title: LT_A_ctrl, Animal B15, Hippocampus

description:
RNAseq batch1
B15_Hipp_RNA


title: E31_Hippo

status: Public on Nov 20 2025

type: genomic

city: Hong Kong

first: Andrew

middle: J.

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Medicine and Therapeutics

country: Hong Kong

institute: Chinese University of Hong Kong

description:
E31
208114950097_R06C02

hyb_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

data_processing:
Raw data were processed with SeSaMe (v1.16.1)
Processed data are presented in the form of beta values.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Hippo

extract_protocol: Genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (D4069, Zymo Research) for blood or EZNA Tissue DNA Kit (D3396-02, Omega Bio-Tek) for solid tissue)

tag: tissue

value: Hippo

tag: treatment


title: LT_A_ctrl, Animal B24, Frontal_cortex

type: SRA

description:
RNAseq batch1
B24_FCTX_RNA

library_source: transcriptomic

data_processing:
Raw sequencing FASTQ files were mapped with STAR98 (v2.7.10b) with default parameters using the Mus musculus genome assembly GRCm39.
Quality control was carried out with the FastQC (v0.11.9) and MultiQC99 (v1.13a) packages.
HTSeq100 (v2.0.2) was used to obtain read counts with default options except ‘mode’ being set to ‘intersection-strict’, and ‘nonunique’ being set to ‘fraction’ for ambiguous reads. Gene counts were filtered for a minimum of at least 10 reads in a minimum number of samples, with the minimum number based on the number of animals constituting the smallest comparator group size in the experiment.
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts
Supplementary files format and content: CSV metadata file

molecule: polyA RNA

extract_protocol:
The tissues were retrieved from RNAlater (AM7021, Thermo Fisher Scientific, US), combined with the TRIzol reagent (15596018, Thermo Fisher Scientific, US) or the lysis buffer of the RNAqueous kit (AM1912, Thermo Fisher Scientific, US), homogenized using the TissueLyser II system (Qiagen, US), and total RNA extraction was performed following the instructions in the vendor’s manuals.
Total RNA samples were sent for library preparation and sequencing by Novogene (Novogene Biology Information Technology Co., Ltd., Beijing, China). Libraries were prepared with a poly(A) selection strategy using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770, New England Biolabs, US).


title: EM_3

city: Beijing

first: Jie

last: Li

address: 8 Xishiku Rd., Xicheng District

country: China

institute: Peking University First Hospital

description:
Library name: EM_3
EM_LI

data_processing:
CLC Genomics Workbench 22.0.1
Assembly: hg38
Supplementary files format and content: FPKM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: eutopic endometrium

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) , 1μg of total RNA was used for the construction of RNA libraries
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: eutopic endometrium


title: EM_5

description:
Library name: EM_5
EM_XIE


title: kidney, db/db_rep6

city: Amsterdam

first: Alessandra

last: Tammaro

state: AZ

address: Meibergdreef 05

department: Department of pathology

country: Netherlands

institute: Amsterdam University Medical Center

description: Library name: K48_db/db_rep6

data_processing:
Sequencing reads were trimmed with BBDuk (BBTools version 36.84, Bushnell B., sourceforge.net/projects/bbmap/).
Mapping to the mouse genome (built GRCh38.101) was performed with RNA STAR, version 2.7.3a, using default parameters.
Gene count was performed with HTSeq, version 2.16.2.
Assembly: mouse genome (built GRCh38.101)
Supplementary files format and content: htseq counts

source_name: kidney

extract_protocol:
Total RNA was extracted from cells seeded in 6-well plates using Agencourt RNAdvance Tissue kit (Beckman Coulter Life sciences #A32646).
100 ng was used to generate libraries using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen #193.384).
QuantSeq

value: kidney

tag: genotype

value: db/m


title: LT_A_ctrl, Animal B15, Hypothalamus

description:
RNAseq batch1
B15_HTH_RNA

source_name: Hypothalamus

value: Hypothalamus


title: E25_Adipose

description:
E25
208114950097_R05C02

scan_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

source_name: Adipose

value: Adipose


title: OMA_2

description:
Library name: OMA_2
OSA_GUO

source_name: ectopic endometrium

value: ectopic endometrium


title: DFFM_ALVAC_pre

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

country: USA

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to rhesus macaque genome (Ensembl Mmul_8.0.1 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Genome_build: Ensembl Mmul_8.0.1 release 88.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
RNA was extracted from PAXgene samples using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s instructions.
GLOBINclear kit (Ambion, Austin, TX, USA) was used to remove globin transcript. Libraries were loaded on Illumina Truseq Paired-End stranded mRNA Kits and sequenced in 2 x 51 base paired-end runs on an Illumina HiSeq 2500 sequencer with an average of 20 million reads per sample.

tag: animal id

value: DFFM

tag: gender

value: M

tag: nb. of challenges to infection

value: ALVAC group

tag: timepoint

value: Pre Vacc

tag: batch

tag: vaccine

value: ALVAC


title: LT_A_ctrl, Animal B15, Frontal_cortex

description:
RNAseq batch1
B15_FCTX_RNA


title: E7_Adipose

description:
E7
208114950097_R04C02

label_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array


title: E25_FCTX

description:
E25
208114950097_R03C02

source_name: FCTX

value: FCTX


title: kidney, db/db_rep4

description: Library name: K33_db/db_rep4


title: EM_2

description:
Library name: EM_2
EM_GUO


title: kidney, db/db_rep5

description: Library name: K42_db/db_rep5


title: LT_A_Ex, Animal B14, Circulating_WBCs

description:
RNAseq batch1
B14_WBC_RNA


title: OMA_1

description:
Library name: OMA_1
OSA_GU


title: kidney, db/db_rep3

description: Library name: K23_db/db_rep3


title: E7_FCTX

description:
E7
208114950097_R02C02


title: EM_1

description:
Library name: EM_1
EM_GU


title: LT_A_Ex, Animal B14, Skeletal_muscle

description:
RNAseq batch1
B14_SkeletalMuscle_RNA


title: E31_FCTX

description:
E31
208114950097_R01C02


title: kidney, db/db_rep2

description: Library name: K11_db/db_rep2


title: LT_A_Ex, Animal B14, Hippocampus

description:
RNAseq batch1
B14_Hipp_RNA

source_name: Hippocampus

value: Hippocampus


title: kidney, db/db_rep1

description: Library name: K09_db/db_rep1


title: HeLa cells siRNA MTR4 rep2

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
Sequence reads were aligned to hg19 using STAR
Sequencing is polyA RNAs (including mRNAs and several ncRNAs). The analysis focused on ncRNAs (even though the sequencing contains more data).
Differential ncRNAs were detected on both strands by comparing WT vs MTR4 depleted cells using normR package (enrichR function, binsize of 500 bp, FDR of 1e-5)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
mtr4_ncrna_all12_filtered_bs500_fdr05.bed (contains the list of ncRNAs upregulated in siMTR4 condition)

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in DMEM medium (Sigma-Aldrich) supplemented with FCS 10% and penicillin/streptomycin.

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using KAPA RNA Stranded mRNA-Seq Kit

treatment_protocol: siRNAs were transfected using Interferin

tag: cell line

value: HeLa

value: siRNA MTR4


title: E25_WBC

description:
E25
208114950097_R06C01

source_name: WBC

value: WBC


title: LT_A_Ex, Animal B14, Hypothalamus

description:
RNAseq batch1
B14_HTH_RNA


title: kidney, db/m_rep8

description: Library name: K08_db/m_rep8

value: db/db


title: HeLa cells siRNA MTR4 rep1


title: E7_WBC

description:
E7
208114950097_R05C01


title: E35_Hippo

description:
E35
208114950097_R04C01

value: Hippo


title: kidney, db/m_rep7

description: Library name: K07_db/m_rep7

value: kidney


title: LT_A_Ex, Animal B13, Circulating_WBCs

description:
RNAseq batch1
B13_WBC_RNA


title: OMA_5

description:
Library name: OMA_5
OSA_XIE


title: E21_Adipose

description:
E21
208114950097_R03C01


title: HeLa cells input shZFC3H1 IP

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner
peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and peak file

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody using ChIP-IT high sensitivity (Active Motif).
Libraries were prepared using Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Rad21 chip-seq were supplemented with lentiviral particles for expression of control shRNA, ZFC3H1 shRNA or MTR4 shRNA.

tag: chip antibody

value: none (input)

value: shRNA ZFC3H1


title: LT_A_Ex, Animal B14, Kidney

description:
RNAseq batch1
B14_Kid_RNA

source_name: Kidney

value: Kidney


title: LT_A_Ex, Animal B13, Skeletal_muscle

description:
RNAseq batch1
B13_SkeletalMuscle_RNA


title: kidney, db/m_rep5

description: Library name: K05_db/m_rep5


title: LT_A_Ex, Animal B13, Kidney

description:
RNAseq batch1
B13_Kid_RNA


title: HeLa cells input shMTR4 IP

value: shRNA MTR4


title: LT_A_Ex, Animal B13, Hippocampus

description:
RNAseq batch1
B13_Hipp_RNA


title: kidney, db/m_rep3

description: Library name: K03_db/m_rep3


title: E9_FCTX

description:
E9
208114950095_R06C02


title: HeLa cells sh MTR4 RAD21 IP

value: Rad21 (Abcam ab992)


title: LT_A_Ex, Animal B13, Hypothalamus

description:
RNAseq batch1
B13_HTH_RNA

value: Hypothalamus


title: kidney, db/m_rep2

description: Library name: K02_db/m_rep2


title: E35_FCTX

description:
E35
208114950095_R05C02


title: HeLa cells siRNA Scrambled rep2

value: siRNA Scrambled


title: LT_A_Ex, Animal B14, Frontal_cortex

description:
RNAseq batch1
B14_FCTX_RNA


title: HeLa cells input sh Control

value: shRNA control


title: HeLa cells siRNA Scrambled rep1


title: kidney, db/m_rep1

description: Library name: K01_db/m_rep1


title: kidney, db/m_rep6

description: Library name: K06_db/m_rep6


title: LT_Y_ctrl, Animal A58, Circulating_WBCs

description:
RNAseq batch1
A58_WBC_RNA


title: HeLa cells shControl RAD21 IP


title: E21_WBC

description:
E21
208114950095_R04C02


title: kidney, Old_mice_supplemented_with_NAM_rep8

data_processing:
Sequencing reads were trimmed with BBDuk (BBTools version 36.84, Bushnell B., sourceforge.net/projects/bbmap/).
/). Mapping to the mouse genome (built GRCh38.101) was performed with RNA STAR [86], version 2.7.3a, using default parameters.
Gene count was performed with HTSeq [87], version 2.16.2.
Assembly: mouse genome (built GRCh38.101)
Supplementary files format and content: htseq counts

