to HG38


title: R400_CD4

description:
Library name: R400
mapped to HG38


title: Male 3mos Striatum NT 1 IP m6A-eCLIPseq


title: R386_CD4

description:
Library name: R386
mapped to HG38


title: Male 3mos Striatum R62 2 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L002, H033

description: Library name: KR_SGI_B004_L002_5GEX_H033


title: R383_CD4

description:
Library name: R383
mapped to HG38


title: PBMCs, Korean cohort, B004_L002, H032

description: Library name: KR_SGI_B004_L002_5GEX_H032


title: Male 3mos Striatum R62 1 input m6A-eCLIPseq


title: R381_CD4

description:
Library name: R381
mapped to HG38


title: Male 3mos Striatum NT 4 input m6A-eCLIPseq


title: R378_CD4

description:
Library name: R378
mapped to HG38


title: R379_CD4

description:
Library name: R379
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H045

description: Library name: KR_SGI_B004_L001_5GEX_H045


title: PBMCs, Korean cohort, B004_L002, H031

description: Library name: KR_SGI_B004_L002_5GEX_H031


title: R385_CD4

description:
Library name: R385
mapped to HG38


title: PBMCs, Caucasian, B004_L001, LONZA3038097

description: Library name: KR_SGI_B004_L001_5GEX_LONZA3038097


title: R380_CD4

description:
Library name: R380
mapped to HG38


title: R377_CD4

description:
Library name: R377
mapped to HG38


title: R397_CD4

description:
Library name: R397
mapped to HG38


title: Male 3mos Striatum NT 3 input m6A-eCLIPseq


title: Male 3mos Striatum R62 4 input m6A-eCLIPseq


title: R387_CD4

description:
Library name: R387
mapped to HG38


title: R384_CD4

description:
Library name: R384
mapped to HG38


title: R376_CD4

description:
Library name: R376
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H044

description: Library name: KR_SGI_B004_L001_5GEX_H044


title: R374_CD4

description:
Library name: R374
mapped to HG38


title: R382_CD4

description:
Library name: R382
mapped to HG38


title: Male 3mos Striatum NT 1 input m6A-eCLIPseq


title: R373_CD4

description:
Library name: R373
mapped to HG38


title: R372_CD4

description:
Library name: R372
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H043

description: Library name: KR_SGI_B004_L001_5GEX_H043


title: Male 3mos Striatum NT 2 input m6A-eCLIPseq


title: R375_CD4

description:
Library name: R375
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H042

description: Library name: KR_SGI_B004_L001_5GEX_H042


title: R371_CD4

description:
Library name: R371
mapped to HG38


title: R369_CD4

description:
Library name: R369
mapped to HG38


title: Male 2mos Cortex TDP-43 IP ASO 3 m6A-eCLIPseq

value: TDP-43 ASO injected


title: R370_CD4

description:
Library name: R370
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H041

description: Library name: KR_SGI_B004_L001_5GEX_H041


title: PBMCs, Korean cohort, B004_L001, H040

description: Library name: KR_SGI_B004_L001_5GEX_H040


title: R367_CD4

description:
Library name: R367
mapped to HG38


title: R368_CD4

description:
Library name: R368
mapped to HG38


title: R366_CD4

description:
Library name: R366
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H039

description: Library name: KR_SGI_B004_L001_5GEX_H039


title: Male 2mos Cortex TDP-43 IP ASO 2 m6A-eCLIPseq


title: R365_CD4

description:
Library name: R365
mapped to HG38


title: Male 2mos Cortex TDP-43 IP ASO 1 m6A-eCLIPseq


title: R364_CD4

description:
Library name: R364
mapped to HG38


title: R363_CD4

description:
Library name: R363
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H038

description: Library name: KR_SGI_B004_L001_5GEX_H038


title: Male 2mos Cortex CTRL 2 IP m6A-eCLIPseq

value: PBS injected


title: Male 2mos Cortex CTRL 3 IP m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L001, H037

description: Library name: KR_SGI_B004_L001_5GEX_H037


title: R361_CD4

description:
Library name: R361
mapped to HG38


title: R359_CD4

description:
Library name: R359
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H036

description: Library name: KR_SGI_B004_L001_5GEX_H036


title: R360_CD4

description:
Library name: R360
mapped to HG38


title: PBMCs, Korean cohort, B004_L001, H035

description: Library name: KR_SGI_B004_L001_5GEX_H035


title: R362_CD4

description:
Library name: R362
mapped to HG38


title: R356_CD4

description:
Library name: R356
mapped to HG38


title: R355_CD4

description:
Library name: R355
mapped to HG38


title: R358_CD4

description:
Library name: R358
mapped to HG38


title: Male 2mos Cortex TDP-43 ASO 3 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L001, H034

description: Library name: KR_SGI_B004_L001_5GEX_H034


title: Male 2mos Cortex TDP-43 ASO 1 input m6A-eCLIPseq


title: PBMCs, Korean cohort, B004_L001, H033

description: Library name: KR_SGI_B004_L001_5GEX_H033


title: Male 2mos Cortex TDP-43 ASO 2 input m6A-eCLIPseq


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, LPS 6h, biol rep 1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads. Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: library-size normalized counts

source_name: Bone marrow-derived M0 macrophage

growth_protocol: Bone marrow was isolated from the hindlimb of mice and were cultured in medium containing M-CSF for 7 days.

extract_protocol:
RNA was extracted using RNeasy micro Kit (Qiagen, 74004) according to the manufacturer's instruction.
0.5µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library V6 preparation following manufacture’s protocol (Vazyme).

treatment_protocol: Bone marrow-derived macrophage were treated with or without LPS (1 µg/ml) for 6h.

value: Bone marrow-derived M0 macrophage

value: GPRC5B knock out

value: LPS (1 µg/ml), 6h


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, LPS 6h, biol rep 2


title: PBMCs, Korean cohort, B004_L001, H032

description: Library name: KR_SGI_B004_L001_5GEX_H032


title: Male 2mos Cortex CTRL 2 input m6A-eCLIPseq


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, basal, biol rep 1

value: vehicle (H20), 6h


title: Bone marrow-derived M0 macrophage, control, LPS 6h, biol rep 3

value: control


title: PBMCs, Korean cohort, B004_L001, H031

description: Library name: KR_SGI_B004_L001_5GEX_H031


title: Bone marrow-derived M0 macrophage, control, LPS 6h, biol rep 2


title: Male 2mos Cortex CTRL 1 IP m6A-eCLIPseq


title: PBMCs, Caucasian, B003_L002, LONZA3038097

description: Library name: KR_SGI_B003_L002_5GEX_LONZA3038097


title: Bone marrow-derived M0 macrophage, control, LPS 6h, biol rep 1


title: R357_CD4

description:
Library name: R357
mapped to HG38


title: PBMCs, Korean cohort, B003_L002, H030

description: Library name: KR_SGI_B003_L002_5GEX_H030


title: Bone marrow-derived M0 macrophage, control, basal, biol rep 3


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, LPS 6h, biol rep 3


title: Bone marrow-derived M0 macrophage, control, basal, biol rep 2


title: Male 2mos Cortex CTRL 3 input m6A-eCLIPseq


title: Male 2mos Striatum TDP-43 ASO 2 total RNA-seq

description: 1 hemisphere was used to extract RNA

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

source_name: Striatum

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

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

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


title: Male 2mos Striatum TDP-43 ASO 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Resident peritoneal macrophage, control, basal, bio rep 3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm39
Supplementary files format and content: library-size normalized counts

