title: A4-2

city: hefei

first: Chengcheng

last: Ma

address: jixi road

institute: anhui chest hospital

description:
Library name: sample11
negative_control-2 (FPKM)

data_processing:
Base calling was performed using Illumina CASAVA software (v1.8.2) with default parameters. Raw FASTQ files were processed with in-house Perl scripts to remove reads containing adapter sequences, reads with >10% poly-N, and low-quality reads (Q-score < 20 in more than 50% of bases). Quality metrics (Q20, Q30, GC content, and sequence duplication levels) were calculated using FASTQC (v0.11.9).
Clean reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using HISAT2 (v2.0.5) with default parameters (--rna-strandness RF). Only reads with perfect matches or up to one mismatch were retained.
Transcripts were assembled and quantified using StringTie (v1.3.3) with default settings. Gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Assembly: GRCm38 (mm10)
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Mus musculus

source_name: Lung tissue

extract_protocol:
After 24 h of treatment, total RNA was extracted from mouse lung tissue samples using Trizol and subjected to RNA sequencing.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: Lung tissue

value: lung homogenate

tag: genotype

value: wild type

tag: group

value: Negative Control Group


title: A4-3

status: Public on Dec 02 2025

type: SRA

country: China

description:
Library name: sample12
negative_control-3 (FPKM)

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: cell type

tag: batch


title: chp_24hr_UM_rep2

city: Columbus

first: Rachel

middle: D

last: Dreher

state: OH

address: 575 Children's Crossroad

country: USA

institute: Nationwide Children's Hospital

description: Library name: sample 65

data_processing:
Low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include log2FoldChange, p-values adjusted and other the statistics generated by DESeq2 for each sample

organism: Homo sapiens

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate. TTC466 cells were grown in RPMI-1640 + 10% FBS + PSQ. CHP-100 cells were grown in McCoys 5A Medium + 10% heat inactivated FBS + PSQ.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol:
Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or UM171, or OG-L002. Cells were harvested for RNA extraction after designated treatment time
KO cell lines were generated via CRISPR/Cas9 gene editing and electroporation delivery and are stable polyclonal populations that were seeded at 30% then harvested once confluent.

tag: cell line

value: Ewing sarcoma

value: LSD1 knockdown

tag: treatment


title: A3-5

description:
Library name: sample8
depolymerase-2 (FPKM)

value: Drug Control Group


title: A3-6

description:
Library name: sample9
depolymerase-3 (FPKM)


title: A3-1

description:
Library name: sample7
depolymerase-1 (FPKM)


title: chp_24hr_UM_rep1

description: Library name: sample 64


title: A2-8

description:
Library name: sample6
treatment-3 (FPKM)

value: Treatment Group


title: chp_6hr_UM_rep2

description: Library name: sample 62


title: chp_KOresc_rep1

description: Library name: sample 73

value: LSD1 KO

value: pMSCV_puro empty vector


title: chp_DMSO_rep2

description: Library name: sample 59

value: wildtype

value: DMSO


title: A1-4

description:
Library name: sample3
positive_control-3 (FPKM)

value: Positive Control Group (Model)


title: chp_6hr_UM_rep1

description: Library name: sample 61


title: chp_DMSO_rep1

description: Library name: sample 58


title: chp_96hr_UM_rep2

description: Library name: sample 68


title: Protoplast,globular somatic embryos (GSE),rep1

city: Guangzhou

first: xiaobing

last: wang

address: Higher Education Mega center, Panyu, Guangzhou

institute: Guangzhou University of Chinese Medicine

description:
Library name: Sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw data was filtered, compared, quantified, and analyzed using the official Cell Ranger software to obtain the gene expression matrix for each cell. Subsequently, Seurat was employed for cell filtering, normalization, cluster classification, differential expression gene analysis of each cluster, and marker gene screening. Cell Ranger was utilized for quality control of sequencing data, where reads with low sequencing quality were removed. Preliminary statistical analyses were performed on the number of reads measured and the sequencing quality of each sample. Cell Ranger software harnessed the Spliced Transcripts Alignment to a Reference (STAR) tool to align cDNA sequence fragments to the reference genome of P. cablin.
Assembly: GZUCM_PCab_1.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Pogostemon cablin

source_name: globular somatic embryos

extract_protocol:
Protoplast suspensions were prepared from P. cablin GSE and CSE using the enzymatic hydrolysis method. To prepare the protoplast cleaning solution, 20 μL of 500× BSA and 3.43 mL of ddH2O were added to 6.25 mL of 0.8 M mannitol. The solution was then pre-cooled in a refrigerator at 4°C. To prepare the enzyme solution, cellulose R10 (0.075 g), pectinase (0.025 g), 3.125 mL of 0.8 M mannitol, 500 μL of 0.1 M MES (pH 5.7), 500 μL of 0.2 M KCl, and 870 μL of ddH2O were weighed or measured and put into a 15 mL centrifuge tube and incubate the tube in a 55℃-water bath for 10 minutes, with vortexing and mixing performed twice during this period. Once the solution had cooled to room temperature, 25 μL of 500× BSA and 50 μL of 1 M CaCl2 were added. The solution was then mixed thoroughly and filtered through a 0.22 μm filter into another 15 mL centrifuge tube. The P. cablin GSE and CSE were washed twice with protoplast washing solution. Subsequently, they were transferred to centrifuge tubes containing enzyme solution and incubated on a shaking table at 30 ℃ with 75 rpm in the dark for 0.5-24 h. A 5 μL aliquot of 0.4% trypan blue staining solution was mixed with 5 μL of protoplast suspension. Cell concentration and viability rates were then determined using the Countess® II automated cell counter. Protoplasts with greater than 80% viability were used for 10x single-cell library construction within 30 min.
To construct scRNA-seq library, barcode-encoded gel beads were mixed with a blend of cells and enzymes and subsequently separated by oil to form Gel Beads-In-Emulsions (GEMs) within a reservoir. After being dissolved, the gel beads freed the capture sequence that incorporated the barcode sequence, and this sequence was later converted into cDNA through reverse transcription. The samples were then labeled. The gel beads were crushed, and the oil droplets were broken up, after which PCR amplification was performed, with the cDNA serving as the template. All GEMs were then mixed to construct sequencing library. The cDNA was enzymatically cleaved into 200-300 bp fragments and subjected to second-generation sequencing library construction steps, followed by PCR to obtain the DNA library. The Illumina HiSeq2500 sequencing platform (Genedenovo Biotechnology Co., Ltd, Guangzhou, China) was utilized to conduct high-throughput sequencing of the prepared libraries.

value: globular somatic embryos

tag: sample type

value: Protoplast


title: A1-3

description:
Library name: sample2
positive_control-2 (FPKM)


title: chp_6hr_UM_rep3

description: Library name: sample 63


title: chp_DMSO_rep3

description: Library name: sample 60


title: A1

description:
Library name: sample1
positive_control-1 (FPKM)


title: chp_CRWT_rep2

description: Library name: sample 56

value: CRISPR WT


title: chp_CRWT_rep1

description: Library name: sample 55


title: treatment-group3

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

description:
Library name: P6
T cell cultured with NF-L-activated macrophage supernatants

data_processing:
Data analysis was performed by R (v.4.2.1) software and limma (v.3.54.2) software packages.
Assembly: GRCm39
Supplementary files format and content: including read count for each sample

source_name: T cell

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods, followed by rigorous quality control of the RNA samples. The quality control primarily involves quantification using a Nanodrop and detection of RNA integrity using an Agilent 4200 TapeStation
Utilizing the structural characteristic that most eukaryotic mRNA carries a polyA tail, Oligo(dT) magnetic beads are used to enrich mRNA with a polyA tail. Subsequently, the obtained mRNA is randomly fragmented using divalent cations. Using the fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA is synthesized in the 1st Strand Enzyme reverse transcriptase system. Then, the second strand of cDNA is synthesized using 2nd Strand Enzyme and dNTPs. The purified double-stranded cDNA undergoes end repair, A-tail addition, and ligation of sequencing adapters. cDNA fragments of approximately 200-300 bp are selected, PCR amplified, and the PCR products are purified again to finally obtain the library. Afterwards, the library is quantified using a Qubit 2.0 Fluorometer and diluted to 1.5 ng/ul. The insert size of the library is detected using an Agilent 4200 TapeStation to ensure library quality. Finally, Illumina sequencing is performed on the qualified library after library inspection.

