title: shNC

city: Dalian

first: Mengyi

last: Tang

address: 467 Zhongshan Road

institute: the Second Affiliated Hospital of Dalian Medical University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq 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 N base 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). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: Hisat2 (v2.0.5).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung cancer

growth_protocol: All cells were routinely cultured in Roswell Park Memorial Institute medium-1640 (RPMI1640) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and streptomycin (all these reagents were obtained from Gibco, Invitrogen, Inc, California, USA) and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol (Transgen, China) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: lung cancer

value: lung cancer cell line

value: routine culture


title: 134208, 3c, 24 Hours, 500um, rat29, Left Hemisphere

status: Public on Feb 05 2024

type: SRA

city: EAST LANSING

first: Erin

middle: K

last: Purcell

state: MI

address: 775 WOODLOT DRIVE

department: Biomedical Engineering

country: USA

institute: MICHIGAN STATE UNIVERSITY

library_source: transcriptomic

data_processing:
Sequencing adapters were trimmed using Cutadapt (v2.3). FastQC (v0.11.8) was used to ensure the quality of data.
Reads are mapped to the reference genome Rattus_norvegicus.Rnor_6.0.9, using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1). Alignment options follow ENCODE standards for RNA-seq.
FastQC is used in an additional post-alignment step to ensure that only high-quality data gets used for expression quantitation and differential expression.
Data was pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis is performed using DESeq2, using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini–Hochberg FDR (Padj) <0.05).
Assembly: Rnor_6.0.9
Supplementary files format and content: deseq2_raw_counts.txt

molecule: total RNA

organism: Rattus norvegicus

source_name: Brain Tissue

growth_protocol: Single shank ‘Michigan’-style probes (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size, 100 µm site spacing, Neuronexus Technologies) were stereotaxically implanted in the motor cortex (M1) of male Sprague–Dawley rats (aged 12–14 weeks). Animals were isoflurane anesthetized and a craniotomy was performed over M1 (+3.0 mm anterior posterior, 2.5 medio lateral from Bregma), dura was resected, and the probe was stereotaxically inserted to a depth of 2 mm from the cortical surface.

extract_protocol:
RNA was extracted from LCM-collected tissue using a specialized RNAstorm extraction kit (Cell Data Sciences).
cDNA library preparation and RNA sequencing was carried out by the University of Michigan Advanced Genomics Core. cDNA libraries were prepped using a Takara SMART-stranded kit and subsequently subjected to 150 paired-end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol:
At the terminal time point, animals were deeply anesthetized with sodium pentobarbital, perfused with 4% paraformaldehyde transcardially, and the brains were extracted. Following graded sucrose protection (5%–20%) and cryo-embedding, the brains were sliced via cryostat (Leica) as 20 µm thick sectionsand mounted on SuperfrostTM Plus slides (Fisher Scientific). Six tissue sections (n = 6) were collected for analysis at each time point (24 h, n = 3 rats; 1 week, n = 5 rats; 6 weeks, n = 4 rats) in addition to six samples collected from naïve, unimplanted rats. Depth of collection spanned the implant shank (∼600–1700 µm from cortical surface).
Tissue near the implant injury, or ‘interfacial’ (within 100 µm) was extracted using LCM (Zeiss Palm MicroBeam IV). Distal tissue of an approximately equivalent total surface area was extracted from ∼500 µm away from the implant site to assess distance-dependent effects. These samples were collected and pooled from four smaller sections obtained at locations equidistant from the implant site. Using similar collection methods, control tissue from naïve brains was used to compare implanted tissue to unimplanted tissue.

tag: strain

value: Sprague-Dawley

tag: cell type

value: Brain Tissue

tag: genotype

value: WT

tag: treatment

value: Silicon Microelectrode Implant  (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size,100 µm site spacing, Neuronexus Technologies)

tag: time

value: 24 Hours


title: H3_ChIP_P0_KO_rep1

city: Bunkyo-ku

first: Soichiro

last: Yamanaka

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeqX output.
ChIP-seq reads were trimmed down to 50 bp from 3' end, using Seqkit v0.10.2, Cutadapt v1.18, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.3.4.1 Only uniquely mapping reads were retained. No mismatch was allowed.
To normalized coverage plots (reads per million, rpm) (bigWig file format) were created by deeptools v3.5.0.
Peaks were called uing homer v4.10 with following settings: -style histone, -size 1000, -minDist 2500
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file
Supplementary files format and content: bed : bed files with peak coordinates

molecule: genomic DNA

organism: Mus musculus

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at P0

growth_protocol: Male germ cells were isolated from Mvh-Venus transgenic mouse at indicated developmental timepoints for Morc1 KO or Morc1 het mice

extract_protocol:
Germ cells were fixed with 1% FA. Chromatin fraction was extracted after processing with sonication. Chromatin extract was served for immunoprecipitation with H3K9me3 antibody. DNA was purified from co-precipitaed fraction.
ChIP-seq library was prepared using QIAseq ultralow input library kit (QIAGEN), following manufacturer's instruction.

tag: tissue

value: testis

tag: developmental stage

tag: antibody

value: MBL, #MABI0301


title: 134207, 3, 24 Hours, 100um, rat29, Left Hemisphere


title: shPCDH1

country: China

organism: Homo sapiens

tag: cell line

value: PCDH1 knockdown


title: Control_rep1

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Trimmed reads were further mapping to hg38 genome using hisat2 v2.1.0
The read counts of each gene was quantified by HTseq v0.11.2
Assembly: hg38
Supplementary files format and content: Excel file includes differentially expressed gene list

source_name: Homo sapiens

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 medium supplemented with 50 µg/ml streptomycin, 50 IU/ml penicillin and 10% fetal calf serum at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Total RNA was isolated and purified from cultured cells using TRIzol reagent (Invitrogen #15596026) following the manufacturer's procedure.
KAPA Hyper Prep Kit (KAPA #KK8504) was used to generate the sequencing libraries following the manufacturer’s instructions.

treatment_protocol: Kasumi-1 cells were seeded into 6-well plates overnight before PHF19 shRNA or scrambled control shRNA transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.

value: Homo sapiens

value: acute myeloblastic leukemia cell


title: SC11vsCS1_HA-Rds2vsNotag_WT_20180502_rep2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description: Biological replicate 2 of 2.  HA-Rds2 occupancy by ChIP-chip in WT cells. HA-Rds2 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

hyb_protocol: standard protocol

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
BED description: A genome browser-ready file for HA-Rds2 occupancy by ChIP-chip (HA-Rds2/no tag) in WT cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP samples were blunted as follow. 40 µL of ChIP DNA were added to 70 µL of blunting mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: Strains were grown in YPD to an OD600 ≈0.7. Cells were washed twice in water, resuspended in YEP containing 2% ethanol, and grown for 3 h. The culture was poured in a 50mL Falcon tube containing 1.4mL 37% formaldehyde and incubated on a rotating wheel for 30 min. Crosslinking was stopped by adding 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells were pelleted at 4'C, 3000 rpm, resuspended in 40mL ice-cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stored at -80'C.

