title: GPR34, TREM2KO, Myelin, rep 4

city: South San Francisco

first: Thomas

last: Sandmann

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

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Library name: HSA-000028233
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

value: iPSC-derived microglia

value: GPR34+TREM2 KO

value: Myelin

tag: replicate


title: Kc167, mock cell, bio rep1

status: Public on Jul 21 2026

type: SRA

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

country: USA

institute: NIH

description: Library name: Kc167_mock_RNAseq_R1.fastq.gz

library_source: transcriptomic

data_processing:
FASTQ files were trimmed using Trim Galore (v0.6.10) with default settings
The resulting reads were mapped to the FlyBase r6-52 reference genome using HISAT2 v2.2.1 with default parameters.
Aligned reads were counted using subread featureCounts v2.0.6 with optimized parameters, “-t exon” option was used to quantify for RNA-seq, and “-s1” option specifically for this sense-stranded library.
Counts tables were used as input files for the downstream differential analysis.
Counts tables from independent nascent RNA-seq experiments were independently imported into DESeq2 v1.40.1 in R4.3.0 version and normalized by design “~treatment” and with otherwise default parameters. DEGs were those with FDR < 0.05.
Assembly: Flybase r6-52
Supplementary files format and content: bigwg

molecule: total RNA

organism: Drosophila melanogaster

growth_protocol: Kc167 cells are grown in CCM3 media (Cytiva) at 25°C.

extract_protocol:
RNA was extracted from transfected Kc167 cells using the RNeasy Mini Kit (Qiagen).
Unfragmented RNA-seq libraries were created from 60-100ng of RNA using the Ovation RNA-seq Systems 1-16 for Model Organisms (Nugen), as described in Chen et al., 2018.

treatment_protocol: Cells were transfected with appropriate dsRNA and incubated at 25°C for 3d before harvesting RNA.

tag: cell line

tag: cell type

value: hemocyte

tag: treatment

value: GFP dsRNA


title: AB12161

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample23

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

molecule: polyA RNA

organism: Homo sapiens

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.

tag: tissue

value: CSF

tag: diagnosis

value: RRMS

tag: patient

tag: category

value: MS

tag: batch


title: Heart_low_salt_1

city: New York

first: Evan

middle: C

last: Palmer-Young

state: NY

address: 525 E 68th St

institute: Cornell University

description: Library name: R3

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.

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

value: L


title: AB12162

description: Library name: Sample24


title: AB12157

description: Library name: Sample22

value: PPMS


title: TREM2KO, Myelin, rep 4

state: California

description:
Library name: HSA-000028230
TREM2 KO, Myelin

tag: Sex

tag: genotype

value: TREM2 KO


title: Heart_high_salt_2

description: Library name: R2

value: H


title: TREM2KO, PBS, rep 4

description:
Library name: HSA-000028229
TREM2 KO, PBS

value: PBS


title: AB12156

description: Library name: Sample21


title: GPR34KO, Myelin, rep 4

description:
Library name: HSA-000028227
GPR34 KO, Myelin

value: GPR34 KO


title: Heart_high_salt_1

description: Library name: R1


title: AB12155

description: Library name: Sample20


title: Control_4

description: Library name: 1_27_R5_S235

source_name: Kidney

value: Kidney

value: C


title: Aldosterone_4

description: Library name: 1_27_R4_S234

value: A


title: Control_3

description: Library name: 1_27_R2_S233


title: GPR34KO, PBS, rep 4

description:
Library name: HSA-000028226
GPR34 KO, PBS

value: female

value: iPSC-derived microglia


title: WT, Myelin, rep 4

description:
Library name: HSA-000028224
WT, Myelin

value: WT

value: Myelin


title: AB12152

description: Library name: Sample17

value: CSF

value: CIS


title: AB12153

description: Library name: Sample18

value: MS


title: AB12154

description: Library name: Sample19


title: Aldosterone_3

description: Library name: 1_27_R1_S232


title: AB12151

description: Library name: Sample16


title: Control_2

description: Library name: 1_12_R5_S231


title: AB12150

description: Library name: Sample15

value: RRMS


title: Aldosterone_2

description: Library name: 1_12_R4_S230


title: AB12149

description: Library name: Sample14


title: TREM2KO, Myelin, rep 3

description:
Library name: HSA-000028218
TREM2 KO, Myelin


title: Control_1

description: Library name: 1_12_R2_S229


title: TREM2KO, PBS, rep 3

description:
Library name: HSA-000028217
TREM2 KO, PBS


title: AB12148

description: Library name: Sample13


title: AB12147

description: Library name: Sample12


title: AB12146

description: Library name: Sample11


title: GPR34KO, PBS, rep 3

description:
Library name: HSA-000028214
GPR34 KO, PBS


title: AB12145

description: Library name: Sample10


title: Planktonic untreated - rep 2

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: Untreated


title: WT, Myelin, rep 3

description:
Library name: HSA-000028212
WT, Myelin


title: WT, PBS, rep 3

description:
Library name: HSA-000028211
WT, PBS


title: Planktonic untreated - rep 1


title: GPR34, TREM2KO, Myelin, rep 2

description:
Library name: HSA-000028209
GPR34/TREM2 KO, Myelin

value: GPR34+TREM2 KO


title: GPR34, TREM2KO, PBS, rep 2

description:
Library name: HSA-000028208
GPR34/TREM2 KO, PBS


title: AB12142

description: Library name: Sample7

value: Active PPMS


title: Biofilm farnesol treated - rep 1

value: 50 mM Farnesol for 24 h


title: Atopic dermatitis 2

type: RNA

city: Seoul

first: Hye Li

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

description: Lesional skin biopsy obtained from a patient with atopic dermatitis

hyb_protocol: Following fragmentation, 0.75 µg of labeled cRNA was hybridized to the Human HT-12 v4.0 Expression BeadChip for 17 h at 58°C according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the Illumina BeadArray Reader confocal scanner.

data_processing:
Raw intensity data were extracted using Illumina GenomeStudio software (v2011.1, Gene Expression Module v1.9.0).
Array probes transformed by logarithm and normalized by quantile method.

label: biotin

source_name: human skin

label_protocol: Total RNA was amplified and labeled to generate biotinylated cRNA using the TargetAmp Nano Labeling Kit for Illumina Expression BeadChip (Epicentre, Madison, WI, USA) according to the manufacturer’s instructions.

extract_protocol: Skin tissues were homogenized, and total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions.

tag: disease

value: Atopic dermatitis


title: GPR34, TREM2KO, PBS, rep 4

description:
Library name: HSA-000028232
GPR34/TREM2 KO, PBS

value: PBS


title: Biofilm untreated - rep 2


title: TREM2KO, PBS, rep 2

description:
Library name: HSA-000028205
TREM2 KO, PBS

value: TREM2 KO


title: Atopic dermatitis 1


title: Biofilm untreated - rep 1


title: Healthy control skin 6

description: Library name: HC6

data_processing:
Raw sequencing reads were processed using the Galaxy platform (https://usegalaxy.org). Adapter sequences and low-quality bases were trimmed using Cutadap. Reads were aligned to the human reference genome (GRCh38) using HISAT2.
Assembly: GRCh38
Supplementary files format and content: csv file include raw counts for each sample

source_name: skin

extract_protocol:
Total RNA was extracted from skin using the Rneasy Plus Mini Kit (Qiagen), according to the manufacturer's instructions.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Reagent Kit (Agilent Technologies) according to the manufacturer's protocol.