extract_protocol:
Total RNA was extracted from 10-20 mg of kidney tissue using Agencourt RNAdvance Tissue kit (Beckman Coulter Life sciences #A32646).
100 ng was used to generate libraries using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen #193.384).
QuantSeq

tag: age

value: Old

value: NAM supplement


title: E9_Adipose

description:
E9
208114950097_R02C01

value: Adipose


title: HeLa cells shZFC3H1 RAD21 IP

value: HeLa


title: kidney, db/m_rep4

description: Library name: K04_db/m_rep4


title: E21_FCTX

description:
E21
208114950097_R01C01

value: FCTX


title: LT_Y_ctrl, Animal A58, Skeletal_muscle

description:
RNAseq batch1
A58_SkeletalMuscle_RNA


title: HeLa cells CTCF IP

value: CTCF (Diagenode C15410210-50)

value: untreated


title: kidney, Old_mice_supplemented_with_NAM_rep7


title: E9_WBC

description:
E9
208114950095_R03C02

value: WBC


title: E32_Hippo

description:
E32
208114950095_R02C02

value: Hippo


title: HeLa cells input ZCCHC8 IP

value: none (input)


title: E30_Adipose

description:
E30
208114950095_R01C02


title: LT_Y_ctrl, Animal A58, Kidney

description:
RNAseq batch1
A58_Kid_RNA


title: kidney, Old_mice_supplemented_with_NAM_rep6

value: kidney


title: LT_A_Ex, Animal B13, Frontal_cortex

description:
RNAseq batch1
B13_FCTX_RNA


title: HeLa cells ZCCHC8 IP

value: ZCCHC8 (Bethyl A301-805A)


title: LT_Y_ctrl, Animal A58, Hippocampus

description:
RNAseq batch1
A58_Hipp_RNA

value: Hippocampus


title: E23_Adipose

description:
E23
208114950095_R06C01


title: E30_FCTX

description:
E30
208114950095_R05C01


title: kidney, Old_mice_supplemented_with_NAM_rep4


title: kidney, Old_mice_supplemented_with_NAM_rep5


title: HeLa cells input ZFC3H1/CTCF IP

description: HeLa cells input for ZFC3H1 IP and for CTCF IP.


title: LT_Y_ctrl, Animal A58, Frontal_cortex

description:
RNAseq batch1
A58_FCTX_RNA


title: LT_Y_ctrl, Animal A58, Hypothalamus

description:
RNAseq batch1
A58_HTH_RNA


title: kidney, Old_mice_supplemented_with_NAM_rep3


title: LT_Y_ctrl, Animal A57, Circulating_WBCs

description:
RNAseq batch1
A57_WBC_RNA


title: E23_FCTX

description:
E23
208114950095_R04C01


title: E32_FCTX

description:
E32
208114950095_R03C01


title: kidney, Old_mice_supplemented_with_NAM_rep2


title: HeLa cells Input MTR4 IP


title: HeLa cells MTR4 IP

value: MTR4 (Abcam ab70552)


title: LT_Y_ctrl, Animal A57, Kidney

description:
RNAseq batch1
A57_Kid_RNA

value: Kidney


title: E30_WBC

description:
E30
208114950095_R02C01


title: kidney, Old_mice_supplemented_with_NAM_rep1


title: kidney, Old_mice_rep8

value: control


title: E32_WBC

description:
E32
208114950095_R01C01


title: mES_LA_G609G_homo_CBSOE_exp2_r2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: fmES_LA_G609G_homo_CBSOE_exp2_r2

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010) was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of millon reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Assembly: Assembly: mm10 from UCSC genome
Supplementary files format and content: Supplementary files format and content: BigWig files and normalized DESEQ2 excel file

growth_protocol: ESCs were maintained on 0.2% gelatin coated plate in Knockout DMEM medium (Thermo Fisher Scientific, 10829018) containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement (Thermo Fisher Scientific, 10828028), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
RNA libraries for RNA-seq were preced using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: E14_NKX2_5_EmGF_ mESCs

tag: cell type

value: CBS_OE Viral infection


title: mES_LA_G609G_homo_CBSOE_exp2_r1

description: Library name: fmES_LA_G609G_homo_CBSOE_exp2_r1


title: mES_LA_G609G_homo_exp2_r2

description: Library name: emES_LA_G609G_homo_exp2_r2


title: kidney, Old_mice_rep7

value: Old


title: LT_Y_ctrl, Animal A57, Frontal_cortex

description:
RNAseq batch1
A57_FCTX_RNA


title: A45_Adipose

description:
A45
208114950092_R05C02

value: Adipose


title: kidney, Old_mice_rep6


title: LT_Y_ctrl, Animal A56, Circulating_WBCs

description:
RNAseq batch1
A56_WBC_RNA


title: mES_LA_G609G_homo_exp2_r1

description: Library name: emES_LA_G609G_homo_exp2_r1


title: kidney, Old_mice_rep5


title: A43_Adipose

description:
A43
208114950092_R04C02


title: A47_Adipose

description:
A47
208114950092_R06C02


title: mES_Ctr_Lmna_exp2_r2

description: Library name: dmES_Ctr_Lmna_exp2_r2

value: Lmna+/+


title: A45_FCTX

description:
A45
208114950092_R03C02

value: FCTX


title: mES_Ctr_Lmna_exp2_r1

description: Library name: dmES_Ctr_Lmna_exp2_r1


title: kidney, Old_mice_rep4


title: A42_FCTX

description:
A42
208114950092_R02C02


title: LT_Y_ctrl, Animal A56, Hippocampus

description:
RNAseq batch1
A56_Hipp_RNA


title: LT_Y_ctrl, Animal A56, Kidney

description:
RNAseq batch1
A56_Kid_RNA


title: LT_Y_ctrl, Animal A56, Hypothalamus

description:
RNAseq batch1
A56_HTH_RNA

value: Hypothalamus


title: LT_Y_ctrl, Animal A57, Hypothalamus

description:
RNAseq batch1
A57_HTH_RNA


title: kidney, Old_mice_rep3


title: kidney, Old_mice_rep2


title: ES_Lmna_Cbs_OE_RNA_seq_r2

description: Library name: ES_Lmna_Cbs_OE_RNA_seq_r2

value: CBS_OE viral transfection


title: LT_Y_ctrl, Animal A57, Hippocampus

description:
RNAseq batch1
A57_Hipp_RNA


title: ES_Lmna_Cbs_OE_RNA_seq_r1

description: Library name: ES_Lmna_Cbs_OE_RNA_seq_r1


title: A47_WBC

description:
A47
208114950092_R01C02

value: WBC


title: A45_WBC

description:
A45
208114950092_R06C01


title: kidney, Old_mice_rep1


title: LT_Y_ctrl, Animal A56, Frontal_cortex

description:
RNAseq batch1
A56_FCTX_RNA


title: kidney, Young_mice_rep6

value: Young


title: LT_Y_ctrl, Animal A55, Skeletal_muscle

description:
RNAseq batch1
A55_SkeletalMuscle_RNA


title: A42_WBC

description:
A42
208114950092_R05C01


title: mES_LA_G609G_homo_exp1_r2

description: Library name: cmES_LA_G609G_homo_exp1_r2


title: kidney, Young_mice_rep5


title: LT_Y_ctrl, Animal A55, Kidney

description:
RNAseq batch1
A55_Kid_RNA


title: mES_LA_G609G_homo_exp1_r3

description: Library name: cmES_LA_G609G_homo_exp1_r3


title: kidney, Young_mice_rep4


title: mES_LA_G609G_homo_exp1_r1

description: Library name: cmES_LA_G609G_homo_exp1_r1


title: E36_Adipose

description:
E36
208114950092_R04C01


title: LT_Y_ctrl, Animal A55, Hypothalamus

description:
RNAseq batch1
A55_HTH_RNA


title: E6_Adipose

description:
E6
208114950092_R02C01


title: kidney, Young_mice_rep3


title: mES_LA_G609G_het_exp1_r2

description: Library name: bmES_LA_G609G_het_exp1_r2


title: LT_Y_ctrl, Animal A55, Frontal_cortex

description:
RNAseq batch1
A55_FCTX_RNA


title: E22_FCTX

description:
E22
208114950092_R01C01


title: mES_LA_G609G_het_exp1_r1

description: Library name: bmES_LA_G609G_het_exp1_r1


title: kidney, Young_mice_rep2


title: kidney, Young_mice_rep1


title: E6_FCTX

description:
E6
208114950091_R06C02


title: LT_Y_ctrl, Animal A53, Circulating_WBCs

description:
RNAseq batch1
A53_WBC_RNA


title: LT_Y_ctrl, Animal A53, Skeletal_muscle

description:
RNAseq batch1
A53_SkeletalMuscle_RNA


title: E36_WBC

description:
E36
208114950091_R05C02


title: im_TEC, Nnmt-OE_TGFβ_rep3

growth_protocol: Conditionally immortalized TECs were maintained in DMEM/F12 medium (Thermo Fisher #21331020) with 10% fetal bovine serum (FBS, Thermo Fisher), 5 ug/ml insulin and transferrin, 5 ng/ml sodium selenite (Thermo Fisher #41400045), 40 pg/ml triiodo-thyrionine (Sigma-Aldrich #T5516), 36 ng/ml hydrocortisone (Sigma-Aldrich #H0135), 20 ng/ml epidermal growth factor (Sigma-Aldrich #E9644), 2mM L-glutamine (Thermo Fisher #25030081) and 1% penicillin/streptomycin (Thermo Fisher #15140122) and IFNgamma (10 ng/ml, Prospec #CYT-358) at 33°C, 5% CO2. Before being seeded for experiments, cells were grown at restrictive conditions (37°C, 5% CO2, in the absence of IFNgamma) for 7 days, to downregulate SV40 large T antigen activity.