extract_protocol: Cell pellets were resuspended in 400 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed using a vortex for 2 hrs at 4C. The lysate was then sonicated 30 cycles, 30 sec ON and 30 sec OFF at High settings (Diagenode Bioruptor). Soluble fragmented chromatin was recovered by centrifugation. 350 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 3.5 μL (1%) were saved as Input sample. 20 μL of Dynabeads coated with protein G pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 200uL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 50°C for 1 hr and subsequently subjected to Proteinase K (5.5 μL 20% SDS, 7.5 μL 10 mg/mL Proteinase K) digestion at 50°C for 1 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

treatment_protocol: 2% ethanol for 3 h

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 gsm1{delta}::KanMX [RDS2 tagged with three HA epitopes at the N-terminus]

value: anti-HA (F7 from Santa-Cruz; 15uL)


title: ChIP-seq_ES_JB_Input

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

data_processing:
ChIP-seq were mapped on the mouse genome (mm39 masked  for JF1 SNPs)using Bowtie2 .
Alignments filtering was realized with samtools (view -q 20).
peaks were called using MACS1.4.2. (--nomodel --shiftsize 73 --pvalue 1e-5 ) and the coverage was computed using bamCoverage (--normalizeUsing RPKM --extendReads 200  --ignoreDuplicates  --binSize 20).
Assembly: mm39
Supplementary files format and content: bigWig

growth_protocol: ES cell lines were maintained in gelatin-coated dishes with ESGRO complete plus medium (Millipore, SF001-500P) containing LIF, BMP4, and a GSK3-β inhibitor. ES-derived neural precursor cells were generated using in vitro corticogenesis as described in Montibus et al 2021 (PMID: 32405722).

extract_protocol:
ChiP-seq experiments on native chromatin were performed on ESC and NPC for the JF1xB6 genetic backgrounds as previously in Le Boiteux et al., 2021 (PMID: 33720519).
Library preparation (TruSeq® ChIP Sample Preparation) and sequencing on a HiSeq 2500 instrument (Illumina) were performed by MGX, according to the manufacturer’s recommendations

value: ES cells

value: JF1 x C57BL/6

tag: chip antibody


title: 134206, 2c, 24 Hours, 500um, rat25, Right Hemisphere


title: ChIP-seq_D12_JB_H3K4me3

value: ES-derived neural precursor cells

value: In vitro corticogenesis Day 12

value: H3K4me3 (Diagenode  030-050)


title: H3_ChIP_E165_het_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (+/-) mice at E16.5


title: NORMAL-TEMP-816-X Male

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks, which is provided here

molecule: polyA RNA

source_name: NORMAL-temporal lobe

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

value: NORMAL-temporal lobe

tag: Sex

value: Male

tag: source of_material

value: autospy material from patient with history of brain tumor


title: SC175vsCS1_HA-Gsm1vsNoTag_WT_20180502_rep1

description: Biological replicate 1 of 2.  Gsm1-HA occupancy by ChIP-chip in WT cells. Gsm1-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

data_processing:
BED description: A genome browser-ready file for Gsm1-HA occupancy by ChIP-chip (Gsm1-HA/no tag) in WT cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 [GSM1 tagged with three HA epitopes at the C-terminus]


title: ChIP-seq_ES_JB_H3K4me3


title: SC11vsCS1_HA-Rds2vsNotag_WT_20180502_rep1

description: Biological replicate 1 of 2.  HA-Rds2 occupancy by ChIP-chip in WT cells. HA-Rds2 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: NORMAL-PONS-953-X Female

source_name: NORMAL-pons

value: NORMAL-pons

value: Female


title: 134205, 2, 24 Hours, 100um, rat25, Right Hemisphere

value: Sprague-Dawley

value: Brain Tissue

value: WT

value: Silicon Microelectrode Implant  (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size,100 µm site spacing, Neuronexus Technologies)

value: 24 Hours


title: H3_ChIP_E165_KO_rep1

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at E16.5

value: testis

value: MBL, #MABI0301


title: NORMAL-PONS-928-X Male


title: ChIP-seq_ES_JB_H3K4me2

value: ES cells

value: JF1 x C57BL/6

value: H3K4me2 (abcam Ab32356)


title: H3_ChIP_E135_KO_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at E13.5


title: H3_ChIP_E135_KO_rep1


title: H3_ChIP_E135_het_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (+/-) mice at E13.5


title: 134204, 1c, 24 Hours, 500um, rat25, Left Hemisphere

value: 24 hours


title: DU145 cell，HuR KO4-3

city: Chongqing

first: Song

last: Guojing

address: Gaotan Yan Street

institute: The First Affiliated Hospital of the Army Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: The Excel table includes TPM values for all sample

growth_protocol: All cells  were maintained in a CO2 incubator at 37° C with either 1640  with 10%  FBS and 1% penicillin‒streptomycin solution

extract_protocol:
Total RNA was extracted using TRIzol reagent  and use for RNA-seq.
RNA libraries for RNA-seq were prepared using SMAARTER mRNA-seq library prep kit following manufacture‘s protocols

treatment_protocol: PC3 and DU145 cells used CRISPR/Cas9 technology to knock out HuR.

value: Prostate cancer cell

value: HuR KO


title: NORMAL-pituitary-A16-32 Male

source_name: NORMAL-pituitary

value: NORMAL-pituitary

value: Male

value: autospy material from patient with history of brain tumor


title: 134203, 1, 24 Hours, 100um, rat25, Left Hemisphere


title: ChIP-seq_D12_BJ_Input

extract_protocol:
ChiP-seq experiments on native chromatin were performed on ESC and NPC for the B6xJF1 genetic backgrounds as previously in Le Boiteux et al., 2021 (PMID: 33720519).
Library preparation (TruSeq® ChIP Sample Preparation) and sequencing on a HiSeq 2500 instrument (Illumina) were performed by MGX, according to the manufacturer’s recommendations

value: ES-derived neural precursor cells

value: C57BL/6 x JF1

value: In vitro corticogenesis Day 12


title: NORMAL-PONS-816-X Male

value: NORMAL-pons


title: ChIP-seq_D12_BJ_H3K4me3

value: H3K4me3 (Diagenode  030-050)


title: NORMAL-pituitary-A14-31 Female

value: Female


title: DU145 cell，HuR KO4-2


title: H3_ChIP_E135_het_rep1

value: testis


title: ChIP-seq_D12_BJ_H3K4me2


title: H3_ChIP_E165_het_rep1

value: MBL, #MABI0301


title: DU145 cell，HuR KO4-1


title: H3K9me3_ChIP_P3_KO_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (-/-) mice at P3

value: Active Motif, #39161


title: H3K9me3_ChIP_P3_KO_rep1


title: ChIP-seq_ES_BJ_H3K4me3

value: ES cells


title: ChIP-seq_ES_BJ_Input


title: NORMAL-FRONTAL-E03 Male

source_name: NORMAL-frontal

value: NORMAL-frontal

value: resection of epilesy foci


title: NORMAL-PARIETAL-928-X Male

source_name: NORMAL-parietal lobe

value: NORMAL-parietal lobe


title: ChIP-seq_ES_BJ_H3K4me2

value: H3K4me2 (abcam Ab32356)


title: DU145 cell，sgControl-2

value: Prostate cancer cell

value: WT


title: H3K9me3_ChIP_P3_het_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (+/-) mice at P3