value: skin


title: Biofilm farnesol treated - rep 2


title: GPR34KO, Myelin, rep 2

description:
Library name: HSA-000028203
GPR34 KO, Myelin

value: GPR34 KO


title: JZ26071533_HC_N4_HC_N4

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

country: China

institute: Sichuan University

description:
Library name: sample12
processed per-sample gene expression table

data_processing:
Raw sequencing reads were quality controlled, adapter-trimmed and filtered to remove low-quality reads using the sequencing provider's standardized RNA-seq processing workflow.
Clean reads were mapped to the Homo sapiens reference genome GRCh38/hg38 using the sequencing provider's standardized RNA-seq alignment workflow.
Gene-level expression was quantified and normalized as FPKM values. The final processed files consist of compressed per-sample expression tables for 12 peripheral blood bulk RNA-seq samples and were used for downstream transcriptomic validation and cell-type deconvolution analyses.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: Each .xlsx.gz file is a gzip-compressed processed expression table for one bulk RNA-seq sample. The files contain gene-level expression values generated from the peripheral blood bulk RNA-seq validation cohort.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from peripheral blood samples using the FastPure Cell/Tissue Total RNA Isolation Kit V3 (Vazyme). RNA integrity was assessed using an Agilent 4200 Bioanalyzer, and RNA concentration was quantified using Qubit (Thermo Scientific).
RNA purification, reverse transcription, library construction and sequencing were performed by Wuxi Xuzhenda Technologies Co., Ltd. mRNA-focused sequencing libraries were prepared from 1 ug total RNA using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme, NR606-02). Poly(A)+ mRNA was enriched using oligo-dT-attached magnetic beads and fragmented. First-strand cDNA was synthesized using reverse transcriptase and random primers, followed by second-strand cDNA synthesis with dUTP incorporation. Double-stranded cDNA was purified with CleanNGS magnetic beads, end-repaired, phosphorylated, A-tailed, ligated to sequencing adapters, treated with UDG enzyme before PCR amplification, and size-selected to obtain 200-300 bp fragments. Libraries were quantified using the Qubit 3.0 dsDNA HS Assay and checked for size distribution using an Agilent BioAnalyzer. Sequencing was performed on a GeneMind SURFSeq 5000 platform to generate 2 x 150 bp paired-end reads.

value: peripheral blood

tag: subject status

value: HC

tag: cohort

value: Validation

value: F

tag: age（years）

tag: donor type

value: healthy control

tag: clinical sample_id


title: Healthy control 2

description: Normal skin biopsy obtained from a healthy control

value: Normal


title: Healthy control skin 5

description: Library name: HC5


title: JZ26071532_HC_N3_HC_N3

description:
Library name: sample11
processed per-sample gene expression table

value: M


title: GPR34KO, PBS, rep 2

description:
Library name: HSA-000028202
GPR34 KO, PBS

value: female

value: iPSC-derived microglia

tag: replicate


title: Healthy control skin 4

description: Library name: HC4


title: WT, Myelin, rep 2

description:
Library name: HSA-000028200
WT, Myelin

tag: cell type

value: WT

value: Myelin


title: JZ26071531_HC_N2_HC_N2

description:
Library name: sample10
processed per-sample gene expression table


title: WT, PBS, rep 2

description:
Library name: HSA-000028199
WT, PBS

tag: treatment


title: JZ26071530_HC_N1_HC_N1

description:
Library name: sample9
processed per-sample gene expression table

tag: tissue


title: Whole Blood, ID3, D1, Placebo, 2hour

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

description: Library name: VA0000200034

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

tag: individual

tag: age

value: Placebo

tag: time

value: Day 1

tag: timepoint

value: 2 hour

tag: reaction type

value: ISRR

tag: reaction type_severity

value: Mild


title: GPR34, TREM2KO, Myelin, rep 1

description:
Library name: HSA-000028197
GPR34/TREM2 KO, Myelin

tag: Sex

tag: genotype

value: GPR34+TREM2 KO


title: JZ26071529_SAF_4_SAF_4

description:
Library name: sample8
processed per-sample gene expression table

value: peripheral blood

tag: subject status

value: SAF

value: Deceased donor

tag: post-transplant time_(years)

tag: maintenance immunosuppressive_regimen

value: Tacrolimus + mycophenolate mofetil + corticosteroids


title: Healthy control skin 1

description: Library name: HC1

value: skin


title: LPSRA_2

city: Wilmington

first: Deepthi

last: Alapati

state: DE

address: 1600 Rockland Road

department: Pediatrics

institute: Nemours Children's health

description:
Library name: Sample7
DA17_B_Imm

data_processing:
Quality control was performed using FastQC, and reads were trimmed for quality and adapter sequences using cutadapt. Human contamination was assessed using bowtie2, and perfectly matching human reads were removed. Remaining reads were aligned to the rat reference genome (rnor6) using STAR, and gene-level counts were generated with RSEM. Differential expression analysis was performed using edgeR. Ensembl IDs were mapped to rat gene names primarily using the Uniprot.org mapping algorithm.
Assembly: the rat reference genome (rnor6)
Supplementary files format and content: Tab limited text file
Supplementary files format and content: DA14_Imm_vs_DA17_Imm_tmm_normalized_counts.txt

source_name: Lung

extract_protocol:
mRNA was extracted using QIAGEN RNeasy microkit
libraries were prepared using the Illumina SMARTer Stranded Total RNA-seq kitV2 – Pico input mammalian. Libraries were sequenced as paired-end 2×150 bp reads with a target depth of ~50 million reads.

value: Lung

value: Lipopolysaccharide


title: GPR34, TREM2KO, PBS, rep 1

description:
Library name: HSA-000028196
GPR34/TREM2 KO, PBS

value: female

value: iPSC-derived microglia

value: PBS


title: JZ26071528_SAF_3_SAF_3

description:
Library name: sample7
processed per-sample gene expression table

tag: cohort

value: Validation

value: F

tag: age（years）

tag: donor type

value: Living donor


title: Psoriasis skin 7

description: Library name: PSO7


title: Healthy control 1

tag: disease

value: Normal


title: LPSRA_1

description:
Library name: Sample6
DA17_A_Imm

tag: treatment


title: LPSRA_5

description:
Library name: Sample10
DA17_E_Imm

tag: tissue


title: TREM2KO, Myelin, rep 1

description:
Library name: HSA-000028194
TREM2 KO, Myelin

tag: cell type

value: TREM2 KO

value: Myelin

tag: replicate


title: JZ26071527_SAF_2_SAF_2

description:
Library name: sample6
processed per-sample gene expression table

value: M

tag: clinical sample_id


title: Healthy control skin 3

description: Library name: HC3


title: Psoriasis skin 6

description: Library name: PSO6


title: LPSRA_4

description:
Library name: Sample9
DA17_D_Imm


title: NSRA_5

description:
Library name: Sample5
DA14_E_Imm

value: Normal saline


title: TREM2KO, PBS, rep 1

description:
Library name: HSA-000028193
TREM2 KO, PBS


title: JZ26071526_SAF_1_SAF_1

description:
Library name: sample5
processed per-sample gene expression table

value: peripheral blood

value: SAF


title: NSRA_4

description:
Library name: Sample4
DA14_D_Imm


title: Psoriasis skin 5

description: Library name: PSO5


title: Healthy control skin 2

description: Library name: HC2


title: LPSRA_3

description:
Library name: Sample8
DA17_C_Imm


title: JZ26071525_CAMR4_CAMR4

description:
Library name: sample4
processed per-sample gene expression table

value: CAMR

value: Tacrolimus + mycophenolate mofetil + corticosteroids


title: Psoriasis skin 4

description: Library name: PSO4

value: skin


title: NSRA_3

description:
Library name: Sample3
DA14_C_Imm

value: Lung


title: GPR34KO, Myelin, rep 1

description:
Library name: HSA-000028191
GPR34 KO, Myelin

value: female

value: GPR34 KO


title: GPR34KO, PBS, rep 1

description:
Library name: HSA-000028190
GPR34 KO, PBS

value: iPSC-derived microglia

value: PBS


title: JZ26071524_CAMR3_CAMR3

description:
Library name: sample3
processed per-sample gene expression table

value: Validation

value: Deceased donor


title: NSRA_2

description:
Library name: Sample2
DA14_B_Imm


title: Psoriasis skin 3

description: Library name: PSO3


title: WT, Myelin, rep 1

description:
Library name: HSA-000028188
WT, Myelin

value: WT


title: JZ26071523_CAMR2_CAMR2

description:
Library name: sample2
processed per-sample gene expression table

value: Living donor


title: Psoriasis skin 2

description: Library name: PSO2


title: WT, PBS, rep 1

description:
Library name: HSA-000028187
WT, PBS


title: JZ26071522_CAMR1_CAMR1

description:
Library name: sample1
processed per-sample gene expression table


title: Psoriasis skin 1

description: Library name: PSO1


title: Rhizopus microsporus gcn5 mutant RNA-seq replicate 1

status: Public on Jul 20 2026

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description:
Library name: gcn5db1
RNA-seq replicate 1, gcn5 mutant R. microsporus

data_processing:
Raw reads aligned to Rhimi59_2_AssemblyScaffolds.fasta with HISAT2. Raw counts per gene quantified with featureCounts v2.x against Rhimi59_2 gene annotation.
DESeq2 v1.36.x. Comparisons: set1a_vs_WT, set1db_vs_WT, gcn5db_vs_WT. Significance: |log2FC| > 1, FDR < 0.05. All comparisons in deseq2_results_HistRm.csv.
Assembly: Rhizopus microsporus NCBI assembly Rhimi59_2 (Rhimi59_2_AssemblyScaffolds.fasta; 79 scaffolds). Gene annotation: Rhimi59_2 JGI MycoCosm official gene models.
Supplementary files format and content: raw_counts_RNAseq_HistRm.csv: tab/comma-separated, GeneID rows × 12 sample columns (featureCounts raw counts). deseq2_results_HistRm.csv: columns = comparison, GeneID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj.

