title: Hippocampus, polyA-enriched RNA-Seq, 1044

description: Library name: 1044-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1043

status: Public on Jul 20 2026

type: SRA

city: Boston

first: Alexander

last: Knyshov

address: 72 E Concord St

department: Medicine

country: USA

institute: Boston University

description: Library name: 1043-plus

library_source: transcriptomic

data_processing:
Trimmomatic 0.39 was used to trim adaptors and low-quality reads
STAR 2.7.10b was used to align trimmed reads to the human reference genome (GRCh38)
RSEM 1.3.3 with Ensembl v108 annotation was used to calculate transcript-based gene expression
Circular RNAs were called using circexplorer3/CLEAR 1.0.1
Assembly: GRCh38
Supplementary files format and content: csv files include linear RNA TPM and circular RNA FPB values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: hippocampus

extract_protocol:
We used human brain samples with the age range of 54-110 years old. Frozen hippocampal tissues were collected from a coronal section of the caudal hippocampus at the level of the lateral geniculate nucleus at the Boston University Alzheimer’s disease Research Center (BU-ADRC). After RNA extraction, RNA was purified using RNeasy Mini Kits (Qiagen), and the RNA integrity number was calculated using an RNA 6000 Pico assay on a Bioanalyzer 2100 (Agilent Technologies).
Total RNA Seq Library Prep:  Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA is depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.  Samples are then fragmented using heat and magnesium.  1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated and the library is amplified.  Strands marked with dUTPs are not amplified, allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing. All libraries were prepared in a strand-specific manner. RNA Seq Library Prep for PolyA+ and PolyA- sequencing: Using the Kapa RNA HyperPrep Kit with RiboErase, rRNA is depleted starting from 500ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA. Following rRNA depletion, mRNA is selected by oligo-dT beads using the KAPA mRNA HyperPrep kit. After the first and second capture, the PolyA minus fraction is kept. After the PolyA captures, the minus fractions are concentrated using the Zymo RNA Clean and Concentrator Kit. Both the PolyA plus and minus fractions are fragmented using heat and magnesium. Following first-strand synthesis with random primers, second-strand synthesis, and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the Agilent Tapestation.

tag: tissue

value: hippocampus

tag: rqn

tag: age

tag: Sex

value: Male

tag: ad status

value: AD

tag: batch


title: Hippocampus, polyA-enriched RNA-Seq, 1040

description: Library name: 1040-plus

value: Control


title: Hippocampus, polyA-enriched RNA-Seq, 1039

description: Library name: 1039-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1037

description: Library name: 1037-plus

value: Female


title: Hippocampus, polyA-enriched RNA-Seq, 1035

description: Library name: 1035-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1038

description: Library name: 1038-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1034

description: Library name: 1034-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1032

description: Library name: 1032-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1033

description: Library name: 1033-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1031

description: Library name: 1031-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1030

description: Library name: 1030-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1027

description: Library name: 1027-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1028

description: Library name: 1028-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1029

description: Library name: 1029-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1024

description: Library name: 1024-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1025

description: Library name: 1025-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1022

description: Library name: 1022-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1021

description: Library name: 1021-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1019

description: Library name: 1019-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1017

description: Library name: 1017-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1020

description: Library name: 1020-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1015

description: Library name: 1015-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1016

description: Library name: 1016-plus


title: Heart_low_salt_2

status: Public on Jul 21 2026

city: New York

first: Evan

middle: C

last: Palmer-Young

state: NY

address: 525 E 68th St

institute: Cornell University

description: Library name: R4

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
We used the PreProcSEQ  pipeline to prepare raw sequencing files for further  analysis. Library read quality was visualized using MultiQC .  Reads were trimmed using Trimmomatic to remove Illumina adapter sequences and the first and last 3 bp of each read. Reads less than 36 bp in length or with average per-base quality scores below 15 were excluded. Reads were mapped to transcripts of the NCBI reference genome for Rattus norvegicus (GCF_036323735.1 (Refseq)) using Salmon  followed by construction of the gene expression matrix with tximeta.
Assembly: GCF_036323735.1
Supplementary files format and content: Read count matrix with one row per gene locus and one column per sample . Separate files for heart and kidney for low salt experiment; and for aldosterone-treated kidneys.

molecule: total RNA

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Papilla dissected from one kidney or piece of ventricle removed from heart. Tissue incubated overnight at 4 oC[EP12.1] in RNAlater (Invitrogen AM7020). Tissue was transferred to lysis buffer, stored at -70 oC, lysed with two freeze-thaw cycles and disrupted manually with forceps. Samples were centrifuged (12.1 rcf, 2 min) and the supernatant passed through an 18-gauge needle.   Total RNA was isolated using a PureLink RNA Mini kit (Invitrogen #12183018A).   For RNAseq the samples were treated with DNase I.
RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA). Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina NovaSeq X plus sequencer with single-end 50 cycles.

treatment_protocol: Female Sprague-Dawley rats (120-200 g) were maintained on synthetic diets (Harlan Teklad) containing control Na (Na content 0.4%) or low Na (Na content 0.01 – 0.02%) for 7 d.  Some animals on control-Na diet were implanted with osmotic minipumps (Alzet model 2002) infusing aldosterone at a rate of 12 ug/day.

value: Heart

tag: treatment

value: L


title: GPR34, TREM2KO, Myelin, rep 3

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Library name: HSA-000028221
GPR34/TREM2 KO, Myelin

data_processing:
Raw data (FASTQ files) were processed using nf-core/rnaseq v3.11.2 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020) with GRCh38 genome sequences and gene annotations from Gencode version 42. To deduplicate unique molecular identifiers, the following umitools_bc_pattern was used: ^(?P.{6})(?P.{4}).*
To account for the fact that the QuantSeq 3' mRNA-Seq library protocol only captures a 3' tag from each transcript, the following custom argument was included in the nf-core/rnaseq workflow: extra_star_align_args: --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA.
The following custom arguments were passed to the salmon quantitation step of the workflow: extra_salmon_quant_args: --noLengthCorrection The nf-core/rnaseq workflow produces a SummarizedExperiment R object that is serialized to disk.
To generate the processed data file, this object was read into an R session, library sizes were estimated with the edgeR::normLibSizes function (version 4.4.2) using the TMM method and counts per million were returned with the edgeR::cpm function.
Assembly: GRCh38
Supplementary files format and content: Excel (XLSX) file with three worksheets: sample annotations, raw count matrix, normalized count matrix (CPM)

source_name: iPSC-derived microglia

growth_protocol: iPSC-derived microglia (iMG) were differentiated from a human, female iPSC line (Thermo Fisher Scientific, A18945, hereafter referred to as iPSC line 1) using a previously published and validated protocol66. iPSCs were maintained on matrigel-coated plates (Corning, CB356238) according to the manufacturer’s specifications in mTeSR-plus (STEMCELL Technologies, 100-0276). Culture medium was replenished every day with fresh medium. Cells were passaged every 5–7 days using Gentle cell dissociation (STEMCELL Technologies, 100-0485) or ReLeSR (STEMCELL Technologies, 100-0484) according to the manufacturer’s specifications. For all in vitro experiments, iPSCs were cultured in 5% O2, 5% CO2 at 37°C. At ~80% confluence hematopoietic differentiation was started. On Day 4 cells were sorted for marker CD235a and replated on matrigel coated plates into Hematopoietic Kit Medium B (STEMCELL Technologies, 05310) containing 10µM ROCK inhibitor (ATCC, Y27632) at 500,000 cells per well of a 6-well plate. From this point onward all steps from STEMCELL Technologies protocol were followed to generate highly pure HPCs.  Collected HPCs were confirmed to be >90% positive for marker CD43, seeded directly onto astrocyte feeder layers to generate iMG, and thereafter maintained in IMDM (Thermo Fisher Scientific, 31980030) supplemented with 10% FBS, 1X Penicillin/Strepyomycin, 20ng/mL hIL3 (Peprotech), 20ng/mL hGMCSF (Peprotech), and 20ng/mL hM-CSF (Peprotech).

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, 74034), and RNA quality was assessed using the TapeStation High Sensitivity RNA ScreenTape (Agilent, 5067-5579)
Library preparation was conducted in a 96-well PCR plate using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, A01173), incorporating the UMI second-strand synthesis module to identify and remove PCR duplicates, following the manufacturer’s protocol. Briefly, total RNA was used as input for oligo-dT priming during reverse transcription, followed by RNA removal. Unique Molecular Identifiers (UMIs) were introduced during second-strand synthesis, and cDNA was purified using magnetic beads, followed by 15 cycles of PCR with dual indexes and PCR purification with 0.8x magnetic beads. Library quantity and quality were assessed using TapeStation High Sensitivity D1000 ScreenTape (Agilent, 5067-5584). Libraries were pooled in equimolar ratios, and the sequencing pool underwent an additional 0.8x magnetic bead purification to remove residual adapter contamination. Sequencing was performed on an Illumina NextSeq 550 System High-Output Kit (SE, 75 bp, dual indexes) with a 5% PhiX spike-in by SeqMatic (Fremont, CA, USA).

treatment_protocol: gRNA sequences targeting AAVS1, GPR34, or TREM2 were identified using the IDT CRISPR-Cas9 guide RNA design checker, ordered from IDT, and re-suspended in TE buffer at 100uM. Guides were complexed with Alt-R Sp Cas9 (IDT, 1081059) and subsequent RNP was delivered into iMG by nucleofection using Lonza’s P3 Primary Cell 4D-Nucleofector X Kit (V4SP3960). iMG were maintained for 24-h in Deepwell Protein LoBind plates (Eppendorf, 951032107) and thereafter collected and centrifuged to remove dead cells. Cells were plated in relevant assay plates and maintained for 9 days with half medium changes every 2 days. WT, GPR34 KO, TREM2 KO, and GPR34/TREM2 KO induced microglia (iMG) cultured in microglia maintenance media were treated with either PBS or myelin (25 µg/mL) for 48 hours. For each sample, RNA was extracted from a pool of two replicate wells, each seeded with 25,000–30,000 cells.