source_name: Resident peritoneal macrophage

growth_protocol: Resident peritoneal macrophages were isolated from peritoneal lavageResident peritoneal macrophages were isolated from peritoneal lavage fluid using the mouse peritoneum macrophage isolation Kit (Miltenyi, 130-110-434) according to the manufacturer’s protocol.

extract_protocol:
RNA was extracted using RNeasy micro Kit (Qiagen, 74004) according to the manufacturer's instruction.
1µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library V8 preparation following manufacture’s protocol (Vazyme).

value: Resident peritoneal macrophage

value: wild-type

value: no treatment


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, basal, biol rep 2


title: PBMCs, Korean cohort, B003_L002, H029

description: Library name: KR_SGI_B003_L002_5GEX_H029


title: Bone marrow-derived M0 macrophage, control, basal, biol rep 1


title: Resident peritoneal macrophage, GPRC5B knock out, basal, bio rep 3

value: GPRC5B-Knock out


title: Resident peritoneal macrophage, control, basal, bio rep 1


title: PBMCs, Korean cohort, B003_L002, H027

description: Library name: KR_SGI_B003_L002_5GEX_H027


title: Resident peritoneal macrophage, GPRC5B knock out, basal, bio rep 2


title: Male 2mos Cortex CTRL 1 input m6A-eCLIPseq

value: Brain

value: Cortex


title: PBMCs, Korean cohort, B003_L002, H026

description: Library name: KR_SGI_B003_L002_5GEX_H026

value: blood

value: PBMCs


title: Male 2mos Striatum CTRL 3 total RNA-seq

description: 1 hemisphere was used to extract RNA

value: Striatum


title: Male 2mos Striatum TDP-43 ASO 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L002, H025

description: Library name: KR_SGI_B003_L002_5GEX_H025


title: Glioblastoma B11

city: Los Angeles

first: David

last: Craig

state: CA

address: 1450 Biggy St, 2nd Floor

department: Department of Translational Genomics

institute: University of Southern California

data_processing:
Sequencing data was analyzed using the 10X Genomics spaceranger pipeline.
Assembly: GRCh38
Supplementary files format and content: .cloupe: Loupe Browser file for visualization of spatial transcriptomics data.
Supplementary files format and content: filtered_feature_bc_matrix.h5: File contains gene expression data for only barcodes that are within tissue regions in the spatial grid.
Supplementary files format and content: raw_feature_bc_matrix.h5:  File contains gene expression data for all barcodes
Supplementary files format and content: metrics_summary.csv:  File contains sequencing summary metrics for
Supplementary files format and content: scale_factors_json.json: File contains scale factor and pixel information for visualizing the spatial sample.
Supplementary files format and content: tissue_hires_image.png: Downsampled full resolution image of sample.
Supplementary files format and content: tissue_positions_list.csv:  File contains position information for spatial barcodes. The first column contains the sequence of the barcode associated to the spot. Column 2 indicates whether the spot is in a tissue area. Columns 3-6 refer to the array in the full resolution image. Column 3 is the row coordinate. Column 4 is the column coordinate. Column 5 is the row pixel coordinate. Column 6 is the column pixel coordinate.
Supplementary files format and content: integrated_glioma_samples_cohortA.rds: Sequencing data for the 11 samples in cohort A were initially analyzed using the 10X Genomics spaceranger pipeline. Output data files for all cohort A samples were imported in R to individual Seurat objects, normalized with SCTransform, and integrated using the Seurat reciprocal PCA integration method.
Supplementary files format and content: integrated_glioblastoma_samples_cohortB.rds: Sequencing data for the six samples in cohort B were initially analyzed using the 10X Genomics spaceranger pipeline. Output data files for all cohort B samples were imported in R to individual Seurat objects, normalized with SCTransform, and integrated using the Harmony method.
Library strategy: Visium CytAssist Spatial Gene Expression for FFPE

source_name: glioma

extract_protocol:
Formalin-fixed parrafin-embedded tissues were sectioned at 5 micron thickness and applied to glass slides, according to the 10X Genomics Visium CytAssist Tissue Preparation Guide.
Sequencing libraries were prepared using the 10X Genomics Visium CytAssist protocol according to manufacturer's instructions.

value: glioma


title: Glioblastoma B10

description: Visium CytAssist Spatial Gene Expression for FFPE


title: Resident peritoneal macrophage, GPRC5B knock out, basal, bio rep 1


title: Glioblastoma B9


title: PBMCs, Korean cohort, B003_L002, H024

description: Library name: KR_SGI_B003_L002_5GEX_H024


title: Glioblastoma B8


title: Male 2mos Striatum CTRL 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Bone marrow-derived M0 macrophage, GPRC5B knock out, basal, biol rep 3


title: Resident peritoneal macrophage, control, basal, bio rep 2


title: PBMCs, Korean cohort, B003_L002, H028

description: Library name: KR_SGI_B003_L002_5GEX_H028


title: Male 2mos Striatum CTRL 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L002, H023

description: Library name: KR_SGI_B003_L002_5GEX_H023


title: Male 2mos Striatum CTRL 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Female 3mos Cortex R62 5 total RNA-seq

description: 1 hemisphere was used to extract RNA

source_name: Cortex

value: No Treatment


title: Glioblastoma B6


title: Monocytes from HIV+/ART subject (non-smoker) CHI0400, Day 0

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes
Assembly: Hg19
Supplementary files format and content: RSEM Count file is in Text

source_name: peripheral blood

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen)
Sequencing library preparation for SLCLs was completed using the Quantseeq RNA-seq library preparation kit.