title: Normal-frontal-cortex 1359-X Male

source_name: NORMAL-cortex

value: NORMAL-cortex

value: Male

value: autospy material from patient with history of brain tumor


title: DU145 cell，sgControl-1


title: NORMAL-frontal lobe-1292-X Female

source_name: NORMAL-frontal lobe

value: NORMAL-frontal lobe


title: PC3 cell，HuR KO1-3

value: HuR KO


title: NORMAL-Cerebellum-928-X Male

source_name: NORMAL-Cerebellum

value: NORMAL-Cerebellum


title: WT_Retina_LG_24mo_24

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 24

data_processing:
Post quality check, reads were mapped to the reference transcriptome using kallisto. Alignments were imported into R and processed with tximport and the Mus musculus Ensembl annotation (GRCm39/Ensembl v104) to summarize gene counts.
Lowly expressing genes were filtered out by only retaining genes that had an average expression greater than 1 CPM in each experimental group.
Differential expression analysis of liver samples was performed with the edgeR and limma-voom pipeline, and thresholds of 0.05 p-value and 1.5-fold change (abs(log2FC) > 0.58) were used to determine significantly differential genes. For retinal samples, the edgeR and limma-voom pipeline and thresholds of 0.05 p-value and 1.25-fold change (abs(log2FC) > 0.32) were used to determine significantly differential genes.
Assembly: GRCm39/Ensembl v104
Supplementary files format and content: Tab-delimited text files containing transcript level counts, gene level counts, or normalized gene level counts-per-million results.

source_name: mouse retina

growth_protocol: In a diet experiment, 6 or 12 month old male C57BL/6J mice were fed a high glycemic index (HGI) or low glycemic index (LGI) diet for 1 or 12 months, respectively.  The LGI diet consisted of 70% amylose and 30% amylopectin and the HGI diet consisted of 100% amylopectin.  Mice were pair-fed to ensure equal consumption in both HGI and LGI diet groups.

extract_protocol:
RNA was isolated from 100mg of liver tissue or whole retina using a RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.  RNA purity and concentration were assessed using a NanoDropTM spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).  A 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA) was used with RNA screentapes to generate RNA integrity numbers (RIN) for RNA samples. All RNA samples selected for RNA-seq library preparation had a RIN greater than 7.
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: After 1 or 12 months of dietary intervention, mice were fasted for 6 hours and euthanized.  Tissues were collected and snap frozen in liquid nitrogen for gene expression analysis.

tag: diet

value: low glycemic index

value: Retina

tag: replicate


title: WT_Retina_LG_24mo_22

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 22


title: H3K9me3_ChIP_P3_het_rep1

value: testis


title: H3K9me3_ChIP_P0_KO_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (-/-) mice at P0

value: Active Motif, #39161


title: WT_Retina_LG_24mo_23

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 23


title: WT_Retina_LG_24mo_21

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 21


title: WT_Retina_HG_24mo_20

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 20

value: high glycemic index


title: PC3 cell，HuR KO1-1


title: H3K9me3_ChIP_P0_het_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (+/-) mice at P0


title: H3K9me3_ChIP_P0_het_rep1


title: H3K9me3_ChIP_P0_KO_rep1


title: NORMAL-Cerebellum-816-X Male


title: DU145 cell，sgControl-3


title: WT_Retina_HG_24mo_18

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 18


title: WT_Retina_HG_24mo_19

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 19


title: H3K9me3_ChIP_E165_KO_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (-/-) mice at E16.5


title: NORMAL-Cerebellum-1292-X Female

value: Female


title: PC3 cell，sgControl-2


title: H3K9me3_ChIP_E165_KO_rep1


title: PC3 cell，HuR KO1-2


title: WT_Retina_HG_24mo_17

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 17


title: PC3 cell，sgControl-1


title: NORMAL-912-X-Cerebellum Male


title: HPAF-II siCtrl rep3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description:
HPAF-II cells silenced with siCtrl for 48 hours rep3
HPAF_siCtrl_3

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg38
Supplementary files format and content: PANC1_deseq2_norm_with_annotations.txt: Gene expression values normalized by DESeq2 unsing FAST DB v2022_1 annotations
Supplementary files format and content: HPAF_deseq2_norm_with_annotations.txt: Gene expression values normalized by DESeq2 unsing FAST DB v2022_1 annotations

source_name: Pancreas

growth_protocol: PANC-1 and HPAF-II cells were cultured in RPMI 1640 (Euroclone) supplemented with 10% FBS (Gibco), 100 U/ml Penicillin (Euroclone), 100 mg/ml streptomycin (Euroclone), Non-Essential Amino Acids 100x (Thermo Fischer) and 50 U/ml gentamycin  (Aurogene) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted and DNAse treatment using RNeasy Mini Kit (Qiagen)
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA)

treatment_protocol: PANC-1 cells were silenced for QKI and RBFOX2 (40nM) for 48 hours. HPAF-II cell silenced with siCtrl.

value: Pancreas

value: HPAF-II

value: human pancreatic adenocarcinoma

tag: tumor

value: PDAC

value: silenced with siCtrl for 48 hours


title: H3K9me3_ChIP_E165_het_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (+/-) mice at E16.5


title: HCD - hfq-3XFLAG #2

city: Jena

first: Eric

last: Ruhland

address: Winzerlaer Str. 2

country: Germany

institute: Friedrich Schiller University Jena

description: molecule: Hfq bound RNA

library_source: other

data_processing:
CLC Genomics Workbench v 22.0.2
Sequence reads were trimmed for adaptor sequence/low quality sequence
trimmed sequence reads were mapped to K. pneumoniae MGH78578 genome using CLC genomic workbench (parameters: mismatch cost 2; Insertion cost 3; deletion cost 3; length fraction 0.8; similarity fraction 0.8)
Read count extraction using CLC workbench
Assembly: NCBI Reference Sequence: NC_009648.1 - NC_009653.1
Supplementary files format and content: xlsx file includes raw counts for each sample

molecule: other

organism: Klebsiella pneumoniae subsp. pneumoniae

growth_protocol: Growth in LB-Medium, 200 rpm shaking, 37 °C until OD 0.25 or OD 2

extract_protocol:
CoIP: cells were disrupted using glass beads, lysae was incubated with α-FLAG Antibody following protein G Sepharose. Solution was washed, RNA fraction was PCI extracted and DNase digested and again PCI extracted.
NEBNext Small RNA Library Prep Set for Illumina
RIP-Seq


title: HPAF-II siCtrl rep2

description:
HPAF-II cells silenced with siCtrl for 48 hours rep2
HPAF_siCtrl_2


title: H3K9me3_ChIP_E165_het_rep1


title: WT_Retina_HG_7mo_8

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 8

value: WT


title: HCD - hfq-3XFLAG #1

description: molecule: Hfq bound RNA


title: WT_Retina_HG_7mo_7

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 7

value: Male


title: H3K9me3_ChIP_E135_KO_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (-/-) mice at E13.5