title: mES_Ctr_LA_exp1_r2

description: Library name: amES_Ctr_LA_exp1_r2


title: LT_Y_ctrl, Animal A55, Hippocampus

description:
RNAseq batch1
A55_Hipp_RNA


title: E34_WBC

description:
E34
208114950091_R04C02


title: LT_Y_ctrl, Animal A52, Skeletal_muscle

description:
RNAseq batch1
A52_SkeletalMuscle_RNA


title: im_TEC, Nnmt-OE_TGFβ_rep1


title: mES_LA_G609G_het_exp1_r3

description: Library name: bmES_LA_G609G_het_exp1_r3


title: mES_Ctr_LA_exp1_r1

description: Library name: amES_Ctr_LA_exp1_r1


title: LT_Y_ctrl, Animal A52, Kidney

description:
RNAseq batch1
A52_Kid_RNA


title: im_TEC, Nnmt-OE_rep3

value: Nmt-OE


title: ES_shCbs_Lmna_KO_RNA_seq_r1

description:
003_03Lmna_KO_shCbs_v_Lmna_Ctr_Differen_Deseq2.xlsx
03ES_Lmna_KO_shCbs_RNA_seq_mergRPKM_mm10.bw

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010) was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of millon reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files
Supplementary files format and content: Excel file from differential expression analysis

source_name: mouse embryonic stem cells

growth_protocol: ES_shCbs_Lmna_KO, Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF for 2 days. mESC were preplated for 50min and collected for RNA extraction.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
Hieff NGS C102P1 Ultima Dual-mode mRNA
polyA RNA-seq

value: mouse embryonic stem cells

value: shCbs


title: E22_Adipose

description:
E22
208114950092_R03C01


title: LT_Y_ctrl, Animal A52, Hippocampus

description:
RNAseq batch1
A52_Hipp_RNA

value: Hippocampus


title: E6_WBC

description:
E6
208114950091_R03C02


title: ES_shCbs_Lmna_KO_RNA_seq_r2


title: mES_Ctr_LA_exp1_r3

description: Library name: amES_Ctr_LA_exp1_r3


title: E34_Adipose

description:
E34
208114950091_R02C02


title: E16_Adipose

description:
E16
208114950091_R01C02


title: im_TEC, Nnmt-OE_rep2


title: Day10_EB_Lmna_KO_CTH_KD_scRNA_seq_r1

library_source: transcriptomic single cell

data_processing:
Raw fastq files were mapped and de-multiplexed by the use of cellRanger (v.7.1.0) count function (settings –expected-cells 3000  and refdata-gex-mm10-2020-A genome.
The filtered feature matrixes were used as input files to merge the data using the Seurat (v. 4.3.0). Low-quality cells were discarded by filtering selected only cells expressing genes higher than 900 genes per cells. Clusters were found with the function FindClusters (resolution=0.5, random.seed=1 and algorithm=1). The UMAP or TSNE plots were generated using RunUMAP and RunTSNE (dims=1.30, n.neighbors= 30).
The feature plots were generated using FeaturePlot in R. Cell type annotation was performed based on the expression of a panel of lineage genes published before:  cardiomyocytes (TnnT+, Myl7+, Myl4+), endothelial cells (Pecam1+, Cdh5+), fibroblasts (Col3a1+, Lum+), smooth muscle cells (Acta2+), neuron progenitor cells (Sox1+), neuron (Dcc+), erythrocytes (Hba-a2+), hepatocytes (Ttr+), hepatic progenitor cells (Krt7+, Krt19+), Mono/MΦ(Cd14+).
Assembly: refdata-gex-mm10-2020-A genome.
Supplementary files format and content: txt demultiplexed files output from CellRanger

source_name: Day10  embryoid bodies differentiated from mouse embryonic stem cells

growth_protocol: shControl, shControl_Lmna-/-, and shCth_Lmna-/- Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs were dissociated by 0.05% trypsin-EDTA followed by preplating to obtain single mESCs and differentiation were perfomed using hanging drop method. Embryoid bodies (EBs) at day10 were collected for single cell experiment.

extract_protocol:
Day10 EBs differentiated shControl, shControl Lmna-/-, shCth Lmna-/- mESCs were digested with Collagenase I . Cell solutions were FACS sorted for single live cells with SYTOX™ Blue Dead Cell Stain (1:2000, Thermo Fisher Scientific, S34857) and then diluted at a density of 1000 cells/µl in 0.4% BSA.
8000 cells were used for library preparation according to the Chromium Next GEM Single Cell 3' Kit v3.1 (10xGenomics, 1000269) with the Chromium Next GEM Chip G Single Cell Kit (10xGenomics, 1000127) and sequenced on a BGISEQ-500 platform.

value: Mouse embryonic stem cells

value: Lmna-/-

value: pLKO


title: LT_Y_ctrl, Animal A52, Hypothalamus

description:
RNAseq batch1
A52_HTH_RNA


title: im_TEC, Nnmt-OE_rep1


title: E12_Adipose

description:
E12
208114950091_R06C01


title: Day10_EB_Lmna_KO_scRNA_seq_r1

value: Day10  embryoid bodies differentiated from mouse embryonic stem cells

value: WT


title: LT_Y_ctrl, Animal A52, Circulating_WBCs

description:
RNAseq batch1
A52_WBC_RNA


title: im_TEC, mock transduced_TGFβ_rep3


title: Day10_EB_Control_scRNA_seq_r1


title: im_TEC, Nnmt-OE_TGFβ_rep2


title: E16_FCTX

description:
E16
208114950091_R05C01


title: LT_Y_ctrl, Animal A51, Skeletal_muscle

description:
RNAseq batch1
A51_SkeletalMuscle_RNA


title: E12_FCTX

description:
E12
208114950091_R04C01


title: im_TEC, mock transduced_TGFβ_rep2


title: ES_CTH_OE_RNA_seq_r2

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010)  was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of millon reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files and normalized_quantify excel file

growth_protocol: ES_shControl , ES_shControl Lmna_KO, ES_shCth Lmna_KO, and CTH OE Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF for 2 days. mESC were preplated for 50min and collected for RNA extraction.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
Hieff NGS C102P1 Ultima Dual-mode mRNA

value: CTH OE


title: Microglia, TDP-43_Q331K, 3Months, rep3

city: Trento

first: Manuela

last: Basso

address: via sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
The raw RNA-sequencing data from astrocytes and oligodendrocytes were analyzed using the standard pipeline provided by Lexogen for the Corall and Corall v2 library preparation kits. The pipeline is available on GitHub here. Gene expression quantification (read counts) was performed using featureCounts v2.0.1 with the parameters -s 0 -t exon -g gene_name. Samples with fewer than 5 million reads assigned by featureCounts were excluded from further analysis.
For microglia samples, RNA sequencing was performed using the Lexogen QuantSeq protocol. Unique Molecular Identifiers (UMIs) were removed with UMI-tools v1.0.1. Gene quantification was done with STAR v2.7.7a, using the Ensembl GRCm39 genome (accessed March 2021). The resulting gene counts were analyzed using the DESeq2 package in R, and normalized counts were obtained via variance stabilizing transformation (VST) as implemented in DESeq2.
For the analysis of the Omomyc bulk RNA-seq data, we used the standard nf-core/rnaseq pipeline (v3.18). The used reference genome was GRCm38.p6, with the Gencode annotation file (vM25). Furthermore, we set the additional parameters defined in the documentation for the Watchmaker mRNA Library Prep Kit with Twist UMI Adapter System to improve the accuracy of the quantification. For the trimming, fastp was set. Other parameters were left to default.
Assembly: mm10
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Oligo
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Astro
Supplementary files format and content: Tab-delimited file (tsv) with TPM (samples on columns) for Oligo
Supplementary files format and content: Tab-delimited file (tsv) with TPM (samples on columns) for Astro
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Microglia
Supplementary files format and content: Tab-delimited file (tsv) with DESeq2 norm. counts (samples on columns) for Microglia
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for purified astrocytes vehicle and treated with Omomyc
Supplementary files format and content: Tab-delimited file (tsv) with DESeq2 norm. counts (samples on columns) for purified astrocytes vehicle and treated with Omomyc

source_name: Mouse cortices

extract_protocol:
To obtain a high RNA quality and yield with small cell amounts, we used the Single Cell RNA Purification Kit (Norgen Biotek Corporation, Thorold, ON, Canada) according to the manufacturer’s instructions. RNA was quantified with Qubit fluorometer (Thermo Fisher Scientific, Inc.). Finally, RNA quality was assessed with Agilent 2100 Bioanalyzer HS for RNA. Omomyc: After 14 days, primary astrocytes were replated (4 × 10⁵ cells/well), treated the next day with 40 μM Omomyc for 48 h, and harvested for RNA extraction (Total RNA Purification Kit, Norgen Biotek).
Astrocytes and oligodendrocytes: Poly(A) RNA-seq library prep was performed according to the manufacturer’s protocol (Lexogen CORALL mRNA-Seq V2 Library Prep Kits with UDIs cat. N. 177-182), adding Unique Molecular Identifier during the linker ligation step. Microglia: Poly(A) RNA-seq Lexogen QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina. For Omomyc-treated and control cells, 1000ng of total RNA was used for Poly(A) enrichment and RNA-seq library preparation according to the Watchmaker mRNA Library Prep Kit protocol. For library construction, the Twist UMI Adapter System (Twist Bioscience) was included in the protocol. Final sequencing libraries were quantified with Qubit DNA HS Kit, analyzed on a Perkin Elmer LabChip GXII, pooled in equimolar amounts, and sequenced on a lane of SP Novaseq6000 flow cell, obtaining an average of 40 million PE150 reads (clusters) per sample.

value: Mouse cortices

tag: time

value: 3 Months

value: Microglia


title: E22_WBC

description:
E22
208114950091_R03C01


title: E16_WBC

description:
E16
208114950091_R02C01


title: im_TEC, mock transduced_rep3


title: E12_WBC

description:
E12
208114950091_R01C01


title: ES_shCth_Lmna_KO-_RNA_seq_r2


title: im_TEC, mock transduced_rep2


title: ES_CTH_OE_RNA_seq_r1


title: Microglia, TDP-43_Q331K, 3Months, rep1


title: LT_Y_ctrl, Animal A52, Frontal_cortex

description:
RNAseq batch1
A52_FCTX_RNA


title: Microglia, TDP-43_Q331K, 10Months, rep4

value: 10 Months


title: E31_Adipose

description:
E31
208114950083_R06C02

value: Adipose


title: Microglia, TDP-43_Q331K, 10Months, rep3


title: im-TEC, TGFβ_SAM_rep3

source_name: im-TEC

value: im-TEC

value: TGFβ + SAM


title: ES_shControl_Lmna_KO_RNA_seq_r2


title: E19_Adipose

description:
E19
208114950083_R05C02


title: im_TEC, mock transduced_rep1


title: ES_shCth_Lmna_KO_RNA_seq_r1


title: E5_Adipose

description:
E5
208114950083_R04C02


title: im-TEC, TGFβ_SAM_rep2


title: im_TEC, mock transduced_TGFβ_rep1


title: ES_shControl_RNA_seq_r2


title: Microglia, TDP-43_Q331K, 10Months, rep1


title: Microglia, TDP-43_Q331K, 3Months, rep2


title: E19_FCTX

description:
E19
208114950083_R03C02

value: FCTX


title: ES_shControl_RNA_seq_r1

value: mouse embryonic stem cells


title: Astrocytes, TDP-43_Q331K, 10Months, rep2

description:
73-ACSA2-Q331K-10M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv

source_name: Mouse cortices and spinal cords

value: Mouse cortices and spinal cords

value: Astrocytes


title: im-TEC, SAM_rep3

value: LUN.