value: T cell

value: NF-L-activated macrophage supernatants


title: treatment-group2

description:
Library name: P5
T cell cultured with NF-L-activated macrophage supernatants


title: chp_CRKO_rep3

description: Library name: sample 54

value: CRISPR KO


title: A4-1

description:
Library name: sample10
negative_control-1 (FPKM)

value: Lung tissue

value: lung homogenate

value: wild type


title: treatment-group1

description:
Library name: P4
T cell cultured with NF-L-activated macrophage supernatants


title: control-group3

description:
Library name: P3
T cell cultured with control macrophage supernatants

value: control macrophage supernatants


title: chp_CRKO_rep2

description: Library name: sample 53

value: Ewing sarcoma


title: control-group1

description:
Library name: P1
T cell cultured with control macrophage supernatants


title: a673_KQ_AEresc_rep3

description: Library name: sample 51

value: K661Q/A539E LSD1 rescue


title: control-group2

description:
Library name: P2
T cell cultured with control macrophage supernatants


title: A2-3

description:
Library name: sample5
treatment-2 (FPKM)

value: Treatment Group


title: chp_CRKO_rep1

description: Library name: sample 52

value: LSD1 KO


title: a673_KQ_AEresc_rep1

description: Library name: sample 49


title: a673_Nullresc_rep3

description: Library name: sample 48

value: wt LSD1 rescue


title: heart from treated NIID mouse, biol rep 3

city: Changsha

first: Yongcheng

last: Pan

state: Hunan

address: 87 Xiangya Rd

institute: Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University

description: Library name: TgTre_Heart_3

data_processing:
Raw reads were processed by fastp to get clean reads
Assembly: Paired-end clean reads were mapped to GRCm38 or GRCh38 by HISAT2, and assembled by StringTie
Supplementary files format and content: Processed gene expression data for all samples are available in TXT format

source_name: heart

extract_protocol:
Total RNA was extracted from mice brain tissue using Trizol reagent (Invitrogen) according to the manufacturer's protocol.
An amount of 1ug of total RNA per sample was processed for library preparation using VAHTS Universal V10 RNA-seq Library Prep Kit following the manufacturer’s recommendations

value: heart

value: cas9 and nlc-sgRNAs


title: a673_Nullresc_rep2

description: Library name: sample 47


title: heart from treated NIID mouse, biol rep 2

description: Library name: TgTre_Heart_2


title: heart from treated NIID mouse, biol rep 1

description: Library name: TgTre_Heart_1


title: heart from untreated NIID mouse, biol rep 3

description: Library name: TgCtl_Heart_3

value: cas9 and ctl-sgRNAs


title: heart from untreated NIID mouse, biol rep 1

description: Library name: TgCtl_Heart_1


title: heart from untreated NIID mouse, biol rep 2

description: Library name: TgCtl_Heart_2


title: a673_Nullresc_rep1

description: Library name: sample 46


title: a673_WTresc_rep3

description: Library name: sample 45

value: wildtype

value: pMSCV_puro empty vector


title: a673_WTresc_rep2

description: Library name: sample 44


title: a673_WTresc_rep1

description: Library name: sample 43


title: heart from control mouse, biol rep 2

description: Library name: Ctl_Heart_2

value: cas9 and ctl/nlc-sgRNAs


title: a673_KOresc_rep3

description: Library name: sample 42


title: cortex from treated NIID mouse, biol rep 3

description: Library name: TgTre_Ctx_3

source_name: cortex

value: cortex


title: a673_KOresc_rep2

description: Library name: sample 41


title: a673_KOresc_rep1

description: Library name: sample 40


title: cortex from treated NIID mouse, biol rep 2

description: Library name: TgTre_Ctx_2


title: heart from control mouse, biol rep 1

description: Library name: Ctl_Heart_1


title: a673_OG_rep3

description: Library name: sample 39

value: LSD1 inhibition


title: a673_OG_rep2

description: Library name: sample 38


title: cortex from treated NIID mouse, biol rep 1

description: Library name: TgTre_Ctx_1


title: cortex from untreated NIID mouse, biol rep 2

description: Library name: TgCtl_Ctx_3


title: cortex from untreated NIID mouse, biol rep 3

description: Library name: TgCtl_Ctx_4


title: a673_OG_rep1

description: Library name: sample 37


title: chp_CRWT_rep3

description: Library name: sample 57

value: CRISPR WT


title: a673_KQ_AEresc_rep2

description: Library name: sample 50


title: a673_96hrUM_rep3

description: Library name: sample 36

value: LSD1 knockdown


title: cortex from untreated NIID mouse, biol rep 1

description: Library name: TgCtl_Ctx_2


title: a673_96hrUM_rep2

description: Library name: sample 35


title: cortex from control mouse, biol rep 2

description: Library name: Ctl_Ctx_2


title: a673_96hrUM_rep1

description: Library name: sample 34


title: cortex from control mouse, biol rep 3

description: Library name: Ctl_Ctx_3


title: FXTAS-TRAP, Rep3, 6m, Cerebellum

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

description:
Library name: 19149FL-173-01-06
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-06

data_processing:
Sequencing reads were aligned to the mm10 mouse genome using TopHat v2.1.1. The number of reads aligned to each gene was tabulated using FeatureCount v1.5.3. All reads mapped to gene bodies were used for differential gene expression analysis using R package DEseq2 v1.30.1.
Assembly: Mus musculus 10 (mm10)
Supplementary files format and content: Tap-delimited text files include  raw read counts for each sample

source_name: Cerebellum

extract_protocol:
RNA of brain tissues were extracted by using TRIzol™ Reagent following the standard protocol. In TRAP procedure, cortex and cerebellum were dissected in pre-cold PBS buffer and homogenized in PBS containing 50 mM Tris (pH 7.5), 100 mM KCl, 12 mM MgCl2 and 1% Nonidet P-40, 1 mM DTT, 100 U/mL Ribolock RNase inhibitor, 100 μg/mL cycloheximide, and 1 tab/5 mL SigmaFast protease inhibitor cocktail (with EDTA). The homogenates were kept on ice for more than 15min and centrifuged at 13000 rpm for 10 min at 4 ℃ to remove nuclei and cell debris. Approximate 50 μL of S1 supernatant was kept for input RNA isolation and the remaining supernatant was pre-cleared with Protein G Dynabeads at 4°C on a rotator for 30 mins. The S2 supernatant was incubated with 10ul HA antibody (Roche, # Anti-HA (12CA5)) on a rotator at 4 ℃ for 2 hours followed by incubating with protein G beads for additional 2 hours at the same condition. Afterwards, the beads were collected and washed 3 times with High Salt Buffer (HSB: 50 mM Tris (pH 7.5), 300 mM KCl, 12 mM MgCl2 and 1% Nonidet P-40, 1 mM DTT, 50 U/mL Ribolock RNase inhibitor, and additional 3X wash by using Extra High Salt Buffer (EHSB: identical to HSB but containing additional 300 mM NaCl). Per each wash, beads were rotated gently at 4°C for 2 mins. During the last wash, 10% beads were saved for western blot, and remaining beads were used for RNA isolation by TRIzol™ Reagent.
RNA libraries for bulk RNA-Seq and TRAP-Seq were prepared according to the manufacturer’s protocol NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.

value: Cerebellum

tag: developmental stage

value: 6-7 months

tag: Sex

value: male

value: GABAergic neuron

value: FMRpolyG+RNA (+/-);Gad2-Cre (+)


title: heart from control mouse, biol rep 3

description: Library name: Ctl_Heart_3


title: a673_24hrUM_rep3

description: Library name: sample 33

value: Ewing sarcoma


title: Control-TRAP, Rep3, 6m, Cerebellum

description:
Library name: 19149FL-173-01-05
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-05

value: Control


title: a673_24hrUM_rep1

description: Library name: sample 31


title: cortex from control mouse, biol rep 1

description: Library name: Ctl_Ctx_1


title: a673_24hrUM_rep2

description: Library name: sample 32


title: a673_6hrUM_rep1

description: Library name: sample 28


title: a673_6hrUM_rep2

description: Library name: sample 29


title: Control-TRAP, Rep1, 6m, Cerebellum

description:
Library name: 19149FL-173-01-02
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-02


title: Control-TRAP, Rep2, 6m, Cerebellum

description:
Library name: 19149FL-173-01-03
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-03


title: a673_6hrUM_rep3

description: Library name: sample 30


title: a673_DMSO_48hr_rep3

description: Library name: sample 27

value: DMSO


title: FXTAS-TRAP, Rep3, 6m, Cortex

description:
Library name: 19149R-118-12
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-12

source_name: Cortex

value: Cortex


title: a673_DMSO_rep6

description: Library name: sample 24


title: FXTAS-TRAP, Rep2, 6m, Cortex

description:
Library name: 19149R-118-10
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-10


title: a673_DMSO_rep5

description: Library name: sample 23


title: Control-TRAP, Rep2, 6m, Cortex

description:
Library name: 19149R-118-09
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-09


title: a673_DMSO_rep4

description: Library name: sample 22


title: a673_DMSO_rep3

description: Library name: sample 21


title: FXTAS-TRAP, Rep1, 6m, Cortex

description:
Library name: 19149R-118-07
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-07


title: a673_DMSO_rep2

description: Library name: sample 20


title: Control-TRAP, Rep3, 3m, Cerebellum

description:
Library name: 19149R-122-29
Column name in 3m_Cerebellum_TRAP_raw_read_counts.txt: 19149R-122-29

value: 3-4 months


title: FXTAS-TRAP, Rep2, 6m, Cerebellum

description:
Library name: 19149FL-173-01-04
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-04