title: HCD - wt #2

description: molecule: Hfq bound RNA

value: wt


title: HPAF-II siCtrl rep1

description:
HPAF-II cells silenced with siCtrl for 48 hours rep1
HPAF_siCtrl_1


title: PC3 cell，sgControl-3

value: Prostate cancer cell


title: WT_Retina_HG_7mo_6

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 6


title: HCD - wt #1

description: molecule: Hfq bound RNA


title: PANC-1 siRBFOX2 rep3

description:
PANC-1 cells silenced for RBFOX2 for 48 hours rep3
siRBFOX2_3

source_name: Pancreas; Duct

value: Pancreas; Duct

value: human pancreatic epitheliod carcinoma cell line

value: silenced for RBFOX2 for 48 hours


title: H3K9me3_ChIP_E135_KO_rep1


title: WT_Retina_HG_7mo_5

description: Retina tissue from Male mice fed high glycemic index diet, replicate no 5

value: Retina


title: H3K9me3_ChIP_E135_het_rep2

source_name: ChIP-seq for H3K9me3 using gonocyte from Morc1 (+/-) mice at E13.5

value: testis


title: LCD - hfq-3XFLAG #1

description: molecule: Hfq bound RNA


title: PANC-1 siRBFOX2 rep2

description:
PANC-1 cells silenced for RBFOX2 for 48 hours rep2
siRBFOX2_2


title: PANC-1 siRBFOX2 rep1

description:
PANC-1 cells silenced for RBFOX2 for 48 hours rep1
siRBFOX2_1


title: H3K9me3_ChIP_E135_het_rep1

value: Active Motif, #39161


title: NORMAL-Cerebellum-897-X Male

value: NORMAL-Cerebellum

value: autospy material from patient with history of brain tumor


title: WT_Retina_LG_7mo_4

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 4

value: low glycemic index


title: NORMAL-Cerebellum-514-X Male


title: WT_Retina_LG_7mo_3

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 3


title: LCD - wt #2

description: molecule: Hfq bound RNA


title: ATAC-seq_P3_KO_rep2

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeqX output.
ATAC-seq reads were trimmed down to 25 bp from 3' end, using Seqkit v0.10.2, Cutadapt v1.18, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.3.4.1 Only uniquely mapping reads were retained. No mismatch was allowed.
To normalized coverage plots (reads per million, rpm) (bigWig file format) were created by deeptools v3.5.0.
Peaks were called uing homer v4.10 with following settings: -style dnase, -size 500, -minDist 1000
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file
Supplementary files format and content: bed : bed files with peak coordinates

source_name: ATAC-seq using gonocyte from Morc1 (-/-) mice at P3

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., 2013, 2015). In brief, nuclei isolated from germ cells were processed with DNA tagmentation enzyme (Illumina)
Tagmented DNA were amplified by a PCR reaction with barcoded primer sets.


title: ATAC-seq_P3_KO_rep1


title: PANC-1 siQKI rep3

description:
PANC-1 cells silenced for QKI for 48 hours rep3
siQKI_3

value: silenced for QKI for 48 hours


title: LCD - wt #1

description: molecule: Hfq bound RNA


title: HCD - untreated #2

data_processing:
computation of coverage and difference between neighboring nucleotides
local mixima of differences annotated as TSS
manual curation of predicted TSS
DOI: 10.5281/zenodo.8388882
Assembly: NCBI Reference Sequence: NC_009648.1 - NC_009653.1
Supplementary files format and content: xlsx file containing the TSS, their classification and associated genes

extract_protocol:
RNA extraction using the Hot Phenol methode, follwowing DNase treatment and PCI extraction.
RNA samples were fragmented using ultrasound, treated with T4 Polynucleotide Kinase, Terminator Exonuclease, poly(A) tailed and 5' triphosphate removed, adapter ligated to 5' ends and cDNAs were synthesized using oligo(dT) adapters.
dRNA-seq (doi: 10.1093/nar/gky765)


title: ATAC-seq_P3_het_rep2

source_name: ATAC-seq using gonocyte from Morc1 (+/-) mice at P3


title: WT_Liver_LG_24mo_56

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 56

source_name: mouse liver

value: Liver


title: ATAC-seq_P3_het_rep1


title: WT_Retina_LG_7mo_1

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 1


title: PANC-1 siQKI rep2

description:
PANC-1 cells silenced for QKI for 48 hours rep2
siQKI_2

value: PDAC


title: PANC-1 siQKI rep1

description:
PANC-1 cells silenced for QKI for 48 hours rep1
siQKI_1


title: LCD - hfq-3XFLAG #2

description: molecule: Hfq bound RNA


title: HCD - untreated #1


title: ATAC-seq_P0_KO_rep2

source_name: ATAC-seq using gonocyte from Morc1 (-/-) mice at P0


title: PANC-1 siCtrl rep3

description:
PANC-1 cells silenced with siCtrl for 48 hours rep3
siCTRL_3

value: silenced with siCtrl for 48 hours


title: HCD - TEXtreatment #1

value: TEX


title: PANC-1 siCtrl rep2

description:
PANC-1 cells silenced with siCtrl for 48 hours rep2
siCTRL_2


title: ATAC-seq_P0_KO_rep1


title: WT_Liver_LG_24mo_53

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 53

value: Male

value: WT


title: PANC-1 siCtrl rep1

description:
PANC-1 cells silenced with siCtrl for 48 hours rep1
siCTRL_1


title: ATAC-seq_P0_het_rep2

source_name: ATAC-seq using gonocyte from Morc1 (+/-) mice at P0


title: Diencephalon

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Quality control, UMI counting of Ensemble genes and aggregation of samples were performed by count and aggr functions in the Cell Ranger software
Assembly: Human: GRCh38
Supplementary files format and content: Count matrices, barcodes, and features

source_name: Diencephalon

extract_protocol:
Cells were loaded onto a Chromium Single cell 3’ chip (Chromium Chip B Single Cell Kit, 10x Genomics, PN-1000154) with Chromium Single Cell 3’ Library & Gel Bead kit v3 (10x Genomics, PN-1000075) and proceeded according to manufacturer’s instructions.
cDNA library was generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead kit v3 (10x Genomics, PN-1000078) according to manufacturer’s instructions.

value: Diencephalon

tag: age


title: WT_Liver_LG_24mo_54

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 54


title: ATAC-seq_P0_het_rep1


title: LCD - TEXtreatment #2

value: wt


title: LCD - untreated #2


title: WT_Liver_HG_24mo_52

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 52

value: high glycemic index


title: hDiO_d100_aggr

description: 10x Genomics

source_name: hiPS cell-deerived regionalized organoids

value: Day 100


title: WT_Retina_LG_7mo_2

description: Retina tissue from Male mice fed low glycemic index diet, replicate no 2

value: Retina


title: ATAC-seq_E165_KO_rep2

source_name: ATAC-seq using gonocyte from Morc1 (-/-) mice at E16.5

value: testis


title: HCD - TEXtreatment #2


title: LCD - untreated #1


title: WT_Liver_HG_24mo_50

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 50


title: WT_Liver_LG_24mo_55

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 55


title: Control Placenta Site Sample D7

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: one merged expression matrix for all samples

data_processing:
Sequencing was performed on NovaSeq 6000 (Pair-end, 100 base pairs per read).
The digital expression matrix was generated by demultiplexing, barcode processing, and gene unique molecular index counting using the Cellranger count pipeline (version 4.0.0, 10X Genomics).
Multiple samples were merged using the Cellranger aggr pipeline.
Assembly: hg38
Supplementary files format and content: raw expression values in sparse matrix format
Supplementary files format and content: metadata in csv format for the donor, disease state, and celltype annotations for each cell

source_name: placenta/decidua

extract_protocol:
The placenta biopsies was mechanically disassociated and enzymatically digested by incubating in digestion media of 2.5% trypsin, 300 U/mL collagenase, and 200 ug/mL DNAse in PBS for 90 minutes at 37oC in 5% CO2. Red blood cell lysis buffer was added to eliminate red blood cells. The cells were strained through a 100uM nylon mesh strainer. The cells were frozen for later use. At time of processing, the frozen cells were thawed and resuspended in an ideal cell concentration of 700-1200 cells/uL for single-cell sequencing.
scRNA-seq libraries were generated using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cells were loaded accordingly following the 10X Genomics protocol with an estimated targeted cell recovery of 6000 cells.