value: female

tag: cell type

value: iPSC-derived microglia

tag: genotype

value: GPR34+TREM2 KO

value: Myelin

tag: replicate


title: GPR34, TREM2KO, PBS, rep 3

description:
Library name: HSA-000028220
GPR34/TREM2 KO, PBS

value: PBS


title: WT, PBS, rep 4

description:
Library name: HSA-000028223
WT, PBS

value: WT


title: Hippocampus, polyA-enriched RNA-Seq, 1013

description: Library name: 1013-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1012

description: Library name: 1012-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1011

description: Library name: 1011-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1008

description: Library name: 1008-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1009

description: Library name: 1009-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1004

description: Library name: 1004-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1006

description: Library name: 1006-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1000

description: Library name: 1000-plus


title: Hippocampus, total RNA-Seq, 1223

description: Library name: 1223


title: Hippocampus, polyA-enriched RNA-Seq, 1002

description: Library name: 1002-plus


title: Hippocampus, total RNA-Seq, 1221

description: Library name: 1221


title: Hippocampus, polyA-enriched RNA-Seq, 1001

description: Library name: 1001-plus


title: Hippocampus, total RNA-Seq, 1220

description: Library name: 1220


title: Hippocampus, total RNA-Seq, 1219

description: Library name: 1219


title: Hippocampus, total RNA-Seq, 1218

description: Library name: 1218


title: Hippocampus, total RNA-Seq, 1217

description: Library name: 1217


title: Hippocampus, polyA-enriched RNA-Seq, 1141

description: Library name: 1141-plus


title: Hippocampus, total RNA-Seq, 1216

description: Library name: 1216

value: Other


title: Hippocampus, total RNA-Seq, 1211

description: Library name: 1211


title: Hippocampus, total RNA-Seq, 1210

description: Library name: 1210


title: Hippocampus, total RNA-Seq, 1209

description: Library name: 1209


title: Hippocampus, total RNA-Seq, 1207

description: Library name: 1207


title: Hippocampus, total RNA-Seq, 1205

description: Library name: 1205


title: Hippocampus, total RNA-Seq, 1204

description: Library name: 1204


title: AB12144

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample9

library_source: transcriptomic single cell

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the human reference genome (GRCh38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies. Differential expression analysis was conducted using the Seurat package in R, which included scaling, principal component analysis, and clustering to identify cell populations and marker genes.
Assembly: refdata-cellranger-GRCh38-1.2.0
Supplementary files format and content: SPID_metadata_annotated.txt

source_name: CSF

extract_protocol:
Human CSF samples were obtained from 14 patients diagnosed with MS, and from 2 CSF inflammatory and 2 peripheral inflammatory donors at Rabin Medical Center hospital, Israel. CSF samples were collected via lumbar puncture by trained medical personnel and were processed within 2-4 hours from collection. CSF samples were diluted with sterile PBS and centrifuged at 350 x g for 5 minutes at 4°C to pellet cells. The supernatant was washed, counted, and used immediately for FACS staining. Sorting gate was immune cells CD45+.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

value: CSF

tag: diagnosis

value: Active PPMS

tag: patient

tag: category

value: MS


title: GPR34KO, Myelin, rep 3

description:
Library name: HSA-000028215
GPR34 KO, Myelin

value: GPR34 KO


title: Planktonic farnesol treated - rep 1

city: Merced

first: Clarissa

last: Nobile

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

data_processing:
Base calling and fastq files were generated using Real-time analyis (RTA) and bcl2fastq softwares respectivley
Raw counts for genes were obtained using the Lexogen Bluebee pipeline (the steps of the pipeline are described below)
Read trimming was performed using bbduk v35.92 with parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=r, trimq=10, minlength=20
Raw and trimmed read quality was assessed using FastQC v0.11.5
Trimmed reads were aligned to reference genome for C. albicans SC5314 (Assembly version A21) using STAR v2.5.2a using parameters:  --outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
Gene counts were obtained using HTSeq-count v0.6.0 with parameters: -m intersection-nonempty -s yes -f bam -r pos
Raw gene counts were normalized and processed using DESeq2 v1.34.0 with log2 folgchange estimation using apeglm (v1.16.0) and p-value corrected for multiple testing using IHW (v1.22.0)
Genome_build: C_albicans_SC5314_A21
Supplementary_files_format_and_content: Raw gene counts text file

organism: Candida albicans

source_name: Fungal cells

growth_protocol: Biofilms were grown in triplicate on the bottoms of sterile flat-bottomed 12-well non-tissue culture treated polystyrene plates. After the initial 90 min adherence period, the wells were gently washed with PBS and fresh RPMI medium with or without 50 mM farnesol was added to each well. The plates were grown at 37 °C with shaking at 250 rpm in an ELMI shaker for 24 h, after which the OD600 of biofilm biomass formed measured. To induce hyphal formation, stationary phase yeast form cells of C. albicans strains were diluted 1:10 in fresh RPMI liquid medium and incubated at 37°C for 4 h with shaking in the presence or absence of farnesol at 30 mM. All experiments were performed three times.

extract_protocol:
RNA was extracted using RiboPure RNA purification according to manufacturuer`s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was farnesol treated for 24 hours for biofilms and another replicate farnesol treated for 4 hours.