title: Microglia, TDP-43_Q331K, 10Months, rep2


title: E5_FCTX

description:
E5
208114950083_R02C02


title: im-TEC, SAM_rep2

value: DIM.


title: im-TEC, TGFβ_NAM_rep3

value: TGFβ + NAM


title: E31_WBC

description:
E31
208114950083_R01C02

value: WBC


title: im-TEC, TGFβ_NAM_rep2


title: E19_WBC

description:
E19
208114950083_R06C01


title: im-TEC, SAM_rep1

value: SAM


title: Astrocytes, TDP-43_Q331K, 6Months, rep5

description:
50-ACSA2-Q331K-6M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv

value: 6 Months


title: Astrocytes, TDP-43_Q331K, 6Months, rep4

description:
49-ACSA2-Q331K-6M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: E5_WBC

description:
E5
208114950083_R05C01


title: ES_shControl_Lmna_KO_RNA_seq_r1

value: pLKO


title: shCtrl_231

city: Tian Jin

first: Yang

last: Ou

address: Weijin road

institute: Nankai university

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping： The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) . The expression level of genes was calculated by RSEM (v1.2.8)
Gene Annotation: Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors;Time Series and WGCNA analysis: Time Series analysis was performed by Mfuzz (v2.34.0), and gene co-expression network analysis was performed by WGCNA (v1.48).
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq [6] under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001.
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each sample

extract_protocol:
RNA was harvested using Trisol(Solarbio).
Experimental Procedure 1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).


title: Astrocytes, TDP-43_Q331K, 10Months, rep1

description:
72-ACSA2-Q331K-10M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: E35_Adipose

description:
E35
208114950083_R04C01


title: GLP2-1 12M

city: Yokohama

first: Jonathan

last: Moody

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description:
Library name: TFHS000883
10x genomics 5' single-cell

data_processing:
Sequence reads from all samples were processed by Cell Ranger (10X Genomics). Seurat (v 5.1.0) was used to aggregate and analyze the processed data following the official vignettes (https://satijalab.org/seurat/articles/sctransform_vignette.html). Specifically, PCA analysis was performed to identify clusters, and 20 gene clusters (0–20) were projected on Uniform Manifold Approximation and Projection (UMAP) space with the normalized gene expression. Gene ontogeny analysis was performed using clusterProfiler (v4.12.6)
Samples were identified using freemuxlet v0.1 against a list of 1000genomes SNPs and matched to patient genotypes.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix files

source_name: intestinal mucosa

extract_protocol:
balloon-assisted enteroscopy to obtain intestinal mucosa biopsy. The intestinal tissue was washed with Ca2+, Mg2+-free Hank’s balanced salt solution (HBSS) (Nacalai Tesque, 17460-15) to remove fecal content. After washing, the intestinal tissue was incubated with HBSS containing 1 mM dithiothreitol (Invitrogen, 15508-013) and 1 mM EDTA (Nacalai Tesque, 06894-85) for 15 min at 37°C. The supernatant of the solution was harvested for epithelial cells by passing through a 100-μm cell strainer into a 50-mL Falcon tube. At the same time, the tissues without the epithelial cells were washed with HBSS and dissolved into solutions by incubation with HBSS containing 2.5% fetal bovine serum (FBS) (Thermo Fisher Scientific, 10270-106) and penicillin/streptomycin (Nacalai Tesque, 26253-84), 1.0 mg/mL collagenase Type3 (Worthington, 032-22364), and 0.1 mg/mL DNase (Sigma-Aldrich, DN25) for 60 min at 37 °C. The dissolved solution and digested tissues were homogenized by vigorous shaking and passed through a 100-m cell strainer into a 50-mL Falcon tube. The solution was centrifuged at 1,700 rpm for 5 min at 4°C , the supernatant was removed, and resuspended in RPMI-1640 (Nacalai Tesque, 00-5523-02) containing 10% FBS and penicillin/streptomycin (Nacalai Tesque, 26253-84) (16, 17).
Isolated single cell suspensions of IE and LP cells were pooled and incubated with a Fixable Viability Dye eFluor (eBioscience, 65-0865-14) for 15 min at 4 °C. Live cells were sorted using BD FACS Aria-II (BD Bioscience) and loaded into Chromium Controller (10X Genomics). RNA-seq libraries were prepared using Chromium single-cell 5’ gene expression library preparation (human) according to the manufacturer’s instructions (10X Genomics). The libraries were then sequenced using a DNBSEQ (MGI Tech).

value: intestinal mucosa


title: shzeb1_231

value: Knockdown Zeb1


title: Astrocytes, TDP-43_Q331K, 6Months, rep2

description:
47-ACSA2-Q331K-6M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: scRNA-seq L001 of KI-str-3

city: GuangZhou

first: Jiawei

address: No. 601 West Huangpu Avenue, Tianhe District,

department: Guangdong-Hong Kong-Macau Institute of CNS Regeneration (GHMICR)

institute: JINAN University

data_processing:
We utilized CellRanger software (v6.0.1) to align the raw reads to the pig (Sus scrofa) reference genome obtained from Ensembl (https://www.ensembl.org).
Doublets were identified using DoubletFinder(v2.0.3).
Cell clustering and single-cell differential expression analysis were completed using Seurat(v4.3.0).
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: CellRanger output files (barcodes.tsv, genes.tsv, matrix.mtx)

organism: Sus scrofa

source_name: striatum

extract_protocol:
Approximately 500 mg of tissue was cut from fresh frozen pig striatum using sterile disposable scalpels on dry ice and weighed. The pig striatum was homogenized in ice-cold homogenization buffer (0.25M sucrose, 5 mM CaCl2, 3 mM MgAc2, 10mM Tris-HCL pH 8.0, 0.1 mM EDTA, 1x protease inhibitor, and 1U/ul Ribolock RNase inhibitors) using a glass-on-glass dounce homogenizer, 10 strokes of the A pestle followed by 10 strokes of the B pestle. The homogenates were passed through a 70-μM cell strainer for collection of the nuclear fraction. The nuclear fraction was mixed with an equal volume of 50% iodixanol and placed on a 30-33% iodixanol solution for 20 minutes at 10,000 × g at 4°C. Nuclei were collected from the 30-33% iodixanol interface after removal of the myelin layer from the top of the gradient. Nuclei were resuspended in nuclei wash and resuspension buffer (0.04% bovine serum albumin, 0.2 U/ul Ribolock RNase inhibitors, 500 mM mannitol, and 0.1 mM PMSF Protease inhibitor in phosphate-buffered saline) and pelleted at 500×Gs for 5 minutes at 4°C. To remove cell debris and large clumps, nuclei were passed through a 40-μM cell strainer. The concentration of nuclei was determined manually using a trypan blue counterstain and a hemocytometer. Nuclei concentration was adjusted to 700-1200 nuclei/μL and immediately followed by the 10X Genomics® Single Cell Protocol.
Illumina-ready sequencing libraries were generated using the Single Cell 3' protocol. A Single Cell 3' library contained standard Illumina paired-end constructs beginning and ending at P5 and P7. The Single Cell 3' 16 bp 10x barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used for paired-end sequencing.

value: striatum

value: KI


title: scRNA-seq L001 of KI-str-2


title: Astrocytes, TDP-43_Q331K, 6Months, rep1

description:
46-ACSA2-Q331K-6M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: E20_Adipose

description:
E20
208114950083_R03C01

value: Adipose


title: im-TEC, TGFβ_NAM_rep1

value: im-TEC


title: im-TEC, NAM_rep3

value: NAM


title: im-TEC, TGFβ_SAM_rep1

value: TGFβ + SAM


title: E8_Adipose

description:
E8
208114950083_R02C01


title: scRNA-seq L001 of KI-str-1


title: Astrocytes, TDP-43_Q331K, 6Months, rep3

description:
48-ACSA2-Q331K-6M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv

value: Mouse cortices and spinal cords


title: scRNA-seq L001 of WT-str-3

value: WT


title: im-TEC, NAM_rep2


title: E20_FCTX

description:
E20
208114950083_R01C01

value: FCTX


title: Astrocytes, TDP-43_Q331K, 3Months, rep4

description:
20-ACSA2-Q331K-3M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv

value: 3 Months

value: Astrocytes


title: E8_FCTX

description:
E8
208114950078_R06C02


title: scRNA-seq L001 of WT-str-1


title: E20_WBC

description:
E20
208114950078_R04C02

value: WBC


title: Astrocytes, TDP-43_Q331K, 3Months, rep1

description:
16-ACSA2-Q331K-3M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: TGFb + S-adenosyl methionine (SAM) treated cells, 23_TGFb_SAM

hyb_protocol: 200ng of converted DNA was used to proceed to the Infinium HD methylation assay protocol following manufacturer recommendations.

scan_protocol: Arrays were scanned using the iScan from Illumina.

data_processing:
Methylation Data were processed in GenomeStudio V2011.1 (Illumina).
processed value definition: Average beta

label: Cy5 and Cy3

source_name: Renal tubular epithelial cells

label_protocol: Bisulfite conversion was performed on 500ng of DNA using the EZ-96 DNA Methylation MagPrep Kit (Zymo # D5040) and following manufacturer recommendations.

extract_protocol: DNA extraction from cells was performed on using Agencourt DNAdvance Tissue Kit (Beckman Coulter #A48705) following manufacturer recommendations. DNA was quantified using the Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermo Fisher # 10398702).

value: Renal tubular epithelial cells


title: im-TEC, TGFβ_rep1

value: TGFβ


title: im-TEC, TGFβ_rep3


title: im-TEC, TGFβ_rep2


title: E35_WBC

description:
E35
208114950078_R05C02

data_processing:
Raw data were processed with SeSaMe (v1.16.1)
Processed data are presented in the form of beta values.