organism: Rhizopus microsporus

source_name: mycelium

growth_protocol: Rhizopus microsporus WT and deletion strains (set1 mutant, gcn5 mutant) were cultured in PDA medium at 30°C under standard conditions. Biomass for ChIP-seq and RNA-seq was harvested from mid-log phase liquid cultures.

extract_protocol:
Total RNA was extracted from mid-log-phase cultures. Ribosomal RNA was depleted. Strand-specific paired-end RNA-seq libraries (150 bp) were prepared and sequenced.
Standard Illumina library preparation from ChIP DNA or rRNA-depleted RNA. Paired-end 150 bp sequencing.

treatment_protocol: No drug or chemical treatment was applied. Standard growth until mid-log phase for all strains.

tag: strain

value: gcn5 mutant

value: GCN5 deletion (SAGA acetyltransferase)

value: mycelium


title: Rhizopus microsporus set1 mutant allele db RNA-seq replicate 3

description:
Library name: set1db3
RNA-seq replicate 3, set1 mutant R. microsporus

value: set1 mutant

value: SET1 deletion allele db


title: Rhizopus microsporus set1 mutant allele db RNA-seq replicate 2

description:
Library name: set1db2
RNA-seq replicate 2, set1 mutant R. microsporus


title: Rhizopus microsporus set1 mutant allele a RNA-seq replicate 3

description:
Library name: set1a3
RNA-seq replicate 3, set1 mutant R. microsporus

value: SET1 deletion allele a


title: Rhizopus microsporus set1 mutant allele a RNA-seq replicate 2

description:
Library name: set1a2
RNA-seq replicate 2, set1 mutant R. microsporus


title: Rhizopus microsporus set1 mutant allele a RNA-seq replicate 1

description:
Library name: set1a1
RNA-seq replicate 1, set1 mutant R. microsporus


title: Rhizopus microsporus WT RNA-seq replicate 3

description:
Library name: WT3
RNA-seq replicate 3, WT R. microsporus

value: wild-type


title: Rhizopus microsporus gcn5 mutant RNA-seq replicate 3

description:
Library name: gcn5db3
RNA-seq replicate 3, gcn5 mutant R. microsporus


title: Rhizopus microsporus WT RNA-seq replicate 2

description:
Library name: WT2
RNA-seq replicate 2, WT R. microsporus


title: Rhizopus microsporus set1 mutant allele db RNA-seq replicate 1

description:
Library name: set1db1
RNA-seq replicate 1, set1 mutant R. microsporus


title: Rhizopus microsporus WT RNA-seq replicate 1

description:
Library name: WT1
RNA-seq replicate 1, WT R. microsporus


title: NSRA_1

description:
Library name: Sample1
DA14_A_Imm

value: Normal saline


title: LL rep1

city: Chaozhou

first: Xiaoting

last: Zheng

state: Guangdong

address: Qiaodong

institute: Hanshan Normal University

description: Library name: Sample 4

data_processing:
BMKCloud online platform and Trinity software
Raw sequence reads were trimmed for adaptor sequences, poly-N sequences, and low-quality reads using in-house Perl scripts on BMKCloud platform to obtain high-quality clean reads.
Clean reads were de novo assembled into transcriptome using Trinity software with default parameters (min_kmer_cov set to 2).
Gene functional annotation was performed across NR, Pfam, KOG/COG/eggNOG, Swiss-Prot, KEGG, and GO databases.
Gene expression levels were quantified and read counts were calculated using RSEM software.
Assembly: de novo assembled transcriptome (Trinity)
Supplementary files format and content: Tab-delimited text file includes raw gene read counts for each sample

organism: Tradescantia spathacea

source_name: leaf

extract_protocol:
RNA was harvested using Total RNA Extractor (Trizol) Kit (Sangon Biotech). 1 μg RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

value: leaf


title: LL rep2

description: Library name: Sample 5


title: LL rep3

description: Library name: Sample 6


title: Rhizopus microsporus gcn5 mutant RNA-seq replicate 2

description:
Library name: gcn5db2
RNA-seq replicate 2, gcn5 mutant R. microsporus


title: FL rep1

description: Library name: Sample 1


title: 7 days maize seedling, rep2, easy-Multiome, atac

city: ATHENS

first: Robert

middle: J.

last: Schmitz

state: GA

address: B416 Davison Life Sciences Department of Genetics University of Georgia 120 East Green Street

department: Genetics

institute: University of Georgia

description: Library name: Zm_seedling_rep2_eMultiATAC

library_source: genomic single cell

data_processing:
RNA sequencing data analysis
For RNA-seq data, Index 2 and the first 10 bp of Read 2 were concatenated to generate a new FastQ file containing the cell barcode and UMI (CB_UMI.fastsq). Then the CB_UMI.fastq and Read 1 files were used to generate the gene expression matrix by mapping the reads to B73 AGP v5 maize reference genome19 with STARsolo20. We specified the following parameters in STARSolo to filter the UMI, filter empty cells, and count unique mapping reads: --soloUMIfiltering MultiGeneUMI_CR, --soloCellFilter EmptyDrops_CR. The filtered expression data was analyzed using the Seurat (v4) R package21. Potential low-quality nuclei or empty droplets were filtered. Specifically, cells with gene counts below a threshold calculated as the median gene count minus two times the median absolute deviation, and cells with UMI counts less than the lower 10% percentile of total UMI counts, were filtered out. Additionally, cells with organelle gene counts comprising more than 15% of the total gene count were excluded. The preprocessed datasets were normalized using SCTransform before the RunPCA for principal component analysis (PCA). Subsequently, the doublets were identified by the DoubletFinder R package, and removed from downstream analysis. We prepared two replicates for each library and integrated them using the Harmony R package. The integrated dataset was then processed using RunUMAP (reduction = "harmony", dims = 1:20) for Uniform Manifold Approximation and Projection (UMAP) dimension reduction, FindNeighbors (reduction = "harmony", dims = 1:30) to obtain the Nearest-neighbor graph, and FindClusters to identify distinct cell populations.
ATAC sequencing data analysis
The raw data processing followed the previously described method5. In brief, raw BCL files were demultiplexed and converted into fastq format using the default settings of the 10X Genomics tool cellranger-atac makefastq (v1.2.0). Initial read processing, including adaptor/quality trimming, mapping, and barcode attachment/correction, was carried out with cellranger-atac count (v1.2.0) using the B73 AGP v5 maize reference genome19. Properly paired mapped reads with a mapping quality greater than 30 were retained using samtools view (v1.6; -f 3 -q 30)91, while also retaining reads with alternate hit XA tags to avoid biasing downstream analysis due to the whole genome duplication events during soybean evolution. Duplicate fragments were collapsed on a per-nucleus basis using picardtools (http://broadinstitute.github.io/picard/) MarkDuplicates (v2.16; BARCODE_TAG=CB REMOVE_DUPLICATES=TRUE). Reads mapping to mitochondrial and chloroplast genomes were counted for each barcode and then excluded from downstream analysis. BAM alignments were then converted to single base-pair Tn5 integration sites in BED format by adjusting coordinates of reads mapping to positive and negative strands by +4 and -5, respectively, and retaining only distinct Tn5 integration sites for each individual barcode.
The R package Socrates was used for nuclei identification and quality control5. The BED file containing single base-pair Tn5 integration sites was imported into Socrates along with the maize GFF gene annotation and the genome index file. To identify bulk-scale ACRs in Socrates, the callACRs function was employed with the following parameters: genome size=8.0e8, shift=-75, extsize=150, and FDR=0.1. This step allowed us to estimate the fraction of Tn5 integration sites located within ACRs for each nucleus. Metadata for each nucleus were collected using the buildMetaData function, with a TSS (Transcription Start Site) window size of 1 kb (tss.window=1000). Sparse matrices were then generated with the generateMatrix function, using a window size of 500. High-quality nuclei were identified based on the following criteria: a minimum of 1,000 Tn5 insertion sites per nucleus, at least 20% of Tn5 insertions within 2 kb of TSSs, and at least 20% of Tn5 insertions within ACRs across all datasets. Additionally, a maximum of 20% of Tn5 insertions in organelle genomes was allowed.
Assembly: Zea mays B73 v5
Supplementary files format and content: AH15AH17_eMultiATAC_Zm_seedling_cpm4.ACR_acr2gene.annotated.uniqACR.txt contains the list of peaks from ATAC data
Supplementary files format and content: AH15AH17_eMultiATAC_Zm_seedling_cpm4_ACR_sparse.rds cantians the ACR x cells matrix for the ATAC data
Supplementary files format and content: AH15AH17_eMultiRNA_Zm_seedling.MergedSeuratObjs.cluster.RDS contains final seurate objs for merged two replicates.
Supplementary files format and content: AH15AH17_eMulti_Zm_seedling.LabelShared.cells.ATAC.metadata.txt contains the ATAC metadata
Supplementary files format and content: AH15AH17_eMulti_Zm_seedling.LabelShared.cells.RNA.metadata.txt contains the RNA metadata
Supplementary files format and content: eMultiRNA_Zm_seedling-rep1_barcodes.tsv contains the barcode id for RNA rep1
Supplementary files format and content: eMultiRNA_Zm_seedling-rep1_features.tsv contains the gene information for RNA rep1
Supplementary files format and content: eMultiRNA_Zm_seedling-rep1_matrix.mtx contains the cell x gene count matrix for RNA rep1
Supplementary files format and content: eMultiRNA_Zm_seedling-rep2_barcodes.tsv contains the barcode id for RNA rep2
Supplementary files format and content: eMultiRNA_Zm_seedling-rep2_features.tsv  contains the gene information for RNA rep2
Supplementary files format and content: eMultiRNA_Zm_seedling-rep2_matrix.mtx contains the cell x gene count matrix for RNA rep2