tag: strain

value: 40 mM Farnesol for 4 h


title: Hippocampus, total RNA-Seq, 1195

description: Library name: 1195

value: hippocampus

value: Male


title: Hippocampus, total RNA-Seq, 1186

description: Library name: 1186

value: Female

value: AD


title: Hippocampus, total RNA-Seq, 1183

description: Library name: 1183


title: Hippocampus, total RNA-Seq, 1179

description: Library name: 1179


title: Planktonic farnesol treated - rep 2


title: Hippocampus, total RNA-Seq, 1176

description: Library name: 1176


title: Hippocampus, total RNA-Seq, 1174

description: Library name: 1174


title: Hippocampus, total RNA-Seq, 1171

description: Library name: 1171


title: Hippocampus, total RNA-Seq, 1166

description: Library name: 1166


title: Hippocampus, total RNA-Seq, 1172

description: Library name: 1172


title: Hippocampus, total RNA-Seq, 1168

description: Library name: 1168


title: Hippocampus, total RNA-Seq, 1165

description: Library name: 1165

value: Control


title: Hippocampus, total RNA-Seq, 1152

description: Library name: 1152


title: Hippocampus, total RNA-Seq, 1156

description: Library name: 1156


title: Hippocampus, total RNA-Seq, 1149

description: Library name: 1149


title: Hippocampus, total RNA-Seq, 1150

description: Library name: 1150


title: Hippocampus, total RNA-Seq, 1147

description: Library name: 1147


title: Hippocampus, total RNA-Seq, 1145

description: Library name: 1145


title: Hippocampus, total RNA-Seq, 1140

description: Library name: 1140


title: Hippocampus, total RNA-Seq, 1139

description: Library name: 1139


title: Hippocampus, total RNA-Seq, 1136

description: Library name: 1136


title: Hippocampus, total RNA-Seq, 1141

description: Library name: 1141


title: Hippocampus, total RNA-Seq, 1130

description: Library name: 1130


title: Hippocampus, total RNA-Seq, 1129

description: Library name: 1129


title: Hippocampus, total RNA-Seq, 1127

description: Library name: 1127


title: Hippocampus, total RNA-Seq, 1128

description: Library name: 1128


title: Hippocampus, total RNA-Seq, 1215

description: Library name: 1215


title: Hippocampus, total RNA-Seq, 1122

description: Library name: 1122


title: Hippocampus, total RNA-Seq, 1121

description: Library name: 1121


title: Hippocampus, total RNA-Seq, 1118

description: Library name: 1118


title: Hippocampus, total RNA-Seq, 1116

description: Library name: 1116


title: Hippocampus, total RNA-Seq, 1114

description: Library name: 1114


title: Hippocampus, total RNA-Seq, 1113

description: Library name: 1113


title: Hippocampus, total RNA-Seq, 1109

description: Library name: 1109


title: Hippocampus, total RNA-Seq, 1112

description: Library name: 1112


title: Hippocampus, total RNA-Seq, 1124

description: Library name: 1124


title: Hippocampus, total RNA-Seq, 1108

description: Library name: 1108


title: Hippocampus, total RNA-Seq, 1107

description: Library name: 1107


title: Hippocampus, total RNA-Seq, 1105

description: Library name: 1105


title: Hippocampus, total RNA-Seq, 1103

description: Library name: 1103


title: Hippocampus, total RNA-Seq, 1102

description: Library name: 1102


title: Hippocampus, total RNA-Seq, 1098

description: Library name: 1098


title: Hippocampus, total RNA-Seq, 1095

description: Library name: 1095


title: Hippocampus, total RNA-Seq, 1094

description: Library name: 1094


title: Hippocampus, total RNA-Seq, 1091

description: Library name: 1091


title: Hippocampus, total RNA-Seq, 1093

description: Library name: 1093


title: Hippocampus, total RNA-Seq, 1090

description: Library name: 1090


title: Hippocampus, total RNA-Seq, 1087

description: Library name: 1087


title: Hippocampus, total RNA-Seq, 1086

description: Library name: 1086


title: Hippocampus, total RNA-Seq, 1085

description: Library name: 1085


title: Hippocampus, total RNA-Seq, 1084

description: Library name: 1084


title: Hippocampus, total RNA-Seq, 1082

description: Library name: 1082


title: Hippocampus, total RNA-Seq, 1081

description: Library name: 1081


title: Hippocampus, total RNA-Seq, 1080

description: Library name: 1080


title: Hippocampus, total RNA-Seq, 1079

description: Library name: 1079


title: Hippocampus, total RNA-Seq, 1077

description: Library name: 1077


title: Hippocampus, total RNA-Seq, 1075

description: Library name: 1075


title: Hippocampus, total RNA-Seq, 1074

description: Library name: 1074


title: Hippocampus, total RNA-Seq, 1073

description: Library name: 1073


title: Hippocampus, total RNA-Seq, 1072

description: Library name: 1072


title: Hippocampus, total RNA-Seq, 1071

description: Library name: 1071


title: Hippocampus, total RNA-Seq, 1070

description: Library name: 1070


title: Hippocampus, total RNA-Seq, 1069

description: Library name: 1069


title: Hippocampus, total RNA-Seq, 1068

description: Library name: 1068


title: Hippocampus, total RNA-Seq, 1067

description: Library name: 1067


title: Hippocampus, total RNA-Seq, 1066

description: Library name: 1066


title: Hippocampus, total RNA-Seq, 1065

description: Library name: 1065


title: Hippocampus, total RNA-Seq, 1064

description: Library name: 1064


title: Hippocampus, total RNA-Seq, 1063

description: Library name: 1063


title: Hippocampus, total RNA-Seq, 1059

description: Library name: 1059


title: Hippocampus, total RNA-Seq, 1061

description: Library name: 1061


title: Hippocampus, total RNA-Seq, 1060

description: Library name: 1060


title: Hippocampus, polyA-enriched RNA-Seq, 1026

description: Library name: 1026-plus


title: Hippocampus, total RNA-Seq, 1058

description: Library name: 1058


title: Hippocampus, total RNA-Seq, 1057

description: Library name: 1057


title: Hippocampus, total RNA-Seq, 1056

description: Library name: 1056


title: Hippocampus, total RNA-Seq, 1054

description: Library name: 1054


title: Hippocampus, total RNA-Seq, 1052

description: Library name: 1052


title: Hippocampus, total RNA-Seq, 1050

description: Library name: 1050


title: Hippocampus, total RNA-Seq, 1051

description: Library name: 1051


title: Hippocampus, total RNA-Seq, 1049

description: Library name: 1049


title: Hippocampus, total RNA-Seq, 1048

description: Library name: 1048


title: Hippocampus, total RNA-Seq, 1047

description: Library name: 1047


title: Hippocampus, total RNA-Seq, 1045

description: Library name: 1045


title: Hippocampus, total RNA-Seq, 1046

description: Library name: 1046


title: Hippocampus, total RNA-Seq, 1044

description: Library name: 1044


title: Hippocampus, total RNA-Seq, 1043

description: Library name: 1043


title: Hippocampus, total RNA-Seq, 1040

description: Library name: 1040


title: Hippocampus, total RNA-Seq, 1039

description: Library name: 1039


title: Hippocampus, total RNA-Seq, 1038

description: Library name: 1038


title: Liver non-parenchymal cells from Hep-ADKTg mouse

city: College Station

first: Chaodong

last: Wu

state: TX

address: 373 Olsen Blvd

department: Nutrition

institute: Texas A&M University

description: Library name: 12_Tg_C_S12

data_processing:
Cell Ranger Software Suite v6.1.2 was used for sample demultiplexing, FASTQ alignment, cell barcode processing and unique molecular identifier counting. Cell barcodes were identified automatically based on the distribution of UMI counts.
After Cell Ranger processing, 15,663 cells from the Hep-ADKWT sample and 17,462 cells from the Hep-ADKTg sample were retained. Ambient RNA contamination was removed using SoupX v1.5.2.
Filtered expression matrices were imported into R v4.1.0 and analyzed using Seurat v4.0.2. UMI counts were normalized using NormalizeData with a scale factor of 10,000 followed by log1p transformation, and the top 2,000 variable genes were identified using the vst method.
Expression values were scaled using ScaleData. Principal component analysis was performed using RunPCA, and UMAP was generated using the top 50 principal components. Harmony v0.1.0 was used to correct batch effects, and clustering was performed using the smart local moving algorithm implemented in Seurat FindClusters with a resolution of 0.1.
Assembly: Mus musculus GRCm38/mm10; verify the exact Cell Ranger reference package against the Cell Ranger web_summary.html before submission.
Supplementary files format and content: Filtered feature-barcode matrices in 10x Genomics Matrix Market format, including matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz for the Hep-ADKWT and Hep-ADKTg samples.

organism: Mus musculus

source_name: liver

growth_protocol: Male hepatocyte-specific ADK-overexpressing mice (Hep-ADKTg) and control Hep-ADKWT mice were maintained under 12-h light/12-h dark cycles with lights on at 06:00 and were fed a standard chow diet. Mice were used for sample collection at 5 months of age.

extract_protocol:
Liver non-parenchymal cells were isolated from 5-month-old male Hep-ADKTg and Hep-ADKWT mice using a collagenase digestion method and were prepared as single-cell suspensions for 10x Genomics library preparation.
Single-cell suspensions were processed using the 10x Genomics Chromium Controller with v3 chemistry. Single-cell libraries were sequenced on an Illumina NextSeq 500 platform at the Texas A&M Institute for Genome Sciences and Society Molecular Genomics Core.

treatment_protocol: Hep-ADKTg mice carried hepatocyte-specific overexpression of adenosine kinase driven by the albumin promoter. Hep-ADKWT mice served as genotype-matched controls. No additional pharmacological or dietary treatment was applied before sample collection.

value: liver

value: liver non-parenchymal cells

value: Hep-ADKTg

value: standard chow diet


title: Liver non-parenchymal cells from Hep-ADKWT mouse

description: Library name: 11_WT_C_S11

value: Hep-ADKWT


title: Hippocampus, total RNA-Seq, 1037

description: Library name: 1037


title: N2A_96hr_Rep3

city: Burlington

first: Princess

last: Rodriguez

state: Vermont

address: 89 Beaumont Avenue

department: Microbiology and Molecular Genetics

institute: University of Vermont

description:
Library name: T96.s6
Samples were actually sequenced with the Singular Genomics G4 sequencer

data_processing:
Raw sequencing data was processed using the nf-core/rnaseq pipeline v3.14.0 using the Nextflow workflow manager v23.04.2. Raw reads were assessed with FASTQC v0.12.1 and aligned to the mm39 reference genome using Salmon v1.10.1.
Differential gene expression analysis was performed using DESeq2 1.52.0.
Multiple hypothesis testing was controlled using the Benjamini–Hochberg false discovery rate (FDR), and genes were considered significantly differentially expressed (DEGs) if they meet both an adjusted p-value threshold (FDR < 0.05) and an absolute log2 fold change ≥ 1.
Assembly: mm39
Supplementary files format and content: merged tab-delimited files containing quantified raw counts for each sample

growth_protocol: N2A-A5 acceptor cells were cultured at 37°C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, 11965118) supplemented with 10% fetal bovine serum (FBS; Gibco 16000044), 1% Penicillin Streptomycin (Pen/Strep; Gibco 15140122), 1% Sodium Pyruvate (Gibco, 11360070), and 10 µg/mL blasticidin (Thermo Fisher, R21001).

extract_protocol:
Total RNA was extracted from undifferentiated (0 hour) and differentiated (96 hours) N2A-A5 cells using the RNeasy Plus Micro Kit (Qiagen, 74034).
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and RNA integrity was assessed (RIN ≥ 7) with the Agilent Bioanalyzer. Ribosomal RNA was depleted and libraries were prepared using the Takara SMARTer Stranded Total RNA-Seq Kit v2 – Pico Mammalian. Libraries were sequenced on the Singular Genomics G4 platform to generate pair-end 150 bp reads to a target depth of ~50 million reads per sample.

treatment_protocol: N2A-A5 cells were differentiated for 96 hours by seeding in differentiation culture media without blasticidin, supplemented with 1% FBS and 10 µM retinoic acid (MedChem, HY14649)

tag: time

value: 96 hr

tag: cell line


title: Hippocampus, total RNA-Seq, 1035

description: Library name: 1035


title: N2A_96hr_Rep2

description:
Library name: T96.s5
Samples were actually sequenced with the Singular Genomics G4 sequencer

value: differentiation culture media without blasticidin, supplemented with 1% FBS and 10 µM retinoic acid


title: Hippocampus, total RNA-Seq, 1034

description: Library name: 1034


title: N2A_96hr_Rep1

description:
Library name: T96.s4
Samples were actually sequenced with the Singular Genomics G4 sequencer


title: Hippocampus, total RNA-Seq, 1033

description: Library name: 1033


title: N2A_0hr_Rep3

description:
Library name: T0.s3
Samples were actually sequenced with the Singular Genomics G4 sequencer

value: 0 hr


title: Hippocampus, total RNA-Seq, 1032

description: Library name: 1032


title: Hippocampus, total RNA-Seq, 1031

description: Library name: 1031


title: N2A_0hr_Rep1

description:
Library name: T0.s1
Samples were actually sequenced with the Singular Genomics G4 sequencer


title: Hippocampus, total RNA-Seq, 1030

description: Library name: 1030


title: Hippocampus, total RNA-Seq, 1076

description: Library name: 1076


title: N2A_0hr_Rep2

description:
Library name: T0.s2
Samples were actually sequenced with the Singular Genomics G4 sequencer


title: Donor 12 RINSC 4 Gy

city: Kingston

first: Michael

last: Antosh

state: RI

address: 2 Lippitt Rd

institute: University of Rhode Island

description: Library name: Sample 120

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

source_name: Whole blood

growth_protocol: Sampled from donors under IRB protocol IRB-AAAS5693 at Columbia University.

extract_protocol:
Blood samples preserved in PAXgene RNA stabilization reagent were sent to Azenta, where total RNA was extracted followed by globin reduction.
QIAGEN Fast Select rRNA HMR and Globin Kit, plus NEGNext Ultra II RNA Library preparation kit.  Note: sequencer model number listed may be incorrect.

treatment_protocol: Each sample was irradiated with 42% photons and 58% neutrons, at either the RINSC source or the RARAF source.

value: Whole blood

tag: irradiation site

value: RINSC

tag: radiation dose_(gy)


title: Hippocampus, total RNA-Seq, 1029

description: Library name: 1029

tag: tissue

tag: rqn


title: Donor 12 RARAF 4 Gy

description: Library name: Sample 119

value: RARAF

tag: age

tag: Sex


title: Donor 12 RINSC 2 Gy

description: Library name: Sample 118


title: Hippocampus, total RNA-Seq, 1027

description: Library name: 1027

tag: ad status

tag: batch


title: Donor 12 RARAF 2 Gy

description: Library name: Sample 117


title: Hippocampus, total RNA-Seq, 1026

description: Library name: 1026


title: Hippocampus, total RNA-Seq, 1028

description: Library name: 1028


title: Hippocampus, total RNA-Seq, 1025

description: Library name: 1025


title: Donor 12 RINSC 1 Gy

description: Library name: Sample 116


title: Donor 12 RARAF 1 Gy

description: Library name: Sample 115


title: Hippocampus, total RNA-Seq, 1024

description: Library name: 1024


title: Donor 12 RARAF 0.5 Gy

description: Library name: Sample 113


title: Donor 12 RINSC 0 Gy

description: Library name: Sample 112


title: Donor 12 RINSC 0.5 Gy

description: Library name: Sample 114


title: Hippocampus, total RNA-Seq, 1021

description: Library name: 1021


title: Hippocampus, total RNA-Seq, 1022

description: Library name: 1022


title: Hippocampus, total RNA-Seq, 1019

description: Library name: 1019


title: Donor 12 RARAF 0 Gy

description: Library name: Sample 111


title: Hippocampus, total RNA-Seq, 1020

description: Library name: 1020


title: HiC GN, etv1_KD, FANS, IVE+day8, rep1

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

library_source: genomic

data_processing:
Hi-C reads were aligned to the mm10 reference genome with Bowtie2 and HiC-Pro. Uniquely mapped paired-end reads were assigned to MboI restriction fragments and valid pairs with a minimum genomic distance of 1Kb were filtered for PCR duplicates. Interaction matrices were normalized using Knight-Ruiz (KR) matrix balancing and observed divided by expected (o/e) transformation and visualized using hic files in Juicebox
Assembly: mm10
Supplementary files format and content: hic files

molecule: genomic DNA

source_name: cerebellum

extract_protocol:
The cerebellum from postnatal day 6 or 22 mice or cerebellar vermis from mice at day 1 to 28 after electroporation were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony). The genomic DNA was digested with MboI and re-ligated after the biotin fill-in reaction, followed by sonication. The fragmented DNA was then subjected to biotin-IP.
Hi-C libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 1 to 28 after electroporation.