title: a673_iLuc_rep3

description: Library name: sample 18

value: luciferase knockdown

value: iLuc shRNA


title: Control-TRAP, Rep2, 3m, Cerebellum

description:
Library name: 19149R-122-28
Column name in 3m_Cerebellum_TRAP_raw_read_counts.txt: 19149R-122-28


title: a673_DMSO_rep1

description: Library name: sample 19

value: wildtype


title: a673_iLuc_rep2

description: Library name: sample 17


title: a673_DMSO_48hr_rep2

description: Library name: sample 26


title: FXTAS-TRAP, Rep1, 3m, Cerebellum

description:
Library name: 19149R-122-25
Column name in 3m_Cerebellum_TRAP_raw_read_counts.txt: 19149R-122-25


title: FXTAS-TRAP, Rep2, 3m, Cerebellum

description:
Library name: 19149R-122-27
Column name in 3m_Cerebellum_TRAP_raw_read_counts.txt: 19149R-122-27


title: FXTAS-TRAP, Rep1, 6m, Cerebellum

description:
Library name: 19149FL-173-01-01
Column name in 6m_Cerebellum_TRAP_raw_read_counts.txt: 19149FL-173-01-01


title: Control-TRAP, Rep1, 3m, Cerebellum

description:
Library name: 19149R-122-26
Column name in 3m_Cerebellum_TRAP_raw_read_counts.txt: 19149R-122-26


title: Control-TRAP, Rep4, 3m, Cortex

description:
Library name: 19149R-122-15
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-15


title: a673_iLSD1_rep2

description: Library name: sample 14

value: iLSD1 shRNA


title: a673_DMSO_48hr_rep1

description: Library name: sample 25


title: a673_CRWT_rep6

description: Library name: sample 12


title: Control-TRAP, Rep3, 3m, Cortex

description:
Library name: 19149R-122-13
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-13


title: FXTAS-TRAP, Rep3, 3m, Cortex

description:
Library name: 19149R-122-14
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-14


title: a673_iLuc_rep1

description: Library name: sample 16


title: a673_CRWT_rep5

description: Library name: sample 11


title: a673_iLSD1_rep1

description: Library name: sample 13


title: SPF_5

first: Yunxia

last: Li

address: No. 1 Nongda Road

department: College of Animal Science and Technology

institute: Hunan Agricultural University

description: specific pathogen-free pig replicate 3

data_processing:
Reads were processed using the Cell Ranger 6.0.1 pipeline with default and recommended parameters.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Sus scrofa

source_name: adipose

extract_protocol:
Adipose tissue were transported in In sterile culture dish with 10 ml 1× DPBS solution (Solarbio, cat. no. D1040) on ice  to remove the residual MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008), then minced on ice.  We used dissociation enzyme 0.25% Trypsin (Hyclone, cat. no. SH30042.01) and 10 ug/mL Recombinant DNase I  (RNase-free) (TaKaRa, cat. no. 2270B) dissolved in DPBS with 5% Fetal Bovine Serum (FBS, Thermo Fisher  Scientific, cat. no. SV30087.02) to digest the tissues. XX tissues were dissociated at 37 ℃ with a shaking speed of  50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield  and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by  1× Red Blood Cell Lysis buffer (Thermo Fisher Scientific, cat. no. 00-4333-57) . Dissociated cells were washed  with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar  Fluorescence Cell Analyzer (Aber Instruments).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell  was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA  molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA  synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with  UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA  synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly  interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell  barcode and UMI. All the remaining procedures including the library construction were performed according to the  standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a  High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo  Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were  generated. The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).

value: adipose

value: specific pathogen-free pig


title: SPF_3

description: specific pathogen-free pig replicate 2


title: Control-TRAP, Rep1, 6m, Cortex

description:
Library name: 19149R-118-08
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-08


title: Control-TRAP, Rep2, 3m, Cortex

description:
Library name: 19149R-122-12
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-12


title: a673_CRWT_rep4

description: Library name: sample 10

value: CRISPR WT


title: FXTAS-TRAP, Rep2, 3m, Cortex

description:
Library name: 19149R-122-11
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-11


title: FXTAS-TRAP, Rep4, 3m, Cortex

description:
Library name: 19149R-122-16
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-16


title: Control-TRAP, Rep3, 6m, Cortex

description:
Library name: 19149R-118-11
Column name in 6m_Cortex_TRAP_raw_read_counts.txt: 19149R-118-11


title: HFA_4

description: human-flora-associated pig replicate 3

value: human-flora-associated pig


title: HFA_3

description: human-flora-associated pig replicate 2


title: Control-TRAP, Rep1, 3m, Cortex

description:
Library name: 19149R-122-10
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-10


title: a673_iLSD1_rep3

description: Library name: sample 15

value: LSD1 knockdown


title: HFA_1

description: human-flora-associated pig replicate 1


title: FXTAS-TRAP, Rep1, 3m, Cortex

description:
Library name: 19149R-122-09
Column name in 3m_Cortex_TRAP_raw_read_counts.txt: 19149R-122-09

value: male


title: GF_3

description: germ-free pig replicate 3

value: germ-free pig


title: a673_CRWT_rep2

description: Library name: sample 8


title: GF_2

description: germ-free pig replicate 2


title: OPLC_4,The only blood sample from a patient with primary lung cancer _4

city: Xining City

first: husai

address: No. 55, South Street, Chengzhong District, Xining City, Qinghai Province

institute: Qinghai Red Corss  Hospital

description: Library name: Sample 12

data_processing:
The raw data format of Nanopore sequencing offmachine data is POD5 format, which contains all raw sequencing signals, through dorado (version: 0.8.2) software performs (Base Calling) analysis and converts POD5 format data into FASTQ format, which contains the base information of sequencing sequences (reads) and their corresponding sequencing quality information, and Pychopper (version 2.7.9) is used to prune ONT reads and recognize full-length tools. Only reads with sequence quality value less than 10 and sequences with length less than 50bp screened by chopper (version 0.7.0) were retained for subsequent analysis.
The ONT reads were aligned to ensembl reference genome mRatBN7.2 using minimap2 (version 2.27-r1193) (Li 2018) in spliced alignment mode with the command ‘mnimap2 -ax splice -uf -k14’. The detection of alternatively spliced isoforms and is implemented using the Pinfish package (github.com/nanoporetech/pinfish). The output of polished transcripts is provided in the GTF format，and transcripts assembled by long-read assembly were merged using StringTie (version 2.1.6) (Pertea et al. 2015) merge to obtain a non-redundant pool of transcripts across samples. Then, gffcompare (version 0.12.6; Parameters: -G,-R) (Pertea & Pertea 2020) were used to compare non-redundant transcripts with known transcripts of the genome to find new transcripts and new genes. Finally, we identified the transcripts as new and known by classcode's [uxijo] and [c=], and finally merged them together for subsequent analysis.
We used DESeq2 (version 1.30.1) (Love et al. 2014) to analyze the differences in transcripts and genes between the two groups. A statistical cutoff of Fold change ≥ 2 and FDR ≤ 0.05 was used to find differentially expressed genes (DEGs) and differential transcript expression (DTEs). Differential transcript usage (DTU) was performed using DEXSeq (Li et al. 2015) as implemented within IsoformSwitchAnalyzeR (version 2.2.0) (Vitting-Seerup & Sandelin 2019). We use gffcompare (version 0.12.6) (Pertea & Pertea 2020) identification of transcripts as input, A difference in isoform fraction (dlF) value between the two conditions and an FDR adjusted p-value were calculated for Each isoform. We considered isoforms with an adjusted P value lower than 0.05 as exhibiting DTU, regardless of dIF. At the gene level, the lowest adjusted p-value of any isoform was considered to be the p-value for the gene, therefore genes with at least one significant isoform were considered significant.
SUPPA2 (version 2.3) (Trincado et al. 2018) was used for calling AS differences. For each identified AS event, the splicing level was defined by Percentage of Spliced-In (PSI) while the mean difference of splicing levels between two groups was measured by ΔPSI (dPSI) and by the P-value from independent T-tests against PSIs in the two groups. We screened out the difference AS with dPSI ≥ 0.05 and P value ≤ 0.05 for analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
For each sample, 500 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9 μl with nuclease free water. Reactions were prepared (9 μl total RNA, 1 μl 10 μM VNP primer, 1 μl 10 mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. 1 μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, then held at 4°C. DNA library were set up for each cDNA (2 μl PR1 Primer, 2 μl PR2 Primer, 20 μl first-strand cDNA, 25 μl LongAmp Taq 2x master mix, 1 μl nuclease free water), and cycled for [3 min at 94°C] ×1 cycle, [15 s at 94°C, 15 s at 50°C, 2 min at 65°C] ×12 cycles, [10 min at 65°C] ×1 cycle, then held at 4°C. cDNA were added barcodes using the Native Barcode Kit 96 V14 (SQK-NBD114.96) following manufacturer’s guidelines. Each barcoded DNA was purified in 1× Ampure XP Beads, eluted in 20 μl of nuclease free water and quantified using Qubit. Finally, 300 fmol of adapter ligated library was loaded onto a PromethION flow cell.
For Long‑read sequencing, the libraries were prepared for following the manufacturer's instructions and applied to MinION system sequencing.