value: peripheral blood

value: monocyte

value: placebo


title: Male 2mos Striatum TDP-43 ASO 1 total RNA-seq

description: 1 hemisphere was used to extract RNA

value: TDP-43 ASO injected


title: Female 3mos Cortex R62 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0430, Day 0

value: galantamine


title: Glioblastoma B7


title: Female 3mos Cortex R62 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0146, Day 0


title: PBMCs, Korean cohort, B003_L002, H022

description: Library name: KR_SGI_B003_L002_5GEX_H022


title: Monocytes from HIV+/ART subject (non-smoker) CHI0187, Day 0


title: PBMCs, Korean cohort, B003_L002, H021

description: Library name: KR_SGI_B003_L002_5GEX_H021


title: Monocytes from HIV+/ART subject (non-smoker) CHI0271, Day 0


title: PBMCs, Korean cohort, B003_L002, H020

description: Library name: KR_SGI_B003_L002_5GEX_H020


title: Monocytes from HIV+/ART subject (non-smoker) CHI0336, Day 0


title: Female 3mos Cortex R62 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0319, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0368, Day 196 (Wk 28)


title: PBMCs, Korean cohort, B003_L002, H019

description: Library name: KR_SGI_B003_L002_5GEX_H019


title: Female 3mos Cortex R62 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0368, Day 112 (Wk 16)


title: Female 3mos Cortex NT 5 total RNA-seq

description: 1 hemisphere was used to extract RNA

value: Non-transgenic


title: Monocytes from HIV+/ART subject (non-smoker) CHI0368, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0423, Day 84 (Wk 12)


title: Female 3mos CortexNT 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0423, Day 112 (Wk 16)


title: PBMCs, Korean cohort, B003_L002, H017

description: Library name: KR_SGI_B003_L002_5GEX_H017


title: Monocytes from HIV+/ART subject (non-smoker) CHI0138, Day 112 (Wk 16)


title: PBMCs, Korean cohort, B003_L002, H016

description: Library name: KR_SGI_B003_L002_5GEX_H016


title: Monocytes from HIV+/ART subject (non-smoker) CHI0138, Day 84 (Wk 12)


title: Female 3mos Cortex NT 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0025, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0423, Day 0


title: PBMCs, Korean cohort, B003_L001, H030

description: Library name: KR_SGI_B003_L001_5GEX_H030


title: Female 3mos Cortex NT 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0025, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0138, Day 0


title: Female 3mos Cortex NT 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0025, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0405, Day 196 (Wk 28)


title: Female 3mos Striatum R62 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Caucasian, B003_L001, LONZA3038097

description: Library name: KR_SGI_B003_L001_5GEX_LONZA3038097


title: Monocytes from HIV+/ART subject (non-smoker) CHI0405, Day 84 (Wk 12)


title: PBMCs, Korean cohort, B003_L001, H028

description: Library name: KR_SGI_B003_L001_5GEX_H028


title: Monocytes from HIV+/ART subject (non-smoker) CHI0405, Day 112 (Wk 16)


title: PBMCs, Korean cohort, B003_L001, H027

description: Library name: KR_SGI_B003_L001_5GEX_H027


title: PBMCs, Korean cohort, B003_L002, H018

description: Library name: KR_SGI_B003_L002_5GEX_H018


title: Monocytes from HIV+/ART subject (non-smoker) CHI0405, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0444, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0444, Day 112 (Wk 16)


title: Female 3mos Striatum R62 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0444, Day 84 (Wk 12)


title: PBMCs, Korean cohort, B003_L001, H025

description: Library name: KR_SGI_B003_L001_5GEX_H025


title: PBMCs, Korean cohort, B003_L001, H029

description: Library name: KR_SGI_B003_L001_5GEX_H029


title: Female 3mos Striatum R62 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0397, Day 196 (Wk 28)


title: Female 3mos Striatum R62 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L001, H024

description: Library name: KR_SGI_B003_L001_5GEX_H024


title: Female 3mos Striatum NT 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L001, H023

description: Library name: KR_SGI_B003_L001_5GEX_H023


title: Monocytes from HIV+/ART subject (non-smoker) CHI0384, Day 196 (Wk 28)


title: Female 3mos Striatum NT 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0397, Day 84 (Wk 12)


title: Female 3mos Striatum R62 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0384, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0383, Day 196 (Wk 28)


title: PBMCs, Korean cohort, B003_L001, H021

description: Library name: KR_SGI_B003_L001_5GEX_H021


title: Female 3mos Striatum NT 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0444, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0384, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0383, Day 112 (Wk 16)


title: PBMCs, Korean cohort, B003_L001, H020

description: Library name: KR_SGI_B003_L001_5GEX_H020


title: Female 3mos Striatum NT 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L001, H022

description: Library name: KR_SGI_B003_L001_5GEX_H022


title: Monocytes from HIV+/ART subject (non-smoker) CHI0397, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0383, Day 84 (Wk 12)


title: Female 3mos Striatum NT 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L001, H026

description: Library name: KR_SGI_B003_L001_5GEX_H026


title: Monocytes from HIV+/ART subject (non-smoker) CHI0397, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0383, Day 0


title: PBMCs, Korean cohort, B003_L001, H019

description: Library name: KR_SGI_B003_L001_5GEX_H019


title: Monocytes from HIV+/ART subject (non-smoker) CHI0267, Day 196 (Wk 28)


title: Male 3mos Cortex R62 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0267, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0267, Day 84 (Wk 12)


title: Male 3mos Cortex R62 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0224, Day 196 (Wk 28)


title: PBMCs, Korean cohort, B003_L001, H018

description: Library name: KR_SGI_B003_L001_5GEX_H018


title: Monocytes from HIV+/ART subject (non-smoker) CHI0267, Day 0


title: PBMCs, Korean cohort, B003_L001, H017

description: Library name: KR_SGI_B003_L001_5GEX_H017


title: Monocytes from HIV+/ART subject (non-smoker) CHI0224, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0384, Day 112 (Wk 16)


title: Male 3mos Cortex R62 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B003_L001, H016

description: Library name: KR_SGI_B003_L001_5GEX_H016


title: Male 3mos Cortex R62 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0224, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0224, Day 0


title: PBMCs, Caucasian, B002_L002, LONZA3038016

description: Library name: KR_SGI_B002_L002_5GEX_LONZA3038016


title: PBMCs, Korean cohort, B002_L002, H015

description: Library name: KR_SGI_B002_L002_5GEX_H015


title: Monocytes from HIV+/ART subject (non-smoker) CHI0233, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0233, Day 0


title: Male 3mos Cortex R62 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0233, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0233, Day 196 (Wk 28)


title: PBMCs, Korean cohort, B002_L002, H014

description: Library name: KR_SGI_B002_L002_5GEX_H014


title: Male 3mos Cortex NT 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0228, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0228, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0228, Day 196 (Wk 28)


title: PBMCs, Korean cohort, B002_L002, H013

description: Library name: KR_SGI_B002_L002_5GEX_H013


title: Male 3mos Cortex NT 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0228, Day 0