value: placenta/decidua

tag: disease state

value: third trimester

value: mixed


title: ATAC-seq_E165_KO_rep1


title: LCD - TEXtreatment #1

tag: strain


title: ATAC-seq_E165_het_rep2

source_name: ATAC-seq using gonocyte from Morc1 (+/-) mice at E16.5


title: Control Placenta Site Sample D3

tag: cell type


title: Control Placenta Site Sample D2

tag: genotype


title: WT_Liver_HG_7mo_39

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 39


title: Accreta Opposite Site Sample D6

source_name: placenta/decidua/myometrium

value: placenta/decidua/myometrium

tag: treatment


title: ATAC-seq_E165_het_rep1


title: WT_Liver_HG_7mo_38

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 38


title: ATAC-seq_E135_KO_rep2

source_name: ATAC-seq using gonocyte from Morc1 (-/-) mice at E13.5


title: Occipital Cortex, NHP2

city: Philadelphia

first: James

last: Wilson

state: Pennsylvania

address: 125S 31st St

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and feature counting were all done using the 10X Genomics CellRanger software (v5.0.1)
Assembly: Mmul_10
Supplementary files format and content: cellrange output in MEX format, containing tab-delimited text files of cell barcode, feature (gene) annotation, and cell-feature read count

molecule: nuclear RNA

organism: Macaca mulatta

source_name: occipital cortex

extract_protocol:
For nucleus isolation, buffers were typically prepared as described below, cooled in advance, and then supplemented immediately prior to use to make “complete” buffers at a final concentration of 1 mM dithiothreitol, 0.8 U/µl RNase inhibitor (Protector RNase Inhibitor; Roche, Indianapolis, IN, USA), and 1X protease inhibitor (complete Mini EDTA-free, Roche).  For these assays ~25 mg of frozen tissue was minced with a scalpel and transferred to a pre-chilled 2-mL Dounce homogenizer with 1 mL of cold complete lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8.0, and 0.1% Triton X-100). The tissue was homogenized with 10 strokes each of pestle A then B and sequentially passed through pre-wetted 100-µM and 30-µM filters, with the filtered sample collected in a sterile tube. We washed the homogenizer and filters with an additional three volumes of complete lysis buffer, collected with the filtered sample. Two volumes of sample were then layered on top of one volume of cold complete isolation buffer (1.8 M sucrose, 3 mM magnesium acetate, and 10 mM Tris-HCl pH 8.0) and spun at 21 000g for 45 min at 4°C.  We then carefully removed the supernatant and added 100 µL complete resuspension buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, and 20 mM Tris-HCl pH 7.2) to the tube without mixing. We incubated the samples on ice for 10–15 min, fully resuspended the nuclei by gently pipetting up and down 20–30 times, and then counted the nuclei with an automated cell counter (Countess 3, Thermo Fisher). For submission of single-nucleus transcriptomic samples, we adjusted the concentration to ~1×106 nuclei/mL (range of 0.7–1.2×106 nuclei/mL) as per the manufacturer’s sample-loading guidelines.
Library preparation was performed according to the manufacturer's instructions (Single Cell 3' v3.1 protocol, 10x Genomics). Briefly, a single nuclei suspension was loaded alongside a master mix and gel beads. The gel beads and individual nuclei were partitioned into droplets to generate an emulsion. A unique molecular identifier and cell barcode were linked to poly-A RNA and reverse-transcribed into cDNA. The cDNA was recovered from the emulsion using silane Dynabeads, amplified to generate sufficient material for library preparation, and then size selected and purified post-amplification with SPRI-Select beads. A portion of the purified cDNA was then enzymatically fragmented, and partial Illumina adapters were ligated. A final PCR amplification further enriched the libraries and completed the Illumina adapters for sequencing, incorporating a unique sample index for demultiplexing

treatment_protocol: Adult female Indian rhesus macaques (3–4 years old) were dosed via ICM injection with AAV9.UbC.trastuzumab

value: occipital cortex


title: WT_Liver_LG_7mo_36

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 36

value: low glycemic index

value: Liver


title: ATAC-seq_E135_KO_rep1


title: Cerebellum, NHP2

description: 10X Genomics

source_name: cerebellum

value: cerebellum


title: Accreta Opposite Site Sample D4


title: WT_Liver_HG_24mo_51

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 51


title: WT_Liver_LG_7mo_35

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 35


title: Accreta Invasive Site Sample D6


title: ATAC-seq_E135_het_rep1

source_name: ATAC-seq using gonocyte from Morc1 (+/-) mice at E13.5


title: Occipital Cortex, NHP1

description: 10X Genomics


title: WT_Liver_LG_7mo_34

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 34


title: Accreta Invasive Site Sample D4


title: Accreta Invasive Site Sample D5


title: WT_Liver_HG_7mo_40

description: Liver tissue from Male mice fed high glycemic index diet, replicate no 40


title: treated with Flood (excessive watering) [SAMPLE 8-1]

status: Public on Feb 04 2024

type: RNA

city: Iksan

first: Sujeevan

last: Rajendran

address: Muwang-ro

country: Sri Lanka

institute: Wonkwang University

description: Test

data_processing: Ubiquitin was used as the reference. gene expression analysis was performed with the 2^−ΔΔCt method using Bio-Rad CFX Maestro software v.4.0 (Bio-Rad). Baseline and threshold levels were set according to the manufacturer’s instructions.

label: SYBR Green

organism: Solanum lycopersicum

source_name: roots

label_protocol: Reactions (10 µL final volume) were prepared using 5 µL of LaboPass™ SYBR Green Q Master Kit (Cosmogenetech, Dajeon, Korea). 0.5 pmol of a primer pair, and 0.5 µL of cDNA template

extract_protocol: Total RNA was extracted with AccuPrep® Universal RNA Extraction Kit followed by DNase I treatment.

