title: SL469974

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: response bias_day6

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: AO18

status: Public on Feb 07 2025

type: SRA

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
cellranger mkfastq
cellranger count
cellbender
scrublet
doubletFinder
seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv' a tab-delimited text files include list of cell-barcodes and 'features.tsv' a tab-delimited text file include list of genes and 'matrix.mtx' file in a sparse matrix format containing raw counts per gene per cell-barcode.

molecule: total RNA

organism: Mus musculus

source_name: NEOCORTEX

extract_protocol:
Single nuclei were obtained from cortex samples in 1 ml ice cold Nuclei EZ lysis buffer (Sigma, #EZ PREP NUC-101), homogenized using 2 ml glass dounce tissue grinders on ice; 15 times with pestle A and then 15 times with pestle B. The solution was then transferred to a new 2 mL microcentrifuge tube, 1mL nuclei EZ lysis buffer was added, followed by 5-minute incubation on ice, and then centrifuged at 500xg for 5 minutes at 4°C. Supernatants were removed, pellets were resuspended in 1mL nuclei EZ lysis buffer, followed by an additional 5-minute incubation on ice, and centrifuged at 500xg for 5 minutes at 4°C. The supernatant was then discarded, the pellet resuspended in NSB (1X PBS w/ 0.2U/ul RNase inhibitors /1% Ultra-pure BSA) and filtered through a 40um Flowmi Cell strainer (Bel-Art, H13680-0040). Nuclei were then counted on a hemocytometer (iChip) in a 10ul of suspension with 1:1 0.4% Trypan Blue. Nuclei concentration was adjusted for targeted sequencing of 10,000 cells/sample using the 10X Genomics Single Cell 3′ Reagent Kits v3 protocol to prepare libraries. 4 mice/genotype and timepoint were used, using both males and females. Libraries were sequenced using the McDermott Sequencing Core at UT Southwestern.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 10x Genomics). Isolated nuclei were mixed with the 10X  master mix and loaded with partitioning oil and gel beads onto the provided chip. This results in generation of gel bead-in-emulsion (GEMs).  GEMs were then retrotranscripted to cDNA; these contained  Ilumina R1 primer sequence, Unique Molecular Identifier (UMIs) and the 10x Barcode. Silane DynaBeads were used to purify cDNA which were then amplified by PCR. SPRIselect beads were used to select proper sized fragments. Samples were cleaned with 80% ethanol after every amplification step as well. Finally, libraries were constructed and an Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during these final steps.

tag: tissue

value: NEOCORTEX

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype

value: FLX


title: SL469973

city: Ann Arbor

first: Elaine

last: Hebda-Bauer

state: Michigan

address: 205 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

library_source: transcriptomic

data_processing:
Alignment: STAR: 2.7.3a
Quantification of gene-level counts: Subread version 2.0.0
Quality control and filtering: Rstudio (v.1.4.1717, R v. 4.1.1)
Differential expression analysis: limma v.3.48.3
Assembly: Rnor6, annotation: Ensembl v.103
Supplementary files format and content: Filtered log(2) cpm per Ensembl-annotated gene for each F2 hippocampal sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Selectively breeding rats for a high or low propensity to explore a novel environment produced the bHR and bLR lines, respectively, at the University of Michigan (Stead et al., 2006). After 37 generations, an initial set (“F0”) of bHRs and bLRs were chosen from 24 distinct families (12 bHR, 12 bLR) to cross-breed for creating 12 intercross families. Their “F1” offspring were screened for novelty-induced locomotion, and individuals with similarly high or low LocoScores were bred with each other to produce a re-emergence of diverse behavioral phenotypes in the “F2” generation. These 48 F2 litters generated 540 rats, 323 of which were phenotyped as young adults (2-4 months old). Our current study used a subset of these animals (F0: n=24, n=6/phenotype per sex; F2: n=250, n=125/sex) that overlapped with those in previous genetic studies (Chitre et al., 2022; Z. Zhou et al., 2019a) but was distinct from those included in our previous male-only RNA-Seq meta-analysis (Birt et al., 2021).  All procedures were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Animals and approved by the Institutional Animal Care and Use Committee at the University of Michigan.

extract_protocol:
Adults (postnatal days 113-132) were decapitated without anesthesia and brains extracted within two minutes. For the F0s, whole HPC was immediately dissected and flash frozen. For the F2s, whole brains were flash frozen, and then later hole punches from the dorsal and ventral HPC were pooled from four hemisected coronal slabs (-2.12 to -6.04 mm Bregma; (Paxinos & Watson, 2013)) for each animal. RNA was extracted using the Qiagen RNeasy Plus Mini Kit.
A Ribogreen Assay was performed using 2 ml of a 7X dilution to measure RNA concentration and total RNA amount. To measure RNA quality, 2 ml of various dilutions were loaded onto a HS RNA Fragment Analyzer chip. The samples were then normalized to 500ng input into 50ml volume for use in Poly A RNA-seq library reactions that were completed through Second Strand Synthesis and Purification. Diluted samples were used for a PicoGreen assay and loaded onto a HS Caliper chip for quality analysis of the cDNA libraries. Following Kapa qPCR, samples were sequenced on a NovaSeq S4 101PE flowcell targeting an average of 25 million reads.

treatment_protocol: Behavioral data analysis: All F0 and F2 rats were tested for locomotor activity in a novel environment (“LocoScore,” protocol: (Stead et al., 2006)). Exploratory and anxiety-related behaviors were measured on an Elevated Plus Maze (protocol: (Chitre et al., 2022)), including distance traveled (cm), time immobile (sec), and percent time in the open arms. A subset of F2s (n=209) was subsequently tested for Sign Tracking vs. Goal Tracking behavior during the last two days of a week-long Pavlovian Conditioned Approach task (protocol: (Meyer et al., 2012)) using a combined score (“PavCA Index”) summarizing behaviors indicating preference for the conditioned stimuli (lever) vs. unconditioned stimuli (food magazine).

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

value: ST

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: MGH1641_HC

city: Cambridge

first: Matthew

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

data_processing:
Data was aligned to hg19 using TopHat and CuffLinks. The data were then TPM normalized and filtered based on the number of mapped reads and percent mappability
Assembly: hg19
Supplementary files format and content: tab-delimited text file indicates the raw counts per patient

organism: Homo sapiens

source_name: Temporal cortex

extract_protocol:
We used the laser-capture RNA-seq method to profile total RNA of brain neurons similar to what we reported in previous studies. In brief, laser-capture microdissection was performed on human autopsy brain samples to extract neurons. For each temporal cortex (middle gyrus) about 300 pyramidal neurons were outlined in layers V/VI by their characteristic size, shape, and location in HistoGene-stained frozen sections and laser-captured using the Arcturus Veritas Microdissection System (Applied Biosystems) as in previous studies. Total RNA was isolated and extracted with DNase using the Arcturus Picopure method
Libraries were constructed using the TruSeq RNA Library Prep Kit v2

tag: tissue

value: Temporal cortex

tag: cell type

value: Pyramidal neurons

tag: genotype

value: HC


title: MGH1544_HC


title: AG05278_C2XO_4

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

description:
d294; GSE264742_counts.csv.gz
DEG.csv.gz

data_processing:
Read pairs were trimmed using fastp
Read pairs were aligned to the human reference genome (hg38) using hisat2 for allele-specific analysis of phased variants using phaser, or quantified against GENCODE version (v36) using salmon.
DESEQ2 output (log2FoldChange, Wald statistic, p.adjust-value by contrast)
Assembly: hg38
Supplementary files format and content: raw counts per sample
Supplementary files format and content: DEG.csv listing DESEQ2 output (log2FoldChange, Wald statistic, p.adjust-value in multiple experimental and control contrasts):
Supplementary files format and content: fXO = female 45,X vs. euploid samples
Supplementary files format and content: mXO1 = male1 45,X vs. euploid samples
Supplementary files format and content: mXO2 = male2 45,X vs. euploid samples
Supplementary files format and content: fmE1 = female vs. male1 euploid samples
Supplementary files format and content: fmE2 =female vs. male2 euploid samples
Supplementary files format and content: m1m2O = male1 vs. male2 45,X samples
Supplementary files format and content: more details in https://www.biorxiv.org/content/10.1101/2023.03.08.531747v2.full

growth_protocol: Human iPSCs were cultured in feeder-free conditions on GelTrex-coated plates (ThermoFisher Scientific) in mTeSR-1 media (Stem Cell Technologies) in 5% CO2 at 37°C. iPSCs were passaged with 0.5M EDTA at least weekly in small aggregates.

extract_protocol:
RNA was extracted from NCCs using the PureLink RNA Mini Kit (ThermoFisher Scientific).
Libraries were prepared at the UConn Center for Genome Innovation using the Illumina Strand mRNA Kit and 100bp paired-ends reads were sequenced to an average depth of 40 million reads/replicate on the NovaSeq (Illumina).

treatment_protocol: Confluent wells of iPSCs cultured on Geltrex-coated plates in mTeSR-1 medium were singularized with Accutase (ThermoFisher Scientific) and plated on Geltrex coated plates at 4.5-6 x104 cells/cm2 in DMEM/F-12, 1x N2, 1% Glutamax, 1% Non-essential Amino Acids, 1 µM CHIR99021 (StemCell Technologies), 2 µM SB431542 (StemCell Technologies), 1 µM DMH1 (Tocris Bioscience), 20 ng/mL BMP4 (Peprotech), and 10 µM Y-27632 (Tocris Bioscience), for the first two days only. Media was changed daily until day 4 and 5 when the cells were harvested. Round of differentiation indicated in the "differentiation round" field.

tag: cell line

value: NCC

tag: differentiation round

value: D


title: AO17

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative


title: SL469972

tag: hippocampal siide used

value: right

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: MGH1388_HC

tag: tissue

tag: cell type

tag: genotype


title: AG05278_C23XX_4

description:
d293; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round


title: MGH1365_HC


title: AO16

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

value: CKO


title: SL469971

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: AO15

description: 10x Genomics

tag: tissue

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype


title: AG05278_C19XX_4

description:
d275; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: differentiation round


title: AG05278_C9XO_4

description:
d276; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL469970

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: mutant liver healty AlbR26Met_6