title: a673_CRKO_rep6

description: Library name: sample 6

value: LSD1 KO

value: CRISPR KO


title: OPLC_3,The only blood sample from a patient with primary lung cancer _3

description: Library name: Sample 11


title: OPLC_2,The only blood sample from a patient with primary lung cancer _2

description: Library name: Sample 10


title: FXTAS, Rep4, 6m, Hippocampus

description:
Library name: 19149R-87-15
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-15

source_name: Hippocampus

value: Hippocampus

value: 6 months

value: bulk tissue

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: a673_CRKO_rep5

description: Library name: sample 5

value: Ewing sarcoma


title: OPLC_1,The only blood sample from a patient with primary lung cancer _1

description: Library name: Sample 9


title: MPC_4,Blood samples from patients with multiple primary cancers _4

description: Library name: Sample 8


title: SPF_2

description: specific pathogen-free pig replicate 1


title: a673_CRWT_rep3

description: Library name: sample 9


title: MPC_2,Blood samples from patients with multiple primary cancers _2

description: Library name: Sample 6


title: a673_CRKO_rep4

description: Library name: sample 4


title: Control, Rep2, 6m, Hippocampus

description:
Library name: 19149R-87-12
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-12

value: Control


title: a673_CRKO_rep3

description: Library name: sample 3


title: HC_3,Blood sample of a healthy person _3

description: Library name: Sample 3

source_name: Blood sample of a healthy person

value: Blood sample of a healthy person


title: HC_4,Blood sample of a healthy person _4

description: Library name: Sample 4


title: a673_CRWT_rep1

description: Library name: sample 7

value: wildtype


title: MPC_1,Blood samples from patients with multiple primary cancers _1

description: Library name: Sample 5


title: FXTAS, Rep2, 6m, Hippocampus

description:
Library name: 19149R-87-11
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-11


title: a673_CRKO_rep1

description: Library name: sample 1


title: GF_1

description: germ-free pig replicate 1

value: adipose


title: FXTAS, Rep1, 6m, Hippocampus

description:
Library name: 19149R-87-10
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-10


title: HC_2,Blood sample of a healthy person _2

description: Library name: Sample 2


title: HC_1,Blood sample of a healthy person _1

description: Library name: Sample 1


title: RNA-seq_rice_seedling_IAA treatment, rep2

city: Chicago

first: CHUAN

last: HE

state: Illinois

address: 929 East 57th Street, GCIS E313

institute: University of Chicago

description: Library name: IAA_2_RNA_seq

data_processing:
We aligned RNA-seq reads to Oryza sativa (MSU7.0) reference genome using Hisat 2. For paired-end 150 bp reads, 100 bp sequences at the 3' end of the reads were trimmed with the parameter “-3 100”. SAMtools  was used to filter the low quality and duplicated reads using the parameters “-F 4 -q 20”. We determined the Expression level TPM by using Featurecounts . The differential expression level using the R package ‘Deseq2’.
Assembly: Msu7.0
Supplementary files format and content: fastq

organism: Oryza sativa

source_name: seedling

extract_protocol:
A total of 50 ug total RNA for each of the two biological replicates was used for mRNA capture (Dynabeads mRNA DIRECT Purification Kit (Invitrogen)) following the manufacturer′ s instructions with modification. Briefly, 50 ug total RNA was diluted with H2O in 100ul volume and then denatured under 65°C for 2 min, and immediately put on the ice for exactly 2 min. Next, a total of 100ul Dynabeads were washed twice with 200ul lysis/binding buffer provided in the above kit. The washed beads were then eluted in 100ul lysis/binding buffer, which further mixed with the denatured total RNA. Then, the sample was put on the rotor to binding for 15 min at room temperature. After binding, wash buffer B was used to wash the beads for twice. 30ul H2O was used to elute the beads and immediately put on the 75°C for 2min. The eluted mRNA was collected after magnetic separation. The mRNA capture process was repeated as described above to obtain the more purified mRNA.
50ng mRNAs of each replicate were used for the library construction. All these libraries were constructed exactly following the previously published protocols

value: seedling


title: RNA-seq_rice_seedling_IAA treatment, rep1

description: Library name: IAA_1_RNA_seq


title: Control, Rep4, 6m, Hippocampus

description:
Library name: 19149R-87-16
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-16


title: in vivo ARS-1620 xenograft experiment

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

description:
Library name: invivo_ARS1620
10x GEX from human cell-line xenografts grown in immunodeficient mice; includes cellranger outputs, demuxlet calls (*.best), and integrated h5ad

data_processing:
Raw single-cell FASTQ files were used as input into the 10X Cell Ranger pipeline with default parameters. Briefly, reads were aligned to the hg38 transcriptome using STAR generating a filtered feature-barcode matrix and bam alignment file.
Pooled scRNA-Seq experiments were demultiplexed into individual cell lines using Demuxlet with the CB tag, setting the fixed mixing proportion, alpha, to 0.5. Demultiplexing of single cell barcodes into drug treatments using hashtag oligos (HTOs) was performed using pymulti from the scEasyMode python library (https://github.com/johnnyUCSF/scEasyMode) , Multiplexed scRNA-Seq count matrices were processed using scanpy. Counts were normalized (normalize_per_cell) and, log-transformed (log1p). Additionally, droplets predicted as doublets by demuxlet were removed. Normalized count matrices were used to calculate PCA, leiden clusters, and UMAP representations.
Assembly: hg38 cellranger reference
Supplementary files format and content: cellranger counts outputs: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz
Supplementary files format and content: processed anndata objects with cell line and drug treatment calls

source_name: xenograft (mouse host)

growth_protocol: Cell lines were grown in RPMI complete, 10% FBS with 1X Pen-strep. Cells were seeded in 6 well plates at 50k/well for a T0 time point. After 72 hours, cells were harvested by trypsin and counted to arrive at total cell numbers. Growth rates were calculated by the following formula: r = ln(Y t/Y 0)/t. Cell line pooling for GENEVA was performed by harvesting all cell lines simultaneously by trypsin digestion, washing in 1X PBS, counting, and inversely balancing against growth rate. Cells were seeded at specific numbers inverse to the growth rate into a single sterile tube and then mixed well before plating into separate wells in vitro, or injections into different mice for flank xenograft studies. All cell line pooling was performed in less than 2 hours total time to ensure healthy cell pools.

extract_protocol:
ells were prepared for single-cell RNA sequencing by trypsin digestion for 10 minutes at 37C when harvested from in-vitro culture. For harvest of organoids and in-vivo xenograft tumors, cells were harvested by resection, chopping with a razor blade into a slurry, and then resuspension in 1 mg/mL Liberase TM. Suspensions were incubated shaking at 37C at 150 RPM for 45 minutes after which cells were resuspended in ACK buffer and incubated at room temperature for 10 minutes. Resuspension in 1X PBS was performed two times following this for wash and removal of digestion buffers. Cells were passed through a 70 micron mesh filter to arrive at single-cell suspensions.
Cell suspensions were then hashed using HTO oligos or Totalseq-A antibodies. Cell suspensions were assigned unique oligo-HTO or antibody-HTOs at the point of experimentation. Cells were incubated with corresponding HTO conjugate for 20 minutes on ice. Cells were then washed 3X in 1X cold PBS and then recounted. Cells were then pooled together from multiple hashed suspensions such that there were equivalent numbers of cells from each suspension prior to 10X single-cell preparation. All single-cell studies were hashed in this way. GENEVA libraries were prepared according to single-cell RNA sequencing Chromium kit instructions. Modifications were performed after the cDNA step in which the small fractions were harvested and then amplified in separate PCR reactions for enrichment of the hashtag reads, also as specified in Chromium kit. Sequencing was performed for the transcriptome and hashtag libraries at a 95%/5% ratio (transcriptome/hashtag). Sequencing targets were 25,000 reads/cell based on expected cell counts determined by number of cells loaded at input into the chromium kit.

treatment_protocol: In vitro compound treatments were prepared by diluting the compound to final concentration in 1X RPMI complete, 10%FBS, pen-strep with no more than 1% DMSO in the final solution. Combination treatments were prepared in the same way. In vitro treatments received media changes with fresh compound dilutions every 48 hours. In vivo delivery was formulated as specified for the specific study and dosed by standard IP or PO dosing.