value: Shoots

tag: activation agent

value: Flood stressed plants

tag: time


title: Cerebellum, NHP1

description: 10X Genomics

tag: tissue


title: treated with Flood (excessive watering) [SAMPLE 7-2]

description: Test

source_name: Shoots

value: roots

value: Proton stressed plants


title: treated with Flood (excessive watering) [SAMPLE 8-2]

description: Test


title: ATAC-seq_E135_het_rep2

tag: developmental stage


title: Treated with acid (pH 4.2 water) [SAMPLE 6-2]

description: Test

value: Salt stressed plants


title: treated with Flood (excessive watering) [SAMPLE 7-1]

description: Test


title: Treated with acid (pH 4.2 water) [SAMPLE 6-1]

description: Test


title: H07_spegJY039_VEGFA_5GtoT_6U_rU_donor2_PE7_317

city: San Francisco

first: Carl

last: Ward

address: 1650 Owens Street

department: Gladstone-UCSF Institute of Genomic Immunology

institute: Gladstone Institutes

data_processing:
Sequencing reads were demultiplexed through HTSEQ (Princeton University High Throughput Sequencing Database, https://htseq.princeton.edu/) and sequencing adapters were trimmed using Cutadapt (4.1) with the parameter “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”.
To quantify prime editing outcomes, amplicon sequencing reads were aligned to corresponding reference sequences (Supplementary Table 9) with CRISPResso2 (2.2.11) in HDR batch mode using the intended editing outcome as the expected allele (-e) with the parameters “-q 30” and “-discard_indel_reads TRUE”. For each amplicon, the quantification window was centered at the pegRNA nick (“-wc -3”) and the window size (“-w”) was set to 10 + the distance between nicks generated by the pegRNA and the nicking sgRNA. For each amplicon, the same quantification window was used for PE2, PE3, PE4 and PE5 conditions, regardless of whether a complementary strand nick was involved (For PE2 and PE4, a nicking sgRNA was assumed to be the same one used for PE3 and PE5).
The frequency of intended editing without indels was calculated as: (number of non-discarded HDR-aligned reads)/(number of reads that aligned all amplicons). The frequency of total indels was calculated as: (number of discarded reads)/(number of reads that aligned all amplicons).
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: Tab delimited txt file containing CRISPResso2 output summary with the frequencies of intended prime edit and indels for each sample, for details see publication

source_name: T cells

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen 69506) per manufacturer's instructions with an elution volume of 100 µL
To assess editing efficiency, PCR was performed with 25 uL of eluted genomic DNA per sample in an 100 µL PCR reaction with KAPA HiFi HotStart ReadyMix (Roche 9420398001) with the following cycling conditions: 95 C for 3 min, 28 cycles of [98 C for 20 s, 63 C for 15 s, and 72 C for 60 s], followed by 72 C for 2 min. PCR products were purified by SPRI selection (Beckman Coulter B23317) and 2 µL eluted product was used for 8 cycles of additional PCR with KAPA HiFi HotStart ReadyMix to add Illumina sequencing adapters and indices. The final PCR products were purified by SPRI selection, quantified with Qubit 1X dsDNA High Sensitivity (HS) assay kit (Invitrogen Q33230), equimolarly pooled, and sequenced with the MiSeq Reagent Kit v2 300 cycles (Illumina MS-102-2002) with 300 cycles for R1 read, 8 cycles i7 index read and 8 cycles i5 index read.

value: T cells

tag: donor#

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY039_VEGFA_5GtoT_6U_rU


title: F07_spegJY039_VEGFA_5GtoT_6U_rU_donor1_PE7_317


title: G07_spegJY039_VEGFA_5GtoT_6U_rU_donor2_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY039_VEGFA_5GtoT_6U_rU


title: WT_Liver_LG_7mo_33

description: Liver tissue from Male mice fed low glycemic index diet, replicate no 33

value: Male

value: WT


title: E07_spegJY039_VEGFA_5GtoT_6U_rU_donor1_PEmax


title: Treated with acid (pH 4.2 water) [SAMPLE 5-2]

description: Test

value: Control plants


title: Treated with acid (pH 4.2 water) [SAMPLE 5-1]

description: Test


title: D11_spegJY037_VEGFA_5GtoT_standard_donor6_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY037_VEGFA_5GtoT_standard


title: D07_spegJY039_VEGFA_5GtoT_6U_rU_donor6_PE7_317


title: Treated with salt (200mM NaCL water) [SAMPLE 4-2]

description: Test


title: Treated with salt (200mM NaCL water) [SAMPLE 4-1]

description: Test


title: C07_spegJY039_VEGFA_5GtoT_6U_rU_donor6_PEmax


title: Treated with salt (200mM NaCL water) [SAMPLE 3-1]

description: Test


title: D07_spegJY039_VEGFA_5GtoT_6U_rU_donor4_PE7_317


title: Treated with salt (200mM NaCL water) [SAMPLE 3-2]

description: Test


title: C07_spegJY039_VEGFA_5GtoT_6U_rU_donor4_PEmax


title: Control plants [SAMPLE 2-1]

description: Control


title: Control plants [SAMPLE 2-2]

description: Control


title: Control plants [SAMPLE 1-2]

description: Control


title: B11_spegJY037_VEGFA_5GtoT_standard_donor5_PE7_317


title: B07_spegJY039_VEGFA_5GtoT_6U_rU_donor3_PE7_317


title: B07_spegJY039_VEGFA_5GtoT_6U_rU_donor5_PE7_317


title: Control plants [SAMPLE 1-1]

description: Control


title: 2-year-old, Mxra7 KO, scRNAseq

city: Suzhou

first: Yiqiang

last: Wang

address: 111 Ren’ai Road

institute: Xi’an Jiaotong-Liverpool University

description: 10x Genomics

data_processing:
The Cell Ranger software (version 2.0.1, 10X Genomics) was employed for data processing. It facilitated the demultiplexing of cellular barcodes, mapping of reads to the genome and transcriptome using the STAR aligner, and down-sampling of reads as necessary. This process generated normalized aggregate data across samples, ultimately producing a matrix of gene counts.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow samples from 2-month-old and 2-year-old wild-type and Mxra7KO mice (n = 3 to 5 per group) were digested using tissue dissociation solution (RPMI 1640, Thermo Fisher Scientific) to obtain single-cell suspensions. These suspensions were subsequently filtered through 40-μm nylon sterile filters. Cell counts and viability were automatically determined and quality-controlled using a Countess® II Automated Cell Counter.
In accordance with the manufacturer's protocol, Chromium Single Cell 3′ Reagent v2 kits (10X Genomics) were employed to generate barcoded single-cell RNA sequencing (scRNA-seq) libraries. The prepared cell suspension, 10X barcode gel magnetic beads, and oil were added to separate chambers of the Chromium Chip B. Subsequently, gel beads-in-emulsion (GEM) were formed using a microfluidic "double cross" system. The GEMs were then transferred to a thermal cycler for reverse transcription. The 30nt oligo-dT reverse transcription primer on the gel magnetic beads facilitated the conversion of poly-A RNA within the cells into cDNA strands containing barcode and unique molecular identifier (UMI) information. Following this, magnetic bead purification was performed to isolate the cDNA. The purified cDNA was then amplified via PCR, and its concentration and fragment size were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer, respectively.