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

country: France

institute: INSERM

description: 680009 HL-E20

data_processing:
EdgeR for differerential expression after normalization
Assembly: Reads were aligned to mouse reference genome GRCm38 (mm10) and generated counts were pre-processed and normalized.
Supplementary files format and content: txt matrix of normalized abundance of genes in all samples

source_name: Liver

extract_protocol:
mRNA was extracted with Qiagen kit from the indicated samples, following manufacturer instructions. 500 ng total RNA per sample was diluted in RNase- DNase- and protease- free molecular grade water (maximum volume 20 µL). RNA quality was verified with Agilent bioanalyzer Tapestation with RIN and/or Dv200 values; and purity evaluated with Nanodrop considered as valid when OD260/280 was between 1.8 and 2.2. Samples were submitted to ICM platform for sequencing with Illumina NovaSeq X technology (purification of poly-A containing mRNA molecules; 40 million reads/sample, 100 bases each, paired end).
Random primed cDNA library, purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis, adapter ligation and adapter specific PCR, amplification

tag: tissue

value: Liver

tag: group

value: healty

tag: genotype


title: AO14

description: 10x Genomics

value: NEOCORTEX

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative


title: AG09270_XO_4

description:
d274; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: differentiation round


title: MGH1314_HC


title: SL469968

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: MGH1322_HC

tag: tissue

tag: cell type

tag: genotype


title: BN99-25_HC


title: AO13

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

value: FLX


title: AG09270_XY_4

description:
d273; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round


title: AG05278_C9XO_3

description:
d268; GSE264742_counts.csv.gz
DEG.csv.gz

value: C


title: SL469967

tag: hippocampal siide used

value: left

tag: Sex

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: BN98-19_5_HC

tag: tissue

value: Temporal cortex

tag: cell type

value: Pyramidal neurons

tag: genotype

value: HC


title: AG04381_C69XY_1

description:
d448; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

value: NCC

tag: differentiation round

value: E


title: AO11

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

value: CKO


title: BN98-19_11_HC


title: AG05278_C19XX_3

description:
d267; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL483910

data_processing:
Alignment: STAR: 2.7.3a
Quantification of gene-level counts: Subread version 2.0.0
Quality control and filtering: Rstudio (v.1.4.1717, R v. 4.1.1).
Differential expression analysis: limma v.3.48.3
Assembly: Rnor6, annotation: Ensembl v.103
Supplementary files format and content: Filtered log(2) cpm per Ensembl-annotated gene for each F0 hippocampal sample

source_name: whole hippocampus

value: hippcampus

tag: Sex

value: Male

tag: animal strain (lineage)

value: bred High Responder

tag: generation

tag: family

tag: rnaconc

tag: rin

tag: ribosomeperc

tag: mrnaperc


title: AO10

description: 10x Genomics

tag: tissue


title: AO09

description: 10x Genomics


title: AG09270_XO_3

description:
d266; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell type


title: BN12-44_11_HC

tag: genotype


title: BN12-44_5_HC


title: AO12

description: 10x Genomics


title: SL483908


title: AO8

description: 10x Genomics


title: SL483909

value: Female


title: SL483911


title: AG05278_C2XO_3

description:
d263; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line


title: AO7

description: 10x Genomics


title: AG05278_C8XO_3

description:
d264; GSE264742_counts.csv.gz
DEG.csv.gz

tag: differentiation round


title: BN11-15_5_HC


title: AO6

description: 10x Genomics

tag: strain


title: SL483906

value: bred Low Responder


title: BN11-15_11_HC


title: AG05278_C9XO_2

description:
d260; GSE264742_counts.csv.gz
DEG.csv.gz

value: B


title: AO5

description: 10x Genomics

value: NEOCORTEX

tag: age


title: SL483905


title: AG05278_C23XX_3

description:
d262; GSE264742_counts.csv.gz
DEG.csv.gz


title: BN11-04_HC


title: SL469969

value: hippocampus

tag: hippocampal siide used

tag: age(days)

tag: animal strain

value: F2 cross

tag: rat number

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: pf reads

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: SL483904

tag: tissue

tag: Sex

tag: animal strain (lineage)

tag: generation

tag: family

tag: rnaconc

tag: rin

tag: ribosomeperc

tag: mrnaperc


title: AG05278_C19XX_2

description:
d259; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: genotype

tag: differentiation round


title: AG09270_XY_3

description:
d265; GSE264742_counts.csv.gz
DEG.csv.gz

value: C


title: AO4

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

value: FLX


title: SL483903

tag: tissue


title: AO2

description: 10x Genomics


title: SL483902

tag: Sex


title: SL483907

tag: animal strain (lineage)


title: AG09270_XO_2

description:
d258; GSE264742_counts.csv.gz
DEG.csv.gz


title: BN10-22_5_HC

value: Temporal cortex

value: Pyramidal neurons

value: HC


title: BN10-63_HC


title: BN10-70_5_HC


title: AG09270_XY_2

description:
d257; GSE264742_counts.csv.gz
DEG.csv.gz

value: NCC


title: AO3

description: 10x Genomics

value: CKO


title: BN11-93_HC


title: BN10-70_11_HC


title: AG05278_C2XO_2

description:
d255; GSE264742_counts.csv.gz
DEG.csv.gz


title: P0_REP5

description: 10x Genomics

data_processing:
cellranger-atac mkfastq
cellranger-atac count
signac,macs2 (peak generation)
signac
Assembly: mm10
Supplementary files format and content: Respective files differentiated by age in name:'barcodes.tsv.gz' a tab-delimited text files include list of cell-barcodes and 'features.tsv.gz' a tab-delimited text file include list of peaks and 'matrix.mtx.gz' file in a sparse matrix format containing raw counts per peak per cell-barcode.

source_name: Neocortex

extract_protocol:
Nuclei were isolated per modification of Habib et al. 2017(Habib et al. 2017) and Ayhan et al. 2021(Ayhan et al. 2021) protocol. Cortex samples were placed in a 2mL dounce homogenizer on ice with 1 mL ice cold Nuclei EZ lysis buffer (Sigma, #EZ PREP NUC-101), and homogenized; 15-20 times with pestle A and then 15-20 times with pestle B. The solution was then transferred to a clean 2 mL microcentrifuge tube, 1mL nuclei EZ lysis buffer was added, followed by 4-minute incubation on ice, and centrifugation at 500xg (rcf) for 5 minutes at 4°C. The supernatant was then discarded, pellet resuspended in 300uL-1mL Nuclei Wash Buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 10%, Tween-20 1%), then centrifuged 500xg for 5 min at 4C. The supernatant was discarded, and pellet resuspended in chilled diluted Nuclei Buffer (10X genomics) by adding 100uL diluted Nuclei Buffer on ice to allow for natural dissociation for 3-4min. Then the final volume was brought to 300uL-1mL. This was then filtered through a 40um pre-wetted Flowmi Cell strainer into a 1.5mL microcentrifuge tube. Nuclei were then counted on a hemocytometer (iChip) in a 10ul of suspension with 1:1 0.4% Trypan Blue. Nuclei concentration was adjusted for targeted sequencing of 4,000-7,000 nuclei/sample using the 10X Genomics Chromium Single Cell ATAC v1.1-v2 protocol to prepare libraries. 2-3 mice/genotype and timepoint were used, using both males and females. Libraries were sequenced using the McDermott Sequencing Core at UT Southwestern.
Library was performed according to the manufacter’s instructions (single cell ATAC v1.1 and v2 protocol, 10x Genomics). Isolated nuclei were mixed with the transposition mix which was followed by transposition. 10X master mix added and samples were loaded onto chip alongside  partitioning oil and gel beads. This results in generation of gel bead-in-emulsion (GEMs).  GEMs were then cleaned with Silane DynaBeads  followed by size-selection using SPRIselect beads. Samples were cleaned with 80% ethanol. Finally, libraries were constructed with  paired-end constructs with P5 and P7 sequences and a sample index added during the final steps.

value: Neocortex

tag: prep batch

tag: sequencing batch

value: flox control


title: BN10-22_11_HC


title: P0_REP6

description: 10x Genomics


title: SL483900

value: hippcampus

value: Female

tag: generation

tag: family

tag: rnaconc


title: AO1

description: 10x Genomics


title: AG05278_C23XX_2

description:
d254; GSE264742_counts.csv.gz
DEG.csv.gz

value: B


title: SL483899

value: Male

value: bred Low Responder

tag: rin

tag: ribosomeperc

tag: mrnaperc


title: SL483898


title: P0_REP4

description: 10x Genomics

tag: genotype

value: e1 cKO


title: AG05278_C9XO_1

description:
d252; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: differentiation round

value: A


title: BN08-40_11_HC


title: P0_REP3

description: 10x Genomics

tag: strain

tag: age


title: BN06-05_5_HC

tag: tissue


title: AG05278_C19XX_1

description:
d251; GSE264742_counts.csv.gz
DEG.csv.gz


title: P0_REP2

description: 10x Genomics


title: AG09270_XO_1

description:
d250; GSE264742_counts.csv.gz
DEG.csv.gz


title: BN05-12_5_HC


title: AG09270_XY_1

description:
d249; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL483897

tag: Sex

value: bred High Responder

tag: failed qc

value: low RIN


title: P0_REP1

description: 10x Genomics

tag: prep batch


title: BN06-05_11_HC


title: AG05278_C8XO_1

description:
d248; GSE264742_counts.csv.gz
DEG.csv.gz


title: E16_REP4

description: 10x Genomics

tag: sequencing batch


title: AG05278_C8XO_2

description:
d256; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL483894

tag: animal strain (lineage)

tag: generation


title: AG05278_C2XO_1

description:
d247; GSE264742_counts.csv.gz
DEG.csv.gz


title: E16_REP3

description: 10x Genomics


title: BN05-12_11_HC


title: BN03-41_5_HC


title: SL483893

tag: family

tag: rnaconc


title: BN08-40_5_HC


title: SL483901

tag: rin

tag: ribosomeperc


title: SL483895

tag: mrnaperc


title: E16_REP2

description: 10x Genomics

tag: genotype


title: SL483892


title: BN03-41_11_HC

tag: cell type


title: AG05278_C23XX_1

description:
d246; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round


title: SL483891


title: Control_rep3_guide2 (D23-5949-2)