value: xenograft (mouse host)

value: Mixed human cell lines

value: human tumor cells

value: KRAS G12C/D/V/A

value: ARS-1620 treatment


title: MPC_3,Blood samples from patients with multiple primary cancers _3

description: Library name: Sample 7


title: Control, Rep1, 6m, Hippocampus

description:
Library name: 19149R-87-09
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-09

value: male


title: PDO ARS-1620 lung cancer organoid experiment

description:
Library name: pdo_ARS1620
10x Gene Expression from lung cancer PDO pools treated with ARS-1620 at varying doses; includes CellRanger matrix files, demuxlet assignments (*.best), bulk RNA demultiplexing FASTQs, and integrated h5ad

source_name: patient-derived organoid (lung cancer)

value: patient-derived organoid (lung cancer)

value: Mixed PDO models

value: human tumor organoid cells

value: KRAS G12C/G12D/ALK fusion/EGFR L858R

value: ARS-1620 dosage series


title: RNA-seq_rice_seedling_ABA treatment, rep1

description: Library name: ABA_1_RNA_seq


title: Control, Rep4, 6m, Cerebellum

description:
Library name: 19149R-81-32
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-32

value: Cerebellum

value: 6 months

value: bulk tissue


title: RNA-seq_rice_seedling_dark to light 24h, rep2

description: Library name: 24h_2_RNA_seq


title: t0 H2122

description:
Library name: L579
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

library_source: genomic

data_processing:
Raw sequencing reads were aligned and counted to quantify the abundance of each unique sgRNA barcode in the gDNA samples. Raw counts were normalized and corrected for lentiviral transduction and sequencing bias.
A binomial (logit) model was fit to compare sgRNA counts across the Sotorasib-treated and vehicle-treated samples. The sgRNA counts were normalized using bestNormalize, and the resulting fitness scores (Rho values) were aggregated per gene to derive a combined z-score reflecting the gene's dependency in the presence of Sotorasib
Assembly: hg38 cellranger reference
Supplementary files format and content: screen_guides.xlsx contains guide sequences, sgRNA_raw_counts.txt contains the guide counts per library, res_* files include guide results for specified conditions
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: Lung Cancer

growth_protocol: Cell lines were grown in RPMI complete, 10% FBS with 1X Pen-strep. For xenograft formation, cells were prepared at 20 million cells per milliliter. Pooled cell lines (H358, H2122, H23, H441) transduced with the dual sgRNA library were injected subcutaneously at $100~\mu\text{L}$ per flank in a 1:1 ratio of 1X PBS to Matrigel into NSG mice.

extract_protocol:
On day 14, tumors were resected and snap-frozen. Genomic DNA (gDNA) was extracted from the excised tumors for guide RNA sequencing using the NucleoSpin Blood XL kit following manufacturer instructions.
sgRNA sequences were amplified from the gDNA using custom PCR primers. The amplified gRNA library was prepared for sequencing to quantify the relative abundance of each guide RNA in the harvested tumor samples. The libraries were constructed to accommodate the short read length necessary to capture the guide sequence.

treatment_protocol: Sotorasib ($100~mg/\text{kg}$) or vehicle control was administered by daily oral gavage in $100~\mu\text{L}$ volume for 13 days, starting 2 days after tumor implantation. The drug formulation consisted of 10% DMSO, 70% Labrasol, and 20% water.

value: Lung Cancer

value: Cancer Cell Line

value: KRAS G12C

value: T0 (Baseline)


title: FXTAS, Rep4, 6m, Cerebellum

description:
Library name: 19149R-81-31
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-31

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: FXTAS, Rep3, 6m, Hippocampus

description:
Library name: 19149R-87-13
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-13

value: Hippocampus


title: t0 H2030

description:
Library name: L578
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: t0 H441

description:
Library name: L577
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12V


title: RNA-seq_rice_seedling_dark, rep2

description: Library name: 0h_2_RNA_seq

value: seedling


title: Control, Rep3, 6m, Cerebellum

description:
Library name: 19149R-81-30
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-30

value: male

value: Control


title: RNA-seq_rice_seedling_dark to light 8h, rep1

description: Library name: 8h_1_RNA_seq


title: Control, Rep3, 6m, Hippocampus

description:
Library name: 19149R-87-14
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-87-14


title: RNA-seq_rice_seedling_dark, rep1

description: Library name: 0h_1_RNA_seq


title: rice_seedling_IAA treatment ,rep2

description: Library name: IAA_2_ATAC

data_processing:
We aligned ATAC-seq reads to Oryza sativa (MSU7.0) reference genome using Bowtie 2 (version 2.3.2.)(34). For paired-end 150 bp reads, 100 bp sequences at the 3' end of the reads were trimmed with the parameter “-3 100”. SAMtools (version 1.9)(35) was used to filter the low quality and duplicated reads using the parameters “-F 4 -q 20”. The bigwig files were generated by deepTools (version 2.5.3)(36). MACS2 was used for ATAC peak calling. We determined the peaks with high reproducibility scores shared between the two biological replicates by using the IDR (Irreproducibility Discovery Rate). The differential binding events were identified using the R package ‘DiffBind’.
Assembly: Msu7.0
Supplementary files format and content: narrowpeak

extract_protocol:
Freshly collected seedlings were immediately chopped with a razor blade for 5 min in 100 μL lysis buffer (20 mM MES, pH 5.7, 0.6M Mannitol, 10 mM MgCl2, 10 mM KCl, 0.1% 2-mercaptoethanol and 0.2% Triton X-100, 1x PI (protease inhibitor)) on ice (two biological replicates were performed) according to our previous work(10) . Thereafter the chopped slurry was washed into 1 ml lysis buffer in a 1.5ml tube and incubated for 5 min on ice with gentle shaking. The mixture was filtered through a 40-μm filter into a new tube, followed by centrifugation at 500 g for 8 min (4 °C). Then, we resuspended the precipitation with 150 µl wash buffer (20 mM Tris-HCl pH 7.8, 10 mM MgCl2, 60 mM KAc pH 5.6).
The above washed 50,000 nuclei were then tagged with TS-Tn5 at 37ºC for 30 min following the kit’s instructions (Vazyme, TD501). After tagging, the integration products were purified using DNA Purification Kit (ZYMO, D4004) and then amplified using Q5 high fidelity DNA polymerase (New England Biolabs, M0491S) for 10-15 cycles. The libraries were sequenced on Illumina HiSeq X Ten with paired-end reads of 150-bp

value: IAA treatment


title: RNA-seq_rice_seedling_ABA treatment, rep2

description: Library name: ABA_2_RNA_seq


title: t0 H23

description:
Library name: L576
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: rice_seedling_IAA treatment ,rep1

description: Library name: IAA_1_ATAC


title: rice_seedling_ABA treatment ,rep2

description: Library name: ABA_2_ATAC

value: ABA treatment


title: Control, Rep2, 6m, Cerebellum

description:
Library name: 19149R-81-28
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-28


title: in vivo H2122 veh 3R

description:
Library name: L575
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

source_name: Xenograft Tumor

value: Xenograft Tumor

value: Cancer Cells (in vivo)

value: Vehicle (DMSO)


title: a673_CRKO_rep2

description: Library name: sample 2

value: Ewing sarcoma

value: LSD1 KO

value: CRISPR KO


title: rice_seedling_ABA treatment ,rep1

description: Library name: ABA_1_ATAC


title: FXTAS, Rep2, 6m, Cerebellum

description:
Library name: 19149R-81-27
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-27

value: Cerebellum

value: 6 months

value: bulk tissue


title: FXTAS, Rep1, 6m, Cerebellum

description:
Library name: 19149R-81-26
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-26

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: in vivo H2122 veh 3L

description:
Library name: L574
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12C


title: rice_seedling_dark to light 24h ,rep1

description: Library name: 24h_1_ATAC

value: dark to light 24h


title: rice_seedling_dark to light 24h ,rep2

description: Library name: 24h_2_ATAC


title: RNA-seq_rice_seedling_dark to light 24h, rep1

description: Library name: 24h_1_RNA_seq

value: seedling


title: Control, Rep1, 6m, Cerebellum

description:
Library name: 19149R-81-25
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-25

value: male


title: rice_seedling_dark to light 8h ,rep1

description: Library name: 8h_1_ATAC

value: dark to light 8h


title: RNA-seq_rice_seedling_dark to light 8h, rep2

description: Library name: 8h_2_RNA_seq


title: rice_seedling_dark,rep2

description: Library name: 0h_2_ATAC

value: dark


title: in vivo H2122 veh 2L

description:
Library name: L572
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: FXTAS, Rep3, 6m, Cerebellum

description:
Library name: 19149R-81-29
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-29


title: WT_23

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

description: Library name: Snumber23

data_processing:
Sample quality control was performed using the Agilent 2100 Bioanalyzer.
Sequencing was performed on the Illumina NextSeq 500 with Paired End 43bp × 43bp reads.
Sequencing data was demultiplexed using Illumina's bcl2fastq2. De-multiplexed read sequences were then aligned to the Mus Musculous (PAR-masked)/mm10 reference sequence using STAR aligner. Quality control led to one outlier sample (genotype -/-) being removed.
De-multiplexed read sequences were then aligned to the Mus Musculous (PAR-masked)/mm10 reference sequence using STAR aligner.
Quality control led to one outlier sample (genotype -/-) being removed.
Assembly: mm10
Supplementary files format and content: Tab delimited txt files containing the raw counts for each sample.