molecule: genomic DNA

organism: Zea mays

source_name: Seedling

growth_protocol: Soil was saturated with tapwater and placed under a 50/50 mixture of 4100K (Sylvania SupersaverCoolWhite Delux F34CWX/SS, 34W) and 3000K (GE Ecolux w/ starcoat, F40CX30ECO, 40W) lighting. Seedlings were grown under a photoperiod of 16 hours of light, eight hours of dark. The temperature was approximately 25℃ during light hours with a relative humidity of approximately 54%.

extract_protocol:
Briefly, root tissues were finely chopped   with single edge razor blades on ice for approximately 2 minutes in 600 μL of pre-chilled Nuclei Isolation Buffer (NIB; 10 mM MES-KOH, pH 5.4; 10 mM NaCl; 250 mM sucrose; 0.1 mM spermine; 0.5 mM spermidine; 1 mM DTT; 1% BSA; and 0.5% Triton X-100). The homogenate was passed through a 40-μm cell strainer and centrifuged at 500 × g for 5 minutes at 4 °C. The supernatant was discarded, and the pellet was gently resuspended in 500 μL of NIB wash buffer (10 mM MES-KOH, pH 5.4; 10 mM NaCl; 250 mM sucrose; 0.1 mM spermine; 0.5 mM spermidine; 1 mM DTT; and 1% BSA). The suspension was filtered through a 40-μm cell strainer and carefully layered onto 1 mL of 35% Percoll (prepared by mixing 35% Percoll with 65% NIB wash buffer) in a 1.5-mL centrifuge tube. Nuclei were enriched by centrifugation at 500 × g for 10 minutes at 4 °C. Following centrifugation, the supernatant was removed, and the nuclei pellet was resuspended in 10 μL of diluted nuclei buffer (DNB; 10x Genomics, Cat# 2000207). For quality control, 5 μL of the nuclei suspension were diluted tenfold, stained with DAPI (Sigma, Cat# D9542), and examined under a fluorescence microscope using a hemocytometer to assess integrity and concentration. The nuclei concentration was then adjusted to 3,200 nuclei/μL using DNB buffer, and 5 μL (approximately 16,000 nuclei) were used as input for single-cell ATAC-seq library construction.
Briefly, Nuclei were isolated from fresh plant tissues by mechanical chopping in nuclei isolation buffer, followed by filtration, Percoll gradient purification, and washing. Approximately 20,000 purified nuclei were subjected to in situ reverse transcription using a poly(dT)-containing reverse transcription primer and Maxima H Minus Reverse Transcriptase. Following reverse transcription, nuclei were washed to remove excess RNA and reaction components before proceeding with the standard 10X Genomics Chromium Single Cell ATAC library preparation workflow. Tagmentation, GEM generation, linear amplification, and DNA purification were performed according to the manufacturer's protocol (10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kit). RNA- and ATAC-derived libraries were independently amplified using library-specific index primers, with the number of PCR cycles determined by qPCR to minimize amplification bias. Final libraries were purified using SPRI beads and sequenced on an Illumina platform.

treatment_protocol: Seedling tissue extending 1 cm on either side of the first visible node (2 cm total) were harvested between 8 and 9 AM six days after sowing. Around 3-5 seedling were used for each replicate.

value: Seedling

tag: library type

value: ATAC


title: 7 days maize seedling, rep2, easy-Multiome, rna

description: Library name: Zm_seedling_rep2_eMultiRNA

value: mRNA


title: 6 days maize seedling, rep1, easy-Multiome, rna

description: Library name: Zm_seedling_rep1_eMultiRNA


title: HSC_TGFB_Res_rep4

city: Santiago de Compostela

first: Rubén

last: Nogueiras Pozo

state: A Coruña

address: Campus Vida Avenida Barcelona, s/n, CIMUS

department: Fisiology

institute: CIMUS - USC

description:
Library name: Tgfb+R300_9
PhHSCs co-treated with TGF-beta1 and Resmetirom

data_processing:
Raw reads were filtered using SOAPnuke software developed by BGI. The filtering steps included: (1) removing reads containing adaptor sequences (matches ≥ 25%, max 2 mismatches); (2) removing reads with N content > 1%; (3) removing reads containing polyX > 50bp ; and (4) removing low-quality reads where > 40% of bases had a quality score < 20. Reads shorter than 100bp were discarded.
Clean reads were aligned to the human reference genome (GRCh38) for gene expression quantification and raw count calculation.
Inter-sample count normalization and differential expression analysis were performed using the EgoGenomics platform. Statistically significant differentially expressed genes (DEGs) were identified using an absolute fold change threshold greater than 2 (abs(FC) > 2) and an adjusted p-value (Q-value) less than 0.05.
Functional annotation and enrichment analyses were conducted for Gene Ontology Biological Processes (GOBP) based on the identified differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: Individual text files (.txt) containing raw read counts for each gene/transcript per sample, generated by the EgoGenomics platform.

source_name: Liver

growth_protocol: Human primary hepatic stellate cells (PhHSCs) (CyHum19007-SC-P2-Z, BeCytes Biotechnologies) were thawed using Thawing Medium (MHT-NPC50, BeCytes Biotechnologies) following the manufacturer’s guidelines. Subsequently, the cells were seeded and cultured in Growth Medium for Stellate Cells (HMSG-50, BeCytes Biotechnologies). These primary cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from liver tissue using the TRIzol–chloroform method following the manufacturer’s protocol. RNA quality and quantity were assessed using a NanoDrop spectrophotometer (selecting samples with A260/A280 ratios between 1.8 and 2.0). RNA integrity was subsequently confirmed (RIN ≥ 8) prior to library preparation.
DNBSEQ Eukaryotic Strand-specific mRNA library. Total RNA samples were enriched for polyA mRNA using oligo dT beads, followed by mRNA fragmentation. Fragmented mRNA was synthesized into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed incorporating dUTP instead of dTTP to preserve strand specificity. The synthesized cDNA was subjected to end-repair, 3' adenylation, and adaptor ligation before PCR amplification. After library quality control and circularization, the library was amplified to generate DNA nanoballs (DNB) and sequenced on the DNBSEQ platform with a PE100 (paired-end 100bp) strategy.