value: cerebellum

tag: cell type

value: granule neurons

value: etv1 sgRNAs in dCas9-KRAB


title: Hippocampus, total RNA-Seq, 1016

description: Library name: 1016

value: hippocampus

value: Female


title: Donor 11 RARAF 4 Gy

description: Library name: Sample 109

value: Male


title: Donor 11 RINSC 2 Gy

description: Library name: Sample 108


title: Donor 11 RARAF 2 Gy

description: Library name: Sample 107


title: Whole Blood, ID14, D2, Vaccine, 6hour

type: protein

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

institute: NIH

hyb_protocol: Hybridization protocol done in accordance with SomaLogic standard operating procedures and best practices.

scan_protocol: The SomaScan Assay was performed on a Tecan Fluent 780 high throughput automation system according to manufacturer’s instructions. Assay data were normalized using SomaLogic’s standard procedure utilizing adaptive normalization by maximum likelihood (Candia, JPR, 2024 (PMID: 39473295)).

data_processing: Protein abundancy was quantified expressed as Relative Fluorescence Units (RFU) and log2 transformed for comparison analysis. Comparison of each timepoint to the baseline for each reaction separately, or comparisons of the groups with reactions to the vaccine to the no-reaction group at each timepoint were completed in R v4.4.2 using R packages lmerTest v3.1-3 and emmeans v1.10.7 to create a linear mixed effects model using the Satterthwaite approximation. Models were set up as an interaction of response and timepoint while blocking on individual group.  Adjusted p-values calculated using Bonferroni correction did not indicate changes with p<0.05 due to the small sample size and thus p-value was used instead of the adjusted p-value.

label: SOMAmer reagents

molecule: protein

source_name: peripheral blood serum

label_protocol: Label protocol done in accordance with SomaLogic standard operating procedures and best practices.

extract_protocol: Blood samples were collected before (baseline or time 0) the second vaccine dose or placebo injections, and 35 min, 2 h, 6 h and 24 h following injections.  For the vaccine booster, samples were obtained before, 35 min and 2 h after the dose. Blood samples were collected using serum separator tubes (BD Biosciences) for high throughput proteomic analysis using the SomaScan platform (SomaLogic).

tag: individual

value: female

tag: treatment

value: Vaccine

tag: day

value: Day 2

tag: timepoint

value: 6 hour

tag: reaction type

value: ISRR

tag: reaction type severity

value: Severe


title: Hippocampus, total RNA-Seq, 1015

description: Library name: 1015

value: Control


title: Donor 11 RINSC 4 Gy

description: Library name: Sample 110


title: Hippocampus, total RNA-Seq, 1017

description: Library name: 1017

value: AD


title: Hippocampus, total RNA-Seq, 1013

description: Library name: 1013


title: Whole Blood, ID4, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0000310034

data_processing:
Bulk RNA-seq FASTQ files were processed using the OpenOmics/RNA-seek (https://doi.org/10.5281/zenodo.13312679) v1.9.5 pipeline to run QC and quantify gene transcript counts.
Assembly: GRCh38
Supplementary files format and content: RSEM counts

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes for 221 study samples using the QIAsymphony PAXgene Blood RNA Kit and the QIAsymphony SP instrument (both Qiagen) according to the manufacturer instructions including DNase I digestion and Proteinase K treatment.  RNA concentration was determined by Quant-iT RiboGreen assay (ThermoFisher) using a Biotek Synergy H1 plate reader (Agilent Technologies) and RINs assessed using Agilent 4200 TapeStation (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA using Universal Plus mRNA-seq Kit with NuQuant Human Globin AnyDeplete kit (Tecan Genomics) on a Biomek Fx robot (Beckman). First, messenger RNA transcripts were captured, fragmented, and converted to complementary DNA. Following second-strand synthesis and end repair, DNA fragments were ligated with dual-indexed adapters compatible with the Illumina platform. Libraries were subjected to strand selection and removal of globin transcripts, followed by 14 cycles of amplification. Purified libraries were analyzed with the Biotek Synergy H1 plate reader and Agilent 4200 TapeStation (Agilent Technologies) to assess concentration and size distribution, respectively, then normalized and pooled for sequencing. Final molarity of the pool was determined by quantitative polymerase chain reaction using the KAPA library quantification kit (Roche). Paired-end sequencing was performed on the NextSeq 2000 (Illumina) using P3 300 cycles kits in 2 × 150-base pair (bp) format.

value: Whole Blood

value: Vaccine/Placebo

tag: time

value: Day 1/Day 2

value: 24 hour/Baseline

value: Allergic/ISRR

tag: reaction type_severity

value: None/Moderate


title: Hippocampus, total RNA-Seq, 1012

description: Library name: 1012

value: hippocampus


title: Donor 11 RINSC 1 Gy

description: Library name: Sample 106

value: Whole blood

tag: irradiation site

value: RINSC


title: Donor 11 RARAF 1 Gy

description: Library name: Sample 105

value: RARAF

tag: radiation dose_(gy)

value: Male


title: Hippocampus, total RNA-Seq, 1009

description: Library name: 1009

tag: tissue


title: Hippocampus, total RNA-Seq, 1011

description: Library name: 1011

tag: rqn

value: Female


title: Donor 11 RINSC 0.5 Gy

description: Library name: Sample 104

tag: age


title: Whole Blood, ID4, D2, Placebo, 2hour

description: Library name: VA0000330034

tag: Sex

value: female

value: Placebo

value: Day 2

value: 2 hour

value: Moderate


title: Donor 11 RARAF 0.5 Gy

description: Library name: Sample 103


title: Hippocampus, total RNA-Seq, 1008

description: Library name: 1008

tag: ad status


title: Donor 11 RINSC 0 Gy

description: Library name: Sample 102


title: Hippocampus, total RNA-Seq, 1006

description: Library name: 1006

tag: batch


title: Donor 11 RARAF 0 Gy

description: Library name: Sample 101


title: Donor 10 RINSC 4 Gy

description: Library name: Sample 100


title: Donor 10 RARAF 4 Gy

description: Library name: Sample 99


title: Hippocampus, total RNA-Seq, 1002

description: Library name: 1002

value: AD


title: Donor 10 RINSC 2 Gy

description: Library name: Sample 98


title: Hippocampus, total RNA-Seq, 1001

description: Library name: 1001


title: Hippocampus, total RNA-Seq, 1000

description: Library name: 1000


title: Hippocampus, total RNA-Seq, 1142

description: Library name: 1142


title: HiC GN, brd4_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_brd4_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: cerebellum

tag: cell type

value: granule neurons

tag: genotype

value: brd4 sgRNAs in dCas9-KRAB


title: Hippocampus, total RNA-Seq, 1004

description: Library name: 1004


title: Whole Blood, ID14, D1, Placebo, Baseline

tag: individual

tag: treatment

value: Day 1

value: Baseline


title: Hippocampus, total RNA-Seq, 1138

description: Library name: 1138

value: hippocampus


title: Donor 10 RARAF 2 Gy

description: Library name: Sample 97

value: Whole blood


title: Ecig_5_miRNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Sample 20

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: HG38
Supplementary files format and content: tab_delimited text files include Counts for each Sample
Supplementary files format and content: txt files include Counts for each Sample

growth_protocol: Human AC16 cardiomyocytes were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from AC16 cardiomyocytes using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries for RNA-seq w ere prepared using SMARTER mRNA-Seq Library Prep Kitfollow ing manufacturer's protocols.

treatment_protocol: AC16 cardiomyocytes were exposed to electronic cigarette aerosol or filtered air (control) using an air–liquid interface (ALI) system.

tag: cell line

value: e-cigarette aerosol


title: Hippocampus, total RNA-Seq, 1133

description: Library name: 1133

value: Control


title: Hippocampus, total RNA-Seq, 1132

description: Library name: 1132

value: Male


title: Ecig_4_miRNA

description: Library name: Sample 19


title: Donor 10 RARAF 1 Gy

description: Library name: Sample 95

value: RARAF

value: Female


title: Donor 10 RINSC 0.5 Gy

description: Library name: Sample 94

value: RINSC


title: Ecig_3_miRNA

description: Library name: Sample 18


title: Donor 10 RARAF 0.5 Gy

description: Library name: Sample 93


title: Ecig_2_miRNA

description: Library name: Sample 17


title: Donor 10 RINSC 1 Gy

description: Library name: Sample 96


title: Hippocampus, total RNA-Seq, 1126

description: Library name: 1126


title: Ecig_1_miRNA

description: Library name: Sample 16


title: Con_5 _miRNA

description: Library name: Sample 15

value: filtered air


title: Donor 10 RINSC 0 Gy

description: Library name: Sample 92


title: Donor 9 RINSC 4 Gy

description: Library name: Sample 90


title: Donor 10 RARAF 0 Gy

description: Library name: Sample 91


title: Con_4 _miRNA

description: Library name: Sample 14


title: Con_3 _miRNA

description: Library name: Sample 13


title: Hippocampus, total RNA-Seq, 1119

description: Library name: 1119


title: Donor 9 RARAF 4 Gy

description: Library name: Sample 89


title: Con_2 _miRNA

description: Library name: Sample 12


title: Donor 9 RINSC 2 Gy

description: Library name: Sample 88


title: Con_1_miRNA

description: Library name: Sample 11


title: Donor 9 RARAF 2 Gy

description: Library name: Sample 87


title: Hippocampus, total RNA-Seq, 1111

description: Library name: 1111


title: K562_PolIISer2p_KASCnT_Input_T1_plus_biotin_Rep2_(241125_WW_Hs_WW1277)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: K562_PolIISer2p_KASCnT_Input_T1_plus_biotin_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (+biotin+T1 streptavidin beads )