title: PBMCs, Korean cohort, B002_L002, H012

description: Library name: KR_SGI_B002_L002_5GEX_H012


title: Male 3mos Cortex NT 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0205, Day 84 (Wk 12)


title: PBMCs, Korean cohort, B002_L002, H011

description: Library name: KR_SGI_B002_L002_5GEX_H011


title: Monocytes from HIV+/ART subject (non-smoker) CHI0205, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0205, Day 0


title: Male 3mos Cortex NT 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0180, Day 196 (Wk 28)


title: Male 3mos Striatum R62 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0180, Day 112 (Wk 16)


title: Male 3mos Cortex NT 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H009

description: Library name: KR_SGI_B002_L002_5GEX_H009


title: Male 3mos Striatum R62 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H010

description: Library name: KR_SGI_B002_L002_5GEX_H010


title: Monocytes from HIV+/ART subject (non-smoker) CHI0180, Day 84 (Wk 12)


title: Male 3mos Striatum R62 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0169, Day 112 (Wk 16)


title: PBMCs, Korean cohort, B002_L002, H008

description: Library name: KR_SGI_B002_L002_5GEX_H008


title: PBMCs, Korean cohort, B002_L002, H007

description: Library name: KR_SGI_B002_L002_5GEX_H007


title: Monocytes from HIV+/ART subject (non-smoker) CHI0169, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0169, Day 84 (Wk 12)


title: Male 3mos Striatum R62 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0169, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0165, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0205, Day 196 (Wk 28)


title: Male 3mos Striatum R62 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H005

description: Library name: KR_SGI_B002_L002_5GEX_H005


title: Male 3mos Striatum NT 5 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H004

description: Library name: KR_SGI_B002_L002_5GEX_H004


title: Monocytes from HIV+/ART subject (non-smoker) CHI0073, Day 112 (Wk 16)


title: Male 3mos Striatum NT 4 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H003

description: Library name: KR_SGI_B002_L002_5GEX_H003


title: PBMCs, Korean cohort, B002_L002, H006

description: Library name: KR_SGI_B002_L002_5GEX_H006


title: Monocytes from HIV+/ART subject (non-smoker) CHI0165, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0073, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0180, Day 0


title: Male 3mos Striatum NT 3 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H002

description: Library name: KR_SGI_B002_L002_5GEX_H002


title: Monocytes from HIV+/ART subject (non-smoker) CHI0073, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0165, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0042, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0042, Day 112 (Wk 16)


title: Male 3mos Striatum NT 2 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0042, Day 84 (Wk 12)


title: Male 3mos Striatum NT 1 total RNA-seq

description: 1 hemisphere was used to extract RNA


title: PBMCs, Korean cohort, B002_L002, H001

description: Library name: KR_SGI_B002_L002_5GEX_H001


title: Monocytes from HIV+/ART subject (non-smoker) CHI0165, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0092, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0042, Day 0


title: CD8 T cells, CCR2 KO, rep3

city: St. Louis

first: Robyn

last: Klein

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

description: 97.ACAACACACA-GACTACCATC.H2LKCDSX5_ACAACACACA-GACTACCATC

data_processing:
Raw data was analyzed using Partek Flow.
Reads were subjected to base trim and STAR alignment to obtain transcript counts, then normalized.
Assembly: mm39
Supplementary files format and content: tab-demilited text file includes raw counts for each sample
Supplementary files format and content: tab-demilited text file includes Partek E/M values for each sample

source_name: brain

growth_protocol: Mice were infected with WNV-NS5-E218A. Brain tissues were harvested at 30 days post infection.

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: CD8 T cells were magnetically isolated from immune cells processed from brain tissues.

value: brain

value: CD8 T cell

value: CCR2 KO


title: CD8 T cells, CCR2 KO, rep2

description: 96.CCGATATGTC-ATAGCGAGAA.H2LKCDSX5_CCGATATGTC-ATAGCGAGAA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0092, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0073, Day 196 (Wk 28)


title: Diff-AEC2 treated to 480 µg/ml bleomycin, 480_1

city: Sejong-si

first: Yubin

last: Han

address: Sejong-ro 2511

department: College of Pharmacy

country: South Korea

institute: Korea University

description: Library name: 480_1

data_processing:
Prior to analysis, the adapter sequences were removed using the Trimmomatic program, and the ends of the reads were trimmed to remove bases with a base quality of less than 3 and a sliding window trimmer with a window size of bases with base quality less than 3 and the sliding window trim technique with window size=4 and mean quality=15. After that, reads shorter than min length=36 bp were removed to generate trimmed data.
A genomic reference (GRCh38) was used to map the cDNA fragments obtained through RNA-seq experiments. Genomic reference (GRCh38) to map the cDNA fragments is the statistical results of mapping with HISAT2 program, which can process spliced read mapping through Bowtie2 aligner.
By using StringTie program, gene/transcript from a reference gene model can be assembled. After assembly, the abundance of the transcript is expressed as read count and normalized value, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) values.
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: csv files include TPM and FPKM values for each sample
Assembly: hg38

source_name: H7  Embryonic stem cell-derived

growth_protocol: For the diff-AEC2 differentiation, H7 cells were seeded as ratio of 1.0*105/cm2 in vitronecin coated-wells. With differentiation to definitive endoderms for 6 days, anterior foregut endoderm for 4 days, ventralized anterior foregut endoderm for 4 days, and lung progenitor for 7 days, lung progenitor cells were derived with 21 days-submerged culture.This lung progenitor cells can be cryo-stocked or re-seeded in 12 well insert format to derive differentiated AEC2s (diff-AEC2). As seeded same ratio as 1.0*105/cm2 in vitronectin coated-353180 falcon 12 well inserts, lung progenitor cells go through 3 days of stabliization in submerged and differentiated to diff-AEC2 in air-liquid interface for 7 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA Library Prep Kit follwing manufactuer's protocols.

treatment_protocol: Bleomycin (Cayman) stocks of 10 µg/ml in phosphate-buffere saline (PBS) were stored at -20℃ and used for bleomycin treatment. In bleomycin treatment, 500 µl of bleomycin was treated to apical side of inserts for 24 hr.