treatment_protocol: PhHSCs were incubated with culture medium supplemented with recombinant human TGF-β1 (PeproTech, cat. 100-21) at a final concentration of 8 ng/mL for 36 hours. For the co-treatment group, Resmetirom (MGL-3196, MedChemExpress) dissolved in dimethyl sulfoxide (DMSO; Merck, cat. D2653) was added to the medium at a final concentration of 300 µM for the last 24 hours of the 36-hour incubation.

value: Liver

tag: cell line

value: Hepatic Stellate Cell

value: TGF-beta1 36h (8 ng/mL) + Resmetirom (300 uM) 24h


title: HSC_TGFB_Res_rep3

description:
Library name: Tgfb+R300_6
PhHSCs co-treated with TGF-beta1 and Resmetirom


title: HSC_TGFB_Res_rep2

description:
Library name: Tgfb+R300_4
PhHSCs co-treated with TGF-beta1 and Resmetirom


title: HSC_TGFB_Res_rep1

description:
Library name: Tgfb+R300_2
PhHSCs co-treated with TGF-beta1 and Resmetirom


title: HSC_TGFB_rep4

description:
Library name: Tgfb36h_12
PhHSCs treated with TGF-beta1

value: TGF-beta1 36h (8 ng/mL)


title: HSC_TGFB_rep3

description:
Library name: Tgfb36h_8
PhHSCs treated with TGF-beta1


title: HSC_TGFB_rep2

description:
Library name: Tgfb36h_5
PhHSCs treated with TGF-beta1


title: HSC_TGFB_rep1

description:
Library name: Tgfb36h_4
PhHSCs treated with TGF-beta1


title: 6 days maize seedling, rep1, easy-Multiome, atac

description: Library name: Zm_seedling_rep1_eMultiATAC


title: PID031_TM1_T1_1_1

city: Montréal

first: Hamed

last: Najafabadi

state: Québec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: PID031_TM1_T1_1_1

data_processing:
Raw sequencing reads were aligned to reference genomes using the 10x Genomics CellRanger software (v3.0.2). For tumor samples, reads were aligned to the human reference genome (hg38). For PDX samples, a combined human (hg38) and mouse (mm10) reference was used. Unique molecular identifier (UMI) counts were generated by collapsing alignments using CellRanger. For PDX samples, multiplets and mouse cells were removed as identified by the CellRanger pipeline. Only cells with >95% of counts mapped to the human genome were retained.
Quality control metrics were computed using the scuttle (v.1.0.4) package. Cells were retained if they met the following criteria: log10 total counts >3, log10 total features >3, and percentage of mitochondrial reads per cell <20%. Doublet detection was performed using DoubletFinder (v.2.0.3). The doublet rate was estimated based on the number of cells recovered per sample, following the multiplet rate guidelines from the 10x Genomics v3 user guide. Other parameters remained as default, except that the top 50 principal components were used for dimensional reduction.
Assembly: GRCh38 and mm10
Supplementary files format and content: Single cell experiment object with counts and metadata in .rds format

source_name: Tumor

extract_protocol:
Tumor specimens were dissociated into single-cell suspensions prior to single-cell RNA sequencing. Tumor tissue was washed two to three times with Dulbecco’s Phosphate-Buffered Saline (DPBS) and minced into 1–2 mm pieces using a scalpel. Tissue fragments were collected, washed with DPBS, and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, tissue pieces were incubated in enzyme solution composed of Enzymes H, R, and A prepared in RPMI 1640 medium and processed using the gentleMACS Octo Dissociator with Heaters (program 37_h_TDK_1). Following dissociation, cells were filtered through a 70 µm cell strainer to remove undigested material, washed with DPBS, and pelleted by centrifugation. Red blood cells were lysed using ACK lysis buffer, after which cells were washed and resuspended in DPBS supplemented with 1% bovine serum albumin. Cell suspensions were passed through a 40 µm filter to remove remaining debris. Viable cells were counted using Trypan Blue exclusion prior to downstream single-cell RNA sequencing library preparation.
Single-cell cDNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Briefly, single-cell suspensions that passed quality control were loaded onto the Chromium Next GEM Chip along with reverse transcription reagents, gel beads, and partitioning oil, and processed using the Chromium Controller to generate gel bead–in–emulsions (GEMs). Reverse transcription was performed in GEMs, followed by GEM cleanup and cDNA recovery. Full-length cDNA was purified using silane magnetic beads and amplified by PCR. cDNA quality and size distribution were assessed prior to library construction. Amplified cDNA was fragmented, end-repaired, and A-tailed, followed by double-sided size selection using SPRIselect beads. Indexed sequencing libraries were generated by adaptor ligation and sample index PCR amplification. Final libraries were purified and quality controlled prior to sequencing. Libraries were sequenced to a targeted depth of approximately 20,000 reads per cell.

value: Tumor

tag: tumor type

tag: disease state

value: renal cell carcinoma

tag: renal cell_carcinoma_subtype

value: ccRCC

tag: tumor site

value: Brain metastasis

tag: group


title: PID030_TM1_T1_1_1

description: Library name: PID030_TM1_T1_1_1


title: PID029_TP1_T1_1_1

description: Library name: PID029_TP1_T1_1_1

value: chRCC

value: Primary


title: PID028_TP1_T1_1_1

description: Library name: PID028_TP1_T1_1_1


title: PID027_TP1_T1_1_1

description: Library name: PID027_TP1_T1_1_1

value: ccpRCT


title: FL rep3

description: Library name: Sample 3


title: PID026_TP1_T1_1_1

description: Library name: PID026_TP1_T1_1_1


title: Aldosterone_1

description: Library name: 1_12_R1_S228

value: Kidney

value: A

tag: batch


title: PDO OKG146P, shControl and shZFP36L2 pooled together, dedifferentiation, hash tag

first: Qingwen

last: Jiang

address: 417 East 68th Street, 1725

institute: memorial sloan kettering cancer center

description:
Library name: OKG146P_dedifferentiation_HTO
10x Genomics

library_source: other

data_processing:
Raw sequencing data were quantified with Cell Ranger. CellBender (v.0.1.0), an unsupervised method for removing ambient RNA from scRNA-seq data, was used to generate a denoised (i.e., ambient-RNA-corrected) count matrix. CellBender-corrected counts were used in all downstream analysis. Doublets were identified and excluded using DoubletDetection (v3.0).
Cells were designated as outliers if they satisfied at least two of the following five conditions: 1) their log1p(total counts) were either more than 3 median absolute deviations (MADs) below or 5 MADs above the median of their organoid line; 2) their log1p(number of genes expressed) was either more than 3 MADs below or 5MADs above the median; 3) their percent of genes expressed in the top 20% of most highly expressed genes was more than 5 MADs below or above the median; 4) their feature-count distance (the difference between the value of log1p(number of genes expressed) observed, and the value predicted from the regression of log1p(number of genes expressed) on log1p(total counts)) was more than 5 MADs below or above the median; 5) their percentage of mitochondrial counts was both more than 2.5 MADs above the median and above the absolute threshold of 8%. Outliers and any remaining cells with fewer than 500 total counts, fewer than 400 detected genes, or greater than 20% mitochondrial content were excluded.
Assembly: GRCh38
Supplementary files format and content: H5AD file containing cells passing QC, deconvolved sample labels, and raw and CellBender-corrected counts.

molecule: protein

growth_protocol: Patient-derived organoids were cultured and expanded in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). Cells are embedded and plated in 40 μL domes of 3:1 Matrigel (Corning) :HISC medium mixture in suspension culture plates. After Matrigel domes solidified at 37 °C for 30 minutes, HISC medium supplemented with Y-27632 (MedChemExpress) was added to the well. Medium was refreshed every two days.

extract_protocol:
Organoids were dissociated into single cells and incubated with TotalSeq hashtag antibodies (BioLegend, #B0251, #B0252, #B0253) for 30 minutes on ice. Viable (DAPI-negative) cells were sorted using a 130 μm nozzle on a SH800S cell sorter (Sony) into DPBS containing 0.04% BSA. Equal numbers of hashtag-labelled shZFP36L2 and shCtrl cells were pooled per condition and resuspended at 700–1,300 cells/μL for library preparation. Cell viability exceeded 90% as determined by Trypan Blue exclusion.
Single-cell suspensions were loaded onto the Chromium Single Cell 3′ v3.1 platform (10x Genomics) according to the manufacturer's protocol, targeting up to 10,000 cells per sample for droplet-based encapsulation and barcoding. Following reverse transcription, emulsions were broken and cDNA was purified using Dynabeads MyOne SILANE, followed by PCR amplification. Libraries were sequenced on an Illumina NovaSeq platform with the following read configuration: Read 1, 28 cycles; i7 index, 8 cycles; Read 2, 90 cycles.