description: In the processed data file, corresponds to column D23-5949-2

data_processing:
RNA was quantified with Salmon using the hg38 reference. Prior to quantification, we used trimmomatic to remove artifacts associated with the ends of RNA molecules
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with Salmon-quantified raw RNA counts

extract_protocol:
RNA was extracted following manufacturer’s manual, using Direct-zol RNA Miniprep kit
Library prep was performed according to the BioMicroCenter's strategy for preparation, which includes NEB ribosomal depletion and NEB Ultra II library prep kit

treatment_protocol: RNA-seq was collected after CRISPRi knockdown of CSNK2A1, NOTCH1, or CSNK2A1. Controls were non-targeting guide RNAs

value: Neural progenitor cells

value: Control


title: E16_REP1

description: 10x Genomics

tag: strain

tag: age


title: E13_REP6

description: 10x Genomics

tag: tissue


title: UK5136_AD

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: SL483896

tag: Sex


title: Control_rep2_guide1 (D23-5948-1)

description: In the processed data file, corresponds to column D23-5948-1


title: SL483890


title: UK1235_AD


title: E13_REP4

description: 10x Genomics

tag: prep batch


title: SL483889


title: E13_REP5

description: 10x Genomics

tag: sequencing batch


title: SL483888

tag: animal strain (lineage)


title: UK1219_AD


title: Control_rep2_guide2 (D23-5945-2)

description: In the processed data file, corresponds to column D23-5945-2


title: UK1228_AD


title: Control_10hr

city: Chicago

first: Elizabeth

middle: R

last: Jerison

state: Illinois

address: 929 E 57th St

department: Physics

institute: University of Chicago

description:
Library name: Sample2
10X Genomics

data_processing:
Sequencing data was aligned to the zebrafish reference genome (GRCz11) using 10X Genomics Cellranger software (6.1.2).
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Body

extract_protocol:
Collected tissue was transferred to 300 uL of digestion buffer (Final concentration .12 mg/mL Liberase-TL (Millipore Sigma, 5401020001) and 22.5 U/mL DNAse I (Worthington, LS006331) in .25\% Trypsin/EDTA (Gibco, 25200-056)) in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes, and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer (.1\% BSA in PBS) per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30-50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane.
The 10X Genomics Chromium 3' platform and reagents (v3.1 kit) was used for cell encapsulation, reverse transcription, and library preparation, according to manufacturer instructions (manual revision D), with 12 cycles of preamplification. For cell encapsulation, one lane of the 10X chip was used for each treatment group (LPS and control), at a target of 16,000 cells/lane.

value: Body

value: AB

value: 6 dpf

tag: treatment

value: control


title: LPS_10hr

description:
Library name: Sample1
10X Genomics

value: LPS


title: Control_rep1_guide1 (D23-5944-1)

description: In the processed data file, corresponds to column D23-5944-1


title: NOTCH1_rep2_guide1 (D23-5942-1)

description: In the processed data file, corresponds to column D23-5942-1


title: Control_rep1_guide2 (D23-5947-2)

description: In the processed data file, corresponds to column D23-5947-2


title: NOTCH1_rep3_guide2 (D23-5943-2)

description: In the processed data file, corresponds to column D23-5943-2


title: E13_REP3

description: 10x Genomics

value: Neocortex


title: UK1213_AD


title: E13_REP2

description: 10x Genomics


title: NOTCH1_rep3_guide1 (D23-5940-1)

description: In the processed data file, corresponds to column D23-5940-1


title: vir & rep cells, csr-1a mutant, mRNAseq, bio rep1

first: DI

last: RAO

address: Westlake University(Yungu), Hangzhou, Zhejiang Province, China

country: China

institute: Westlake University

data_processing:
Adapters and low-quality bases were removed from the raw sequencing reads using the tool fastp (version 0.20.1) (options: -q 20 -n 0 -u 50 -l 75 -c).
The trimmed reads were then mapped to the reference genome (C. elegans genome WS276) using the Spliced Transcripts Alignment to a Reference (STAR) software (version 2.5.2b). The options applied (--outSAMunmapped Within --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.8 --outFilterMatchNminOverLread 0.8) control parameters such as how unmapped reads are handled, the maximum number of multiple alignments allowed for a read, and the minimum alignment score.
Read counts per gene were calculated using featureCounts, a function of the Subread package (version 2.0.0). This tool assigns reads to genomic features (e.g., genes or exons) and generates a count matrix that tabulates how many reads overlap with each feature.
The read count data was then used for differential gene expression analysis using the DESeq2 R package.
Assembly: C. elegans genome WS276
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: Young adult male Caenorhabditis elegans

growth_protocol: Soreted cells were maintained in egg buffer (118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM Hepes, pH=7.3, osmolarity 340 mOsm)/10% FBS

extract_protocol:
5000 of sorted cells were collected in TRIzol reagent (catalog no.T9424, Sigma) for total RNA extraction
mRNA libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (catalog no.NR605, Vazyme) and  were evaluated using an Agilent 2100 Bioanalyzer System (High Sensitivity DNA Analysis kit).

value: male

value: somatic cells

tag: cell subtype

value: vir & rep cells

value: gfp::sl2::2xflag::aid::csr-1a_delta; him-8; Ex(pnc-1p::wrmScarlet); Ex(pcs-1p::wrmScarlet)

value: With late L4 parental heat-stress


title: UK1202_AD


title: UK1201_AD


title: UK1185_AD


title: vir & rep cells, csr-1a mutant, mRNAseq, bio rep3


title: vir & rep cells, WT, mRNAseq, bio rep2

value: gfp::sl2::2xflag::aid::csr-1a; him-8; Ex(pnc-1p::wrmScarlet); Ex(pcs-1p::wrmScarlet)


title: UK1192_AD


title: UK1181_AD


title: NOTCH1_rep2_guide2 (D23-5939-2)

description: In the processed data file, corresponds to column D23-5939-2

value: Neural progenitor cells


title: NOTCH1_rep1_guide2 (D23-5941-2)

description: In the processed data file, corresponds to column D23-5941-2


title: WT, replicate 1, scRNAseq

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center (CNIO)

description: 10X Genomics

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with BCL Convert (Illumina).
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-flex-multi-frp)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
To isolate liver inflammatory cells, the liver was excised, minced into small pieces, and placed in a tube containing cold DMEM (4.5 g/L glucose) 10% FBS, 0.75 mg/mL collagenase A and 50 ul/mL DNaseI. Then, the solution containing liver pieces was mixed at 37ºC for 30 min at 2000 rpm to digest. On top of a 50 mL falcon, liver tissue was added to nylon mesh strainer and 2-3 ml DMEM media (4.5 g/L glucose) was added. Liver tissue was mashed through the mesh with the plunger from a 3 ml syringe, until volume was brought up to 15 ml with cold DMEM. After centrifugation at 500g for 5 min at 4°C, pellet was resuspended in 1 mL of RBC lysing buffer and incubated 5 min at RT. Reaction was stopped by adding 10 mL of DMEM (4.5 g/L glucose) supplemented with 10% FBS. After centrifugation at 500g for 5 min at 4 °C, supernatant was discarded, and the pellet was resuspended in 15 mL of 38% Percoll in DMEM media (4.5 g/L glucose) supplemented with 10% FBS and underlaid with 70% Percoll in PBS and further centrifuged at 500g for 30 min at 4°C. Interface with mononuclear cells was collected and washed with 15 mL of DMEM media (4.5 g/L glucose) supplemented with 10% FBS. After centrifugation at 500g for 10 min at 4°C, supernatant was discarded and the pellet was washed and finally resuspended in 5% BSA, 2 mM EDTA in Ca2+/Mg2+ -free PBS (MACS buffer). CD45+ cells were isolated using FACSARIA (30M). 5 mice were pooled to obtain the required number of cells.
Fixed cell suspensions obtained with the "Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit" (10xGenomics PN-1000414) were processed with the "Chromium Fixed RNA Profiling Reagent Kit" according to the manufacturer's instructions (10xGenomics, user guide CG000527). Briefly, individual samples were hybridised to *mouse* transcriptome probe sets (Chromium Fixed RNA Kit, 10xGenomics *PN1000496*), multiplexed and encapsulated in gel beads in emulsion (GEMs) in a Chromium iX instrument (10xGenomics). GEM recovery and gene expression library construction were all performed as recommended by the manufacturer. Libraries were sequenced on an Illumina instrument ((Illumina NovaSeq X) by following manufacturer's protocols.

treatment_protocol: Mice were treated with tamoxifen for one week

value: liver

value: immune

value: WT

value: One week of tamoxifen treatment


title: E13_REP1

description: 10x Genomics

value: flox control


title: vir & rep cells, WT, mRNAseq, bio rep3


title: WT, replicate 2, scRNAseq

description: 10X Genomics


title: vir & rep cells, WT, mRNAseq, bio rep1


title: URI(+/D)Hep, replicate 1, scRNAseq

description: 10X Genomics

value: URI(+/delta)Hep


title: Round spermatids, csr-1a mutant, CUT_Tag, bio rep3

library_source: genomic

data_processing:
Adapters and low-quality bases were removed from the raw sequencing reads using the tool fastp (version 0.20.1) (options: -q 20 -n 0 -u 50 -l 75 -c).
The trimmed reads were mapped to the C. elegans genome (WS276) using Bowtie2 (version 2.3.5.1). The options applied (--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700) control parameters such as the alignment mode, sensitivity, and insert size. For spike-in calibration, the trimmed reads were additionally mapped to the human genome (GRCh38).
The mapped files were calibrated using the calculated scale factors and converted to genomic coverage bedgraph files using the bedtools genomecov function.
Normalized bedgraph files were converted to BigWig files using UCSC bedGraphToBigWig. Biological replicates in BigWig files were merged using UCSC BigWigMerge. The density of genome features in each chromosome was calculated with UCSC BigWigSummary from BigWig files. The genome browser views were generated by visualizing the BigWig files in the Integrative Genomics Viewer (IGV)
Read counts were obtained using an R script and normalized to human map reads per million.
Differential Expression Analysis: Differential gene expression analysis was performed using an R script. The significance of differential expression (p-value) was calculated using the Student's t-test.
Assembly: C. elegans genome (WS276); human genome (GRCh38)
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

molecule: genomic DNA

source_name: Caenorhabditis elegans male germline 8-10 h post of Heat-stress

growth_protocol: Round spermatids were dissected 8-10 hours after males were heat-stressed, incubated in an L-15 (catalog no. 21083–027, Gibco) medium containing 15% FBS (catalog no. 10270-106, Gibco), and 1% sucrose, and analyzed with a MoFlo Astrios cell sorter (Beckman Coulter) installed with Moflo Summit 6.3.1.