extract_protocol: Genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (D4069, Zymo Research) for blood or EZNA Tissue DNA Kit (D3396-02, Omega Bio-Tek) for solid tissue)


title: E8_WBC

description:
E8
208114950078_R03C02


title: Astrocytes, TDP-43_Q331K, 3Months, rep2

description:
17-ACSA2-Q331K-3M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: im-TEC, NAM_rep1


title: Oligodendrocytes, TDP-43_Q331K, 6Months, rep4

description:
40-O4-Q331K-6M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv

value: 6 Months

value: Oligodendrocytes


title: TGFb + NNMTi (5-amino-1-methylquinolinium) treated cells, 11_TGFb_NNMTi


title: scRNA-seq L001 of WT-str-2


title: TGFb + S-adenosyl methionine (SAM) treated cells, 24_TGFb_SAM


title: TGFb + NNMTi (5-amino-1-methylquinolinium) treated cells, 12_TGFb_NNMTi


title: Oligodendrocytes, TDP-43_Q331K, 6Months, rep3

description:
39-O4-Q331K-6M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: im-TEC, control_rep3

value: control


title: E32_Adipose

description:
E32
208114950078_R02C02


title: E29_Adipose

description:
E29
208114950078_R01C02


title: Oligodendrocytes, TDP-43_Q331K, 6Months, rep2

description:
38-O4-Q331K-6M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: im-TEC, control_rep2


title: Astrocytes, TDP-43_Q331K, 3Months, rep3

description:
19-ACSA2-Q331K-3M
Astro_ACSA2_Raw_counts.tsv
Astro_ACSA2_tpm.tsv


title: Oligodendrocytes, TDP-43_Q331K, 6Months, rep1

description:
37-O4-Q331K-6M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: TGFb treated cells, 06_TGFb

value: TGFb treated cells


title: im-TEC, control_rep1


title: E29_FCTX

description:
E29
208114950078_R05C01


title: im-TEC, TGFβ_NNMTi_rep3

value: TGFβ + NNMTi


title: TGFb treated cells, 05_TGFb


title: Oligodendrocytes, TDP-43_Q331K, 3Months, rep4

description:
9-O4-Q331K-3M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: E23_WBC

description:
E23
208114950078_R03C01


title: TGFb treated cells, 04_TGFb


title: Control cells, 03_Ctrl

value: Control cells


title: im-TEC, TGFβ_NNMTi_rep2

value: im-TEC


title: E13_Adipose

description:
E13
208114950078_R06C01

value: Adipose


title: Oligodendrocytes, TDP-43_Q331K, 3Months, rep3

description:
8-O4-Q331K-3M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: im-TEC, TGFβ_NNMTi_rep1


title: Oligodendrocytes, TDP-43_Q331K, 3Months, rep1

description:
6-O4-Q331K-3M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: Oligodendrocytes, TDP-43_Q331K, 3Months, rep2

description:
7-O4-Q331K-3M
Oligo_O4_Raw_counts.tsv
Oligo_O4_tpm.tsv


title: E13_FCTX

description:
E13
208114950078_R04C01


title: Control cells, 02_Ctrl


title: hichip_bm_wt

city: Boston

first: Mayuri

last: Yano

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
For ChIP-seq, Paired-end reads were aligned to mouse genome build GRCm38/mm10, using BWA version 0.7.17. The significance of peaks was tested using MACS3 (version 3.0.0a6, https://github.com/taoliu/MACS) with the -B option, a regular TF-binding mode. Peak artifacts were removed (reference locations “black-listed” by the ENCODE consortium https://sites.google.com/site/anshulkundaje/projects/blacklists, ENCFF356LFX). Super enhancers were called using the ROSE algorithm (v2). H3K27ac signal was normalized as Reads Per Million Peak Reads. Bedtools coverage was used to calculate the number of reads in regions of interest. Density profiles were plotted via the Deeptools package.
Assembly: GRCm39/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: bone marrow

extract_protocol:
For ChIP-seq, bead-bound chromatin was then end polished, followed by crosslink reversal and proteinase K digestion, and DNA purification with SPRI select beads
ChIP-seq libraries were prepared by ligating Illumina adaptors with barcoded index PCR

value: bone marrow

value: Lineage negative cells

value: H3K27ac (Millipore, MABE647)


title: im-TEC, TGFβ_rep2


title: TGFb + NNMTi (5-amino-1-methylquinolinium) treated cells, 10_TGFb_NNMTi


title: im-TEC, TGFβ_rep3


title: Control cells, 01_Ctrl


title: hichip_fl_wt

source_name: fetal liver

value: fetal liver

value: WT


title: im-TEC, TGFβ_rep1


title: A82_Colon

description:
A82
208114950084_R06C02

source_name: Colon

value: Colon


title: B1ML3- Replicate 3

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description: Library name: B1ML3

data_processing:
Raw paired-end (PE)   from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.8
Adapters were removed with Trimmomatic v0.39
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: M. circinelloides f. lusitanicus v3.0  (https://mycocosm.jgi.doe.gov/Mucci3/Mucci3.home.html)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics  for every gene

organism: Mucor lusitanicus

source_name: Mycelium

growth_protocol: R7B, ∆dkl, and ∆dfl strains were grown on solid YPG media  at 26 ºC for 24 hours

extract_protocol:
Total RNA was extracted using the NYZ total RNA kit (NYZtech) and subjected to on-column DNase I treatment (Sigma).
RNA sequencing and library preparation was were performed by Novogene (Cambridge, UK) using the Illumina platform.

value: Mycelium


title: hichip_bm_tg

value: Vav-Cre;Ergflox/-


title: im-TEC, NNMTi_rep3

extract_protocol:
Total RNA was extracted from cells seeded in 6-well plates using Agencourt RNAdvance Tissue kit (Beckman Coulter Life sciences #A32646).
100 ng was used to generate libraries using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen #193.384).
QuantSeq

value: NNMTi


title: A82_Hippo

description:
A82
208114950084_R04C02

source_name: Hippo

value: Hippo


title: E29_WBC

description:
E29
208114950078_R02C01

value: WBC


title: rnaseq_WT_FL3

data_processing:
For RNA-seq data analysis, trimmed reads were aligned to the mouse reference genome (GRCm39/mm10) by STAR with default parameters. Aligned reads were mapped to features using HTSeq, and differential expression analyses were performed using the DESeq2. Genes having less than 4 counts were excluded prior to statistical analysis, and differentially expressed genes (DEGs) were selected using as cutoffs the adjusted p-value < 0.05. Heatmaps were performed using pheatmap and list of DEGs was passed to enrichR and clusterProfiler for enrichment analyses.
Assembly: GRCm39/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
For RNA-seq, total RNA was purified using TRIzol and then samples were treated with DNaseI.
RNA-seq Libraries were prepared using SMARTer Stranded Total RNAseq v3 Pico Input Mammalian sample preparation kits from 5ng of purified total RNA.


title: B1ML1- Replicate 1

description: Library name: B1ML1


title: B1ML2- Replicate 2

description: Library name: B1ML2


title: im-TEC, NNMTi_rep2


title: im-TEC, NNMTi_rep1


title: A82_CardiacMuscle

description:
A82
208114950084_R02C02

source_name: CardiacMuscle

value: CardiacMuscle


title: A82_FCTX

description:
A82
208114950084_R03C02

source_name: FCTX

value: FCTX


title: B1M3- Replicate 3

description: Library name: B1M3


title: rnaseq_WT_FL2


title: B1M2- Replicate 2

description: Library name: B1M2


title: E13_WBC

description:
E13
208114950078_R01C01

source_name: WBC


title: rnaseq_WT_FL1


title: A82_SkeletalMuscle

description:
A82
208114950084_R01C02

source_name: SkeletalMuscle

value: SkeletalMuscle


title: im-TEC, control_rep3

value: control


title: im-TEC, control_rep2

value: im-TEC


title: A2ML3- Replicate 3

description: Library name: A2ML3


title: A82_Adipose

description:
A82
208114950084_R06C01

source_name: Adipose

value: Adipose


title: rnaseq_WT_BM3

value: bone marrow


title: rnaseq_WT_BM4

value: Lineage negative cells


title: im-TEC, control_rep1


title: B1M1 - Replicate 1

description: Library name: B1M1


title: A82_HTH

description:
A82
208114950084_R05C02

source_name: HTH

value: HTH


title: rnaseq_WT_FL4

value: fetal liver


title: A82_WBC

description:
A82
208114950084_R05C01


title: A2ML2- Replicate 2

description: Library name: A2ML2


title: ppr4D_rep3

city: Edinburgh

first: Andreas

last: Fellas

address: Swann Building, Max Born Crescent

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
Library name: B5425C_S9
raw files and read count file

data_processing:
Raw reads were quality assessed with FastQC and aligned and mapped to the fission yeast reference genome (972, ASM294v2, GCF_000002945.1) using STAR RNA-seq aligner and SAMtools (Dobin et al., 2013; Li et al., 2009). Generation of gene counts was performed using the featureCounts from Rsubread package and differential expression analysis was carried out using edgeR (Liao et al., 2014; Robinson et al., 2010)
Assembly: ASM294v2
Supplementary files format and content: read counts per gene from featureCounts

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Log phase cultures were harvested from biological triplicates of wild-type, ppr4Δ and cup1-tt cultures.

extract_protocol:
Monarch® Total RNA Miniprep Kit (New England Biolabs T2010S)
Total RNA extraction followed by mRNA selection was performed using NEB Next Poly(A) mRNA Magnetic Isolation Module and cDNA Library was prepared with NEB E7760 NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs E7490) according to manufacturer’s protocol.