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.17 "view" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag-direct for whole cells with CUTAC  V.4 dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v4
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: Cell Signaling Technology, 13499S


title: Ecig_5_mRNA

description: Library name: Sample 10


title: Ecig_4_mRNA

description: Library name: Sample 9


title: Donor 9 RINSC 1 Gy

description: Library name: Sample 86


title: Donor 9 RARAF 1 Gy

description: Library name: Sample 85


title: Ecig_3_mRNA

description: Library name: Sample 8


title: Ecig_2_mRNA

description: Library name: Sample 7


title: Donor 9 RINSC 0.5 Gy

description: Library name: Sample 84


title: Ecig_1_mRNA

description: Library name: Sample 6


title: Donor 9 RARAF 0.5 Gy

description: Library name: Sample 83


title: Con_5_mRNA

description: Library name: Sample 5


title: Donor 9 RINSC 0 Gy

description: Library name: Sample 82


title: Donor 9 RARAF 0 Gy

description: Library name: Sample 81


title: Whole Blood, ID10, D1, Placebo, 35min

value: male

value: Placebo

tag: day

tag: timepoint

value: 35 min

tag: reaction type

value: ISRR

tag: reaction type severity

value: Mild


title: Con_3_mRNA

description: Library name: Sample 3


title: Con_4_mRNA

description: Library name: Sample 4


title: Donor 8 RARAF 4 Gy

description: Library name: Sample 79

tag: irradiation site

tag: radiation dose_(gy)


title: Con_2_mRNA

description: Library name: Sample 2


title: Donor 8 RINSC 4 Gy

description: Library name: Sample 80

tag: tissue


title: Donor 8 RINSC 2 Gy

description: Library name: Sample 78

tag: age


title: Hippocampus, total RNA-Seq, 1097

description: Library name: 1097

tag: rqn

tag: Sex


title: Donor 8 RARAF 2 Gy

description: Library name: Sample 77


title: Donor 8 RARAF 1 Gy

description: Library name: Sample 75


title: Donor 8 RINSC 1 Gy

description: Library name: Sample 76


title: Liver, Pc day 20, biol rep 5

first: Alexis

last: Kaushansky

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children’s Research Institute

description: Library name: sample 10

data_processing:
Data QC, alignment, and peak calling were conducted using the PEPATAC pipeline.
Assembly: mm10
Supplementary files format and content: narrowPeak files (one per sample) generated from peak caller MACS2 during the PEPATAC pipeline.

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver tissue and transposition conducted according to the protocol developed by Corces et al. 2017 Nat Methods.
Library preparation was performed as described by Buenrostro et al. 2015 Curr Protoc Mol Biol. and sequenced by Psomagen using the Illumina NovaSeq 6000 platform for 151-bp paired-end reads

value: Liver

tag: strain

tag: disease state

value: Pc blood-stage

tag: time

value: 20 dpi


title: Liver, Pc day 20, biol rep 4

description: Library name: sample 9


title: Donor 8 RINSC 0.5 Gy

description: Library name: Sample 74

value: Whole blood


title: Con_1_mRNA

description: Library name: Sample 1


title: Donor 8 RARAF 0.5 Gy

description: Library name: Sample 73


title: Liver, Pc day 20, biol rep 3

description: Library name: sample 8


title: Donor 8 RINSC 0 Gy

description: Library name: Sample 72


title: mature DCs, 96h, PFOS , rep3

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: PFOS72_3

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42)human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 38)
Supplementary files format and content: Text file including the normalized counts for each sample.

growth_protocol: THP-1 human monocytic cells were maintained in 100-mm tissue culture dishes in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 µM 2-mercaptoethanol, and 10% heat-inactivated fetal bovine serum (FBS), hereafter referred to as cell culture medium. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ and maintained according to the ATCC recommendations (TIB-202), being passaged twice weekly and reseeded at a density of 2–4×10⁵ viable cells/mL to maintain exponential growth. For differentiation, THP-1 cells were seeded at a density of 1x10^5 cells/mL in T-35 tissue culture flasks and cultured for five days in cell culture medium supplemented with rhIL-4 (1500 U/mL) and GM-CSF (1500 U/mL) to induce differentiation into immature dendritic cells (iDCs).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and total RNA was purified using RNeasy spin columns including on-column DNase digestion. RNA was eluted in RNase-free water and stored at −80 °C until use. RNA concentration and purity were assessed by measuring absorbance at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The A260/A280 and A260/A230 ratios were used to evaluate RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra RNA Library Preparation kit.

treatment_protocol: On day five of differentiation, iDCs were seeded at a density of 1×10⁶ cells/mL in 12-well plates containing complete treatment medium and exposed for 24 h to PFOA (10 µg/mL), PFOS (10 µg/mL), or vehicle control (0.1% DMSO, v/v). Following the initial 24-h exposure, a maturation cocktail consisting of rhIL-4 (3,000 IU/mL), rhGM-CSF (1,500 IU/mL), rhTNF-α (2,000 IU/mL), and ionomycin (200 ng/mL) was added to induce maturation into mature dendritic cells (mDCs). PFAS and control compounds remained present throughout the maturation period. Cells were harvested after 24 or 72 h of maturation, corresponding to total exposure times of 48 and 96 h, respectively.

value: 20 μM PFOS


title: mature DCs, 96h, PFOS , rep1

description: Library name: PFOS72_1


title: Whole Blood, ID10, D2, Vaccine, 6hour

tag: individual

value: Vaccine

value: Day 2

value: 6 hour

tag: batch


title: Whole Blood, ID9, M5, Booster, 2hour

value: female

tag: treatment

value: Booster

value: Month 5

value: 2 hour


title: Liver, Pc day 20, biol rep 2

description: Library name: sample 7


title: Donor 7 RINSC 4 Gy

description: Library name: Sample 70

value: RINSC

value: Female


title: mature DCs, 96h, PFOA , rep2

description: Library name: PFOA72_2

tag: cell line

value: 24.4 μM PFOA


title: Liver, Pc day 20, biol rep 1

description: Library name: sample 6


title: mature DCs, 96h, PFOA , rep3

description: Library name: PFOA72_3


title: Donor 7 RARAF 4 Gy

description: Library name: Sample 69

value: RARAF


title: Donor 7 RINSC 2 Gy

description: Library name: Sample 68


title: Donor 7 RARAF 2 Gy

description: Library name: Sample 67


title: Liver, UI, biol rep 5

description: Library name: sample 5

value: Uninfected


title: Donor 7 RINSC 0.5 Gy

description: Library name: Sample 64


title: mature DCs, 96h, PFOA , rep1

description: Library name: PFOA72_1


title: Donor 7 RARAF 1 Gy

description: Library name: Sample 65


title: Donor 7 RINSC 1 Gy

description: Library name: Sample 66


title: mature DCs, 96h, control, rep3

description: Library name: Ctrl72_3

value: 0.1% DMSO


title: Liver, UI, biol rep 3

description: Library name: sample 3

value: Liver


title: Liver, UI, biol rep 4

description: Library name: sample 4


title: Donor 7 RARAF 0 Gy

description: Library name: Sample 61


title: Donor 7 RINSC 0 Gy

description: Library name: Sample 62


title: Liver, UI, biol rep 2

description: Library name: sample 2


title: Donor 6 RINSC 4 Gy

description: Library name: Sample 60


title: Donor 7 RARAF 0.5 Gy

description: Library name: Sample 63


title: mature DCs, 96h, control, rep2

description: Library name: Ctrl72_2


title: Donor 6 RARAF 4 Gy

description: Library name: Sample 59


title: mature DCs, 48h, PFOS , rep3

description: Library name: PFOS24_3

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42) human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 38)
Supplementary files format and content: Text file including the normalized counts for each sample.


title: Langerhans cells 4

city: East Lansing

first: Axel

middle: Dizan

last: Schmitter-Sanchez

state: MI

address: 775 Woodlot Dr

institute: Michigan State University

description: Library name: LC_4

data_processing:
Reads were aligned to the Ensembl Mouse GRCm39 genome using STAR Aligner. DESeq2 was used to normalize raw counts and determine the differential expression of chemokine receptor genes among the epithelial and Langerhans cell samples.
Assembly: Ensembl Mouse GRCm39
Supplementary files format and content: A tab-delimited text matrix containing raw read counts per gene for each sample.

source_name: Ear epidermis

extract_protocol:
Single cell suspension was collected from four huLangerin-CreER; Rosa-stop-tdTomato; Cx3cr1-GFP; K14-H2B-Cerulean mice during homeostasis. Ears were incubated epidermis side up in 2.5% Trypsin solution at 37°C for 90 min, and the epidermis was removed from the dermis. Single cell suspension was achieved by mincing, cutting, and running the sample through a 70 µm filter. LCs and epithelial cells were sorted using fluorescence-activated cell sorting (FACS) based on their red (LCs) and blue (epithelial cells) fluorescence.
Libraries were prepared using the KAPA mRNA HyperPrep Kit with dUTP-based strand specificity. Libraries were normalized to 10 nM, then loaded onto an Illumina NovaSeq flow cell. The sequencing was performed using 100 bp paired-end sequencing on an Illumina HiSeq NovaSeq.

value: Ear epidermis

tag: cell type

value: Langerhans cells

value: 8 weeks


title: mature DCs, 48h, PFOS , rep2

description: Library name: PFOS24_2

value: 20 μM PFOS


title: Donor 6 RINSC 1 Gy

description: Library name: Sample 56

value: Whole blood


title: Whole Blood, ID10, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: male

value: Placebo/Vaccine

tag: day

value: Day 1/Day 2

tag: timepoint

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/Mild


title: Donor 6 RARAF 2 Gy

description: Library name: Sample 57

value: Female


title: HiC GN, ctrl, FANS, IVE+day8, rep4

description: Library name: Hi-C_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_4

value: cerebellum

value: granule neurons

tag: genotype

value: ctrl sgRNAs in dCas9-KRAB


title: mature DCs, 48h, PFOS , rep1

description: Library name: PFOS24_1


title: Donor 6 RARAF 0.5 Gy

description: Library name: Sample 53

tag: irradiation site

value: RARAF


title: Langerhans cells 2

description: Library name: LC_2


title: mature DCs, 48h, PFOA , rep3

description: Library name: PFOA24_3

value: 24.4 μM PFOA


title: Donor 6 RARAF 0 Gy

description: Library name: Sample 51

tag: radiation dose_(gy)


title: Langerhans cells 3

description: Library name: LC_3

tag: tissue

value: Ear epidermis


title: Langerhans cells 1

description: Library name: LC_1

value: Langerhans cells

tag: age


title: Donor 5 RARAF 4 Gy

description: Library name: Sample 49

value: Male


title: Epithelial cells 4

description: Library name: KTC_4

value: Epithelial cells

value: 8 weeks


title: Donor 5 RINSC 2 Gy

description: Library name: Sample 48

value: Whole blood

value: RINSC


title: Donor 5 RARAF 1 Gy

description: Library name: Sample 45


title: Epithelial cells 2

description: Library name: KTC_2


title: mature DCs, 48h, control, rep3

description: Library name: Ctrl24_3

value: 0.1% DMSO


title: Donor 5 RINSC 0.5 Gy

description: Library name: Sample 44


title: Donor 5 RINSC 0 Gy

description: Library name: Sample 42


title: Donor 4 RINSC 4 Gy

description: Library name: Sample 40


title: immature DCs, 24h, GW7647, rep3

description: Library name: GW_3

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42)human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13 (release 42)
Supplementary files format and content: Text file including the normalized counts for each sample.