treatment_protocol: OKG146P patient-derived primary colorectal cancer organoids expressing doxycycline-inducible shZFP36L2 or shCtrl were cultured in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). All conditions were supplemented with 2 μg/mL doxycycline throughout. Medium was refreshed every two days. Organoids were cultured in HISC medium for 7 days (HISC condition), or in HISC medium for 7 days followed by intestinal growth factor-free (IGFF) medium — containing all base media components but lacking EGF, Noggin, A8301, FGF2, and IGF-I — for 7 days (differentiation condition), or in HISC for 7 days, IGFF for 7 days, then HISC for a further 7 days (dedifferentiation condition).

value: CRC PDO

tag: genotype

value: shControl and shZFP36L2 pooled by hash tags

value: dedifferentiation

value: HTO

tag: hto

value: TotalSeq-B0251 anti-human Hashtag 1 (shControl), TotalSeq-B0252 anti-human Hashtag 2 (shZFP36L2), TotalSeq-B0253 anti-human Hashtag 3 (sample excluded from downstream analysis)


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 12hrs, replicate 3

description: Library name: MSK107Li_SLAM_28

data_processing:
Adapter trimming and quality filtering: Raw sequencing reads were trimmed for adapters and low-quality bases using Trim Galore.
Alignment and T>C quantification: Trimmed reads were aligned to the GRCh38 reference genome using Slamdunk (via the nf-core/slamseq pipeline v1.0.0 in Nextflow), which performs conversion-aware mapping, alignment filtering, multimapper recovery, SNP calling to mask genomic T>C variants, and quantification of total and T>C-converted reads. Read counts were generated at the UTR level and collapsed to the gene level. 3′ UTR annotations and pipeline configurations followed Muhar et al. (2018).
Background correction: Gene-level T>C conversion rates were background-corrected using matched unlabeled samples (shCtrl corrected with unlabeled shCtrl; shZFP36L2 corrected with unlabeled shZFP36L2).
RNA half-life estimation: Due to residual 4sU retention in Matrigel causing delayed peak labeling, t=2 h was used as the first effective decay time point for genes peaking at t=2 h in control samples (n=5,888 genes). Half-lives were calculated by fitting a single-exponential decay model to t=2, 5, and 12 h time points using t½ = ln(2)/k, where k is the fitted first-order decay constant.
Assembly: GRCh38
Supplementary files format and content: CSV file with halflife calculated for each gene in shCtrl or shZFP36L2 organoids.

extract_protocol:
Total RNA was subsequently isolated using a standard TRIzol-based extraction protocol.
Purified RNA was subjected to chemical derivatization according to the SLAMseq Kinetics Kit – Catabolic Kinetics Module manufacturer’s instructions. Briefly, 4sU-labeled RNA was alkylated with iodoacetamide (IAA) under the recommended reaction conditions to modify incorporated 4sU residues prior to library preparation. Alkylated RNA was purified and used as input for sequencing library construction. The SLAMseq chemistry enables reverse transcriptase to incorporate G opposite alkylated 4sU during cDNA synthesis, resulting in diagnostic T>C conversions in sequencing reads derived from newly labeled transcripts. Sequencing libraries were generated from total RNA using the QuantSeq 3′ mRNA-seq V2 Library Prep Kit FWD with Unique Dual Indices according to the manufacturer’s instructions. This protocol uses oligo(dT)-primed first-strand synthesis, followed by RNA removal, random-primed second-strand synthesis, bead purification, and PCR amplification to generate strand-specific Illumina-compatible libraries enriched for the 3′ ends of polyadenylated transcripts. Unique dual indices were introduced during PCR amplification. Libraries were prepared from total RNA without prior poly(A) enrichment or rRNA depletion, consistent with the QuantSeq workflow.

treatment_protocol: For the catabolic labeling experiment, organoids were labeled with 500 μM 4sU for 6 h, with fresh 4sU-containing medium supplied every 2 h to maintain labeling efficiency. At the end of labeling, one set of samples was harvested immediately as the t0 time point. To measure mRNA decay kinetics, 4sU-containing medium was removed and organoids were washed by adding 3 mL warm PBS and incubating for 10 min to allow residual labeling medium to equilibrate out. The PBS was then replaced with HISC medium containing 50 mM uridine and samples were harvested at 2 h, 5 h, and 12 h. At each timepoint, medium was removed completely and organoids were lysed directly in the culture well by adding 1 mL TRIzol and pipetting 15 times to fully dissolve the Matrigel domes. Lysates were transferred to pre-labeled 1.5 mL tubes, snap-frozen, and stored at −80 °C until RNA extraction.

value: chase for 12hrs


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 12hrs, replicate 2

description: Library name: MSK107Li_SLAM_27


title: PDO OKG146P, shControl and shZFP36L2 pooled together, dedifferentiation, mRNA

description:
Library name: OKG146P_dedifferentiation_mRNA
10x Genomics

value: mRNA


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 12hrs, replicate 1

description: Library name: MSK107Li_SLAM_26


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 12hrs, replicate 3

description: Library name: MSK107Li_SLAM_25

value: shCtrl


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 12hrs, replicate 2

description: Library name: MSK107Li_SLAM_24


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 5hrs, replicate 3

description: Library name: MSK107Li_SLAM_22

value: chase for 5hrs


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 12hrs, replicate 1

description: Library name: MSK107Li_SLAM_23


title: FL rep2

description: Library name: Sample 2

value: leaf


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 5hrs, replicate 1

description: Library name: MSK107Li_SLAM_20


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 5hrs, replicate 2

description: Library name: MSK107Li_SLAM_21


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 5hrs, replicate 3

description: Library name: MSK107Li_SLAM_19


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 5hrs, replicate 2

description: Library name: MSK107Li_SLAM_18


title: AB12143

description: Library name: Sample8

value: CSF

tag: diagnosis

value: Active PPMS

tag: patient

tag: category

value: MS


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 5hrs, replicate 1

description: Library name: MSK107Li_SLAM_17

tag: cell type

tag: treatment


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 2hrs, replicate 2

description: Library name: MSK107Li_SLAM_15

value: chase for 2hrs


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 2hrs, replicate 3

description: Library name: MSK107Li_SLAM_16


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 2hrs, replicate 2

description: Library name: MSK107Li_SLAM_12


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 2hrs, replicate 1

description: Library name: MSK107Li_SLAM_14


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 2hrs, replicate 3

description: Library name: MSK107Li_SLAM_13


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 2hrs, replicate 1

description: Library name: MSK107Li_SLAM_11


title: MSK107Li PDO cells, shZFP36L2, no 4sU label, replicate 2

description: Library name: MSK107Li_SLAM_10

value: no 4sU label


title: MSK107Li PDO cells, shZFP36L2, no 4sU label, replicate 1

description: Library name: MSK107Li_SLAM_9


title: MSK107Li PDO cells, shCtrl, no 4sU label, replicate 2

description: Library name: MSK107Li_SLAM_8


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 0hrs, replicate 3

description: Library name: MSK107Li_SLAM_6

value: chase for 0hrs


title: MSK107Li PDO cells, shCtrl, no 4sU label, replicate 1

description: Library name: MSK107Li_SLAM_7


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 0hrs, replicate 2

description: Library name: MSK107Li_SLAM_5


title: MSK107Li PDO cells, shZFP36L2, 4sU label for 6hrs, chase for 0hrs, replicate 1

description: Library name: MSK107Li_SLAM_4


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 0hrs, replicate 3

description: Library name: MSK107Li_SLAM_3


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 0hrs, replicate 2

description: Library name: MSK107Li_SLAM_2


title: MSK107Li PDO cells, shCtrl, 4sU label for 6hrs, chase for 0hrs, replicate 1

description: Library name: MSK107Li_SLAM_1


title: OKG146N, frameshift ZFP36L2-ADAR, replicate3

description:
Library name: OKG146N_fsZFP36L2_ADAR_3
OKG146N_hypertribe.csv

data_processing:
Adapter trimming: Raw sequencing reads were trimmed for adapters and low-quality bases using Cutadapt (v4.8).
Alignment: Trimmed reads were aligned to the hg38 reference genome and construct sequences using STAR (v2.7.11b).
Editing site identification: RNA editing sites were identified using GATK HaplotypeCaller (v3.8.1.0), retaining only A-to-G substitutions on the forward strand and U-to-C substitutions on the reverse strand. Known genomic variants annotated in dbSNP (human_9606_b144_GRCh38p2) were excluded.
Statistical testing: Editing frequency at each site was assessed using a Beta-binomial test with Benjamini–Hochberg multiple testing correction.
Assembly: GRCh38
Supplementary files format and content: CSV file containing per-site RNA editing analysis results for all detected sites in indicated PDO lines, comparing wild-type ZFP36L2 (test) to frameshift mutant ZFP36L2 (fs-ZFP36L2, ctrl). Columns include Ensembl gene ID, gene symbol, genomic feature (exon/intron/utr3/utr5), editing site ID (chromosome:position_substitution), number of editing events in the gene, editing frequency difference (wt ZFP36L2 minus fs-ZFP36L2), mean editing frequency in fs-ZFP36L2 and wt ZFP36L2 conditions, nominal p-value (Beta-binomial test), and Benjamini-Hochberg adjusted p-value.