treatment_protocol: YES 32 ℃

value: yeast

tag: strain

value: strain B5425


title: rnaseq_WT_BM2

value: WT


title: ppr4D_rep2

description:
Library name: B5425B_S8
raw files and read count file


title: A2ML1- Replicate 1

description: Library name: A2ML1

value: Mycelium


title: rnaseq_WT_BM1


title: A2M3- Replicate 3

description: Library name: A2M3


title: A81_HTH

description:
A81
208114950084_R03C01


title: ppr4D_rep1

description:
Library name: B5425A_S7
raw files and read count file


title: A81_Colon

description:
A81
208114950084_R04C01

value: Colon


title: rnaseq_Tg_BM4

value: Vav-Cre;Ergflox/-


title: A81_Hippo

description:
A81
208114950084_R02C01

value: Hippo


title: A2M2- Replicate 2

description: Library name: A2M2


title: rnaseq_Tg_BM2


title: rnaseq_Tg_BM3


title: cup1tt_rep2

description:
Library name: B5005B_S5
raw files and read count file

value: strain B5005


title: cup1tt_rep1

description:
Library name: B5005A_S4
raw files and read count file


title: Yeast_RT - Replicate 3

description: Library name: RT3


title: A81_SkeletalMuscle

description:
A81
208114950074_R05C02


title: A2M1 - Replicate 1

description: Library name: A2M1


title: rnaseq_Tg_BM1


title: WT_rep3

description:
Library name: 972C_S3
raw files and read count file

value: wildtype 972

value: strain 972


title: Yeast_RT - Replicate 2

description: Library name: RT2


title: WT Unengrafted Control

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description:
WT_Unengrafted_1
snRNA-seq

data_processing:
STARsolo to align reads to GRCm38.
Assembly: GRCm38
Supplementary files format and content: *.tar.gz archives include barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

source_name: mouse brain

extract_protocol: To prepare samples for single-nucleus RNA sequencing, dissected striata were pooled and placed in 1 mL of ice-cold Nuclei Isolation Buffer (NIB), consisting of 10 mM HEPES pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.10% IGEPAL, 1x cOmplete EDTA-free protease inhibitor cocktail (Roche), and 0.2 U/uL Protector RNase Inhibitor (Roche). Tissue was manually triturated with a P1000 pipette, then incubated for 10 minutes on ice. Samples were then centrifuged for 3 minutes at 600g/rcf. The nuclei pellets were resuspended in 500 uL NIB, then incubated for 3 more minutes on ice. Nuclei were centrifuged for 3 minutes at 600g/rcf, then resuspended in DMEM/F-12. Nuclei were then incubated with 7-Aminoactinomycin D (7-AAD) (Invitrogen) added 1:1000, then sorted on the BD FACSAria Fusion (BD Biosciences). Sorted nuclei were counted and loaded onto a 10X Genomics Chromium controller to generate single-nucleus gel beads in emulsion (10X Genomics). Libraries were prepared using 10X Genomics’ Chromium Single Cell 3’ Reagent Kit v3.1.

value: Brain

value: Unengrafted


title: A81_Adipose

description:
A81
208114950074_R04C02

value: Adipose


title: WT+hGPC 2

description:
WT_HumanFetal_2
snRNA-seq

value: Transplanted with hGPCs


title: cup1tt_rep3

description:
Library name: B5005C_S6
raw files and read count file


title: Yeast_RT- Replicate 1

description: Library name: RT1


title: WT_rep1

description:
Library name: 972A_S1
raw files and read count file


title: A87_WBC

description:
A87
208114950074_R03C02

value: WBC


title: A81_FCTX

description:
A81
208114950084_R01C01

value: FCTX


title: WT+hGPC 1

description:
WT_HumanFetal_1
snRNA-seq


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate C

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: Library name: WT_Anaerobic_C

data_processing:
All paired-end FASTQ files were processed through the same pipeline. Reads were trimmed using Trimmomatic version 0.3  with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming, the reads were aligned to the Z. mobilis ZM4 genome sequence (GenBank accession GCF_003054575.1) using bwa-mem (version 0.7.17-h5bf99c6_8)  with default settings. Alignment files were further processed with Picard-tools (version 2.26.10) (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools (version 1.2)  (sort and index commands). Paired aligned reads were mapped to gene locations using HTSeq version 0.6.0. The R package edgeR (version 3.30.3) with default settings was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold (57). Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: GCF_003054575.1
Supplementary files format and content: 20250627_Kiley_RsuR_RNAseq_HTSeq_raw_counts.txt contains the RAW gene counts for the experiments as determined by Htseq-count
Supplementary files format and content: 20250627_Kiley_RsuR_RNAseq_FPKM.txt contains FPKM normalized gene counts for all experiments.

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: bacteria cell

growth_protocol: Strains were grown in ZRDM medium, a modification of Neidhardt medium buffered with 80 mM MES to pH 6.0, and supplemented with a mixture of amino acids (5x supplement EZ, Teknova) and nucleosides (10x ACGU Solution, Teknova). All cultures were incubated at 30º C. The overnigt cultures used to inoculate the cultures were grown under anaerobic conditions.

extract_protocol:
The RNA was extracted, the same day as the cells were harvest, following standard hot phenol:chlorofom protocol, and ethanol precipitated overnight at -80º C. The RNA then was resuspended in RNase free water and treated with DNAse I at 37ºC for 1 hour Then the RNA was reextracted and precipitated as before. The clean RNA was resuspended in RNAse free water.
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. Strand-specific RNA sequencing libraries was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on the flowcell. After clustering, the flowcell was loaded on the Illumina instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Cells were growth under anaerobic conditions (95% N2, 5% CO2) or aerobic conditions (70% N2, 25% O2, and 5% CO2), by bubbling the gas mixtures into the culture. Cells were harvested by collecting 10 mL of cells over 1 mL of cold 5% vol/vol phenol:ethanol mixture

tag: replicate

value: C

value: bacteria cell

tag: oxygen level

value: anaerobic


title: M_PM - Replicate 2

description: Library name: PM2

tag: tissue


title: A80_Colon

description:
A80
208114950074_R02C02

tag: treatment


title: R62 Unengrafted Control

description:
R62_Unengrafted_1
snRNA-seq

tag: genotype


title: A81_CardiacMuscle

description:
A81
208114950074_R06C02

value: CardiacMuscle


title: A80_HTH

description:
A80
208114950074_R01C02

value: HTH


title: M_PM - Replicate 1

description: Library name: PM1

value: Mycelium


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate B

description: Library name: WT_Anaerobic_B

value: B

value: WT


title: R62+hGPC 2

description:
R62_HumanFetal_1
snRNA-seq
GSM6506795_GSM6506796_Sample_R62_FetalCd44_Str_Nuc_1.tar.gz and GSM6506796_GSM6506795_Sample_R62_FetalCd44_Str_Nuc_1.tar.gz are identical.


title: Myc24 - Replicate 3

description: Library name: M24h_3


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate B

description: Library name: WT_Aerobic_B

value: aerobic


title: Myc24 - Replicate 2

description: Library name: M24h_2


title: R62+hGPC 1

description:
R62_FetalCd44_Str_Nuc_1
snRNA-seq
GSM6506795_GSM6506796_Sample_R62_FetalCd44_Str_Nuc_1.tar.gz and GSM6506796_GSM6506795_Sample_R62_FetalCd44_Str_Nuc_1.tar.gz are identical.


title: WT_rep2

description:
Library name: 972B_S2
raw files and read count file

value: wildtype 972

value: yeast


title: ZEB1_KO

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping： The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) . The expression level of genes was calculated by RSEM (v1.2.8)
Gene Annotation: Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors;Time Series and WGCNA analysis: Time Series analysis was performed by Mfuzz (v2.34.0), and gene co-expression network analysis was performed by WGCNA (v1.48).
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq [6] under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001.
Assembly: mm10
Supplementary files format and content: xls files include FPKM values for each sample

source_name: primary cells from tumor

value: primary cells from tumor


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate A

description: Library name: WT_Anaerobic_A

value: A


title: A80_CardiacMuscle

description:
A80
208114950074_R04C01


title: M_PM - Replicate 3

description: Library name: PM3


title: A80_SkeletalMuscle

description:
A80
208114950074_R03C01

value: SkeletalMuscle


title: PYMT


title: Myc - Replicate 3

description: Library name: M2h_3


title: ESC_G609G_homo_H3K9me3_A_r2

description: 11ESC_LmnaG609G_homo_H3K9me3_A_merg2RPKM_mm10.bw

data_processing:
Ttrimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
mapped bam files were merged with bamtools merge (default settings)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome version
Supplementary files format and content: bigWig files

growth_protocol: Control, Lmna KO and Lmna G609G/G609G  Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF for 2 days. mESC were preplated for 50min and collected for Chip-seq

extract_protocol:
ESCs were dissociated by 0.05% trypsin-EDTA followed by preplating for 50min to obtain single mESCs and 1million mESCs were collected for H3K9me3 chip-seq
Libraries were constructed with the NEB Ultra DNA II Library Kit for Illumina (#E7103S/L)

value: mouse embryonic stem cells

value: Lmna G609G/G609G

tag: antibody

value: Abcam, ab8904


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate C

description: Library name: WT_Aerobic_C

value: C


title: Myc24 - Replicate 1

description: Library name: M24h_1


title: A80_Adipose

description:
A80
208114950074_R02C01

value: Adipose


title: ESC_G609G_homo_H3K9me3_A_r1


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate C

description: Library name: DZM0422_Anaerobic_C

value: bacteria cell

value: anaerobic


title: A80_WBC

description:
A80
208114950074_R01C01

value: WBC


title: Myc - Replicate 2

description: Library name: M2h_2

value: Mycelium


title: A41_Colon

description:
A41
208114950056_R06C02

value: Colon


title: Myc - Replicate 1

description: Library name: M2h_1


title: Zymomonas mobilis ∆ZMO_0422 Aerobic RNA-seq Replicate C

description: Library name: DZM0422_Aerobic_C


title: A80_Hippo

description:
A80
208114950074_R06C01

value: Hippo


title: ESC_Lmna_KO_H3K9me3_A_r2

description: 10ESC_LmnaKO_H3K9me3_A_merg2RPKM_mm10.bw

value: Lmna KO


title: A80_FCTX

description:
A80
208114950074_R05C01

value: FCTX


title: Yeast - Replicate 3

description: Library name: Y_3


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate B

description: Library name: DZM0422_Anaerobic_B

value: B


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate A

description: Library name: WT_Aerobic_A

value: WT

value: aerobic


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate A

description: Library name: DZM0422_Anaerobic_A

value: A


title: ESC_Ctr_H3K9me3_A_r2

value: mouse embryonic stem cells

value: Ctr


title: ESC_Lmna_KO_H3K9me3_A_r1

value: Abcam, ab8904


title: Yeast - Replicate 2

description: Library name: Y_2


title: A41_HTH

description:
A41
208114950056_R05C02

value: HTH


title: Zymomonas mobilis ∆ZMO_0422 Aerobic RNA-seq Replicate B

description: Library name: DZM0422_Aerobic_B


title: Yeast - Replicate 1

description: Library name: Y_1


title: PC-tumor

type: RNA

city: Houston

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

institute: The University of Texas M.D. Anderson Cancer Center

description: Section of PC-derived subcutaneous tumor in immunocompetent mouse

hyb_protocol: Followed Xenium In Situ Gene Expression protocol from the manufacturer (CG000582)

scan_protocol: Followed Xenium Analyzer User Guide (CCG000584)

data_processing: Data were processed with the Xenium Analyzer (10x Genomics) and imported into R for further processing using Seurat (v4.4.0), including quality control, normalization, and object construction.