value: H7  Embryonic stem cell-derived

value: Differentiated type 2 alveolar cells

value: WT

value: Bleomycin 480 µg/ml


title: Diff-AEC2 treated to 240 µg/ml bleomycin, 240_2

description: Library name: 240_2

value: Bleomycin 240 µg/ml


title: Monocytes from HIV+/ART subject (non-smoker) CHI0092, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0077, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0077, Day 112 (Wk 16)


title: Diff-AEC2 treated to 240 µg/ml bleomycin, 240_1

description: Library name: 240_1


title: Monocytes from HIV+/ART subject (non-smoker) CHI0077, Day 0


title: Monocytes from HIV+/ART subject (non-smoker) CHI0077, Day 84 (Wk 12)


title: CD8 T cells, CCR2 KO, rep1

description: 95.CCTATAATGC-ATGACTCCTC.H2LKCDSX5_CCTATAATGC-ATGACTCCTC


title: CD8 T cells, WT, rep3

description: 90.GTATGCAGCT-TTCGGAATGA.H2LKCDSX5_GTATGCAGCT-TTCGGAATGA


title: Monocytes from HIV+/ART subject (non-smoker) CHI0063, Day 196 (Wk 28)


title: CD8 T cells, WT, rep2

description: 89.CGCTTCCTAA-GCACTACCAG.H2LKCDSX5_CGCTTCCTAA-GCACTACCAG


title: Monocytes from HIV+/ART subject (non-smoker) CHI0063, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0063, Day 112 (Wk 16)


title: Diff-AEC2 treated to 480 µg/ml bleomycin, 480_2

description: Library name: 480_2


title: Monocytes from HIV+/ART subject (non-smoker) CHI0092, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0063, Day 0


title: Diff-AEC2 treated to 24 µg/ml bleomycin, 24_2

description: Library name: 24_2

value: Bleomycin 24 µg/ml


title: CD8 T cells, WT, rep1

description: 87.AATGTAACCG-TATGCCGGCA.H2LKCDSX5_AATGTAACCG-TATGCCGGCA


title: Diff-AEC2, Control_2

description: Library name: Con_2

value: control


title: Diff-AEC2, Control_1

description: Library name: Con_1

source_name: H7 Embryonic stem cell-derived

value: H7 Embryonic stem cell-derived


title: Monocytes from HIV+/ART subject (non-smoker) CHI0043, Day 196 (Wk 28)

value: peripheral blood


title: ChIPSeq_P7_Testis_Null_Input_rep2

city: Salt Lake City

first: Bradley

middle: R.

last: Carins

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

library_source: genomic

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

molecule: genomic DNA

source_name: testis

extract_protocol:
Tissues/ were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Branson sonifier (0.9 s on/0.1 s off x 7 cycles, average size 300-700 bp).
ChIP-seq libraries were prepared using the NEBNext® Ultra II DNA Library prep for Illumina. 1.0 ng of DNA was used as starting material for input and ip samples. Libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were amplified using 7 cycles on the thermocycler. Libraries were validated using the Agilent Technologies 4150 TapeStation

value: testis

value: Mouse testis at P7

value: Zbtb16 null


title: Monocytes from HIV+/ART subject (non-smoker) CHI0043, Day 112 (Wk 16)

value: monocyte

value: galantamine


title: Monocytes from HIV+/ART subject (non-smoker) CHI0047, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0043, Day 84 (Wk 12)

value: placebo


title: ChIPSeq_P7_Testis_Null_Input_rep1


title: ChIPSeq_P7_Testis_WT_Input_rep2


title: Monocytes from HIV+/ART subject (non-smoker) CHI0047, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0047, Day 84 (Wk 12)


title: ChIPSeq_P7_Testis_WT_Input_rep1


title: Monocytes from HIV+/ART subject (non-smoker) CHI0047, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0370, Day 0


title: Diff-AEC2 treated to 24 µg/ml bleomycin_24_1

description: Library name: 24_1


title: Monocytes from HIV+/ART subject (smoker) CHI0234, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0252, Day 0


title: ChIPSeq_P7_Testis_Null_SOX3_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0196, Day 0


title: ChIPSeq_P7_Testis_Null_SALL4_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0362, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0385, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0385, Day 84 (Wk 12)


title: ChIPSeq_P7_Testis_Null_SALL4_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0085, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0085, Day 84 (Wk 12)


title: ChIPSeq_P7_Testis_WT_RNAPol2Ser2P_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0329, Day 112 (Wk 16)


title: ChIPSeq_P7_Testis_WT_Pan-RNAPol2_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0385, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (non-smoker) CHI0043, Day 0


title: ChIPSeq_P7_Testis_WT_RNAPol2Ser5P_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0329, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0109, Day 112 (Wk 16)


title: ChIPSeq_P7_Testis_WT_TBP_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0329, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0388, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (smoker) CHI0109, Day 0


title: ChIPSeq_P7_Testis_WT_SALL4_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0066, Day 0


title: ChIPSeq_P7_Testis_Null_SOX3_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0388, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0388, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0388, Day 0


title: ChIPSeq_P7_Testis_WT_RNAPol2Ser2P_rep1


title: ChIPSeq_P7_Testis_WT_RNAPol2Ser5P_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0085, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0381, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0381, Day 84 (Wk 12)


title: ChIPSeq_P7_Testis_WT_Pan-RNAPol2_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0107, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0107, Day 196 (Wk 28)


title: ChIPSeq_P7_Testis_WT_TBP_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0107, Day 84 (Wk 12)


title: ChIPSeq_P7_Testis_WT_SOX3_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0381, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0109, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0215, Day 196 (Wk 28)


title: ChIPSeq_P7_Testis_WT_SALL4_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0107, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0215, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0215, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0201, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (smoker) CHI0215, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0381, Day 196 (Wk 28)


title: HTO_Flot2Cre naïve CD4+ T cells, stimulated (0, 0.25, 1 μg/ml), 3 hour

city: Research Triangle Park

first: Michael

middle: B

last: Fessler

state: NC

address: 111 T.W. Alexander Drive

institute: National Institute of Environmental Health Sciences/NIH

description: Cells stimulated with 0, 0.25, or 1 μg/ml of plate-bound anti-CD3 were hash-tagged with barcode sequence 'ACCCACCAGTAAGAC', 'GGTCGAGAGCATTCA', or 'CTTGCCGCATGTCAT', respectively.

data_processing:
fastq.gz files were processed using the “multi” function in cellranger 7.2.0. and the mm10-3.0.0 reference set, allowing for concurrent processing of hashtag and gene expression information.
Assembly: mm10-3.0.0
Supplementary files format and content: Single zipped files containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz are provided for both WT and Cre genotypes.

molecule: protein

source_name: Spleen and lymph nodes

growth_protocol: Primary naïve CD4+ T cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), antibiotics, and 57.2 μM beta-mercaptoethanol in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells stimulated with 0, 0.25, or 1 μg/ml of plate-bound anti-CD3 were hash-tagged with barcode sequence 'ACCCACCAGTAAGAC', 'GGTCGAGAGCATTCA', or 'CTTGCCGCATGTCAT', respectively, within each genotype (WT and Cre). The labeled cells were then pooled to create pooled sample WT and pooled sample Cre.
For pooled sample WT and sample Cre, about 16000 live cells at 3x10^5 cells/ml concentration with more than 80% viabilities loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Controller (10x Genomics, 120263). The cDNA for antibody derived transcripts (ADT) and gene derived transcripts was generated and amplified according to manufacturer’s instructions (10x Genomics and BioLegend). The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ library and gel bead kit v3.1 (10x Genomics, 1000268) and additional reagents recommended in the protocol of Total A-seq (BioLegend). The two libraries were mixed at 9:1 molar ratio (Gene Expression library to ADT library) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read 1: 28; Read 2: 90).