value: bone marrow

value: bone marrow cell

value: Mxra7 KO


title: A11_spegJY037_VEGFA_5GtoT_standard_donor5_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY037_VEGFA_5GtoT_standard


title: A07_spegJY039_VEGFA_5GtoT_6U_rU_donor5_PEmax


title: 2-year-old, WT, scRNAseq

description: 10x Genomics


title: A07_spegJY039_VEGFA_5GtoT_6U_rU_donor3_PEmax


title: F02_spegJY036_RUNX1_5GtoT_6U_rU_donor1_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY036_RUNX1_5GtoT_6U_rU


title: 2-month-old, WT, scRNAseq

description: 10x Genomics


title: G02_spegJY036_RUNX1_5GtoT_6U_rU_donor2_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY036_RUNX1_5GtoT_6U_rU


title: H02_spegJY036_RUNX1_5GtoT_6U_rU_donor2_PE7_317


title: 2-month-old, Mxra7 KO, scRNAseq

description: 10x Genomics


title: KO, replicate 1, scRNA-seq

city: Birmingham

first: Mostafa

middle: Gamal Saadeldin

last: Mohamed

state: Alabama

address: 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

description: 10 X Genomics

data_processing:
Cellranger-7.1.0 (10X Genomics) pipeline was used to align the raw sequencing data to the mm10 mouse reference genome and count the expressed transcripts. Filtered feature-barcode matrix (contains only detected cell-associated barcodes) are provided as the final processed files.
Assembly: Mouse reference (mm10) - 2020-A downloaded from https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps#mouse-ref-2020-a
Supplementary files format and content: tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated from the tibia and femur by flushing a 25G syringe with 1X PBS containing 2% FBS. The red blood cells were removed using ACK lysis buffer before antibody incubation. The cells were then counted and incubated with antibodies. The linage-marker-negative (Lin-) c-kit+ population containing hematopoietic stem and progenitor cells was sorted
Sorted single-cell suspension, 10x barcoded gel beads and oil (10xGenomics Chromium Next GEM Single Cell 3' Kit v3.1 PN 1000268) were loaded into 10x Chromium™ Single Cell Chip to capture single cells into nanoliter-scale oil droplets by 10xChromium X Controller and generate Gel Bead-In-EMulsions (GEMs). cDNA from single cells were synthesized and barcoded by incubation of the GEMs in a thermocycler machine and then purified from GEMs by DynaBeads (10xGenomics PN 2000048). cDNA was pre-amplified by PCR to generate sufficient mass for sequencing library construction. The single-cell cDNA libraries were constructed by following 10xGenomics 3’ NextGem 3.1 version kit instructions. The final constructed 3’-biased single-cell libraries were sequenced by the Illumina Novaseq6000 machine, targeting 50,000 read pairs/cell.

value: Bone marrow

value: 8-weeks old

value: Lin- cKit+

value: Son+/-


title: KO, replicate 2, scRNA-seq

description: 10 X Genomics


title: C11_spegJY037_VEGFA_5GtoT_standard_donor6_PEmax

value: T cells


title: WT, replicate 2, scRNA-seq

description: 10 X Genomics

value: Son+/+


title: D02_spegJY036_RUNX1_5GtoT_6U_rU_donor6_PE7_317


title: D02_spegJY036_RUNX1_5GtoT_6U_rU_donor4_PE7_317


title: D10_spegJY034_RUNX1_5GtoT_standard_donor6_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY034_RUNX1_5GtoT_standard


title: D06h_Dox_old_rep3

city: Stanford

first: Lucy

last: Xu

address: 290 Jane Stanford Way

data_processing:
Sequence reads were trimmed for adapter sequences, low quality, and T-overhang using TrimGalore (v0.6.6).
Trimmed reads were mapped to a custom genome (mm10 with transgene sequences added as chromosomes) using STAR (2.7.10b), allowing for chimeric mapping (minimum length of 25).
Multimapped reads were removed with samtools, then features were counted with Subread.
Counts were normalized using variance stabilizing transformation as implemented in DESeq2 (1.40.1).
Assembly: mm10 with transgene sequences (rtTA, P2A, T2A, E2A) added as chromosomes
Supplementary files format and content: comma-separated text file includes raw counts for each sample
Supplementary files format and content: comma-separated text file includes VST-normalized counts for each sample

source_name: adult brain (subventricular zone)

growth_protocol: Primary neural stem cells were plated onto poly-D-lysine and laminin coated plates in Neurobasal-A media with B27, EGF, bFGF, and penicillin/streptomycin/glutamine.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy kit according to manufacturer’s instructions. 500 ng of each sample was used as input for library construction.
Library construction was performed using the Illumina Stranded mRNA Prep (Ligation) kit (20040534) and IDT for Illumina DNA/RNA UD Indexes, Plate A index adapters, according to manufacturer’s instructions. All samples were pooled, then the pooled library was sequenced across three lanes of an Illumina NovaSeq X Plus with paired-end 150bp reads.

treatment_protocol:
To induce differentiation, cells were treated with media lacking EGF and bFGF, 18h after plating.
To induce OSKM expression, doxycycline was added to the media at 2ug/ml.

value: adult brain (subventricular zone)

tag: cell line

value: primary

value: neural stem cells

value: iOSKM

value: old

value: M

tag: media

value: differentiation media

value: Dox


title: C10_spegJY034_RUNX1_5GtoT_standard_donor6_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY034_RUNX1_5GtoT_standard


title: A48h_Dox_old_rep3

tag: Sex

value: NSC media


title: C02_spegJY036_RUNX1_5GtoT_6U_rU_donor6_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY036_RUNX1_5GtoT_6U_rU


title: C02_spegJY036_RUNX1_5GtoT_6U_rU_donor4_PEmax


title: D06h_Dox_old_rep2

value: F


title: D06h_untr_young_rep3

value: young

value: untr


title: B02_spegJY036_RUNX1_5GtoT_6U_rU_donor5_PE7_317

value: T cells

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY036_RUNX1_5GtoT_6U_rU


title: B10_spegJY034_RUNX1_5GtoT_standard_donor5_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY034_RUNX1_5GtoT_standard


title: A18h_Dox_old_rep4

value: adult brain (subventricular zone)


title: B02_spegJY036_RUNX1_5GtoT_6U_rU_donor3_PE7_317


title: A10_spegJY034_RUNX1_5GtoT_standard_donor5_PEmax


title: E02_spegJY036_RUNX1_5GtoT_6U_rU_donor1_PEmax


title: D06h_untr_young_rep1

value: primary


title: A02_spegJY036_RUNX1_5GtoT_6U_rU_donor5_PEmax


title: D48h_untr_old_rep1

value: neural stem cells


title: A48h_Dox_old_rep1

value: iOSKM


title: D18h_untr_old_rep2

value: old


title: WT, replicate 1, scRNA-seq

description: 10 X Genomics

value: Bone marrow

value: 8-weeks old

value: Lin- cKit+

value: Son+/+


title: H06_spegJY045_RNF2_1T_ins_6U_rU_donor2_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY045_RNF2_1T_ins_6U_rU


title: D06h_Dox_old_rep4

value: M

value: differentiation media

value: Dox


title: A02_spegJY036_RUNX1_5GtoT_6U_rU_donor3_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY036_RUNX1_5GtoT_6U_rU