source_name: subcutaneous tumor

label_protocol: Followed Xenium In Situ for FFPE - Tissue Preparation Guide from the manufacturer (CG000578)

growth_protocol: Five-week-old C57BL/6 mice were maintained in the Department of Veterinary Surgery and Medicine at MD Anderson. 2D-cultured PC cells (3 x 106) were injected subcutaneously into the right dorsal flanks of mice.

extract_protocol: Animals were euthanized, and PC tumors were collected 140 days after transplantation. The excised tumors were fixed and paraffin-embedded for immunostaining. To isolate normal esophagus tissue, 8-week-old mice were euthanized and subjected to cervical dislocation. Longitudinally opened esophagi were washed with phosphate-buffered saline (PBS), fixed, and paraffin-embedded.

value: ESCC


title: ESC_Ctr_H3K9me3_A_r1


title: A41_FCTX

description:
A41
208114950056_R03C02


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , batch3, 10X lane2, STICR

city: San Francisco

first: Alex

last: Pollen

institute: UCSF

description:
Library name: HM2D_3rd_L2_STICR
Raw data for macaque specimens are deposited
clones.h5ad

library_source: other

data_processing:
10X gene expression libraries together with sgRNA and STICR libraries were aligned to the hg38 genome obtained from CellRanger (refdata-gex-GRCh38-2024-A) with feature barcode reference using CellRanger-7.2.0. Aligned counts were then processed with Cellbender(Fleming et al. 2023, PMID: 37550580) for ambient removal. The resulting counts were processed by Scanpy (Wolf et al. 2018, PMID: 29409532) to remove low quality cells containing fewer than 1000 genes, a high abundance of mitochondrial reads (greater than 15% of total transcripts), or a high abundance of ribosomal reads (greater than 40% of total transcripts). Illumina Single Cell CRISPR libraries were aligned using DRAGEN Single Cell RNA v4.4.5 with additional arguments --single-cell-barcode-tag and --single-cell-umi-tag to support downstream individual demultiplexing. Low quality cells that had fewer than 500 genes or high abundance of mitochondrial or ribosomal reads were removed. To align 10X runs with pooled human and rhesus macaque individuals, we made a composite genome using CellRanger mkref function with (1) hg38 (CellRanger refdata-gex-GRCh38-2024-A) and (2) a version of rheMac10 included in a hierarchical alignment and annotated with the Comparative Annotation Toolkit as part of Mao et al. (PMID: 33953399), then filtered with litterbox(https://github.com/nkschaefer/litterbox). Cells identified as cross-species multiplets were removed from downstream analyses. STICR barcodes for lineage tracing experiments were aligned and assigned using the NextClone (Putri et al. 2023) workflow. Individual barcodes were filtered by at least 3 reads supporting a single UMI and at least 2 UMI to call cells with a barcode.
Assembly: GRCh38, RheMac10
Supplementary files format and content: Merged anndata object of cells with assigned sgRNA and lineage barcode, including gene count matrix and metadata including individulal, developmental stages, cellt ype annotation, sgRNA assignment and clonal barcode assignment for experiments containing lineage tracing. For lineage tracing experiments, merged anndata objecta at the clone level at the clonexcell type format.
Supplementary files format and content: Csv files contain sgRNA sequences and target gene information used for sgRNA alignment.

molecule: other

organism:
Macaca mulatta
Homo sapiens

source_name: Cortical neural Progenitors

extract_protocol:
Culture of primary human and macaque neural progenitors were dissociated for 20 min in papain, spun down and resuspended in 0.5% BSA, 5% Trehalose in PBS and sorted with FACSAria Fusion cell sorter (BD) based on GFP (and mCherry) expression. Collected cells were resuspended in 0.02%BSA in PBS and captured following manufacture's protocol.
Gene expression library was constructed according to manufacturer's instructions. sgRNA libraries were separately amplified from each cDNA library. To generate STICR barcode libraries, cDNA library was used as template following protocol described in Delgado et al. 2021, PMID: 34912114.

value: Cortical neural Progenitors


title: Zymomonas mobilis ∆ZMO_0422 Aerobic RNA-seq Replicate A

description: Library name: DZM0422_Aerobic_A

value: bacteria cell


title: Normal esophagus

description: lateral view of esophageal tissue section

source_name: mouse esophagus

value: Normal esophagus


title: A41_CardiacMuscle

city: Hong Kong

first: Andrew

institute: Chinese University of Hong Kong

description:
A41
208114950056_R02C02

value: CardiacMuscle


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , batch3, 10X lane2, sgRNA

description:
Library name: HM2D_3rd_L2_sgRNA
Raw data for macaque specimens are deposited
feature_ref.csv


title: mouse E18.5 mixed striatum, rep litter4_set2

city: Cambridge

first: Margaret

last: Schroeder

address: 77 Massachusetts Avenue

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

description:
Library name: Exp133_mmE18.5_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

data_processing:
Demultiplexed fastq files were generated by the Broad Institute Genomics Platform using Illumina software. 10x Genomics Cell Ranger software version 7.1 was used for alignment and counting via the 10x Genomics Cloud Analysis platform. For samples that were sequenced across several library pools, fastq files were grouped prior to alignment to create one cell-by-gene (cell x gene) counts matrix per sample. CellBender (v0.2.0) remove-background (Fleming et al., 2023) was used to remove ambient RNA and call nuclei with default parameters and expected_cells = 10,000, total-droplets-included = 40,000 and the –cuda flag. CellBender-cleaned cell x gene matrix .h5 files were read into Python in the anndata format using a custom function written by Stephen Fleming (https://github.com/broadinstitute/CellBender/issues/57).
Assembly: Reads were aligned to an optimized mouse reference genome based on the mouse GRCm38 primary sequence assembly (version 2, Pool et al. 2024) or or a modified marmoset mCalja1.2.pat.X assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) provided courtesy of Michael DeBerardine and Fenna Krienen (Princeton Neuroscience Institute) in which mitochondrial genes from CM021961.1 (https://www.ncbi.nlm.nih.gov/nuccore/1820101357/) were annotated using MITOS2113. The marmoset reference genome was generated from the .fasta and .gtf files using Cell Ranger “mkref” v7.1.0 using default parameters without filtering for any gene/transcript biotype and is available at: https://doi.org/10.5281/zenodo.16915694.
Supplementary files format and content: Processed data files are cell x gene count matrices in .h5 format without ambient RNA removal.

source_name: striatum

growth_protocol: Common marmosets were housed in AAALAC-accredited facilities at MIT, in spacious holding rooms with a 12 hour light/dark cycle, temperature 74.0 ± 2.0°F (23.3 ± 1.1°C), relative humidity of 50 ± 20 %, and unrestricted access to food and water. Cages contained a variety of perches and enrichment devices. Procedures were conducted with prior approval by the MIT Committee for Animal Care (CAC) and following veterinary guidelines. Animal work was performed in accordance with protocols approved by MIT’s Committee on Animal Care and NIH guidelines. All postnatal mice were wild-type C57BL/6J originally obtained from Jackson Laboratories and bred in-house. Timed pregnant C57BL/6J females were either obtained from Jackson Laboratories to arrive between gestation day 11 and 15 or were impregnated in house by setting up overnight mating pairs with females in proestrus or estrus phase. Embryos were harvested at E18.5 (18 days after the plug date). Mice were housed in a facility with a light cycle running from 07:00 to 19:00,  temperature 20-22.2°C, humidity 30-70%, and food and water available ad libitum. Postnatal mice were not derived from timed pregnant females. Instead, age was determined during regular pup checks by experienced researchers based on the Jax Mice Pup Appearance Chart.

extract_protocol:
Nuclei were extracted from frozen tissue using the 10x Genomics Chromium Nuclei Isolation Kit (Protocol CG000505, Rev A).
snRNAseq libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Protocol CG000315 Rev C or Rev D) following manufacturer instructions.

treatment_protocol: None; animals were wild-type and allowed to develop normally.

value: striatum

value: nuclei


title: A41_Hippo

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

description:
A41
208114950056_R04C02

value: Hippo


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, batch3, 10X lane2, GEX

description:
Library name: HM2D_3rd_L2_GEX
Raw data for macaque specimens are deposited
merged.h5ad


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_DNA_Index2_Rep1

city: Ithaca

first: Haiyuan

last: Yu

state: New York

address: 237 Tower Road

department: Department of Computational Biology, Weill Institute for Cell and Molecular Biology

institute: Cornell University

description:
Library name: QUASARRseq_eaBC_DNA_Index2_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv

data_processing:
QUASARR-seq data preprocessing includes two main parts: 1. eaBC-TRE-paBC index mapping and 2. RNA aBC/DNA aBC activity measurement. Raw sequencing data was first filtered using fastp using the following parameters "--disable_adapter_trimming --trim_poly_g --cut_right", followed by processing using biodatatools. Briefly, sequence information was retrieved according to the library’s corresponding layout; eaBC-TRE-paBC and unique molecular identifiers (UMIs) for index mapping, and RNA aBCs, DNA aBCs, and UMIs for activity measurements. In index mapping, eaBCs and paBCs were clustered by merging all sequences with a maximum Hamming distance of one for sequencing error tolerance. Partial element sequences were aligned to the reference element sequences. eaBCs and paBCs were then assigned to the TREs. For the multiple minP library set, an additional three-bp minP barcode was used to assign aBCs to their associated minPs. eaBCs and paBCs were regarded as a representation of a given TRE(A), if the number of eaBC-TRE(A)-paBC entries were significantly higher than all other eaBC-TRE(X)-paBC entries for any given TRE(X). In activity measurement, eaBCs and paBCs were extracted and matched to the previously clustered eaBCs and paBCs during index mapping and assigned to their corresponding TRE. All counts generated were subjected to UMI correction to collapse identical copies. The resultant RNA and DNA element counts were then normalized using edgeR to calculate the normalized element counts and logFCs.
Assembly: hg38
Supplementary files format and content: Processed QUASARR-seq files contain per-element DNA input counts, RNA output counts, and activity statistics computed using limma. Element (identifier for tested sequence), DNA1/DNA2 and RNA1/RNA2 (normalized counts from two replicates), limma outputs logFC (log2 fold-change), AveExpr (average log2 abundance), t (moderated t-statistic), P.Value (raw P-value), adj.P.Val (FDR-adjusted P-value), and B (log-odds of differential activity).