source_name: hippocampus

extract_protocol:
Dissected brain tissue was homogenized in Trizol (Thermo Fisher) to protect against RNA degradation. Chloroform (50ul) was then added, and the tissue and shaken for 20 seconds before a 15-minute incubation at room temperature. Samples were centrifuged (14000rpm, 15 minutes at 4°C) and the aqueous phase was transferred to 70% ethanol. RNA extraction was performed using the Qiagen RNasy minikit (cat #74108 Thermo Fisher), while DNA was synthesized using the qScript cDNA Synthesis Kit (cat#101414-100, Quanta Bioscience).
Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

value: hippocampus

value: Female


title: WT_24

description: Library name: Snumber24


title: Control, Rep4, 6m, Cortex

description:
Library name: 19149R-81-16
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-16

value: Cortex

value: Control


title: KO_22

description: Library name: Snumber22


title: Control, Rep3, 6m, Cortex

description:
Library name: 19149R-81-14
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-14


title: KO_21

description: Library name: Snumber21


title: in vivo H2122 veh 1L

description:
Library name: L570
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Xenograft Tumor

value: Cancer Cells (in vivo)

value: Vehicle (DMSO)


title: in vivo H2122 soto 3R

description:
Library name: L569
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Sotorasib


title: WT_20

description: Library name: Snumber20


title: rice_seedling_dark,rep1

description: Library name: 0h_1_ATAC


title: rice_seedling_dark to light 8h ,rep2

description: Library name: 8h_2_ATAC


title: FXTAS, Rep2, 6m, Cortex

description:
Library name: 19149R-81-13
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-13

value: 6 months


title: WT_19

description: Library name: Snumber19


title: Control, Rep2, 6m, Cortex

description:
Library name: 19149R-81-12
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-12

value: bulk tissue


title: in vivo H2122 soto 2R

description:
Library name: L567
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: WT_17

description: Library name: Snumber17


title: KO_18

description: Library name: Snumber18


title: KO_16

description: Library name: Snumber16


title: WT_15

description: Library name: Snumber15


title: FXTAS, Rep1, 6m, Cortex

description:
Library name: 19149R-81-11
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-11

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: WT_14

description: Library name: Snumber14


title: in vivo H2122 soto 2L

description:
Library name: L566
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12C


title: FXTAS, Rep3, 6m, Cortex

description:
Library name: 19149R-81-15
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-15


title: KO_12

description: Library name: Snumber12


title: KO_13

description: Library name: Snumber13


title: Control, Rep1, 6m, Cortex

description:
Library name: 19149R-81-09
Column name in FXTAS_bulk_raw_read_counts.txt: 19149R-81-09


title: in vivo H2122 veh 1R

description:
Library name: L571
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: Control, Rep4, 3m, Hippocampus

description:
Library name: 21154R-01-36
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-36

value: Hippocampus

value: 3 months


title: in vivo H2122 soto 1R

description:
Library name: L565
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: WT_10

description: Library name: Snumber10


title: WT_11

description: Library name: Snumber11


title: in vivo H2122 soto 1L

description:
Library name: L564
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: KO_9

description: Library name: Snumber9


title: KO_8

description: Library name: Snumber8


title: FXTAS, Rep3, 3m, Hippocampus

description:
Library name: 21154R-01-34
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-34

value: male


title: WT_5

description: Library name: Snumber5


title: FXTAS, Rep4, 3m, Hippocampus

description:
Library name: 21154R-01-35
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-35


title: in vivo H2030 veh 3R

description:
Library name: L563
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: KO_6

description: Library name: Snumber6


title: KO_4

description: Library name: Snumber4


title: in vivo H2030 veh 3L

description:
Library name: L562
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: in vivo H2122 soto 3L

description:
Library name: L568
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: in vivo H2030 veh 2L

description:
Library name: L560
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: WT_3

description: Library name: Snumber3


title: Control, Rep3, 3m, Hippocampus

description:
Library name: 21154R-01-33
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-33


title: WT_1

description: Library name: Snumber1


title: Sucnr1-KO S8

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcl2fastq-1.8.4 pipeline (Illumina).
Sequencing adapter contaminations and the first 6 nucleotides at the 5’end were removed with cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38.99
Supplementary files format and content: Ensembl gene and transcript IDs, and RSEM-estimated raw counts for 55,471 annotated genes, in each sample.

source_name: Bone marrow

extract_protocol:
Spine, hips, femur, tibia, sternum and humerus were harvested. For each mice, bones were pooled and bone marrow (BM) extracted by crushing the bones in cold PBS followed by filtration with 40µm cell strainer.  After erythrocyte lysis, cells were stained with antibody mixes and FACS-sorted using BD Aria III cell sorter. Total RNA was isolated using the Arcturus Picopure RNA isolation kit (Arcturus – Thermo Fisher) from small numbers of FACS-sorted cells (27000 – 75000).
RNA was amplified with the NEBNext Single cell/Low input RNA libray kit v. 3.0 (NEB#E6420) following the protocol to the fragmentation step. cDNA was fragmented to target size of 150 base pairs with Covaris M220. Libraries were prepared with TruSeq RNA library preparation kit v. 2.0 (RS#122-2001, Illumina) starting the protocol from “perform end repair” to final library. Libraries were sequenced with the NextSeq550 instrument (Illumina) at the GSCT (UiT – The Arctic University of Norway). 3-4 biological replicates were used per experimental group. The quantity of the Illumina libraries was determined using dsDNA - Qubit High Sensitivity and fragment size was determined by Agilent Technologies 2100 Bioanalyzer using the Agilent DNA 1000 chip.

value: Bone marrow

value: Lineage- Sca1+ cKit+ (LSK)


title: Control, Rep2, 3m, Hippocampus

description:
Library name: 21154R-01-32
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-32


title: in vivo H2030 veh 2R

description:
Library name: L561
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: KO_2

description: Library name: Snumber2

value: hippocampus


title: FXTAS, Rep2, 3m, Hippocampus

description:
Library name: 21154R-01-31
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-31


title: WT S6

value: WT


title: A2-1

description:
Library name: sample4
treatment-1 (FPKM)

source_name: Lung tissue

value: Lung tissue

value: lung homogenate

value: wild type

value: Treatment Group


title: Sucnr1-KO S7


title: in vivo H2030 soto 3L

description:
Library name: L558
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Xenograft Tumor

value: Cancer Cells (in vivo)


title: WT S5


title: Control, Rep1, 3m, Hippocampus

description:
Library name: 21154R-01-29
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-29

value: Control


title: Sucnr1-KO S3


title: FXTAS, Rep1, 3m, Hippocampus

description:
Library name: 21154R-01-30
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-30

value: bulk tissue


title: in vivo H2030 soto 1R

description:
Library name: L557
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Sotorasib


title: in vivo H2030 soto 1L

description:
Library name: L556
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12C


title: WT S1


title: Control, Rep4, 3m, Cerebellum

description:
Library name: 21154R-01-22
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-22

value: Cerebellum


title: NIPC 4 hours post perfusion T2-rep 10

city: Melbourne

first: Abdul Waheed

last: Khan

state: Vic

address: 99 Commercial Road

department: Diabetes

country: Australia

institute: Monash University

description: Library name: G4-R10

data_processing:
Sequence reads underwent quality and adapter trimming with skewer. Trimmed reads were mapped to the rat genome using STAR aligner with ensembl annotations to Rattus_norvegicus.mRatBN7.2.108 and gene level RNA count matrix produced using featurecounts
Assembly: Rattus norvegicus mRatBN7
Supplementary files format and content: RNA_countmx.tsv is a tab delimited GeneID~Sample RNA counts matrix

organism: Rattus norvegicus

source_name: Myocardial

extract_protocol:
Left ventricle tissue samples were homogenized in liquid nitrogen. Total RNA was then extracted from homogenized tissue samples of all experimental groups using TRIzol reagent® (Invitrogen Australia, Mt Waverely, Vic, Australia) and Direct-zolTM RNA miniprep kit (Zymo Research; Irvine CA, USA),
NEBNext® Ribo-Zero Magnetic kit (rRNA removal) module (New England Biolabs, Ipswich, MA) was used to enrich mRNA from 1μg of total RNA. Barcoded libraries were generated using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s instructions. Deep sequencing was performed using Illumina NovaSeq PE 150 (San Diego, CA)

treatment_protocol: 1.     IPC (n=20) group of rats underwent two cycles of ischaemia-reperfusion (5 minutes each) before a sustained 13.5-minute ischemia. Successful occlusion was confirmed by observing cardiac akinesia, left ventricular blanching, and electrocardiogram changes. Reperfusion was visually confirmed after removing the suture. Tissue samples from ten rats were collected immediately after preconditioning (T1) and from another ten rats 4 hours post-surgery (T2), representing stunned myocardium. 2. NIPC (n=20) group of rats served as the control, experiencing only the sustained 13.5-minute ischaemic insult without preconditioning cycles. Tissue samples from ten rats were collected immediately after the chest incision (T1) and from another ten rats 4 hours after surgery (T2), representing infarcted myocardium.