extract_protocol:
300 thousand round spermatids per sample were prepared and 30 of 293-F cells were added as spike-in. Cells were washed twice using 1×PBS by gently pipetting, and centrifuged for 5min at 1700×g. Each sample was added with 100μl pre-chilled NE buffer, resuspended by gently pipetting up and down, and incubated on ice for 10 minutes.
The libraries were prepared following the protocol of Hyperactive Universal CUT_Tag Assay Kit for Illumina Pro (catalog no. TD904, Vazyme) and were evaluated using an Agilent 2100 Bioanalyzer System (High Sensitivity DNA Analysis kit).

value: round spermatids

tag: chip antibody

value: H3K9me3 (abcam, #ab8898)

value: 8-10 h post Heat-stress


title: CSNK2A1_rep3_guide2 (D23-5937-2)

description: In the processed data file, corresponds to column D23-5937-2


title: GS(+/D)Hep, replicate 1, scRNAseq

description: 10X Genomics

value: GS(+/delta)Hep


title: RH RRBS MET-2 replicate

city: Toronto

first: Mohsen

last: Hosseini

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
RRBS libraries were quality-checked and sequenced on Illumina HiSeq/NovaSeq platform, generating paired-end reads of 150pb nucleotides.
Raw data were trimmed to remove adapter and low-quality base using Trimmomatic-0.36, followed by quality control assessment with FastQC (v0.11.5). Trimmed reads were aligned to mouse reference genome from Ensembl (GRCm38/mm10) and duplicated reads were removed.
The bismark_methylation_extractor, an auxiliary component of Bismark version 0.16.3, has been utilized to extract methylation data for each cytosine analyzed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain CpG site coordinates, coverage, and methylation values. including CpG sites coordinate, coverage, methylation values

source_name: Bone marrow

growth_protocol: Freshly isolated cells from mouse bone marrow, never cultured

extract_protocol:
The genomic DNA was extracted from mouse HSPCs per condition using QIAamp DNA extraction kit.
Genomic DNA was digested with MspI, and the resulting fragments were end-repaired, A-tailed, and ligated with methylated adapters. After size-selection, bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Zymo Research). The bisulfite-converted DNA was PCR-amplified to enrich for adapter-ligated fragments. Size selection was conducted via gel cutting in order to obtain DNA fragments spanning a range of 220bp to 40bp in length (Meissner, 2008). Following this, the EZ DNA Methylation Gold Kit (Zymo Research) was utilized to convert these fragments to bisulfite. The ultimate DNA library was generated via PCR amplification.

treatment_protocol: Dnmt3aR878H/+ or Dnmt3a+/+ donor WBM cells were transplanted into lethally irradiated recipients in a non-competitive manner from sex-matched littermates. Recipients were either left untreated for five weeks following transplantation or initiated on a one-month course of metformin treatment. Following a month, these mice were euthanized and their bone marrow cells were obtained. Subsequently, the BM was enriched in order to isolate Lin-Kit+ cells (HSPCs). The EasySep mouse hematopoietic progenitor isolation kit (StemCell Technologies, Cat# 19856) was utilized to accomplish this enrichment. Following that, a further enrichment procedure was executed utilizing the c-KIT positive enrichment kit (Cat# 18757, StemCell Technologies).

value: Bone marrow

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

tag: sorting

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing

value: C57BL/6(Dnmt3afl-R878H/+ mice (JAX stock #032289) crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))

value: metformin


title: UK1180_AD

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: NOTCH1_rep1_guide1 (D23-5938-1)

description: In the processed data file, corresponds to column D23-5938-1

value: Neural progenitor cells


title: UK1173_AD


title: RH RRBS MET-1 replicate


title: Round spermatids, csr-1a mutant, CUT_Tag, bio rep2

value: male


title: CSNK2A1_rep2_guide1 (D23-5936-1)

description: In the processed data file, corresponds to column D23-5936-1


title: UK1188_AD


title: CSNK2A1_rep1_guide2 (D23-5935-2)

description: In the processed data file, corresponds to column D23-5935-2


title: UK1169_AD


title: CSNK2A1_rep3_guide1 (D23-5934-1)

description: In the processed data file, corresponds to column D23-5934-1


title: UK1168_AD


title: RH RRBS VEH-4 replicate

value: vehicle (control)


title: Round spermatids, csr-1a mutant, CUT_Tag, bio rep1


title: RH RRBS MET-3 replicate


title: UK1158_AD


title: CSNK2A1_rep2_guide2 (D23-5933-2)

description: In the processed data file, corresponds to column D23-5933-2


title: Round spermatids, WT, CUT_Tag, bio rep3

value: gfp::tev::2xflag::aid::csr-1a; him-8


title: RH RRBS VEH-2 replicate


title: UK1133_AD


title: CSNK2A1_rep1_guide1 (D23-5932-1)

description: In the processed data file, corresponds to column D23-5932-1


title: RH RRBS VEH-1 replicate


title: HNRNPA2B1_rep3_guide2 (D23-5931-2)

description: In the processed data file, corresponds to column D23-5931-2


title: Round spermatids, WT, CUT_Tag, bio rep1

value: round spermatids


title: UK1118_AD


title: WT RRBS  MET-4 replicate

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: DMY konckout male medaka gonda,120dph,small RNA-Seq,biological replicate 2

city: Wuhan

first: Xing

last: Lin

state: Hubei

address: No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province

institute: Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences

description: Library name: 120dph_XYD2_small_RNA

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: ASM223467v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include RPM values for each Sample

organism: Oryzias latipes

source_name: ovary

extract_protocol:
Utilizing Poly (dT) oligo-attached magnetic beads, the mRNA was extracted from the total RNA and enriched. cDNA libraries were then prepared using the TruSeq RNA Sample Preparation Kit (Illumina, USA). Polyacrylamide gel electrophoresis was used to separate short-length RNAs, measuring 17 to 32 bp, from the total RNA. After the chosen segments were ligated to 5’ and 3’ RNA adapters, RT-PCR amplification was carried out.
Utilizing Poly (dT) oligo-attached magnetic beads, the mRNA was extracted from the total RNA and enriched. cDNA libraries were then prepared using the TruSeq RNA Sample Preparation Kit (Illumina, USA). Finally, the cDNA libraries were sequenced using the Illumina Hiseq 2000TM platform after PCR amplification.

value: ovary

value: female

value: DMY konckout


title: DMY konckout male medaka gonda,120dph,small RNA-Seq,biological replicate 3

description: Library name: 120dph_XYD3_small_RNA


title: WT RRBS  MET-3 replicate

value: Bone marrow

value: Mouse HSPCs


title: DMY konckout male medaka gonda,120dph,small RNA-Seq,biological replicate 1

description: Library name: 120dph_XYD1_small_RNA


title: HNRNPA2B1_rep1_guide2 (D23-5929-2)

description: In the processed data file, corresponds to column D23-5929-2


title: WT RRBS  MET-2 replicate

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing


title: HNRNPA2B1_rep3_guide1 (D23-5928-1)

description: In the processed data file, corresponds to column D23-5928-1


title: MGH1801_AD


title: RH RRBS VEH-3 replicate

value: C57BL/6(Dnmt3afl-R878H/+ mice (JAX stock #032289) crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: Round spermatids, WT, CUT_Tag, bio rep2

value: H3K9me3 (abcam, #ab8898)

value: 8-10 h post Heat-stress


title: WT RRBS  VEH-4 replicate


title: MGH1791_AD

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: HNRNPA2B1_rep2_guide2 (D23-5927-2)

description: In the processed data file, corresponds to column D23-5927-2

value: Neural progenitor cells


title: HNRNPA2B1_rep2_guide1 (D23-5930-1)

description: In the processed data file, corresponds to column D23-5930-1


title: HNRNPA2B1_rep1_guide1 (D23-5926-1)

description: In the processed data file, corresponds to column D23-5926-1


title: UK1117_AD


title: WT RRBS  VEH-3 replicate

value: vehicle (control)


title: MGH1673_AD


title: wild type male medaka gonda,120dph,small RNA-Seq,biological replicate 1

description: Library name: 120dph_XY1_small_RNA

source_name: testis

value: testis

value: male

value: WT


title: vir & rep cells, csr-1a mutant, mRNAseq, bio rep2

value: somatic cells

value: vir & rep cells

value: gfp::sl2::2xflag::aid::csr-1a_delta; him-8; Ex(pnc-1p::wrmScarlet); Ex(pcs-1p::wrmScarlet)

value: With late L4 parental heat-stress


title: Control_rep3_guide1 (D23-5949-1)

description: In the processed data file, corresponds to column D23-5949-1

value: Control


title: wild type female medaka gonda,120dph,small RNA-Seq,biological replicate 3

description: Library name: 120dph_XX3_small_RNA

value: ovary

value: female


title: MGH1745_AD


title: MGH1664_AD


title: Control_rep2_guide2 (D23-5948-2)

description: In the processed data file, corresponds to column D23-5948-2


title: WT RRBS  VEH-2 replicate

value: Bone marrow

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: Input ChIP

data_processing:
Illumina base-cell data were processed and demultiplexed using bcl2fastq2 v2.20 and low-quality bases with Phred scores less than 33 were trimmed. 75 bp single-end sequence reads were subsequently mapped to the genome through BWA v0.7.12 algorithm with default settings
Low quality reads were filtered out and PCR duplicates were removed.
Aligned sequencing reads, or tags, were extended to 200bp from the 3’ end, followed by dividing the genome into 32bp bins and counting the number of fragments in each bin
The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-2.
Assembly: mm10
Supplementary files format and content: bigWig files including one file for the input
Supplementary files format and content: narrow peak file containing peaks for each sample

extract_protocol:
LK-enriched BM cells were fixed with 1% formaldehyde for 15 min according to the Active Motif ChIP cell fixation protocol. Fixed cell pellets were submitted to Active Motif (Carlsbad, CA) for ChIP-Seq.
An automated system (Apollo 342, Wafergen Biosystems/Takara) was utilized to prepare Illumina sequencing libraries (described by Bentley et al., (2008)). The resulting DNA libraries were then quantified and sequenced on Illumina's NovaSeq 6000 following a final PCR amplification step.