growth_protocol: Patient-derived CRC organoids were cultured and expanded in human intestinal stem cell (HISC) medium comprising Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:50 B27 Supplement (Thermo Fisher Scientific), 1:100 N2 Supplement (Thermo Fisher Scientific), and 100 μg/mL Primocin (InvivoGen), supplemented with 50 ng/mL EGF (Peprotech), 100 ng/mL Noggin (Peprotech), 500 nM A8301 (Sigma-Aldrich), 50 ng/mL FGF2 (Peprotech), and 100 ng/mL IGF-I (Peprotech). NGS-Wnt (0.5 M, ImmunePrecise N001) and R-spondin (10ng/mL, MBL-J2-004) were additianolly added to HISC media for normal colon organoid culture. Cells are embedded and plated in 40 μL domes of 3:1 Matrigel (Corning) :HISC medium mixture in suspension culture plates. After Matrigel domes solidified at 37 °C for 30 minutes, HISC medium supplemented with Y-27632 (MedChemExpress) was added to the well. Medium was refreshed every two days.

extract_protocol:
Total RNA was extracted from organoids using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was measured using the RiboGreen assay, and RNA quality was assessed using an Agilent Bioanalyzer.
300 ng of total RNA with RIN values of 9.8-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: ZFP36L2-ADAR or fsZFP36L2-ADAR induced by doxycycline at day5 organoid culture for 48hours.

value: Normal colon PDO


title: OKG146N, frameshift ZFP36L2-ADAR, replicate2

description:
Library name: OKG146N_fsZFP36L2_ADAR_2
OKG146N_hypertribe.csv


title: OKG146N, frameshift ZFP36L2-ADAR, replicate1

description:
Library name: OKG146N_fsZFP36L2_ADAR_1
OKG146N_hypertribe.csv


title: OKG146N, Wildtype ZFP36L2-ADAR, replicate3

description:
Library name: OKG146N_ZFP36L2_ADAR_3
OKG146N_hypertribe.csv


title: OKG146N, Wildtype ZFP36L2-ADAR, replicate2

description:
Library name: OKG146N_ZFP36L2_ADAR_2
OKG146N_hypertribe.csv


title: OKG146N, Wildtype ZFP36L2-ADAR, replicate1

description:
Library name: OKG146N_ZFP36L2_ADAR_1
OKG146N_hypertribe.csv


title: CosMX_PID037

description: CosMX-1K library

hyb_protocol: NanoString protocol

scan_protocol: Quality control, cell segmentation, and RNA normalization was performed on AtoMx™ prior to downstream analysis.

data_processing:
The count matrix from the MTSCRCC tumor was loaded into a Seurat object, filtering out cells with fewer than 10 detected features and genes expressed in fewer than 3 cells, and log-normalized using Seurat’s NormalizeData function with a scaling factor of 10,000. Highly variable features (2,000 genes) were identified using the “vst” method and used to compute principal components. The data were then scaled using the ScaleData function. The top 40 principal components were selected based on elbow plots and JackStraw analysis and were used to construct a k-nearest neighbor graph and perform graph-based clustering using the Louvain algorithm at a resolution of 0.5 (FindNeighbors/FindClusters). The resulting shared nearest neighbor (SNN) clusters were characterized by cluster-specific marker genes identified using the FindAllMarkers function. Cells without distinct gene expression profiles, likely due to limited transcript coverage, were labeled as “Undefined”, while other clusters were annotated based on canonical marker genes identified in our CosMx 1K spatial transcriptomics dataset.
Gene counts (PID037_exprMat_file.csv.gz)

label: SMI imaging barcodes

label_protocol: Slides were washed 3 times in PBS and then loaded onto flowcells for cyclic imaging of defined FOVs (0.51 x 0.51 mm) on the CosMx™ Spatial Molecular Imager, resulting in single molecule read-out of detected mRNAs.

extract_protocol: CosMx™ Spatial Molecular Imaging (SMI) was performed as per the supplier’s protocol using the Universal Cell Characterization RNA Panel (Nanostring Technologies). Briefly, 5 µm FFPE sections of the tumor were processed through deparaffinization, antigen retrieval (in Tris-EDTA ph9 for 15 min at 98°C), and Proteinase K digestion (3 ug/mL Proteinase K for 30 min at 40°C) prior to overnight incubation at 37°C with the human Universal Cell Characterization RNA Panel diluted in hybridization Buffer R. The next day, slides were washed twice in 2XSSC/formamide (25 min at 37°C), twice in 2XSSC, and incubated with a segmentation antibody cocktail targeting CD298, B2M, PanCK, CK8/18, CD45, and SYTO13 for 1 hr in a humidity chamber.

tag: tissue

value: mucinous tubular and spindle cell carcinoma


title: P2S2p

city: Milan

first: Mario

last: Faretta

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology (IEO)

description: Library name: MCF10A cells, ChIP P2S2p

library_source: genomic

data_processing:
basecall were performed using bcl2fastq v2.20.0.422 for Novaseq output
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: breast

extract_protocol:
MCF10A cells were cross-linked 10 min at RT by directly adding formaldehyde to the culture medium to a final concentration of 1%. Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with ice-cold PBS and lysed in SDS buffer: 100 mM NaCl, 50 mM Tris–HCl (pH 8), 5 mM EDTA (pH 8), 0.5% SDS and protease inhibitors (10 min, RT). Chromatin lysates were diluted in Triton Dilution Buffer(100 mM Tris–HCl at pH 8, 100 mM NaCl, 5 mM EDTA at pH 8, 5% Triton X-100, and protease inhibitors) by adding ½ V. Sonication was performed with Branson Digital Sonifier 250 to obtain fragments in the range of 500-250 bp. Antibody incubations were performed overnight with the following: anti-Pol II-pS5 (ab5131 Abcam, Cambridge, UK), anti-Pol II-pS2 (A300-654A, Bethyl Laboratories, Montgomery TX, USA), anti-53bp1 (ab36823, Abcam, Cambridge, UK)
Libraries were prepared with NEBNext Ultra II DNA

value: breast

value: Human breast epithelial cell line


title: Input

description: Library name: MCF10A cells, Input


title: P2S5p

description: Library name: MCF10A cells, ChIP P2S5p


title: 53bp1

description: Library name: MCF10A cells, ChIP 53bp1


title: Hippocampus, polyA-depleted RNA-Seq, 1219

city: Boston

first: Alexander

last: Knyshov

address: 72 E Concord St

department: Medicine

institute: Boston University

description: Library name: 1219-minus

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: other

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.