value: Myocardial

value: Wild type

value: ischaemia-reperfusion injury

tag: sample group

value: NIPC 4 hours post perfusion T2


title: NIPC 4 hours post perfusion T2-rep 8

description: Library name: G4-R8


title: in vivo H441 veh 3R

description:
Library name: L555
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12V

value: Vehicle (DMSO)


title: FXTAS, Rep4, 3m, Cerebellum

description:
Library name: 21154R-01-21
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-21

value: 3 months

value: male

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: FXTAS, Rep3, 3m, Cerebellum

description:
Library name: 21154R-01-20
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-20


title: NIPC 4 hours post perfusion T2-rep 5

description: Library name: G4-R5


title: in vivo H2030 soto 3R

description:
Library name: L559
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: in vivo H441 veh 3L

description:
Library name: L554
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: NIPC 4 hours post perfusion T2-rep 9

description: Library name: G4-R9


title: Control, Rep3, 3m, Cerebellum

description:
Library name: 21154R-01-19
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-19


title: NIPC 4 hours post perfusion T2-rep 4

description: Library name: G4-R4


title: in vivo H441 soto 2R

description:
Library name: L552
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: Control, Rep2, 3m, Cerebellum

description:
Library name: 21154R-01-18
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-18


title: NIPC 4 hours post perfusion T2-rep 1

description: Library name: G4-R1


title: WT S2

value: Bone marrow

value: Lineage- Sca1+ cKit+ (LSK)

value: WT


title: in vivo H441 veh 1L

description:
Library name: L553
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Xenograft Tumor

value: Cancer Cells (in vivo)


title: NIPC 4 hours post perfusion T2-rep 2

description: Library name: G4-R2


title: IPC 4 hours post perfusion T2-rep 10

description: Library name: G3-R10

value: IPC 4 hours post perfusion T2


title: NIPC 4 hours post perfusion T2-rep 3

description: Library name: G4-R3


title: FXTAS, Rep1, 3m, Cerebellum

description:
Library name: 21154R-01-16
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-16

value: bulk tissue


title: IPC 4 hours post perfusion T2-rep 8

description: Library name: G3-R8


title: IPC 4 hours post perfusion T2-rep 9

description: Library name: G3-R9


title: IPC 4 hours post perfusion T2-rep 7

description: Library name: G3-R7


title: in vivo H441 soto 1L

description:
Library name: L550
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Sotorasib


title: IPC 4 hours post perfusion T2-rep 5

description: Library name: G3-R5

value: Myocardial


title: IPC 4 hours post perfusion T2-rep 6

description: Library name: G3-R6

value: Wild type


title: in vivo H441 soto 2L

description:
Library name: L551
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: Control, Rep1, 3m, Cerebellum

description:
Library name: 21154R-01-15
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-15

value: Cerebellum

value: Control


title: NIPC 4 hours post perfusion T2-rep 7

description: Library name: G4-R7

value: ischaemia-reperfusion injury

value: NIPC 4 hours post perfusion T2


title: in vivo H23 veh 2R

description:
Library name: L549
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12C

value: Vehicle (DMSO)


title: Control, Rep4, 3m, Cortex

description:
Library name: 21154R-01-08
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-08

value: Cortex

value: 3 months

value: male


title: IPC 4 hours post perfusion T2-rep 4

description: Library name: G3-R4


title: NIPC 4 hours post perfusion T2-rep 6

description: Library name: G4-R6


title: in vivo H23 veh 2L

description:
Library name: L548
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: IPC 4 hours post perfusion T2-rep 3

description: Library name: G3-R3


title: FXTAS, Rep4, 3m, Cortex

description:
Library name: 21154R-01-07
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-07

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: IPC 4 hours post perfusion T2-rep 2

description: Library name: G3-R2


title: IPC 4 hours post perfusion T2-rep 1

description: Library name: G3-R1


title: FXTAS, Rep2, 3m, Cerebellum

description:
Library name: 21154R-01-17
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-17


title: IPC baseline T1-rep 10

description: Library name: G2-R10

value: IPC baseline T1


title: in vivo H23 veh 1R

description:
Library name: L547
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Xenograft Tumor

value: Cancer Cells (in vivo)


title: IPC baseline T1-rep 9

description: Library name: G2-R9


title: in vivo H23 veh 1L

description:
Library name: L546
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: IPC baseline T1-rep 7

description: Library name: G2-R7


title: Control, Rep3, 3m, Cortex

description:
Library name: 21154R-01-05
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-05

value: bulk tissue


title: in vivo H23 soto 3R

description:
Library name: L545
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Sotorasib


title: FXTAS, Rep3, 3m, Cortex

description:
Library name: 21154R-01-06
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-06


title: IPC baseline T1-rep 8

description: Library name: G2-R8

value: Myocardial


title: Control, Rep2, 3m, Cortex

description:
Library name: 21154R-01-04
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-04


title: in vivo H2122 veh 2R

description:
Library name: L573
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: in vivo H23 soto 3L

description:
Library name: L544
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: IPC baseline T1-rep 6

description: Library name: G2-R6

value: Wild type


title: IPC baseline T1-rep 5

description: Library name: G2-R5


title: FXTAS, Rep2, 3m, Cortex

description:
Library name: 21154R-01-03
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-03


title: in vivo H23 soto 1R

description:
Library name: L543
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: IPC baseline T1-rep 3

description: Library name: G2-R3


title: IPC baseline T1-rep 2

description: Library name: G2-R2


title: FXTAS, Rep1, 3m, Cortex

description:
Library name: 21154R-01-02
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-02


title: IPC baseline T1-rep 1

description: Library name: G2-R1


title: Control, Rep1, 3m, Cortex

description:
Library name: 21154R-01-01
Column name in FXTAS_bulk_raw_read_counts.txt: 21154R-01-01


title: NIPC baseline T1-rep 10

description: Library name: G1-R10

value: NIPC baseline T1


title: in vitro H2122 veh

description:
Library name: L541
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Lung Cancer

value: Cancer Cell Line


title: NIPC baseline T1-rep 9

description: Library name: G1-R9

value: ischaemia-reperfusion injury


title: GH4913

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

description:
Library name: GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 5
GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 5

data_processing:
RNA reads were aligned using STAR 2.7.0f with default settings.
Cutadapt was used for adapter trimming and quality control.
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: Excel file of normed counts (RNA-seq)

source_name: adenocarcinoma cells

growth_protocol: Cell lines use typical growth protocols with DMEM 10% FBS. All cells were grown 24h on media with 10% charcoal stripped serum before dexamethasone treatment.

extract_protocol:
Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep.

treatment_protocol: Dexamethasone treatments were 100 nano-molar for 2h.

value: adenocarcinoma cells

value: GRKO GFP-mGR W718S/Y722S

value: Dex 100nM 2h


title: NIPC baseline T1-rep 8

description: Library name: G1-R8


title: in vitro H2122 soto

description:
Library name: L540
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12C


title: GH4912

description:
Library name: GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 4
GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 4


title: NIPC baseline T1-rep 6

description: Library name: G1-R6


title: NIPC baseline T1-rep 7

description: Library name: G1-R7


title: NIPC baseline T1-rep 5

description: Library name: G1-R5


title: in vitro H2030 soto

description:
Library name: L538
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: NIPC baseline T1-rep 3

description: Library name: G1-R3


title: in vitro H2030 veh

description:
Library name: L539
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: Vehicle (DMSO)


title: GH4910

description:
Library name: GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 2
GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 2


title: GH4911

description:
Library name: GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 3
GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 3


title: in vivo H23 soto 1L

description:
Library name: L542
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: GH4909

description:
Library name: GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 1
GRKO GFP-mGR W718S/Y722S 100nM Dex 2h Replicate 1


title: in vitro H441 veh

description:
Library name: L537
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).

value: KRAS G12V


title: NIPC baseline T1-rep 4

description: Library name: G1-R4


title: IPC baseline T1-rep 4

description: Library name: G2-R4

value: IPC baseline T1


title: in vitro H441 soto

description:
Library name: L536
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: GH4908

description:
Library name: GRKO GFP-mGR W718S/Y722S Veh Replicate 5
GRKO GFP-mGR W718S/Y722S Veh Replicate 5

value: Vehicle


title: NIPC baseline T1-rep 2

description: Library name: G1-R2


title: in vitro H23 veh

description:
Library name: L535
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: NIPC baseline T1-rep 1

description: Library name: G1-R1


title: GH4907

description:
Library name: GRKO GFP-mGR W718S/Y722S Veh Replicate 4
GRKO GFP-mGR W718S/Y722S Veh Replicate 4


title: in vitro H23 soto

description:
Library name: L534
Pooled CRISPRi screen data derived from genomic DNA (gDNA) samples. Raw sequencing reads (R1/R2) were merged across technical replicates and aligned to the sgRNA library reference. The final sgRNA read counts for each sample are provided in the merged count matrix (sgRNA_raw_counts.txt), which serves as the input for differential enrichment analysis (results found in res_logit_* files).