treatment_protocol: Cells were exposed for 24 h to 10 µg/mL PFOA or PFOS (corresponding to approximately 24.4 µM and 20.0 µM, respectively) or vehicle control (0.1% DMSO v/v). Following 24 h exposure, cells were collected for transcriptomic analysis.

value: 1 μM GW


title: Donor 4 RINSC 2 Gy

description: Library name: Sample 38


title: immature DCs, 24h, GW7647, rep2

description: Library name: GW_2


title: Donor 4 RARAF 2 Gy

description: Library name: Sample 37


title: Donor 4 RINSC 1 Gy

description: Library name: Sample 36


title: Donor 4 RARAF 1 Gy

description: Library name: Sample 35


title: Donor 4 RINSC 0.5 Gy

description: Library name: Sample 34


title: Donor 4 RARAF 0.5 Gy

description: Library name: Sample 33


title: Donor 5 RINSC 4 Gy

description: Library name: Sample 50


title: Donor 5 RARAF 2 Gy

description: Library name: Sample 47


title: CD103+ Lung DCs Before Cell Culture 5

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

description: Library name: B5

data_processing:
Differential Gene expression and data processing performed in R and Python using DESEQ2
Assembly: Mus musculus GRCm38
Supplementary files format and content: processed data is provided as a .csv file containing gene hit counts normalized via DESEQ2.

source_name: Lung

extract_protocol:
Total lung rna was extraced via qiagen RNAeasy columns following manufacturer's protocol.
Library and sequencing performed by Azenta

value: Lung

value: CD103+ DCs

value: Pre-Culture


title: Donor 5 RINSC 1 Gy

description: Library name: Sample 46


title: mature DCs, 48h, PFOA , rep1

description: Library name: PFOA24_1


title: Donor 5 RARAF 0 Gy

description: Library name: Sample 41


title: Donor 5 RARAF 0.5 Gy

description: Library name: Sample 43


title: CD103+ Lung DCs After 18h Cell Culture 4

description: Library name: A5

value: 18h Post-Culture


title: Donor 4 RINSC 0 Gy

description: Library name: Sample 32


title: immature DCs, 24h, dexamethasone , rep2

description: Library name: DEX_2

value: 150 μg/mL DEX


title: CD103+ Lung DCs Before Cell Culture 4

description: Library name: B4


title: Donor 4 RARAF 0 Gy

description: Library name: Sample 31


title: Donor 4 RARAF 4 Gy

description: Library name: Sample 39


title: Donor 3 RARAF 4 Gy

description: Library name: Sample 29


title: CD103+ Lung DCs Before Cell Culture 3

description: Library name: B3


title: Donor 3 RINSC 2 Gy

description: Library name: Sample 28


title: immature DCs, 24h, PFOS , rep3

description: Library name: PFOS_3

value: 20 μM PFOS


title: CD103+ Lung DCs Before Cell Culture 2

description: Library name: B2


title: Donor 3 RARAF 2 Gy

description: Library name: Sample 27

value: RARAF


title: Donor 3 RINSC 1 Gy

description: Library name: Sample 26


title: immature DCs, 24h, PFOS , rep2

description: Library name: PFOS_2


title: Donor 3 RARAF 1 Gy

description: Library name: Sample 25


title: immature DCs, 24h, GW7647, rep1

description: Library name: GW_1


title: Donor 3 RINSC 0.5 Gy

description: Library name: Sample 24


title: Donor 3 RARAF 0.5 Gy

description: Library name: Sample 23


title: Donor 3 RINSC 0 Gy

description: Library name: Sample 22


title: immature DCs, 24h, dexamethasone , rep3

description: Library name: DEX_3


title: Donor 3 RARAF 0 Gy

description: Library name: Sample 21


title: Donor 2 RINSC 4 Gy

description: Library name: Sample 20

value: Female


title: immature DCs, 24h, PFOA , rep2

description: Library name: PFOA_2

value: 24.4 μM PFOA


title: Control2_good

city: Hangzhou

last: Liu

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: Control2

data_processing:
Quality control；Reads mapping to the reference genome；Novel transcripts Prediction；Gene functional annotation；Quantification of gene expression levels；Differential expression analysis；GO enrichment analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes FPKM values for each Sample

source_name: brain

extract_protocol:
According to the instruction manual of the TRlzol Reagent, RNA was harvested. 1 μg RNA per sample was applied as input material for preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain


title: Donor 2 RARAF 4 Gy

description: Library name: Sample 19


title: immature DCs, 24h, PFOA , rep1

description: Library name: PFOA_1


title: Donor 2 RARAF 2 Gy

description: Library name: Sample 17


title: Control1_good

description: Library name: Control1


title: Donor 2 RINSC 1 Gy

description: Library name: Sample 16


title: immature DCs, 24h, dexamethasone , rep1

description: Library name: DEX_1


title: immature DCs, 24h, control, rep3

description: Library name: Ctrl_3


title: Donor 2 RARAF 1 Gy

description: Library name: Sample 15


title: mature DCs, 96h, PFOS , rep2

description: Library name: PFOS72_2


title: Donor 2 RINSC 0.5 Gy

description: Library name: Sample 14


title: Donor 2 RARAF 0.5 Gy

description: Library name: Sample 13


title: scRNA-seq mouse bone marrow WT normal control

city: Rye

first: Liming

last: H ou

address: 601 Midland Ave

institute: New York Blood Center

description: Library name: S10_WT_Lin_neg

data_processing:
Single cells were barcoded using the 10 Chromium single-cell platform, and cDNA libraries were prepared following the manufacturers instructions (Chromium Single Cell 3 Kits v3.1, 10 Genomics, USA). Bone marrow cells were harvested from 5-10 WT or Lxn-/- mice (either normal or AML mice). Stromal cells were sorted by cell surface marker CD45-, Lin-, Ter119-, and 7-AAD. Live cell counts were further determined using a hemocytometer. Libraries were sequenced on the NovaSeq 6000 (Illumina) platform (paired-end 150bp). The sequencing reads were aligned to the mouse reference genome (mm10) and quantified using CellRanger (v5.0.0, https://www.10xgenomics.com) with default parameters. The filtered count matrix, features, and barcodes of each sample from CellRanger were imported into Seurat (v4.3.0) to create Seurat objects. To accurately characterize the transcriptomic changes of bone marrow and stromal cells at single-cell level in Lxn-/- mice, the cells that meet the following criteria were removed: (1) with less than 1000 or more than 7500 detected features; (2) with mitochondrial transcripts that accounted for more than 10% of the total detected transcripts; (3) predicted to be doublets by Scrublet (v0.2.3). Moreover, the genes detected in less than three cells for each sample were also excluded in the following analysis. All 8 samples (HSPCs and stromal cells before transplantation, GFP+ Mll-Af9 cells and stromal cells after transplantation) were merged together to perform principal component analysis (PCA) and dimensionality reduction analysis. Different HSPC and stromal populations were annotated with known lineage-specific and stromal markers. Cell-cell communication differential analysis was performed with CellChat.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: Processed single-cell RNA-seq count matrix generated by 10x Genomics Cell Ranger pipeline. The .h5 file contains filtered gene-barcode matrices including gene expression counts for high-quality cells. The .tar archive contains the filtered feature-barcode matrix directory, including matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz.

source_name: Bone marrow

extract_protocol:
Bone marrow cells were harvested from 5-10 WT or Lxn-/- mice (either normal or AML mice). Stromal cells were sorted by cell surface marker CD45-, Lin-, Ter119-, and 7-AAD. The hematopoietic cells were Lin- in the normal condition, and GFP+ Lin- in AML condition.
Chromium Single Cell 3 Kits v3.1 (10 Genomics)

value: Bone marrow

value: WT normal Lin- cell control


title: Donor 2 RINSC 0 Gy

description: Library name: Sample 12


title: immature DCs, 24h, control, rep1

description: Library name: Ctrl_1


title: Donor 2 RARAF 0 Gy

description: Library name: Sample 11


title: Donor 1 RINSC 4 Gy

description: Library name: Sample 10


title: Normal liver Patient 4

city: London

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: 1151 Richmond St.

country: Canada

institute: University of Western Ontario

description:
Library name: NL_4
10X Visium v1 (fresh-frozen)

data_processing:
Fastq.gz files were generated and demultiplexed with 10x Genomics software SpaceRanger 1.3.0. Sequencing reads were aligned to the human genome Gencode39.
Samples were integrated per biological condition and clustered using Seurat v4. Region types were determined using cell2location deconvolution using existing single-cell liver atlases. See publication for details.
Assembly: GRCh39
Supplementary files format and content: SpaceRanger output files are provided for each sample. filtered_bc_matrix.h5 is an hdf5 file of the gene expression counts in each spot under the tissue. scalefactors_json is a json file linking the compressed image file to the spot coordinates in tissue_positions_list file. The hires_image ad lowres_image are whole slide fluorescent images showing CD68 protein.
Supplementary files format and content: For each group of samples (BA1, BA2, NL, NonBA), a metadata table (.csv) is provided with cluster IDs and region labels (Scar, Hepatocyte, Cholangiocyte) as well as cell2location scores for hepatocytes, stellate, and cholangiocytes) for each Visium spot that passed QC.
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue was surgically collected during transplant and biobanked (-80). Tissue was thawed then serially sectioned and slices with evident fibrosis were chosen.
Spatially-barcoded cDNAs were immediately brought to the DNA Services Core for amplification, strictly following the 10x Genomics Fresh Frozen Visium Spatial Gene Expression protocol (v1). The amplified cDNAs were enzymatically fragmented and converted into sequencing-ready, dual-indexed libraries through standard end-repair, A-tailing, adaptor ligation, and PCR. The final libraries were quantitated on Qubit (Life Technologies, Grand Island, NY) and the average size determined on the AATI Fragment Analyzer (Agilent Technologies, Santa Clara, CA). The libraries were pooled by calculated capture spot coverage via Loupe Browser and the pool diluted to 5nM concentration, then further quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA).  The final pool was sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) to a length of 28nt (read 1, contains the spot barcode and unique molecular identifier used for removing PCR duplicates), 10nt for each index (libraries contain unique dual indexes to prevent index switching) and 150nt for read 2 (the cDNA read) to a minimum depth of at least 50,000 cDNA reads per spot.