growth_protocol: K-562 (CCL-243; ATCC) cells were cultured in IMDM (30-2005; ATCC) supplemented with 10% FBS (30-2020; ATCC) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (15596026; Invitrogen) following the manufacturer’s instructions. Plasmid DNA was extracted from cells as previously described (PMID: 9591124).
QUASARR-seq requires the generation of a pre-transfected DNA eaBC-TRE-paBC index library for barcode-element index generation, as well as a minimum of four libraries per replicate: two RNA libraries targeting the eaBC and paBC transcripts, respectively, and two DNA libraries targeting the eaBC and paBC inputs, respectively. To construct an eaBC-TRE-paBC index, pre-transfected eaBC-TRE-paBC libraries were generated prior to electroporation. Total RNA was extracted from cells using TRIzol Reagent following the manufacturer’s instructions. To remove contaminating plasmid DNA, RNA was treated with DNase I (AM2222; Invitrogen) and subsequently purified using RNeasy Mini Kit (74104; QIAGEN). Reverse transcription was performed with the DNase-treated RNA (for eaBC and paBC quantification libraries) as the template using SuperScript III Reverse Transcriptase (18080093; Invitrogen). Plasmid DNA was extracted from cells as previously described (PMID: 9591124). A first primer extension was performed with the pre-transfected (for eaBC-TRE-paBC index library) and extracted (for eaBC and paBC quantification libraries) DNA as the templates. Reactions were treated with Exonuclease I (M0293; New England Biolabs) to remove unused primer and purified using DNA Clean & Concentrator-5 (D4013; Zymo Research Corp.). A second primer extension was performed with the products of the reverse transcription (RNA libraries) and the first primer extension (DNA libraries) as the templates, respectively. Reactions were again treated with Exonuclease I and purified using DNA Clean & Concentrator-25 (D4033; Zymo Research) and DNA Clean & Concentrator-5 for the RNA and DNA libraires, respectively. Finally, low-cycle PCR was performed to add sequencing adapters, followed by acquisition of 2 × 150 bp reads on an Illumina NovaSeq X Plus.

treatment_protocol: QUASARR-seq input libraries were electroporated into K-562 using Amaxa Cell Line Nucleofector Kit V (VCA-1003; Lonza Group AG) with a Lonza Amaxa Nucleofector II Device using program T-016. The manufacturers’ Amaxa Cell Line Nucleofector Kit V protocol for ATCC K-562 was followed, except for each electroporation, 1 x 10^6 cells received 20 μg of QUASARR-seq library. Five electroporations were carried out per technical replicate, two technical replicates per biological replicate. Cells for different biological replicates were cultured and electroporated on separate days. Following a 6-hour incubation period, cells were harvested by pooling samples for the same technical replicate to remove variance introduced during electroporation. Following three washes with 1X PBS (10010023; Gibco), each technical replicate was parsed out where 4 x 10^6 cells were used for RNA libraries and 1 x 10^6 cells were used for DNA libraries. Cell pellets were snap-frozen with LN2 and stored in −80°C until library preparation.


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_RNA_Index2_Rep2

description:
Library name: QUASARRseq_eaBC_RNA_Index2_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv


title: A41_Adipose

description:
A41
208114950056_R06C01

value: Adipose


title: mouse E18.5 mixed thalamus, rep litter3_set2

description:
Library name: Exp133_mmE18.5_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: thalamus

value: thalamus


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , batch3, 10X lane1, STICR

description:
Library name: HM2D_3rd_L1_STICR
Raw data for macaque specimens are deposited
clones.h5ad


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_RNA_Index2_Rep1

description:
Library name: QUASARRseq_eaBC_RNA_Index2_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , batch3, 10X lane1, sgRNA

description:
Library name: HM2D_3rd_L1_sgRNA
Raw data for macaque specimens are deposited
feature_ref.csv


title: A83_WBC

description:
A83
208114950056_R05C01

value: WBC


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_DNA_Index2_Rep2

description:
Library name: QUASARRseq_paBC_DNA_Index2_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv


title: mouse E18.5 mixed striatum, rep litter3_set2

description:
Library name: Exp133_mmE18.5_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, batch3, 10X lane1, GEX

description:
Library name: HM2D_3rd_L1_GEX
Raw data for macaque specimens are deposited
merged.h5ad


title: low salt night fed ZT4 rep1

status: Public on Nov 25 2025

city: Irvine

first: Kousha

last: Changizi

state: California

address: Donald Bren Hall

department: ICS/IGB

institute: University of California, Irvine

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

source_name: Colon

extract_protocol:
Total RNA was extracted from the colon with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

value: Colon

value: low salt night fed


title: A79_Hippo

description:
A79
208114950056_R02C01

source_name: Hippo


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_DNA_Index2_Rep2

description:
Library name: QUASARRseq_eaBC_DNA_Index2_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv


title: H3-3A_A15G_M_1yo_whole_blood

city: Philadelphia

first: Kelly

middle: J

last: Clark

state: PA

address: 3501 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital of Philadelphia

hyb_protocol: Day one consists of denaturing and neutralizing bisulfite converted DNA samples to prepare them for amplification. The denatured DNA is isothermally amplified in an overnight step. Day two begins by fragmenting the amplified product using end-point fragmentation to avoid over-fragmenting the sample. After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4 degrees C. The precipitated DNA is then resuspended in hybridization buffer. The array is then prepared for hybridization in a capillary flow-through chamber. Samples are applied to an array; the loaded array is incubated overnight in the Illumina Hybridization Oven. Day three begins with “washing” the hybridized array; unhybridized and non-specifically hybridized DNA is washed away to prepare the chip for staining and extension. Extend and Stain (Xstain) consists of single-base extension of the oligos on the array, using the captured DNA as a template, incorporates detectable labels on the array and determines the genotype call for the sample.

scan_protocol: Beadchips are then loaded into the Illumina iScan, which scans the array using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores. The iScan Reader uses a laser to excite the fluor of the single-base extension product on the beads of the BeadChip sections. Light emissions from these fluors are then recorded in high-resolution images of the BeadChip sections.

data_processing:
Data from these images are analyzed using Illumina’s GenomeStudio Methylation Module. IDAT files were processed in R using the minfi package to get beta values. Only probes with detection p-values under 0.05 were used. Probes from X and Y chromosomes and probes with SNPs were filtered out.
minfi-computed beta values

source_name: whole blood

label_protocol: Bisulfite-treated DNA is amplified and loaded onto an Infinium methylation array for the Infinium methylation assay and scanned on the iScan System.

growth_protocol: Fibroblasts were cultured in DMEM. Media was changed every 2-3 days, and cells were split at ~70% confluency.

extract_protocol: Fibroblast DNA was extracted with Qiagen DNeasy Blood and Tissue Kit. Whole blood DNA was extracted on the Biomek FX using the Agencourt Genfind chemistry and methodologies.

value: whole blood


title: A79_Colon

description:
A79
208114950056_R04C01


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_DNA_Index2_Rep1

description:
Library name: QUASARRseq_paBC_DNA_Index2_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv


title: A79_HTH

description:
A79
208114950056_R03C01


title: mouse E18.5 mixed thalamus, rep litter1_set2

description:
Library name: Exp110_mmE18.5_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse E18.5 mixed cortex, rep litter3_set2

description:
Library name: Exp133_mmE18.5_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: cortex

value: cortex


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_RNA_Index2_Rep2

description:
Library name: QUASARRseq_paBC_RNA_Index2_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv


title: A79_FCTX

description:
A79
208114950056_R01C01

source_name: FCTX

value: FCTX


title: H3-3A_Q125R_F_2yo_whole_blood


title: mouse E18.5 mixed striatum, rep litter1_set2

description:
Library name: Exp110_mmE18.5_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: control_M_5yo_whole_blood

value: WT


title: mouse E18.5 mixed cortex, rep litter1_set2

description:
Library name: Exp110_mmE18.5_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: K-562_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_RNA_Index2_Rep1

description:
Library name: QUASARRseq_paBC_RNA_Index2_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv


title: A41_SkeletalMuscle

description:
A41
208114950056_R01C02

source_name: SkeletalMuscle

value: SkeletalMuscle


title: A79_CardiacMuscle

description:
A79
208114950055_R06C02

source_name: CardiacMuscle


title: Pre-transfected_pDEST-QUASARR-luc-gfp_pGAPDH-pMYC-pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC-TRE-paBC_DNA_Index2

description:
Library name: QUASARRseq_eaBC-TRE-paBC_DNA_Index2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_paBC_limma_logFC.tsv
QUASARR_pGAPDH_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pMYC_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv
QUASARR_pAPOBEC3F_CNPL-TRE202-TRE5-TRE6_eaBC_limma_logFC.tsv


title: mouse 90wks female MO, rep 230130_aged_11F

description:
Library name: Exp106_mmaged_3B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: MO

value: MO


title: control_F_1yo_whole_blood


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_eaBC_DNA_Index1_Rep2

description:
Library name: QUASARRseq_eaBC_DNA_Index1_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A79_SkeletalMuscle

description:
A79
208114950055_R05C02


title: mouse 90wks male thalamus, rep 230130_aged_10M

description:
Library name: Exp106_mmaged_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_eaBC_RNA_Index1_Rep2

description:
Library name: QUASARRseq_eaBC_RNA_Index1_Rep2
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A79_Adipose

description:
A79
208114950055_R04C02

source_name: Adipose


title: mouse E18.5 mixed cortex, rep litter1_set1

description:
Library name: Exp110_mmE18.5_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: control_F_33yo_whole_blood


title: control_F_7yo_whole_blood_2


title: H3-3B_R8C_F_33yo_whole_blood

value: H3-3B p.R8C


title: H3-3A_A111V_F_7yo_whole_blood


title: A38_Colon

description:
A38
208114950055_R02C02


title: K-562_pDEST-QUASARR-luc-gfp_pMYC_CNPL-TRE202-MRE_eaBC_RNA_Index1_Rep1

description:
Library name: QUASARRseq_eaBC_RNA_Index1_Rep1
Biomaterial_Vector_minP(s)_TRE(s)_Target_Molecule_Index_Replicate
QUASARR_CNPL-TRE202-MRE_eaBC_limma_logFC.tsv


title: A79_WBC

description:
A79
208114950055_R03C02

source_name: WBC