treatment_protocol: Mouse naive CD4+ T cells were stimulated for 3 hours with varying concentrations (0, 0.25, or 1 μg/ml) of plate-bound anti-CD3. A fixed dose of soluble anti-CD28 (1 μg/ml) was provided under the conditions of 0.25 or 1 μg/ml of plate-bound anti-CD3.

value: Spleen and lymph nodes

value: primary naive CD4+ T cells

value: Cre

value: 3 hour stimulation with varying concentrations (0, 0.25, or 1 μg/ml) of plate-bound anti-CD3. A fixed dose of soluble anti-CD28 (1 μg/ml) was provided under the conditions of 0.25 or 1 μg/ml of plate-bound anti-CD3.

tag: library type

value: HTO

tag: hto

value: TotalSeq-A301 anti-mouse Hashtag 1, TotalSeq-A302 anti-mouse Hashtag 2, TotalSeq-A303 anti-mouse Hashtag 3


title: HTO_Flot2WT naïve CD4+ T cells, stimulated (0, 0.25, 1 μg/ml), 3 hour

value: WT


title: GEX_Flot2Cre naïve CD4+ T cells, stimulated (0, 0.25, 1 μg/ml), 3 hour

value: mRNA


title: Monocytes from HIV+/ART subject (smoker) CHI0030, Day 196


title: Monocytes from HIV+/ART subject (smoker) CHI0201, Day 112 (Wk 16)


title: ChIPSeq_P7_Testis_WT_SOX3_rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0201, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0030, Day 112 (Wk 16)


title: GEX_Flot2WT naïve CD4+ T cells, stimulated (0, 0.25, 1 μg/ml), 3 hour


title: Monocytes from HIV+/ART subject (smoker) CHI0030, Day 84 (Wk 12)


title: mouse_lung

city: Carlsbad

first: Dennis

last: Eastburn

address: 5928 Pascal Court, Suite 100

institute: BioSpyder Technologies, Inc

description:
Tissue_3
TempO-LINC

data_processing:
*library strategy: TempO-LINC
To generate TempO-LINC single-cell expression data, barcoded reads are demultiplexed using an in-house developed software. Briefly, index associated reads are scanned to find the sequences of the barcodes, while allowing an offset of 3 nucleotides from their expected positions and 1 mismatch from their expected sequence. Reads featuring the same barcode combination are pooled together into barcode associated clusters. A cell calling read threshold is established based on inflection point analysis of a ranked barcode distribution plot (knee plot). Cell associated reads are then aligned to the reference human or mouse whole transcriptome TempO-Seq probe sequences using bwa v. 0.7.17 (mem algorithm, parameters: -v 1 -c 2 -L 100). Unique molecular identifiers (UMIs) are used to collapse the reads originating from the same transcript and remove any PCR duplicates. For each single-cell alignment, the probes featuring a UMI count >0 are considered indicative of an expressed/detected gene. Cell count tables are generated using the software featureCount v 2.0.1.
Assembly: GRCm38
Supplementary files format and content: Read count table matrix files stored as H5 archive

source_name: lung

extract_protocol:
Fresh tissue was isolated from an 8-week-old ICR (CD-1®) mouse following IACUC-approved protocols. The harvested tissues included one cerebral cortex hemisphere (65 mg), one half of a kidney (45 mg), and one lung lobe (50 mg), which were immediately snap-frozen on dry ice. The frozen tissues, along with 75 µL of RNase Inhibitor V2 (S2 Genomics, 100-288-916), were then placed in the Dissociation Chamber of a pre-cooled standard Nuclei Isolation Cartridge (S2 Genomics, 100-063-287) and inserted into the pre-cooled Singulator 100TM (S2 Genomics, 100-060-817). Nuclei were isolated from the tissues using the Low Volume Nuclei Isolation protocol. Following isolation, the nuclei suspension was recovered from the Singulator cartridge and centrifuged at 500 rcf for 5 minutes at 4°C. The supernatant was removed, and the kidney and lung nuclei pellets were resuspended in 1 mL of Nuclei Storage Reagent (S2 Genomics, 100-063-405) supplemented with RNase inhibitor (1 U/µL). The brain nuclei were further processed using Debris Removal Stock Reagent (S2 Genomics 100-253-628) to eliminate myelin debris, according to the manufacturer's instructions. Finally, the nuclei were counted, and their viability was determined using AO/PI staining with the Nexcelom K2. The nuclei samples were subsequently fixed via the TempO-LINC Fixation protocol as described below, and stored at -80oC.
Nuclei were fixed using the TempO-LINC Fixation Kit (BioSpyder Technologies Inc., cat# 202392). Fixed, cryopreserved mouse nuclei were thawed and barcoded with the TempO-LINC barcoding protocol. Briefly, nuclei were hybridized with the Mouse Whole Transcriptome v1.1 (30,162 probe pairs, BioSpyder, cat# 201186) DO pool and placed in an incubator overnight for 16 hours at 45oC.  Next, 100,000 nuclei were transferred and prepped for TempO-LINC Barcoding. Nuclei were equally distributed across the 48 wells of the TempO-LINC Barcode 1 plate at 2,083 nuclei/well. Following three rounds of ligation-based barcoding, nuclei were then distributed for direct PCR amplification at 1000 nuclei/well. PCR primers contained both Illumina sequencing adapters as well as dual indices that also served as the fourth TempO-LINC barcode.

value: lung

tag: age

value: 8 weeks

tag: strain

value: ICR (CD-1) mouse


title: Monocytes from HIV+/ART subject (smoker) CHI0182, Day 196 (Wk 28)

value: peripheral blood


title: Monocytes from HIV+/ART subject (smoker) CHI0030, Day 0


title: Monocytes from HIV+/ART subject (smoker) CHI0201, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0182, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0173, Day 196 (Wk 28)


title: mouse_kidney

description:
Tissue_2
TempO-LINC

source_name: kidney

value: kidney


title: EZH2KO_MBC_D39

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Pre-processing of sequencing results to generate gene expression count matrices was performed using the 10x genomics Cell Ranger v7.1.0 pipeline and aligning to the mm10-2020-A mouse reference genome.
Further processing was done with Seurat v4.3.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10-2020-A
Supplementary files format and content: 10x Genomics mRNA output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Memory B cells

extract_protocol:
At the indicated time point spleens and lymph nodes from a pool of 5 mice were processed and memory B cells were isolated by FACS.
10x 5’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics 1000263) according to the instructions provided.