treatment_protocol: Bone marrow cells procured from female murine subjects that underwent transplantation were subjected to a treatment regimen lasting for a duration of one month, with and without the administration of metformin.  Following the initial procedure, the bone marrow (BM) cells underwent a specific enrichment process to isolate Lin-Kit+ cells(HSPCs). This enrichment was achieved using the EasySep mouse hematopoietic progenitor isolation kit (StemCell Technologies, Cat# 19856). Subsequently, an additional enrichment step was performed using the c-KIT positive enrichment kit (StemCell Technologies, Cat# 18757).


title: UK1104_AD

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: MGH1519_AD


title: wild type female medaka gonda,120dph,small RNA-Seq,biological replicate 1

description: Library name: 120dph_XX1_small_RNA


title: RH MET-2 replicate ChIP

value: C57BL/6(Dnmt3afl-R878H/+ mice (JAX stock #032289) crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))

value: metformin


title: Control_rep2_guide1 (D23-5945-1)

description: In the processed data file, corresponds to column D23-5945-1

value: Neural progenitor cells


title: Control_rep1_guide1 (D23-5947-1)

description: In the processed data file, corresponds to column D23-5947-1


title: wild type male medaka gonda,120dph,small RNA-Seq,biological replicate 2

description: Library name: 120dph_XY2_small_RNA

value: testis

value: male

value: WT


title: RH MET-1 replicate ChIP


title: MGH1411_AD


title: WT RRBS  MET-1 replicate


title: Control_rep1_guide2 (D23-5944-2)

description: In the processed data file, corresponds to column D23-5944-2

value: Control


title: DMY konckout male medaka gonda,30dph,small RNA-Seq,biological replicate 3

description: Library name: 30dph_XYD3_small_RNA

value: ovary

value: DMY konckout


title: MGH1399_AD


title: RH VEH-2 replicate ChIP

value: Bone marrow

value: vehicle (control)


title: MGH1387_AD


title: MGH1363_AD


title: DMY konckout male medaka gonda,30dph,small RNA-Seq,biological replicate 1

description: Library name: 30dph_XYD1_small_RNA

value: female


title: RH VEH-1 replicate ChIP

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing


title: NOTCH1_rep2_guide2 (D23-5942-2)

description: In the processed data file, corresponds to column D23-5942-2


title: DMY konckout male medaka gonda,30dph,small RNA-Seq,biological replicate 2

description: Library name: 30dph_XYD2_small_RNA


title: NOTCH1_rep3_guide2 (D23-5940-2)

description: In the processed data file, corresponds to column D23-5940-2


title: wild type female medaka gonda,120dph,small RNA-Seq,biological replicate 2

description: Library name: 120dph_XX2_small_RNA


title: wild type male medaka gonda,30dph,small RNA-Seq,biological replicate 3

description: Library name: 30dph_XY3_small_RNA


title: wild type male medaka gonda,30dph,small RNA-Seq,biological replicate 2

description: Library name: 30dph_XY2_small_RNA


title: NOTCH1_rep1_guide1 (D23-5941-1)

description: In the processed data file, corresponds to column D23-5941-1


title: WT MET-2 replicate ChIP

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: wild type male medaka gonda,120dph,small RNA-Seq,biological replicate 3

description: Library name: 120dph_XY3_small_RNA


title: wild type male medaka gonda,30dph,small RNA-Seq,biological replicate 1

description: Library name: 30dph_XY1_small_RNA


title: WT MET-1 replicate ChIP


title: BN13-10_AD

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: MGH1360_AD


title: WT VEH-1 replicate ChIP


title: WT VEH-2 replicate ChIP


title: NOTCH1_rep2_guide1 (D23-5939-1)

description: In the processed data file, corresponds to column D23-5939-1

value: Neural progenitor cells


title: wild type female medaka gonda,30dph,small RNA-Seq,biological replicate 3

description: Library name: 30dph_XX3_small_RNA


title: NOTCH1_rep3_guide1 (D23-5943-1)

description: In the processed data file, corresponds to column D23-5943-1


title: CSNK2A1_rep3_guide1 (D23-5937-1)

description: In the processed data file, corresponds to column D23-5937-1


title: wild type female medaka gonda,30dph,small RNA-Seq,biological replicate 2

description: Library name: 30dph_XX2_small_RNA


title: BDL-SenA-3

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: cholangiocyte

extract_protocol:
Total RNA was isolated using TRIzol (Vazyme, Nanjing, China) according to the manufacturer’s instructions and then and purified by lithium chloride (Sigma, Missouri, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cholangiocyte

value: BDL plus senkyunolide A


title: NOTCH1_rep1_guide2 (D23-5938-2)

description: In the processed data file, corresponds to column D23-5938-2


title: BDL-SenA-2


title: BN12-27_AD


title: MGH1362_AD


title: BN11-78_AD


title: DMY konckout male medaka gonda,10dph,small RNA-Seq,biological replicate 3

description: Library name: 10dph_XYD3_small_RNA


title: BDL-3

value: BDL


title: BN11-38_AD


title: wild type female medaka gonda,30dph,small RNA-Seq,biological replicate 1

description: Library name: 30dph_XX1_small_RNA

value: WT


title: CSNK2A1_rep1_guide1 (D23-5935-1)

description: In the processed data file, corresponds to column D23-5935-1


title: CSNK2A1_rep2_guide2 (D23-5936-2)

description: In the processed data file, corresponds to column D23-5936-2


title: DMY konckout male medaka gonda,10dph,small RNA-Seq,biological replicate 2

description: Library name: 10dph_XYD2_small_RNA

value: ovary


title: DMY konckout male medaka gonda,10dph,small RNA-Seq,biological replicate 1

description: Library name: 10dph_XYD1_small_RNA

value: DMY konckout


title: BN11-97_AD


title: BDL-1


title: BN11-21_AD


title: CSNK2A1_rep1_guide2 (D23-5932-2)

description: In the processed data file, corresponds to column D23-5932-2


title: wild type male medaka gonda,10dph,small RNA-Seq,biological replicate 3

description: Library name: 10dph_XY3_small_RNA

value: testis

value: male


title: wild type male medaka gonda,10dph,small RNA-Seq,biological replicate 2

description: Library name: 10dph_XY2_small_RNA


title: BN07-54_AD


title: CSNK2A1_rep2_guide1 (D23-5933-1)

description: In the processed data file, corresponds to column D23-5933-1


title: Sham-3

value: sham


title: Sham-2


title: HNRNPA2B1_rep3_guide1 (D23-5931-1)

description: In the processed data file, corresponds to column D23-5931-1


title: wild type male medaka gonda,10dph,small RNA-Seq,biological replicate 1

description: Library name: 10dph_XY1_small_RNA


title: BN07-42_AD


title: BN10-16_AD


title: BN11-27_AD


title: BDL-SenA-1


title: wild type female medaka gonda,10dph,small RNA-Seq,biological replicate 3

description: Library name: 10dph_XX3_small_RNA

value: female


title: HNRNPA2B1_rep2_guide2 (D23-5930-2)

description: In the processed data file, corresponds to column D23-5930-2


title: BN05-19_AD


title: CSNK2A1_rep3_guide2 (D23-5934-2)

description: In the processed data file, corresponds to column D23-5934-2


title: RH MET-2 replicate

data_processing:
The readings were mapped to the mm10 reference genome using the STAR (v2.5) program
The HTSeq v0.6.1 software was utilized to tally the number of reads that were aligned to each individual gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample

growth_protocol: Freshly isolated HSPCs from mouse bone marrow, never cultured

extract_protocol:
RNA extraction from enriched murine HSPC was performed using the RNeasy Plus Mini Kit (QIAGEN, Cat #74136) following the instructions provided by the manufacturer.
Libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina, and sequencing was performed using the NovaSeq 6000 S4 with PE150 BP sequencing system.

treatment_protocol: The dataset was derived from an in vivo competition experiment after 1 month of treatment, with 2 animals per treatment groups.

value: Bone marrow

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: C57BL/6(Dnmt3afl-R878H/+ mice (JAX stock #032289) crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))

value: metformin


title: RH MET-1 replicate

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing


title: RH VEH-2 replicate

value: vehicle (control)


title: wild type female medaka gonda,10dph,small RNA-Seq,biological replicate 2

description: Library name: 10dph_XX2_small_RNA


title: 6-2816vd-148_T

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: Strand orientation: reverse

data_processing:
Basecalls performed using Illumina RTA.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities
Expression values were computed using a pseudo-alignment to the reference transcriptome using Kallisto version 0.43.0
Assembly: GRCh38

source_name: lung adenocarcinoma

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen)
cDNA libraries were prepared from total RNA using a PolyA selection and the Illumina TruSeq Stranded RNA Kit and were further amplified for sequencing.

value: lung adenocarcinoma

tag: reference genome

value: Gencode 26

tag: strand orientation

value: non stranded

tag: quantification

value: paired-end


title: 4-10314vd-763_T

description: Strand orientation: reverse


title: DMY konckout male medaka gonda,120dph,RNA-Seq,biological replicate 3

description: Library name: 120dph_XYD3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: ASM223467v1
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Utilizing Poly (dT) oligo-attached magnetic beads, the mRNA was extracted from the total RNA and enriched. cDNA libraries were then prepared using the TruSeq RNA Sample Preparation Kit (Illumina, USA).
The cDNA libraries were sequenced using the Illumina Hiseq 2000TM platform after PCR amplification.