title: GH4906

description:
Library name: GRKO GFP-mGR W718S/Y722S Veh Replicate 3
GRKO GFP-mGR W718S/Y722S Veh Replicate 3


title: GH4905

description:
Library name: GRKO GFP-mGR W718S/Y722S Veh Replicate 2
GRKO GFP-mGR W718S/Y722S Veh Replicate 2


title: 29 week-NCAR-control-14dn-rep4

city: Potomac

first: Jennifer

last: Smith

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 29-NCAR-r4
library name V2: 22
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

data_processing:
Step 1: RNA-seq data were processed using R packages using a custom workflow using SnakeMake workflow management system for reproducibility. The workflow included adapter read trimming using Trimmomatic (Bolger, Lohse and Usadel, 2014).
Step 2: Sequences were reference aligned to GRCh using STAR (Dobin et al., 2013)
Step 3: Transcripts were quantified at gene-level resolution using the R software package featureCounts (Liao, Smyth and Shi, 2014). Read duplicates were removed by using –ignoreDups setting in R:featureCounts.
Step 4: RNA-seq QC was performed using MultiQC, dupRadar and GATK estimate of library complexity.
Step 5: Next, data for some samples were excluded based on data quality (technical omissions) as indicated in the methods section of the manuscript. Data were omitted for three reasons:  1) RNA quality score (RQS) < 8; 2) low RNA integrity (RIN) <6 and 3) low RNA-seq quality based on the analysis of metrics in Step 4.
Step 6: RNA-seq data from all 24 AD-iCAP batches were merged into a single file and several preprocessing steps were performed in R to detect and correct technical noise in the data to reduce error as described below in the following steps. First, genes were filtered to remove those below the limit of detection. To do this, ERCC controls were removed and a histogram of expression levels for each gene across all patient samples was generated, showing a bimodal curve indicating some genes were below the limit of detection. A threshold was selected to separate the curves corresponding to 35 counts and genes were filtered to remove those below this threshold for greater than 10% of the samples.
Step 7: Next, data for a subset of samples were excluded based on patient class uncertainty. Samples with class uncertainty included those with conflicting amyloid beta (Aβ) pathology from cerebrospinal fluid (CSF) and positron emission tomography (PET) imaging, CSF Aβ₄₂ values near the diagnostic threshold, or absence of Aβ data at the time of blood draw. Codes include: F1, those with conflicting PET and CSF data for presence of AB pathology;  F2, no AB pathology data at time of blood draw or only CSF AB42 data that is close to threshold; F3, longitudinal AB data show transition from AD  to normal pathology; F4, CSF AB42 value is close to threshold of pathogenic levels.
Step 8: Counts were adjusted to correct for GC bias using either full quantile normalization (FQN) or conditional quantile normalization (CQN) determined by the R-EdgeR package.
Step 9: Data were normalized for heteroskedasticity by variance transformation (VST) using the DESeq2 package and batch corrected using the removeBatchEffect function from the R package Limma (Ritchie et al., 2015).
Step 10: For RNA-seq data generated with mouse plasma, differential expression analysis was performed using R-DESeq2 (Love, Huber and Anders, 2014). GSEA analysis was applied using the R-fgsea package. Raw gene-level counts were normalized using the median-of-ratios method, and a negative binomial generalized linear model was fit with design ~ condition. Wald tests were used to evaluate pairwise contrasts between conditions, and p-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate. Genes with FDR < 0.05 were considered differentially expressed.
Assembly: GRCh
Supplementary files format and content: For RNA-seq data generated with human plasma, processed data included are: 1) feature_counts data containing raw feature counts (ADSBIRII.completeData.20180223.rds) and 2) processed/normalized data (as described) (all.cqn.vst_12032024_2.rds). Both are R data files.
Supplementary files format and content: For RNA-seq data generated with mouse plasma, processed data included are: 1) feature_counts data containing  raw feature counts (feature_counts_GEO2.csv and feature_counts_GEO.csv) and  2) results of differential expression analysis ( log2 fold change and FDR values). Both are .csv files with filenames corresponding to experimental condition (e.g. 2wk,29HEMI_NCAR,cqn.csv)

source_name: iCell Neurons

growth_protocol: Indicator cells were a commercially available, pan-neuronal population of human neurons (glutamatergic and GABAergic) derived from induced pluripotent stem cells (iPSCs) (iCell Neurons from Fujifilm (formerly Cellular Dynamics International (CDI)). Cells were grown according to manufacturer’s instructions with a modification to the culture duration described below. 12-well Eppendorf moat plates were coated with 0.01% poly-L-ornithine solution (Sigma P4957) for 1 h followed by 3.3 µg/mL laminin (Sigma L2020) for 1 h. Next, iCell neurons were thawed and plated a density of 488,875 cells/well in a total volume of 1 mL/well. Medium was exchanged 24 h after plating. Cells were treated after culturing for a total of 48 h.

extract_protocol:
For experiments with human plasma samples, RNA was isolated manually using an RNeasy Micro kit (Qiagen) and for experiments with mouse plasma samples, automated RNA isolation was performed using a MagMax mirVana kit (Invitrogen, A27828) on either a KingFisher Flex or a Kingfisher Duo Prime liquid handling robot as per the manufacturer’s recommendation (Thermo Fisher Scientific). Total RNA was stored at -80°C.
100 - 250 ng of total RNA from each iCAP sample was used for automated library preparation and RNA sequencing (RNA-seq) performed by Covance/Labcorp. Strand-specific library prep was performed with PolyA selection using TruSeq RNA Library Prep kit (Illumina) with unique dual indices (IDT) and resulting DNA samples were pooled and spread evenly across lanes and sequenced on a HiSeq 4000 (Illumina) with paired-end 150 bp reads yielding 20-30 M total reads per sample.

treatment_protocol: Cells were exposed to 5% plasma containing 0.2 mg/mL heparin sodium salt (Stem Cell Technologies, 07980) in PBS for 6 h.

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: mouse

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: normal

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: 29 week-HEMI-case-14dn-rep3

description:
Library name: 29-HEMI-r3
library name V2: 21
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

tag: cell type

value: MCI


title: SF11_con_2

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

country: Germany

institute: IKMB

description: Library name: SF11_con_2

data_processing:
nf-core pipeline rnaseq
We used Tophat 2 and Bowtie 2 to align reads.
Reads were mapped to mouse genome (MGI assembly version 10) using Tophat program.
Expression counts were normalized by library size.
Normalized gene expression values of the transcripts were computed by HTSeq
Assembly: GRCh38
Supplementary files format and content: comma separated values of the raw reads for each samples
Supplementary files format and content: comma separated values concerning sample information

source_name: colon

growth_protocol: Two guide RNAs (gRNAs) targeting exon 2 of the human IL22RA1 gene were designed and cloned into the gRNA–Cas9 co-expressing plasmid PX458 . To generate the universal donor plasmid for CRISPaint-mediated knockout, pCRISPaint-mNeon-PuroR was digested with BamHI to obtain the backbone, and the CMV-EGFP-T2A-PuroR fragment obtained from the plasmid VB200426 was inserted into the backbone. The mixture of the gRNA plasmid, selector plasmid , and universal donor plasmid was introduced into cells using the NEPA21 electroporation system (NEPAGENE), as previously described.

extract_protocol:
Total RNA was extracted from colonic organoids using the RNeasy Mini Kit (Qiagen). RNA quantity and integrity were assessed using RiboGreen and TapeStation; only samples with RIN >7.0 were used.
Stranded mRNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq Stranded mRNA Sample Prep Kit, following the manufacturer’s protocol.

treatment_protocol: For the rescue and Reg3a treatment experiments, human colonic organoids were treated with rmReg3a and rhREG3A. The stimuli were added 24 hours before the start of the colony-forming assay and continued throughout the experiment.

tag: tissue

value: colon

tag: cell line

value: organoid

value: intestinal organoid

tag: treatment

value: CTRL

tag: batch


title: SY8_IL22_2

description: Library name: SY8_IL22_2


title: 12 week-NCAR-control-14dn-rep4

description:
Library name: 12-NCAR-r4
library name V2: 20
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number


title: 12 week-HEMI-case-14dn-rep3

description:
Library name: 12-HEMI-r3
library name V2: 24
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: preAD


title: SF13_IL22_3

description: Library name: SF13_IL22_3


title: GH4903

description:
Library name: GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 3
GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 3

value: adenocarcinoma cells

tag: genotype

value: GRKO GFP-mGR  P643A

value: Dex 100nM 2h


title: 21 week-NCAR-control-14dn-rep4

description:
Library name: 21-NCAR-r4
library name V2: 23
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-NCAR-control-14dn-rep3

description:
Library name: 21-NCAR-r3
library name V2: 18
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)


title: SF13_con_2

description: Library name: SF13_con_2

tag: tissue

tag: cell line

tag: treatment

tag: batch


title: 29 week-HEMI-case-14dn-rep4

description:
Library name: 29-HEMI-r4
library name V2: 16
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: GH4902

description:
Library name: GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 2
GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 2

tag: genotype