treatment_protocol: Mice were infected with 15,000 virus forming units of influenza A/PR8/34 (PR8).

value: Memory B cells

tag: time point

value: Day 39

tag: antibodies/tags

value: CD19-CRE, EZH2-fl/fl

tag: sorting markers

value: CD19+ IgD- CD138- CD38+ FAS- GL7- HA/NP_tetramer+


title: Monocytes from HIV+/ART subject (smoker) CHI0182, Day 112 (Wk 16)

value: monocyte

value: placebo


title: Monocytes from HIV+/ART subject (smoker) CHI0173, Day 112 (Wk 16)


title: mouse_brain_cortex

description:
Tissue_1
TempO-LINC

source_name: one cerebral cortex hemisphere

value: one cerebral cortex hemisphere


title: Monocytes from HIV+/ART subject (smoker) CHI0079, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (smoker) CHI0173, Day 0

value: galantamine


title: Monocytes from HIV+/ART subject (smoker) CHI0173, Day 84 (Wk 12)


title: EZH2KO_MBC_D14

value: Day 14


title: Monocytes from HIV+/ART subject (smoker) CHI0079, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0079, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0017, Day 196 (Wk 28)


title: Monocytes from HIV+/ART subject (smoker) CHI0079, Day 0


title: CTRL_MBC_D14


title: Monocytes from HIV+/ART subject (smoker) CHI0017, Day 112 (Wk 16)


title: KO+PBS 24hr bio rep 4

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

data_processing:
Quality control metrics were performed on raw sequencing reads using fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene
Assembly: mm10
Supplementary files format and content: Excel file that contains matrix of raw counts of all samples (5 WT, 5 KO, 5 KO+PBS, 5 KO+lacripep)

source_name: Cornea

extract_protocol:
Total RNA was collected  and purified using RNAaqueous and DNase reagents according to the manufacturer’s instructions (Ambion, Houston, TX, USA)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Cornea

value: Aire KO

value: PBS


title: Monocytes from HIV+/ART subject (smoker) CHI0017, Day 0


title: KO+PBS 24hr bio rep 3


title: Monocytes from HIV+/ART subject (smoker) CHI0018, Day 84 (Wk 12)


title: Monocytes from HIV+/ART subject (smoker) CHI0003, Day 196 (Wk 28)


title: KO+PBS 24hr bio rep 1


title: Monocytes from HIV+/ART subject (smoker) CHI0018, Day 0


title: CTRL_MBC_D39

value: mRNA


title: Monocytes from HIV+/ART subject (smoker) CHI0003, Day 112 (Wk 16)


title: Monocytes from HIV+/ART subject (smoker) CHI0003, Day 84 (Wk 12)


title: Old_HSC_CD150H_RRBS_rep4

city: Boston

first: Wenhao

last: Zhang

state: MA

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

department: Genetics

institute: Harvard Medical School

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

source_name: Hematopoietic stem cells

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

value: Hematopoietic stem cells


title: WT 5wk bio rep3

value: WT

value: untreated


title: Old_HSC_CD150H_RRBS_rep3


title: KO 5wk bio rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0003, Day 0

value: peripheral blood


title: Old_HSC_CD150L_RRBS_rep4


title: WT 5wk bio rep2


title: Monocytes from HIV+/ART subject (smoker) CHI0182, Day 0


title: Blood_Recipient_young_HSCs_10M_TX_RRBS_rep4

source_name: whole blood

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

value: whole blood


title: Blood_Recipient_young_HSCs_10M_TX_RRBS_rep3


title: Old_HSC_CD150L_RRBS_rep3


title: Blood_Recipient_young_HSCs_10M_TX_RRBS_rep2


title: KO+PBS 24hr bio rep 2


title: Monocytes from HIV+/ART subject (smoker) CHI0017, Day 84 (Wk 12)


title: 9674_cort

city: Cincinnati

first: Hyacinth

middle: Idu

last: Hyacinth

state: Ohi

address: 3230 Eden Avenue

department: Neurology

institute: University of Cincinnati

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

source_name: cort

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

value: No

value: cort

tag: disease state

value: AA

tag: stress exposure

value: RSD


title: Monocytes from HIV+/ART subject (smoker) CHI0018, Day 196 (Wk 28)

value: monocyte

value: placebo


title: Blood_Recipient_young_HSCs_10M_TX_RRBS_rep1


title: Monocytes from HIV+/ART subject (smoker) CHI0018, Day 112 (Wk 16)


title: Blood_Recipient_old_HSCs_10M_TX_RRBS_rep4


title: 9674_hip

source_name: hip

value: hip


title: Blood_Recipient_old_HSCs_10M_TX_RRBS_rep3


title: KO 5wk bio rep2


title: Blood_Recipient_old_HSCs_10M_TX_RRBS_rep2


title: 9636_cort

value: Ctrl


title: Blood_Recipient_old_HSCs_10M_TX_RRBS_rep1


title: Male_WT_Pooled

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: Library name: MAE3_S3

data_processing:
The single-cell transcriptomic data measured on the Illumina NextSeq 500 machine was pre-processed and analyzed following a standard workflow and using the Seurat software package (version 3.1.4) in R (3.6.1). All samples passed the quality filters and were retained for the subsequent data analysis steps; the processed data covers 3337 single cells in total. Outlier cells with unique feature counts over 2500 or less than 200 were filtered out. Moreover, cells with more than 5% mitochondrial gene counts were filtered out. For data normalization, a global-scaling normalization method that adjusts the feature expression measurements for each cell by applying a centered log ratio (CLR) transformation was employed.
Assembly: mm10
Supplementary files format and content: Processed data is provided in the .txt file format containing the normalized gene count matrix for each sample.
Library strategy: Drop-seq

growth_protocol: Tg2576 mice (B6;SJL-Tg(APPSWE)2576Kha) heterozygous transgenic mice of both genders, and wildtype littermate controls, were purchased from Taconics (9 per genotype/gender). Mice were housed in dedicated facilities under specific pathogen-free conditions for 1 week to acclimatize. Mice always had ad libitum access to standard mouse food (Ssnif, # V 1534-300) and water. All mouse experiments were performed according to the European FELASA guidelines for animal experimentation and had been approved by the local institutional Animal Experimentation Ethics Committee, and by the overseeing Luxembourg government agencies. Offspring was let age until 24 weeks.