value: ovary

tag: genotype


title: WT VEH-2 replicate

tag: cell line

tag: cell type

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: BN03-30_AD

data_processing:
Data was aligned to hg19 using TopHat and CuffLinks. The data were then TPM normalized and filtered based on the number of mapped reads and percent mappability
Assembly: hg19
Supplementary files format and content: tab-delimited text file indicates the raw counts per patient

value: Temporal cortex

value: Pyramidal neurons

value: AD


title: BDL-2

value: cholangiocyte

value: BDL


title: U266_cgRNA_Sample_D_S9

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

data_processing:
The reads were mapped by STAR 2.27a and read counts per gene were quantified using Human Ensembl GRCh38.98 GTF file. In Partek flow, read counts were normalized by adding 1.0E-4 followed by TMM normalization. All results of differential gene expression analysis utilized Partek’s statistical analysis tool, DESeq2.  For differentially expressed gene list, p-values, FDR, and fold change (FC) filters were applied. The filter was p<0.05, FDR<0.05 and Fold change > 2 for all differential gene expression results. Ingenuity Pathway Analysis software (IPA) was used for pathway analysis.
Assembly: Human Ensembl GRCh38.98
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TMM normalized counts for each Sample

source_name: Cell line

growth_protocol: U266 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), without antibiotics, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
8ug/mL blasticidin and 4ug/mL puromycin, started 4 days after transduction
Libraries for RNA-Seq were prepared with Nugen Universal plus mRNA-Seq Kit to generate strand-specific RNA-seq libraries.  The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library.  Different index adaptors were used for multiplexing samples in one sequencing lane. Sequencing was performed on NovaSeq 6000 for PE 2x150 bp run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.19.1.403 program.

treatment_protocol: After transduction, cells were treated with puromycin and blasticidin to kill non-transduced cells. They were then maintained in media with these selection agents.

value: Cell line

value: Plasma cells

value: control gRNA


title: U266_cgRNA_Sample_E_S10


title: HNRNPA2B1_rep1_guide2 (D23-5926-2)

description: In the processed data file, corresponds to column D23-5926-2

value: Neural progenitor cells


title: DMY konckout male medaka gonda,120dph,RNA-Seq,biological replicate 2

description: Library name: 120dph_XYD2

value: female

value: DMY konckout


title: WT VEH-1 replicate

value: Bone marrow

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing

value: vehicle (control)


title: HNRNPA2B1_rep3_guide2 (D23-5928-2)

description: In the processed data file, corresponds to column D23-5928-2


title: HNRNPA2B1_rep1_guide1 (D23-5929-1)

description: In the processed data file, corresponds to column D23-5929-1


title: wild type male medaka gonda,120dph,RNA-Seq,biological replicate 3

description: Library name: 120dph_XY3

value: testis

value: male

value: WT


title: lung, 8wk, HPS2, cohort_c

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Alignment and quantification using STAR-solo
QC, filtering, integration using scanpy v.1.8.1
Batch effect correction using harmony-pytorch
Assembly: GRCm39
Supplementary files format and content: adata_processed_geo.h5ad is an HDF5 anndata file containing cell- and gene-level metadata as well as sparse counts matrices for the final processed dataset.

source_name: lung

extract_protocol:
Cells were isolated by FACS from dissociated primary mouse lung tissue and sorted buffer for droplet-based scRNA-seq.
poly-A selection was performed on isolated bulk RNA to enrich for mRNA. Subsequently, enriched mRNA was fragmented and Illumina sequencing adapters were ligated before QC and sequencing.

value: lung

tag: batch


title: DMY konckout male medaka gonda,120dph,RNA-Seq,biological replicate 1

description: Library name: 120dph_XYD1

value: ovary


title: HNRNPA2B1_rep2_guide1 (D23-5927-1)

description: In the processed data file, corresponds to column D23-5927-1


title: U266_cgRNA_Sample_C_S8


title: wild type male medaka gonda,120dph,RNA-Seq,biological replicate 2

description: Library name: 120dph_XY2


title: lung, 8wk, C57BL6, cohort_c

tag: age


title: wild type female medaka gonda,10dph,small RNA-Seq,biological replicate 1

description: Library name: 10dph_XX1_small_RNA

tag: tissue


title: metformin replicate 2

description:
Mouse HSPCs
MET_2_matrix.mtx.gz
MET_2_features.tsv.gz
MET_2_barcodes.tsv.gz

data_processing:
The scRNA reads were aligned against the mouse reference sequence mm10 using Cell Ranger (v6.1.2).
Assembly: mm10
Supplementary files format and content: cell ranger output (matrix, features and barcodes) containing Single-Cell Gene Expression  (GEX)  counts  and CD45.1 CD45.2 ADT counts for each sample
Library strategy: CITE-SEQ

extract_protocol:
Murine HSPC were enriched and then CD45.1 + cells (Dnmt3a+/+) and CD45.2 + cells (Dnmt3aR879/+) were marked using TotalSeq™-B antibodies (according to Biolegend's protocol: https://www.biolegend.com/en-us/protocols/totalseq-b-or-c-with-10x-feature-barcoding-technology).
CITE-seq library generation was performed using 10x Genomics Chromium Single Cell 3′ v3.1_CellSurfaceProtein_RevD kit and the Novaseq 6000 sequencing system

treatment_protocol: Bone marrow cells procured from female murine subjects that underwent transplantation were subjected to a treatment regimen lasting for a duration of seven months, with and without the administration of metformin.  Following the initial procedure, the bone marrow (BM) cells underwent a specific enrichment process to isolate Lin-Kit+ cells(HSPCs). This enrichment was achieved using the EasySep mouse hematopoietic progenitor isolation kit (StemCell Technologies, Cat# 19856). Subsequently, an additional enrichment step was performed using the c-KIT positive enrichment kit (StemCell Technologies, Cat# 18757).

tag: strain

value: metformin

tag: library type

value: mRNA


title: WT MET-1 replicate

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: wild type male medaka gonda,120dph,RNA-Seq,biological replicate 1

description: Library name: 120dph_XY1

tag: Sex


title: 2-11974vd-811_T

description: Strand orientation: reverse

value: lung adenocarcinoma

value: Gencode 26

value: non stranded

value: paired-end


title: metformin replicate 2.1

library_source: other

molecule: protein

value: Bone marrow

value: ADT


title: lung, 8wk, C57BL6, cohort_b


title: U266_cgRNA_Sample_A_S6

value: Cell line

value: Plasma cells

value: control gRNA


title: wild type female medaka gonda,120dph,RNA-Seq,biological replicate 3

description: Library name: 120dph_XX3

value: female


title: U266_gRNA2_Sample_E_S5

value: EFNB2 gRNA


title: lung, 60wk, C57BL6, cohort_a


title: metformin replicate 1

description:
Mouse HSPCs
MET_1_matrix.mtx.gz
MET_1_features.tsv.gz
MET_1_barcodes.tsv.gz

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing


title: metformin replicate 1.1


title: wild type female medaka gonda,120dph,RNA-Seq,biological replicate 2

description: Library name: 120dph_XX2

value: ovary

value: WT


title: U266_gRNA2_Sample_D_S4


title: lung, 60wk, HPS2, cohort_a

value: lung


title: U266_cgRNA_Sample_B_S7


title: lung, 60wk, HPS1, cohort_a


title: vehicle replicate 2.1

description:
Mouse HSPCs
VEH_2_matrix.mtx.gz
VEH_2_features.tsv.gz
VEH_2_barcodes.tsv.gz

value: vehicle (control)


title: lung, 60wk, HPS1-2, cohort_a


title: U266_gRNA2_Sample_B_S2


title: wild type female medaka gonda,120dph,RNA-Seq,biological replicate 1

description: Library name: 120dph_XX1


title: vehicle replicate 1.1

description:
Mouse HSPCs
VEH_1_matrix.mtx.gz
VEH_1_features.tsv.gz
VEH_1_barcodes.tsv.gz


title: U266_gRNA2_Sample_C_S3


title: lung, 8wk, HPS1, cohort_d


title: DMY konckout male medaka gonda,30dph,RNA-Seq,biological replicate 2

description: Library name: 30dph_XYD2

value: DMY konckout


title: DMY konckout male medaka gonda,30dph,RNA-Seq,biological replicate 3

description: Library name: 30dph_XYD3


title: Sham-1

value: cholangiocyte

value: sham


title: U266_gRNA2_Sample_A_S1


title: lung, 8wk, HPS1-2, cohort_d


title: DMY konckout male medaka gonda,30dph,RNA-Seq,biological replicate 1

description: Library name: 30dph_XYD1


title: KO2

city: Tokyo

first: Koya

last: Yasukawa

state: --- Select One ---

country: Japan

institute: Tokyo medical and dental university

data_processing:
Sequence reads were checked by using FastQC.
Sequence reads were mapped to GRCm38/mm10 by using STAR.
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

extract_protocol:
Total RNA was extracted from cells by using TRIzol Reagent (Thermo Fisher Scientific). Contaminating DNA was removed by digestion with DNA-free DNA Removal Kit (Thermo Fisher Scientific). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).
RNA libraries for RNA-seq were prepared by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Liver

value: Hepatocellular carcinoma cells

value: Acvr2a knockout


title: wild type male medaka gonda,30dph,RNA-Seq,biological replicate 3

description: Library name: 30dph_XY3

value: testis

value: male


title: lung, 60wk, HPS1-2, cohort_d


title: L024_L027_L034_L035

city: San Francisco

first: Mark

middle: Roberts

last: Looney

address: 513 Parnassus

institute: UCSF

description: 10x Genomics

data_processing:
Alignment to reference genome and Ensembl Annotation (CellRanger 3.0.2)
QC: UMI < 200, mt-genes > 15%, rb-genes > 50%
Normalization and variance stabilization via SCTransform (Seurat 4.3.0)
Multiplet removal (DoubletFinder 2.0)
Assembly: GRCh38 reference genome
Supplementary files format and content: HDF5 feature barcode matrix format

source_name: Lung/ Bone marrow

extract_protocol:
Lungs were enzymatically and mechanically dissociated, bone marrow cells were collected from the trabecular framework of the VBs through passive release. Single cell suspensions were sorted and subsequently used for the 10X encapsulation.
10x encapsulation and library construction were done using Chromium Next GEM Single Cell 3’ Reagent Kits v3.2 per the manufacturer’s instruction.