value: hippocampus

tag: rqn

tag: age

tag: Sex

value: Male

tag: ad status

value: Control


title: Hippocampus, polyA-depleted RNA-Seq, 1223

description: Library name: 1223-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1221

description: Library name: 1221-minus

value: Female


title: Hippocampus, polyA-depleted RNA-Seq, 1220

description: Library name: 1220-minus

value: AD


title: Hippocampus, polyA-depleted RNA-Seq, 1218

description: Library name: 1218-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1217

description: Library name: 1217-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1216

description: Library name: 1216-minus

value: Other


title: Hippocampus, polyA-depleted RNA-Seq, 1215

description: Library name: 1215-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1211

description: Library name: 1211-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1209

description: Library name: 1209-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1207

description: Library name: 1207-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1210

description: Library name: 1210-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1205

description: Library name: 1205-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1204

description: Library name: 1204-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1195

description: Library name: 1195-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1186

description: Library name: 1186-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1183

description: Library name: 1183-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1179

description: Library name: 1179-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1174

description: Library name: 1174-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1172

description: Library name: 1172-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1176

description: Library name: 1176-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1171

description: Library name: 1171-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1165

description: Library name: 1165-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1168

description: Library name: 1168-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1166

description: Library name: 1166-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1156

description: Library name: 1156-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1152

description: Library name: 1152-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1147

description: Library name: 1147-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1145

description: Library name: 1145-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1150

description: Library name: 1150-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1149

description: Library name: 1149-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1140

description: Library name: 1140-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1142

description: Library name: 1142-minus


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

description: Library name: 1141-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1139

description: Library name: 1139-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1138

description: Library name: 1138-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1136

description: Library name: 1136-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1130

description: Library name: 1130-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1132

description: Library name: 1132-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1133

description: Library name: 1133-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1129

description: Library name: 1129-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1128

description: Library name: 1128-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1126

description: Library name: 1126-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1124

description: Library name: 1124-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1127

description: Library name: 1127-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1121

description: Library name: 1121-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1122

description: Library name: 1122-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1119

description: Library name: 1119-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1118

description: Library name: 1118-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1116

description: Library name: 1116-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1114

description: Library name: 1114-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1111

description: Library name: 1111-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1112

description: Library name: 1112-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1109

description: Library name: 1109-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1107

description: Library name: 1107-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1108

description: Library name: 1108-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1105

description: Library name: 1105-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1103

description: Library name: 1103-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1098

description: Library name: 1098-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1097

description: Library name: 1097-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1113

description: Library name: 1113-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1095

description: Library name: 1095-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1094

description: Library name: 1094-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1091

description: Library name: 1091-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1090

description: Library name: 1090-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1087

description: Library name: 1087-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1085

description: Library name: 1085-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1086

description: Library name: 1086-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1083

description: Library name: 1083-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1084

description: Library name: 1084-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1082

description: Library name: 1082-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1102

description: Library name: 1102-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1081

description: Library name: 1081-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1080

description: Library name: 1080-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1079

description: Library name: 1079-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1093

description: Library name: 1093-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1078

description: Library name: 1078-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1077

description: Library name: 1077-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1076

description: Library name: 1076-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1075

description: Library name: 1075-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1073

description: Library name: 1073-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1074

description: Library name: 1074-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1072

description: Library name: 1072-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1071

description: Library name: 1071-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1070

description: Library name: 1070-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1069

description: Library name: 1069-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1068

description: Library name: 1068-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1067

description: Library name: 1067-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1066

description: Library name: 1066-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1065

description: Library name: 1065-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1064

description: Library name: 1064-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1063

description: Library name: 1063-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1060

description: Library name: 1060-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1061

description: Library name: 1061-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1059

description: Library name: 1059-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1058

description: Library name: 1058-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1057

description: Library name: 1057-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1054

description: Library name: 1054-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1056

description: Library name: 1056-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1052

description: Library name: 1052-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1050

description: Library name: 1050-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1051

description: Library name: 1051-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1049

description: Library name: 1049-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1048

description: Library name: 1048-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1047

description: Library name: 1047-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1045

description: Library name: 1045-minus


title: Hippocampus, polyA-depleted RNA-Seq, 1046

description: Library name: 1046-minus


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

description: Library name: 1044-minus


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

description: Library name: 1043-minus


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

description: Library name: 1040-minus


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

description: Library name: 1039-minus


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

description: Library name: 1038-minus


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

description: Library name: 1037-minus


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

description: Library name: 1035-minus


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

description: Library name: 1034-minus


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

description: Library name: 1033-minus


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

description: Library name: 1032-minus


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

description: Library name: 1031-minus


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

description: Library name: 1030-minus


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

description: Library name: 1029-minus


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

description: Library name: 1028-minus


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

description: Library name: 1027-minus


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

description: Library name: 1026-minus


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

description: Library name: 1025-minus


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

description: Library name: 1024-minus


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

description: Library name: 1022-minus


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

description: Library name: 1021-minus


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

description: Library name: 1020-minus


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

description: Library name: 1019-minus


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

description: Library name: 1017-minus


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

description: Library name: 1015-minus


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

description: Library name: 1016-minus


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

description: Library name: 1013-minus


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

description: Library name: 1012-minus


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

description: Library name: 1011-minus


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

description: Library name: 1009-minus


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

description: Library name: 1008-minus


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

description: Library name: 1004-minus


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

description: Library name: 1006-minus


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

description: Library name: 1002-minus


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

description: Library name: 1001-minus


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

description: Library name: 1000-minus


title: Hippocampus, polyA-enriched RNA-Seq, 1223

description: Library name: 1223-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1221

description: Library name: 1221-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1220

description: Library name: 1220-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1219

description: Library name: 1219-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1218

description: Library name: 1218-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1217

description: Library name: 1217-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1216

description: Library name: 1216-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1215

description: Library name: 1215-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1210

description: Library name: 1210-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1209

description: Library name: 1209-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1207

description: Library name: 1207-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1211

description: Library name: 1211-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1205

description: Library name: 1205-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1204

description: Library name: 1204-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1195

description: Library name: 1195-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1186

description: Library name: 1186-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1183

description: Library name: 1183-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1179

description: Library name: 1179-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1176

description: Library name: 1176-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1172

description: Library name: 1172-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1174

description: Library name: 1174-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1171

description: Library name: 1171-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1168

description: Library name: 1168-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1166

description: Library name: 1166-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1165

description: Library name: 1165-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1156

description: Library name: 1156-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1152

description: Library name: 1152-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1150

description: Library name: 1150-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1149

description: Library name: 1149-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1147

description: Library name: 1147-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1145

description: Library name: 1145-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1140

description: Library name: 1140-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1139

description: Library name: 1139-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1138

description: Library name: 1138-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1136

description: Library name: 1136-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1133

description: Library name: 1133-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1132

description: Library name: 1132-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1130

description: Library name: 1130-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1129

description: Library name: 1129-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1128

description: Library name: 1128-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1127

description: Library name: 1127-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1126

description: Library name: 1126-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1124

description: Library name: 1124-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1122

description: Library name: 1122-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1121

description: Library name: 1121-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1119

description: Library name: 1119-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1116

description: Library name: 1116-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1113

description: Library name: 1113-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1114

description: Library name: 1114-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1118

description: Library name: 1118-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1112

description: Library name: 1112-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1111

description: Library name: 1111-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1109

description: Library name: 1109-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1108

description: Library name: 1108-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1107

description: Library name: 1107-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1105

description: Library name: 1105-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1103

description: Library name: 1103-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1142

description: Library name: 1142-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1102

description: Library name: 1102-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1098

description: Library name: 1098-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1097

description: Library name: 1097-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1095

description: Library name: 1095-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1091

description: Library name: 1091-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1094

description: Library name: 1094-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1090

description: Library name: 1090-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1087

description: Library name: 1087-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1093

description: Library name: 1093-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1086

description: Library name: 1086-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1085

description: Library name: 1085-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1084

description: Library name: 1084-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1083

description: Library name: 1083-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1082

description: Library name: 1082-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1081

description: Library name: 1081-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1080

description: Library name: 1080-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1079

description: Library name: 1079-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1078

description: Library name: 1078-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1077

description: Library name: 1077-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1076

description: Library name: 1076-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1075

description: Library name: 1075-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1074

description: Library name: 1074-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1072

description: Library name: 1072-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1073

description: Library name: 1073-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1071

description: Library name: 1071-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1070

description: Library name: 1070-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1069

description: Library name: 1069-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1068

description: Library name: 1068-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1067

description: Library name: 1067-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1066

description: Library name: 1066-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1064

description: Library name: 1064-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1065

description: Library name: 1065-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1063

description: Library name: 1063-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1061

description: Library name: 1061-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1060

description: Library name: 1060-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1059

description: Library name: 1059-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1058

description: Library name: 1058-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1057

description: Library name: 1057-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1056

description: Library name: 1056-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1054

description: Library name: 1054-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1052

description: Library name: 1052-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1051

description: Library name: 1051-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1050

description: Library name: 1050-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1049

description: Library name: 1049-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1048

description: Library name: 1048-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1047

description: Library name: 1047-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1045

description: Library name: 1045-plus


title: Hippocampus, polyA-enriched RNA-Seq, 1046

description: Library name: 1046-plus