value: liver

value: Normal

value: not collected


title: Donor 1 RARAF 4 Gy

description: Library name: Sample 9

value: Whole blood


title: scRNA-seq mouse bone marrow KO normal control

description: Library name: S11_KO_Lin_neg

value: KO normal Lin- cell control


title: Donor 1 RINSC 2 Gy

description: Library name: Sample 8

value: RINSC


title: Donor 1 RARAF 2 Gy

description: Library name: Sample 7


title: scRNA-seq mouse bone marrow KO leukemia stroma

description: Library name: YL_11_KO_Stromal

value: KO leukemia stroma


title: Donor 1 RINSC 1 Gy

description: Library name: Sample 6


title: Donor 3 RINSC 4 Gy

description: Library name: Sample 30

value: Male


title: Normal liver Patient 2

description:
Library name: NL_2
10X Visium v1 (fresh-frozen)


title: Donor 1 RARAF 1 Gy

description: Library name: Sample 5


title: scRNA-seq mouse bone marrow WT leukemia stroma

description: Library name: YL_10_WT_Stromal

value: WT leukemia stroma


title: Normal liver Patient 3

description:
Library name: NL_3
10X Visium v1 (fresh-frozen)


title: CD103+ Lung DCs Before Cell Culture 1

description: Library name: B1

value: Lung

value: CD103+ DCs

value: Pre-Culture


title: Donor 1 RINSC 0.5 Gy

description: Library name: Sample 4

value: Female


title: immature DCs, 24h, PFOS , rep1

description: Library name: PFOS_1

value: 20 μM PFOS


title: Control4_good

description: Library name: Control4

value: brain


title: immature DCs, 24h, PFOA , rep3

description: Library name: PFOA_3

value: 24.4 μM PFOA


title: Donor 1 RARAF 0.5 Gy

description: Library name: Sample 3

value: RARAF


title: Normal liver Patient 1

description:
Library name: NL_1
10X Visium v1 (fresh-frozen)

value: liver


title: scRNA-seq mouse bone marrow MA9 GFP Lin- cells in KO recipients

description: Library name: YL_9_KO_Lin_neg_GFP

value: Bone marrow

value: MA9 GFP Lin- cells in KO recipients


title: Donor 1 RINSC 0 Gy

description: Library name: Sample 2

value: Whole blood


title: Control3_good

description: Library name: Control3


title: Non-BA cholestasis Patient 4

description:
Library name: NonBA_4
10X Visium v1 (fresh-frozen)

value: Alagille Syndrome

value: male


title: Donor 1 RARAF 0 Gy

description: Library name: Sample 1


title: VSL-34F Stool sRNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: VSL-34F

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings.
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix tables with the raw mature miRNA read counts for each sample

source_name: Stool

extract_protocol:
Stool samples were collected in a collection tube containing a nucleic acid stabilizing solution (Norgen Biotek) for subsequent nucleic acid isolation. The returned samples were stored at -80°C. RNA was extracted from 200 µL aliquots using the stool total RNA purification kit (Norgen Biotek Corp.) according to the manufacturer’s protocol. RNA quality and quantity were verified in accordance with the MIQE guidelines (http://miqe.gene-quantification.info/). RNA concentration was quantified using the Qubit microRNA assay kit (Invitrogen) on a Qubit fluorimeter (Invitrogen).
Small RNA-seq libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep for Illumina® (New England Biolabs, Inc.) kit used to convert small RNA transcripts into barcoded cDNA libraries. For each library, 200 ng of RNA were processed as starting material. Each library was prepared with a unique indexed primer. Multiplex adapter ligations, reverse transcription primer hybridization, reverse transcription reaction and PCR amplification were performed according to the manufacturer's protocol. After PCR amplification, the cDNA constructs were purified with the QIAQuick® PCR Purification Kit (QIAGEN), following the modifications suggested by the NEBNext® Multiplex Small RNA Library Prep for Illumina® protocol. Final libraries were loaded on the Bioanalyzer® 2100 (Agilent Technologies) using the DNA High Sensitivity Kit (Agilent Technologies) according to the manufacturer's protocol. Libraries were pooled together (34-plex) and further purified with a gel size selection. A final Bioanalyzer® 2100 run with the High Sensitivity DNA Kit (Agilent Technologies) allowed the assessment of DNA libraries quality regarding size, purity, and concentration. The obtained libraries were subjected to the Illumina sequencing pipeline on Illumina NextSeq500 sequencers (75 cycles, Illumina Inc., USA).

value: Stool

tag: campania region

value: VSL


title: scRNA-seq mouse bone marrow MA9 GFP Lin- cells in WT recipients

description: Library name: YL_8_WT_Lin_neg_GFP

value: MA9 GFP Lin- cells in WT recipients


title: Non-BA cholestasis Patient 3

description:
Library name: NonBA_3
10X Visium v1 (fresh-frozen)

tag: Sex


title: VSL-32F Stool sRNA-Seq

description: Library name: VSL-32F


title: VSL-31F Stool sRNA-Seq

description: Library name: VSL-31F


title: NK cell, Ehmt2-KO

first: Xinhua

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

description: Library name: H3K9me2-KO

data_processing:
The raw sequencing data were processed with fastp (v0.23.4) for quality control and adapter trimming. Cleaned reads were then aligned to the GRCm38/mm10 reference genome using Bowtie2. The resulting alignment files (BAM) were converted to coverage bedgraph files using bedtools (v2.18). Peak calling was performed with SEACR under a stringent threshold of FDR < 0.01, and the identified peaks were annotated using HOMER. Genome-wide CUT&Tag signal profiles were computed and visualized with DeepTools, while the Integrative Genomics Viewer (IGV) was used to inspect CUT&Tag signals at specific gene loci.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig format of normalized signal value
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
Nuclei were prepared according to the manufacturer's instructions of the Hyperactive Universal CUT&Tag Assay Kit (Vazyme).
The sequencing libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following the manufacturer’s instructions

value: Spleen

value: NK cell


title: VSL-30F Stool sRNA-Seq

description: Library name: VSL-30F


title: Non-BA cholestasis Patient 2

description:
Library name: NonBA_2
10X Visium v1 (fresh-frozen)

value: Progressive Familial Intrahepatic Cholestasis (PFIC)

value: female


title: Donor 2 RINSC 2 Gy

description: Library name: Sample 18

data_processing:
Alignment: HISAT2
Quality check: FastQC
Analysis: deseq2
Assembly: GRCh38 Reference Genome
Supplementary files format and content: normalized data,from deseq2 output (csv file)
Supplementary files format and content: read counts (csv file)

value: RINSC

value: Female


title: NK cell, Wild-type

description: Library name: H3K9me2-WT

value: Wild-type


title: VSL-29M Stool sRNA-Seq

description: Library name: VSL-29M


title: Non-BA cholestasis Patient 1

description:
Library name: NonBA_1
10X Visium v1 (fresh-frozen)


title: VSL-28F Stool sRNA-Seq

description: Library name: VSL-28F


title: NK cell, EHMT2-KO rep3

description:
Library name: KO-3
Count.Mouse.txt

data_processing:
Raw RNA-seq data were preprocessed using fastp (v0.23.4), an ultra-fast all-in-one FASTQ preprocessor, with default parameters to ensure high-quality reads. Processed reads were then aligned to the GRCm38/mm10 (for mouse) or GRCh38/hg38 (for human) reference genome using STAR (v2.7.11b), allowing a maximum of 2 mismatches per read alignment. Gene-level quantification was performed using HTSeq (v2.0.3) to generate raw read counts. Differentially expressed genes (DEGs) were identified using DESeq2 R package with the following thresholds: absolute log₂ fold change (|log₂FC|) > 0.5 and Benjamini-Hochberg (BH)-adjusted P value < 0.01.
Assembly: GRCh38/hg38 for Homo sapiens GRCm38/mm10 for Mus musculus
Supplementary files format and content: text format of the raw read count for each gene

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.


title: VSL-27M Stool sRNA-Seq

description: Library name: VSL-27M


title: SNL >2 Patient 4

description:
Library name: BA2_4
10X Visium v1 (fresh-frozen)

value: billiary atresia (BA)


title: VSL-25F Stool sRNA-Seq

description: Library name: VSL-25F


title: NK cell, EHMT2-KO rep2

description:
Library name: KO-2
Count.Mouse.txt


title: VSL-24F Stool sRNA-Seq

description: Library name: VSL-24F


title: SNL >2 Patient 3

description:
Library name: BA2_3
10X Visium v1 (fresh-frozen)

value: liver


title: VSL-23F Stool sRNA-Seq

description: Library name: VSL-23F


title: NK cell, EHMT2-KO rep1

description:
Library name: KO-1
Count.Mouse.txt


title: VSL-21F Stool sRNA-Seq

description: Library name: VSL-21F


title: SNL >2 Patient 2

description:
Library name: BA2_2
10X Visium v1 (fresh-frozen)


title: VSL-20F Stool sRNA-Seq

description: Library name: VSL-20F


title: NK cell, Wild-type rep3

description:
Library name: WT-3
Count.Mouse.txt


title: VSL-18M Stool sRNA-Seq

description: Library name: VSL-18M


title: immature DCs, 24h, control, rep2

description: Library name: Ctrl_2

value: 0.1% DMSO


title: scRNA-seq mouse bone marrow WT stromal normal control

description: Library name: S12_WT_Stromal

value: Bone marrow

value: WT normal stromal control


title: SNL >2 Patient 1

description:
Library name: BA2_1
10X Visium v1 (fresh-frozen)


title: VSL-17M Stool sRNA-Seq

description: Library name: VSL-17M


title: NK cell, Wild-type rep2

description:
Library name: WT-2
Count.Mouse.txt


title: VSL-16M Stool sRNA-Seq

description: Library name: VSL-16M


title: SNL <2 Patient 4

description:
Library name: BA1_4
10X Visium v1 (fresh-frozen)


title: VSL-15M Stool sRNA-Seq

description: Library name: VSL-15M


title: NK cell, Wild-type rep1

description:
Library name: WT-1
Count.Mouse.txt


title: VSL-10M Stool sRNA-Seq

description: Library name: VSL-10M


title: SNL <2 Patient 3

description:
Library name: BA1_3
10X Visium v1 (fresh-frozen)


title: VSL-09M Stool sRNA-Seq

description: Library name: VSL-09M


title: Pancreatic tumor and TME cells, Serpine1 KO - Flex

city: New York

first: Chiara

last: Falcomatà

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Siania

description:
Library name: Sample_3
10x Genomics

data_processing:
Raw FASTQ files were aligned to the reference genome Gex-mm10-2020-A using CellRanger multi v7.0.1 (10x Genomics). Feature barcode matrix files generated by CellRanger were utilized for downstream analyses.
Assembly: Gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic tumor