value: Lung/ Bone marrow

value: HSPCs (Lin- CD34+ cells)


title: BM024_BM027_BM034_BM036

description: 10x Genomics


title: L025_L028_BM_026_BM029

description: 10x Genomics


title: lung, 60wk, C57BL6, cohort_d


title: BM025_BM028_L029

description: 10x Genomics


title: lung, 8wk, HPS2-TG, cohort_f


title: NC1

value: Acvr2a Wild type


title: BM019_BM020_L021_L023

description: 10x Genomics


title: vehicle replicate 2

value: Bone marrow

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

value: mRNA


title: lung, 8wk, C57BL6, cohort_f


title: wild type female medaka gonda,30dph,RNA-Seq,biological replicate 3

description: Library name: 30dph_XX3

value: ovary

value: female

value: WT


title: wild type male medaka gonda,30dph,RNA-Seq,biological replicate 1

description: Library name: 30dph_XY1


title: NC2


title: wild type female medaka gonda,30dph,RNA-Seq,biological replicate 2

description: Library name: 30dph_XX2


title: KO1


title: lung, 8wk, HPS3, cohort_f

value: lung


title: 2.4 brain 4

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

description:
25-Mmu-Li24-03
edgeRglm_GENE_Li24-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

data_processing:
Sequencing reads were trimmed to remove adaptors and low-quality bases
Trimmed reads were aligned to mm10 reference genome using STAR aligner
Differential gene expression analysis was conducted via EdgeR generalized linear model method
For lithium treated mouse brains, two batches were combined using Com-Bat seq.
Assembly: mm10
Supplementary files format and content: excel file from differential gene expression anaylsis conducted in EdgeR

source_name: brain

extract_protocol:
RNA was collected using Direct-zol RNA kit (Zymo Research).
RNA libraries were generated following the Illumina TruSeq RNA Sample preparation guide. mRNA libraries were generated using NEBNext Poly(A) mRNA Magnetic isolation module and NEBNext Ultara RNA library prep kit.

value: brain

value: 2.4 mg/kg LiCO3 diet


title: vehicle replicate 1

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing

value: vehicle (control)


title: L019_L020_BM021_BM023

description: 10x Genomics


title: lung, 8wk, HPS2, cohort_f


title: wild type female medaka gonda,30dph,RNA-Seq,biological replicate 1

description: Library name: 30dph_XX1


title: m-GC, scRNAseq

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

data_processing:
The raw RNA sequencing reads for all samples were aligned to the human reference genome hg19 using the STAR program with standard input parameters. Gene expression levels were quantified by calculating FPKM values (fragments per kilobase of transcript per million fragments mapped) using RSEM software, and the gene annotation reference was GENCODE hg19.
The single-cell RNA-seq data for m-GCs was processed using 10x Genomics Cell Ranger 3.1.0 to handle the raw fastq files. For alignment and gene annotation, the human reference genome used was hg19, in conjunction with Ensembl 87
Assembly: hg19
Supplementary files format and content: Count and FPKM matrix text file, feature barcode matrix text file.

source_name: mature Guide Cells activated from dormant pre-GC

growth_protocol: Human unmobilized peripheral blood samples were collected from healthy donors. Immediately after collection, majority of the red blood cells were removed using lysis buffer and majority of lymphocytes were removed by high-speed centrifugation. The supernatant was removed and the cell pellet was gently rinsed with 1xPBS (pH 7.4) which contains pre-GC.

extract_protocol:
Total RNA were extracted using TRI Reagent protocol (Sigma-Aldrich). Residual DNA contamination was digested by using PerfeCTa DNase I (RNase-free, Quantabio).
RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs (NEB), E7770). Single cell RNA-seq library was constructed using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000268).

treatment_protocol: The cell pellet was gently resuspended in 19 mL hepatic-conditioned medium to activate pre-GCs. The cell suspension was seeded in 100 mm diameter treated culture dishes (Corning, 430293) at 3,000,000 to 5,000,000 cells per dish, and incubated for 14-18 days in a CO2 (5%) incubator at 37oC. The hepatic-conditioned medium was changed every other day. Aggregation of granules near the center of the cells indicates maturation (m-GCs). Co-culture of m-GC and human umbilical cord-derived mesenchymal stromal cells (UC-MSC) at the ratio of 10:1 give rise to giaSC in the presence of hepatic-conditioned medium.


title: 2.4 brain 2

description:
Li-24-05
edgeRglm_GENE_Li24-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: UC-MSC, person 2, replicate 2

source_name: human umbilical cord-derived mesenchymal stromal cells


title: 2.4 brain 1

description:
Li-24-01
edgeRglm_GENE_Li24-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: lung, 8wk, HPS1-2, cohort_f


title: UC-MSC, person 2, replicate 1

value: human umbilical cord-derived mesenchymal stromal cells


title: DMY konckout male medaka gonda,10dph,RNA-Seq,biological replicate 3

description: Library name: 10dph_XYD3

value: DMY konckout


title: lung, 8wk, HPS1, cohort_f


title: wild type male medaka gonda,30dph,RNA-Seq,biological replicate 2

description: Library name: 30dph_XY2

value: testis

value: male


title: lung, 60wk, C57BL6, cohort_e


title: DMY konckout male medaka gonda,10dph,RNA-Seq,biological replicate 1

description: Library name: 10dph_XYD1


title: UC-MSC, person 1, replicate 2


title: 1.8 brain 3

description:
22-Mmu-Li18-02
edgeRglm_GENE_Li18-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: 1.8 mg/kg LiCO3 diet


title: lung, 60wk, HPS3, cohort_e


title: 2.4 brain 3

description:
24-Mmu-Li24-02
edgeRglm_GENE_Li24-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: lung, 60wk, HPS2-TG, cohort_e


title: wild type male medaka gonda,10dph,RNA-Seq,biological replicate 2

description: Library name: 10dph_XY2


title: 1.8 brain 2

description:
Li-18-06
edgeRglm_GENE_Li18-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: wild type male medaka gonda,10dph,RNA-Seq,biological replicate 3

description: Library name: 10dph_XY3


title: wild type male medaka gonda,10dph,RNA-Seq,biological replicate 1

description: Library name: 10dph_XY1


title: AD4_control [reanalysis]

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quantify them against the human reference genome GRCh38 using Cellranger count.
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters. The samples here include reanalysis of samples GSM5242603 and GSM7505845.
Assembly: GRCh38
Supplementary files format and content: counts.csv: Comma-separated values file containing filtered count matrix for each cell.
Supplementary files format and content: md.csv: Comma-separated values file with metadata for each cell, contains cell identification.

source_name: Organoid

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech).
Libraries generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (version 3, 10x Genomics).
Single-cell RNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000.

value: Organoid

tag: developmental stage

value: Day 200

value: iPSC-derived neural retina from organoids

tag: condition

value: Control


title: 1.8 brain 1

description:
Li-18-01
edgeRglm_GENE_Li18-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

tag: treatment


title: UC-MSC, person 1, replicate 1


title: wild type female medaka gonda,10dph,RNA-Seq,biological replicate 3

description: Library name: 10dph_XX3

value: ovary


title: lung, 60wk, HPS1, cohort_e


title: lung, 60wk, HPS2, cohort_e


title: 1.2 brain 3

description:
20-Mmu-Li12-02
edgeRglm_GENE_Li12-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: 1.2 mg/kg LiCO3 diet


title: lung, 60wk, HPS1-2, cohort_e


title: AC_D200

description: Female sample - Pooled 30 organoids for experiment all at Day 200 of differentiation. Organoids developed using IGF1-dependent method of differentiation as published in Darin Zerti, 2020 (DOI: 10.1002/stem.3082).

value: Affected Control

value: Female


title: 1.2 brain 4

description:
21-Mmu-Li12-04
edgeRglm_GENE_Li12-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: brain


title: DMY konckout male medaka gonda,10dph,RNA-Seq,biological replicate 2

description: Library name: 10dph_XYD2

value: female


title: 1.2 brain 2

description:
Li-12-05
edgeRglm_GENE_Li12-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: 1.8 brain 4

description:
23-Mmu-Li18-03
edgeRglm_GENE_Li18-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: wild type female medaka gonda,10dph,RNA-Seq,biological replicate 2

description: Library name: 10dph_XX2

value: WT


title: 1.2 brain 1

description:
Li-12-03
edgeRglm_GENE_Li12-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: Sample 10_Rep3_H460 CVT-11127 Treatment

city: New York

first: BiNGS

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Adapter sequences trimmed with TrimGalore!(v0.6.5)
Gene level read counts are obtained by using Salmon (v1.2.1)
Counts table and DEG analysis completed using DeSeq2 (v1.28.1)
Assembly: hg38
Supplementary files format and content: csv, normalized counts

growth_protocol: H661, H358, H1993,H2228, H2122 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% Pen-strep and 1% Glutmax  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LUAD cell lines were treated with CVT-11127 (10µM for 96 hours), equivalent concentration of DMSO was added to cotrol samples. Cells were maintained in RPMI with 10% fetal bovine serum (FBS) and 1% Pen-strep and 1% Glutmax  in humidified atmosphere with 5% CO2 at 37C

value: NSCLC, LUAD

tag: time

value: Day 4


title: wild type female medaka gonda,10dph,RNA-Seq,biological replicate 1

description: Library name: 10dph_XX1


title: AD3_D210 [reanalysis]

value: Day 210


title: macrophage, GPR35 knockout 3

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

description:
macrophage_KO_3
RNAseq_GPR35_macrophages.txt

data_processing:
Sequencing of libraries was performed using an Illumina HiSeq 2500 platform generating 1x50bp reads.
Assembly: GRCm38 Mus musculus
Supplementary files format and content: tab-delimited txt files include RPKM for each sample

source_name: bone marrow-derived macrophage

extract_protocol:
RNA was extracted using the QIAGEN Rneasy kit (QIAGEN).
RNA libraries were prepared using TruSeq® Stranded mRNA Library Prepas per manufacturer's instructions

value: bone marrow-derived macrophage

value: GPR35 knockout


title: 2C7_D200

description: Male sample - Pooled 30 organoids for experiment all at Day 200 of differentiation. Organoids developed using BMP4-activated method of differentiation as published in Dean Hallam, 2018 (https://doi.org/10.1002/stem.2883).