extract_protocol:
Mice were euthanized in deep anesthesia (150 mg/kg ketamine, 1 mg/kg metedomidine, i.p.) and transcardially perfused with PBS. The mouse cortex was dissected manually, following by its dissociation using the Adult–Brain Dissociation Kit (Miltenyi Biotec) according to manufacturer's instructions. Cells were then resuspended in 0.5% BSA and Drop-seq analysis was applied to obtain single cell RNA-seq data.
The 3′ end enriched cDNA libraries were prepared by tagmentation reaction of 600 pg cDNA library using the standard Nextera XT tagmentation kit (Illumina). Reactions were performed according to the manufacturer's instructions. The PCR amplification cycling programme used was 95°C 30 s, and 12 cycles of 95°C (10 s), 55°C (30 s), and 72°C (30 s), followed by a final extension step of 72°C (5 min). Libraries were purified twice to reduce primers and short DNA fragments with 0.6×and 1×Agencourt AMPure XP beads (Beckman Coulter), respectively, in accordance with the manufacturer's protocol. Finally, purified libraries were eluted in 10 μl Molecular Grade Water. Quality and quantity of the tagmented cDNA library were evaluated using Bioanalyzer High Sensitivity DNA Chip. The average size of the tagmented libraries prior to sequencing was between 400 and 700 bps.
Purified Drop-seq cDNA libraries were sequenced using an Illumina NextSeq 500 machine with the recommended sequencing protocol, except for 6 pM of custom primer (GCCTGTCCGCGGAAGCAGTGGTATCAACG CAGAGTAC) applied for priming of read 1. Paired-end sequencing was performed for the read 1 of 20 bases (covering the random cell barcode 1–12 bases and the rest 13–20 bases of random unique molecular identifier (UMI) and for read 2 of 60 bases of the genes. Raw reads were further demultiplexed and processed using a dedicated Drop-seq computational pipeline.

value: Cortex

tag: Sex

value: Male


title: 9636_hip


title: Female_TG_Pooled

description: Library name: MAE2_S2

value: Female

value: TG


title: Female_WT_Pooled

description: Library name: MAE1_S1


title: 9644_cort


title: WT 5wk bio rep1

value: Cornea


title: 9644_hip


title: B16F10 tumors treated with Cisplatin and BVT948 (combination therapy)

city: Birmingham

first: Nestor

last: Prieto-Dominguez

state: AL

department: Microbiology

institute: The University of Alabama at Birmingham (UAB)

description:
Library name: Com
10x genomics

data_processing:
Bowtie Version 1.1.1 was used with parameter -e80 to align pair-end reads to GRCm38/mm10 reference. Each library was filtered to include only abundant barcodes (>500 counts)
Data normalization was carried out by eliminating putatively stressed or dying cells based on mitochondrila DNA content.
Assembly: GCRm38/mm10 was used as the reference genome sequence for read alignment
Supplementary files format and content: Processed data files include tab-separated values and matrix files. Replicates number correspond to each hashtag and were pooled together on the same .rar file.

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

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

extract_protocol:
Following tumor disaggregation, lysates were incubated with TotalSeq-B0301, B0302, B0303 and B0304 anti-mouse hashtag antibodies (Biolegend) and replicates were pooled. At least 50,000 CD45+ cells were sorted from each group into PBS using BD FACSAria II Cell Sorter.
Cells were loaded into the Chromium Single Cell Controller with Single Cell 3' Gel Beads and Partitioning Oil to generate Gel Bead-in-EMulsion (GEMs) droplets. Next, mRNA and cell-hashing antibody-derived tags (HTOs) were reverse transcribed, barcoded and amplified according to the manufacturer's recommendations. Amplified cDNA was size separated with SPRI beads (Beckman Coulter) into <300 nt fragments with HTOs and >300nt fragments with mRNA-templated cDNA. cDNA sequencing libraries were generated according to 10X Genomics guidelines. Purified HTOs were amplified to append P5 and P7 adapter sequences compatible with the Illumina Flow Cell using a common SI-PCR forward primer and pooled with the cDNA. Libraries were sequenced on an Illumina NextSeq 500 instrument

treatment_protocol: Tumors were treated with two rounds of cisplatin (5mg/kg, ip, once daily for 3 days), BVT948 (10mg/kg, ip, qd), or their combination. Vehicle-treated mice were treated with PBS (ip, qd). Cisplatin rounds were spaced 3 days apart.

value: Melanoma primary tumor

value: Melanoma murine cells

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups


title: B16F10 tumors treated with PBS

description:
Library name: Veh
10x genomics

value: PBS, ip, qd


title: d25 GV H3K36me3_rep3

city: Cambridge

first: Soumen

last: Khan

address: Babraham Hall

department: Epigenetics

country: United Kingdom

institute: Babraham Institute

data_processing:
Mapping of ChIP-seq data was performed with Bowtie v2.2.9 to the mouse GRCm38 genome assembly. Libraries were de-duplicated for analysis.
Assembly: GRCm38
Supplementary files format and content: Allvalid 2kb windows_RPKM_reps.txt
Supplementary files format and content: Histone enriched regions_repset_RPKM.txt

extract_protocol:
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications. Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice. MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer. Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA. Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours. Chromatin was added to the antibody-bound beads and rotated overnight at 4°C. This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours. DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.
Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2, as per the manufacturers recommendations.

tag: developmental stage

value: GV oocytes

value: wildtype


title: B16F10 tumors treated with BVT948

description:
Library name: BVT
10x genomics

value: BVT948, 10 mg/kg, ip, qd


title: d25 GV H3K36me3_rep1


title: 9631_hip

value: No

value: AA


title: C-3_NSN_scRNA-seq

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

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


title: D-30_NSN_scRNA-seq


title: C-8_NSN_scRNA-seq


title: 9631_cort

value: cort


title: 9633_cort


title: 5353_cort

value: SS


title: 5349_cort

value: Ctrl


title: D-15_Inter_scRNA-seq


title: C-7_NSN_scRNA-seq


title: B16F10 tumors treated with Cisplatin

description:
Library name: Cis
10x genomics

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


title: C-6_NSN_scRNA-seq


title: D-34_NSN_scRNA-seq


title: D-14_NSN_scRNA-seq


title: Male_TG_Pooled

description: Library name: MAE4_S4

source_name: Cortex

value: Cortex

value: Male


title: D-11_NSN_scRNA-seq


title: C-12_NSN_scRNA-seq


title: 5349_hip

value: hip


title: 9646_cort

value: RSD


title: D-12_SN_scRNA-seq


title: 9646_hip


title: C-13_SN_scRNA-seq


title: D-9_SN_scRNA-seq


title: d25 GV H3K36me3_rep2


title: C-9_SN_scRNA-seq


title: 9643_hip


title: C-18_SN_scRNA-seq


title: 9643_cort


title: D-13_SN_scRNA-seq


title: 5353_hip