extract_protocol:
Dissected tumor tissues were immersion-fixed in 10% neutral buffered formalin for 24 hours at room temperature and subsequently embedded in paraffin blocks for sectioning. FFPE tissue curls (20 µm thickness) were collected for RNA extraction using the RNeasy FFPE Kit (Qiagen) according to the manufacturer’s instructions. RNA quantity and integrity were assessed using an Agilent TapeStation with High Sensitivity RNA ScreenTape, and samples with DV200 values >30% were considered suitable for downstream analysis.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell Gene Expression Flex protocol (10x Genomics), which is optimized for fixed and FFPE-derived RNA. Briefly, paraffin was removed from tissue sections, and tissues were rehydrated and enzymatically digested to release single cells or nuclei following manufacturer’s instructions. Dissociated single cells or nuclei were incubated with transcriptome-wide probe sets, allowing hybridization to target RNA molecules retained within each cell or nucleus. Barcoded Gel Bead-in-Emulsions (GEMs) were then generated on the Chromium X system, incorporating cell-specific barcodes and unique molecular identifiers (UMIs). Following GEM generation, libraries were amplified by PCR, subjected to sample indexing, and purified according to the manufacturer’s protocol. Final libraries were quantified using Qubit fluorometric analysis (Thermo Fisher Scientific) and Agilent TapeStation, pooled, and sequenced on an Illumina NovaSeq 6000 platform in paired-end mode, targeting 25,000 reads per cell.

value: Pancreatic tumor

value: KPC FC1245 orthotopically injected

value: tumor cells, immune and stromal compartments


title: VSL-08F Stool sRNA-Seq

description: Library name: VSL-08F

value: Stool

value: VSL


title: SNL <2 Patient 2

description:
Library name: BA1_2
10X Visium v1 (fresh-frozen)


title: VSL-07F Stool sRNA-Seq

description: Library name: VSL-07F


title: VSL-06F Stool sRNA-Seq

description: Library name: VSL-06F


title: Pancreatic tumor and TME cells, Serpinb2 KO - Flex

description:
Library name: Sample_2
10x Genomics


title: SNL <2 Patient 1

description:
Library name: BA1_1
10X Visium v1 (fresh-frozen)

value: male


title: VSL-05F Stool sRNA-Seq

description: Library name: VSL-05F


title: Pancreatic tumor and TME cells, control KO - Flex

description:
Library name: Sample_1
10x Genomics


title: scRNA-seq mouse bone marrow KO stromal normal control

description: Library name: S13_KO_Stromal

value: KO normal stromal control


title: VSL-03F Stool sRNA-Seq

description: Library name: VSL-03F


title: PC3, MR* (Unsheared), Rep3

city: Houston

first: Abigail

last: Fabiano

address: 6100 Main St

department: Bioengineering

institute: Rice University

description: Library name: 10277-AF-12

data_processing:
Psuedoalignment was completed using Kallisto and data was processed using DESeq2 in R.
Used tximport to import and transform the data, genes with counts < or =10 were removed.
Transformed count data on the log2 scale via variance stabilizing transform.
Significant genes are denoted as those with a -log10(Padj) > 2.
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: Counts.csv files contain raw counts for each sample, as well as TPM abundance and transcript length.

source_name: prostate tumor

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 1% penstrep, 10 mM HEPES, and 1 mM sodium pyruvate. PC3 cells were maintained in RPMI supplemented with 10% heat-inactivated FBS, 1% penstrep, and 10 mM HEPES. Cells were incubated in humidified conditions at 37C and 5% CO2.

extract_protocol:
RNA was harvested using the Rneasy kit from QIAGEN, with a DNA digestion.
Libraries were constructed by the VANTAGE NGS core at Vanderbilt University Medical Center.

treatment_protocol: MR cells were treated with 10-20 pulses of 3950 dyn/cm2 of high-intensity (HI) FSS every time the cells were passaged, up to ~50-60 passages. MN condition was a static control (same as the parental), simply at a higher passage. MR* (unsheared) condition is the MR cells sheared ~50-60 passages, and then passaged 10 times with no HI FSS treatment. MR-young cells were exposed to HI FSS for ~20 passages.

value: prostate tumor

value: immortalized prostate cancer (bone-met)

value: MR* (Unsheared)

value: x60 FSS, x10 passages no FSS


title: GFB-15572

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

description:
Library name: VT1689
R3

data_processing:
Adapter sequences were removed from raw FASTQ files using Cutadapt (v4.9). Subsequently, high-quality, adapter-trimmed reads were mapped against the mouse reference genome (mm10) using the STARlong utility within the STAR aligner. Quantification of gene expression was performed using FeatureCounts at default parameters for each time points.
Assembly: mm10
Supplementary files format and content: Normalised count matrix

source_name: Brain

growth_protocol: For the total nucleic acids extraction, snap-frozen sEEG electrodes were cut into small pieces using sterile nuclease-free scissors into microfuge tubes and the total nucleic acids were extracted using PicoPure™ RNA Isolation Kit (Thermo KIT0204) according to the manufacturer's instructions with minor modifications.

extract_protocol:
For the RNA purification samples were first treated with DNase I (Thermo EN0521) to remove the DNA and purified using GeneJET RNA Purification Kit (Thermo K0732) according to the manufacturer's instructions. Purified RNA samples were quantified using Qubit high-sensitivity RNA Quantification assay (Thermo Q32852). The quality of the RNA was analysed using Agilent TapeStation systems with high-sensitivity RNA tapes with RIN numbers.
FLASH-seq protocol (https://www.protocols.io/view/bulk-flash-seq-3byl4jynolo5/v2)

value: Brain

value: Cortex


title: VSL-01M Stool sRNA-Seq

description: Library name: VSL-01M


title: VSL-02M Stool sRNA-Seq

description: Library name: VSL-02M


title: PC3, MR* (Unsheared), Rep2

description: Library name: 10277-AF-11


title: LF-34F Stool sRNA-Seq

description: Library name: LF-34F

value: LF


title: GFB-15571

description:
Library name: VT1688
R2


title: LF-32M Stool sRNA-Seq

description: Library name: LF-32M


title: GFB-15570

description:
Library name: VT1687
R1


title: LF-31M Stool sRNA-Seq

description: Library name: LF-31M


title: PC3, MR, Rep3

description: Library name: 10277-AF-9

value: MR

value: x60 FSS


title: PC3, MR* (Unsheared), Rep1

description: Library name: 10277-AF-10


title: LF-30F Stool sRNA-Seq

description: Library name: LF-30F


title: LF-28F Stool sRNA-Seq

description: Library name: LF-28F


title: LF-29F Stool sRNA-Seq

description: Library name: LF-29F


title: PC3, MR, Rep2

description: Library name: 10277-AF-18


title: GFB-15569

description:
Library name: VT1686
R3


title: GFB-15568

description:
Library name: VT1685
R2


title: LF-26M Stool sRNA-Seq

description: Library name: LF-26M


title: LF-25M Stool sRNA-Seq

description: Library name: LF-25M


title: PC3, MR, Rep1

description: Library name: 10277-AF-7


title: PC3, MN, Rep3

description: Library name: 10277-AF-6

value: MN

value: High passage control


title: GFB-15567

description:
Library name: VT1684
R1


title: LF-21F Stool sRNA-Seq

description: Library name: LF-21F


title: SZN-043 70d, replicate 2, nonhep enriched, scRNAseq

city: South San Francisco

first: Russell

last: Fletcher

state: CA

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

description:
Library name: RFSZ-10X-3H
10x Genomics v3 3'

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 8.0.0
Data exploration, normalization, dimension reduction, clustering, DE, and GSEA analyses were done in R (version 4.3.2)
Data from the same animal replicate derived from the hepatocyte-enrichment workflow and from the non-hepatocyte enrichment workflow were combined at the beginning of the analysis.
From the full data set, hepatocytes and non-hepatocytes were subsetted and analyzed separately.
Assembly: GRCm39
Supplementary files format and content: aggregated cellular barcodes from Cellranger output
Supplementary files format and content: feature/genes from Cellranger output
Supplementary files format and content: aggregated UMI matrix from Cellranger output
Supplementary files format and content: log2 of scran + RUVg normalized counts matrix of hepatocytes as tab delimited text file
Supplementary files format and content: hepatocyte QC, batch and experimental condition metadata in tab delimited text file
Supplementary files format and content: log2 of scran + RUVg normalized counts matrix of non-hepatocytes as tab delimited text file
Supplementary files format and content: non-hepatocyte QC, batch, experimental condition, and cell type metadata in tab delimited text file

growth_protocol: Mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). All animal experimentation was in accordance with the ‘‘Guide for the Care and Use of Laboratory Animals’’ prepared by the National Academy of Sciences. Protocols for animal experimentation were approved by the Surrozen Institutional Animal Care and Use Committee. 7-week-old C57Bl/6J female mice were acclimatized 4-5 per cage a minimum of two days prior to the experiment. Mice were kept 12/12-hour light/dark cycle in a 30% to 70% humidity environment and room temperature ranging from 20°C to 26°C.

extract_protocol:
At 24h, 14d, or 70d of the experiment, livers were perfused with a collagenase solution to dissociate the cells, and live cells were then purified by FACS.
Standard 10x Genomics Chromium 3’ v3 scRNA-seq reagents were used. Approximately 2000-4000 cells were loaded per channel. Cells from one animal replicate were captured per channel, and a cell fraction enriched for hepatocytes or for non-hepatocytes from each animal replicate were captured per channel. Standard 10x Genomics Chromium 3’ v3 scRNA-seq RT, cDNA amplification, and sequencing library preparation protocols were followed. Multiplexed sequencing libraries were sequenced on Illumina Hi Seq 4000 S1 lanes, averaging about 50,000 reads per cell.

treatment_protocol: Mice were dosed intraperitoneally once with either 10 mg/kg of an Anti-GFP antibody or with 10 mg/kg of SZN-043 and mice livers were collected at 24-hours, 14-days, 70-days.

value: liver

value: liver cells

tag: strain

value: 6-8 weeks old

value: SZN-043 70d, nonhep enriched, replicate 2


title: LF-23M Stool sRNA-Seq

description: Library name: LF-23M

value: Stool


title: SZN-043 70d, replicate 1, nonhep enriched, scRNAseq

description:
Library name: RFSZ-10X-3G
10x Genomics v3 3'

value: SZN-043 70d, nonhep enriched, replicate 1