value: Late Onset STGD1

value: Male


title: 0.6 brain 4

description:
19-Mmu-Li06-05
edgeRglm_GENE_Li06-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: 0.6 mg/kg LiCO3 diet


title: Sample 10_Rep2_H460 CVT-11127 Treatment


title: Sample 10_Rep1_H460 CVT-11127 Treatment


title: macrophage, wild type 2

description:
macrophage_WT_2
RNAseq_GPR35_macrophages.txt

value: Wild type


title: macrophage, GPR35 knockout 5

description:
macrophage_KO_5
RNAseq_GPR35_macrophages.txt


title: 0.6 brain 3

description:
18-Mmu-Li06-02
edgeRglm_GENE_Li06-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: 0.6 brain 2

description:
Li-06-06
edgeRglm_GENE_Li06-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: P291_32_21-PSA-F5_Log2 Signal

type: RNA

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Gallus gallus

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The five-week feeding trial with 72 male, 1-day-old broiler chickens (Cobb 500, Cobb-Vantress, Weidemar, Germany) was approved by the Animal Welfare Officer of the Justus Liebig University Giessen (approval no.: JLU 862_M). All experimental procedures described followed established guidelines for laboratory animals care and handling.

extract_protocol: Aliquots from the liver (20-30 mg) were used for total RNA extraction using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer´s protocol. Total RNA was analyzed for quantity and quality using an Infinite 200M microplate reader with a NanoQuant plate (both from Tecan, Mainz, Germany).

treatment_protocol: The broilers were randomly assigned to three different groups (4 broilers/cage, 6 cages/group), with a similar mean initial body weight across the groups. The broilers were housed in 2.1 m2 cages with nipple drinkers and feed automates and had free access to feed and water. The floor was covered with hemp-based litter (Hemparada, HempFlax Group B.V., Oude Pekela, Netherlands) which allowed scratching, pecking and dustbathing and was exchanged two times per week during the first two weeks and every two days during the last three weeks of the trial. In addition, broilers were provided with perches in elevated position for resting and sleeping. Light regime followed a schedule of 24 h:0 h, 23 h:1 h, 22 h:2 h, 21 h:3 h, 20 h:4 h, 19 h:5 h (light:dark) at days 1, 2, 3, 4, 5, 6, and 18 h:6 h from day 7 onward and the light intensity was constantly 40 Lux, as recommended by the breeder. The room temperature decreased from 28-29°C on day one, measured at pen height, to 23-24°C on day 35. Infrared lamps (Albert Kerbl GmbH, Buchbach, Germany) were used as additional heat sources during the first 6 days to adjust the temperature at the cage floor to 34°C. Mean relative humidity was 60.0 ± 1.9%. The groups were fed three different nutrient adequate diets containing either 0 (group PSA-F0), 25 (group PSA-F25) or 5% (group PSA-F50) g/kg diet of P. sapidus fruiting bodies in a three-phase feeding system (starter diet form day 1-10, grower diet from day 11-21, finisher diet from day 22-35). The composition of the diets met the broiler’s requirements of nutrients and energy according to the breeder’s recommendations (Cobb-Vantress, 2022). Diets were provided in crumbled form during the first three days, and in pellet form (2 mm diameter) from day 3 until the end of the trial. On days 1, 10, 21 and 35 body weight (individually) and feed intake (per cage) were determined. The feed:gain ratio was calculated from feed intake and body weight gains on cage basis.

value: Liver

value: 50 g/kg diet PSA fruiting bodies


title: P291_35_27-PSA-F5_Log2 Signal


title: Ileum, GPR35 knockout 3

description:
Ileum_KO_3
RNAseq_GPR35_ileum.txt

source_name: Ileum

value: Ileum


title: Ileum, GPR35 knockout 5

description:
Ileum_KO_5
RNAseq_GPR35_ileum.txt


title: Sample 9_Rep1_H460 Control

value: DMSO


title: P291_29_18-PSA-F5_Log2 Signal


title: 0.6 brain 1

description:
Li-06-04
edgeRglm_GENE_Li06-Li00.xlsx
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: P291_36_33-PSA-F5_Log2 Signal


title: 0.0 brain 4

description:
17-Mmu-Li00-06
see other 4 doses
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: 0.0 mg/kg LiCO3 diet


title: Sample 9_Rep2_H460 Control


title: macrophage, GPR35 knockout 1

description:
macrophage_KO_1
RNAseq_GPR35_macrophages.txt


title: Sample 10_Rep3_H2122 CVT-11127 Treatment


title: Ileum, wild type 4

description:
Ileum_WT_4
RNAseq_GPR35_ileum.txt


title: 0.0 brain 2

description:
Li-00-05
see other 4 doses
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx

value: brain


title: 0.0 brain 3

description:
16-Mmu-Li00-02
see other 4 doses
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: Sample 10_Rep2_H2122 CVT-11127 Treatment


title: Ileum, wild type 2

description:
Ileum_WT_2
RNAseq_GPR35_ileum.txt


title: Ileum, GPR35 knockout 1

description:
Ileum_KO_1
RNAseq_GPR35_ileum.txt


title: P291_24_12-PSA-F5_Log2 Signal


title: macrophage, wild type 4

description:
macrophage_WT_4
RNAseq_GPR35_macrophages.txt


title: Sample 9_Rep3_H460 Control


title: 0.0 brain 1

description:
Li-00-01
see other 4 doses
rsem_GENE_CombatSeq_LiBrain_CPM.xlsx


title: P291_26_15-PSA-F5_Log2 Signal


title: Sample 10_Rep1_H2122 CVT-11127 Treatment


title: Ileum, wild type 1

description:
Ileum_WT_1
RNAseq_GPR35_ileum.txt


title: LiCl neuron 4

description:
Mmu-Neur-LiCl4
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv

source_name: neuron

value: neuron

value: 15mM LiCl


title: P291_31_20-PSA-F2-5_Log2 Signal

value: 25 g/kg diet PSA fruiting bodies


title: Sample 9_Rep3_H2122 Control

value: NSCLC, LUAD

value: Day 4


title: P291_33_23-PSA-F2-5_Log2 Signal


title: LiCl neuron 3

description:
Mmu-Neur-LiCl3
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: Sample 9_Rep2_H2122 Control


title: ILS40700FT3-T

description: Strand orientation: forward

source_name: lung squamous cell carcinoma

value: lung squamous cell carcinoma

value: Gencode 26

value: forward

value: single read R1


title: P291_28_17-PSA-F2-5_Log2 Signal


title: ILS40683FT1-T

description: Strand orientation: forward

value: lung adenocarcinoma


title: Sample 9_Rep1_H2122 Control


title: P291_25_14-PSA-F2-5_Log2 Signal


title: LiCl neuron 1

description:
Mmu-Neur-LiCl1
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: ILS39926FT3-T

description: Strand orientation: forward


title: Sample 8_Rep3_H2228 CVT-11127 Treatment


title: LiCl neuron 2

description:
Mmu-Neur-LiCl2
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: P291_22_8-PSA-F2-5_Log2 Signal


title: ILS36726FT2-T

description: Strand orientation: forward


title: P291_20_2-PSA-F2-5_Log2 Signal


title: Sample 8_Rep2_H2228 CVT-11127 Treatment


title: P291_30_19-PSA-F0_Log2 Signal

value: 0 g/kg diet PSA fruiting bodies


title: ILS34047D3-T

description: Strand orientation: forward


title: P291_34_25-PSA-F0_Log2 Signal

value: Liver


title: control neuron 4

description:
Mmu-Neur-Ctrl4
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv

value: Control 1/2 media change


title: control neuron 3

description:
Mmu-Neur-Ctrl3
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: Sample 8_Rep1_H2228 CVT-11127 Treatment


title: COT6ZACG-T

description: Strand orientation: forward


title: control neuron 2

description:
Mmu-Neur-Ctrl2
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: AAEQEAGO-T

description: Strand orientation: forward

source_name: lung large cell carcinoma

value: lung large cell carcinoma


title: Sample 7_Rep3_H2228 Control

value: DMSO


title: Control neuron 1

description:
Mmu-Neur-Ctrl1
LiNeurons_DGE.xlsx
rsem_GENE_LiNeurons.csv


title: Sample 7_Rep2_H2228 Control


title: P291_27_16-PSA-F0_Log2 Signal


title: 30mo sample 5

description:
30mo-C20
edgeRglm_GENE_c30mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv


title: 738_20T

description: Strand orientation: forward

source_name: cutaneous melanoma

value: cutaneous melanoma

value: Gencode 33

value: paired-end


title: HEK293, InducedA76, replicate 4

city: Umea

first: Paulina

middle: H

last: Wanrooij

address: Kemihuset (K), Campus, Umeå Umeå universitet, 901 87 Umeå

country: Sweden

institute: Umea University

data_processing:
Data files were assessed using FastQC, and read alignment was performed using STAR2.5.2b. On the WSL2 platform, featureCounts for Linux was utilized for quantification and generation of counts files.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from 16 frozen cell pellet samples using Qiagen RNeasy Plus kit standard RNA extraction protocol. Initial sample quality control was performed using Qubit and Fragment Analyzer.
RNA libraries were prepared by Azenta Life Sciences using Illumina’s PolyA selection method

value: Kidney

value: Embryonic kidney


title: Sample 7_Rep1_H2228 Control

value: NSCLC, LUAD


title: HEK293, InducedDMSO, replicate 4

value: doxy+DMSO


title: Sample 6_Rep3_H1993 CVT-11127 Treatment

value: Day 4


title: 30mo sample 4

description:
30mo-C19
edgeRglm_GENE_c30mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv

value: brain


title: P291_21_7-PSA-F0_Log2 Signal


title: 30mo sample 3

description:
30mo-C17
edgeRglm_GENE_c30mo-c10mo.xlsx
edgeRglm_GENE_g30mo-g20mo.xlsx
rsem_GENE_TPM_102030Br_CtrlOnly.csv