title: D48h_untr_old_rep2

value: F

value: untr


title: D06h_untr_young_rep2

value: young


title: F06_spegJY045_RNF2_1T_ins_6U_rU_donor1_PE7_317

value: T cells


title: A18h_Dox_old_rep2

value: adult brain (subventricular zone)

value: primary

value: NSC media


title: D06_spegJY045_RNF2_1T_ins_6U_rU_donor6_PE7_317


title: A18h_untr_young_rep3

value: neural stem cells

value: iOSKM


title: D18h_untr_old_rep3

value: old


title: E06_spegJY045_RNF2_1T_ins_6U_rU_donor1_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY045_RNF2_1T_ins_6U_rU


title: D48h_untr_old_rep4


title: A18h_untr_young_rep4


title: A48h_Dox_old_rep2


title: C06_spegJY045_RNF2_1T_ins_6U_rU_donor6_PEmax


title: B06_spegJY045_RNF2_1T_ins_6U_rU_donor5_PE7_317


title: D06_spegJY045_RNF2_1T_ins_6U_rU_donor4_PE7_317


title: A18h_Dox_old_rep3


title: A06_spegJY045_RNF2_1T_ins_6U_rU_donor5_PEmax


title: A18h_Dox_young_rep5


title: G04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor2_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY043_PRNP_G127V_6GtoT_6U_rU


title: D48h_Dox_old_rep3


title: A18h_untr_young_rep2


title: D06h_Dox_old_rep1


title: G06_spegJY045_RNF2_1T_ins_6U_rU_donor2_PEmax


title: A06_spegJY045_RNF2_1T_ins_6U_rU_donor3_PEmax


title: F04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor1_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY043_PRNP_G127V_6GtoT_6U_rU


title: E04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor1_PEmax


title: D06h_untr_old_rep3

value: M


title: D18h_untr_young_rep5

value: differentiation media


title: D04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor4_PE7_317


title: D04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor6_PE7_317


title: D18h_Dox_old_rep3

value: Dox


title: C04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor6_PEmax


title: D48h_untr_young_rep5


title: A18h_Dox_old_rep1


title: C04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor4_PEmax


title: B06_spegJY045_RNF2_1T_ins_6U_rU_donor3_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY045_RNF2_1T_ins_6U_rU


title: A18h_Dox_young_rep3

value: F


title: D18h_untr_old_rep1

value: untr


title: B04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor5_PE7_317


title: C06_spegJY045_RNF2_1T_ins_6U_rU_donor4_PEmax


title: A18h_untr_young_rep1

value: young


title: B04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor3_PE7_317

value: T cells


title: H04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor2_PE7_317


title: D48h_untr_young_rep4

value: adult brain (subventricular zone)


title: D48h_untr_young_rep3

value: primary


title: D48h_Dox_old_rep2


title: D18h_Dox_old_rep2


title: H08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor2_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY047_IL2RB_H134D_Y135F_6U_rU


title: A04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor3_PEmax


title: D18h_untr_young_rep4

value: neural stem cells


title: D06h_untr_old_rep2

value: iOSKM


title: A18h_Dox_young_rep4

value: NSC media


title: E08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor1_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY047_IL2RB_H134D_Y135F_6U_rU


title: G08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor2_PEmax


title: F08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor1_PE7_317


title: A18h_Dox_young_rep1


title: D08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor4_PE7_317


title: A06h_Dox_old_rep4

value: old


title: C08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor6_PEmax


title: D48h_Dox_old_rep1


title: D08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor6_PE7_317


title: D48h_untr_young_rep2


title: C08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor4_PEmax


title: A18h_Dox_young_rep2


title: D18h_untr_young_rep3


title: B08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor3_PE7_317


title: D18h_Dox_old_rep4


title: B08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor5_PE7_317


title: A08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor3_PEmax


title: D06h_untr_old_rep1


title: A08_spegJY047_IL2RB_H134D_Y135F_6U_rU_donor5_PEmax


title: A04_spegJY043_PRNP_G127V_6GtoT_6U_rU_donor5_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY043_PRNP_G127V_6GtoT_6U_rU


title: A18h_untr_old_rep4

value: M


title: D48h_Dox_old_rep4

value: differentiation media


title: H05_spegJY044_FANCF_5GtoT_6U_rU_donor2_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY044_FANCF_5GtoT_6U_rU


title: D18h_Dox_old_rep1

value: Dox


title: D05_spegJY044_FANCF_5GtoT_6U_rU_donor4_PE7_317


title: D18h_untr_young_rep2

value: F


title: A06h_Dox_old_rep3


title: G05_spegJY044_FANCF_5GtoT_6U_rU_donor2_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY044_FANCF_5GtoT_6U_rU


title: D48h_untr_young_rep1

value: young

value: untr


title: D05_spegJY044_FANCF_5GtoT_6U_rU_donor6_PE7_317

value: T cells


title: C05_spegJY044_FANCF_5GtoT_6U_rU_donor4_PEmax


title: E05_spegJY044_FANCF_5GtoT_6U_rU_donor1_PEmax


title: D06h_untr_young_rep5

value: adult brain (subventricular zone)

value: primary


title: A18h_untr_old_rep2

value: neural stem cells


title: C05_spegJY044_FANCF_5GtoT_6U_rU_donor6_PEmax


title: A06h_Dox_old_rep2

value: iOSKM


title: B05_spegJY044_FANCF_5GtoT_6U_rU_donor3_PE7_317


title: D48h_untr_old_rep3


title: D18h_untr_old_rep4


title: A05_spegJY044_FANCF_5GtoT_6U_rU_donor3_PEmax


title: A48h_Dox_old_rep4

value: NSC media


title: A05_spegJY044_FANCF_5GtoT_6U_rU_donor5_PEmax


title: H03_spegJY048_DNMT1_6GtoC_6U_rU_donor2_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY048_DNMT1_6GtoC_6U_rU


title: F05_spegJY044_FANCF_5GtoT_6U_rU_donor1_PE7_317


title: D18h_untr_young_rep1


title: F03_spegJY048_DNMT1_6GtoC_6U_rU_donor1_PE7_317


title: D06h_untr_young_rep4


title: D03_spegJY048_DNMT1_6GtoC_6U_rU_donor6_PE7_317


title: E03_spegJY048_DNMT1_6GtoC_6U_rU_donor1_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY048_DNMT1_6GtoC_6U_rU


title: A18h_untr_old_rep1

value: old


title: B05_spegJY044_FANCF_5GtoT_6U_rU_donor5_PE7_317


title: D03_spegJY048_DNMT1_6GtoC_6U_rU_donor4_PE7_317


title: A18h_untr_old_rep3

value: M


title: C03_spegJY048_DNMT1_6GtoC_6U_rU_donor4_PEmax


title: SVZ-targeted reprogramming, lane 5 (multiplexed scRNA-seq)

data_processing:
CellRanger software (v3.0.2 for whole-body reprogramming or v6.0.2 for SVZ-targeted reprogramming) was used for demultiplexing, barcoded processing, and gene counting. Default settings were used to distinguish cells from background.
Assembly: mm10, with transgene sequences added as additional chromosomes
Supplementary files format and content: tab-separated values files and matrix files

source_name: subventricular zone (adult brain)

extract_protocol:
Live cells were isolated from the SVZ for single-cell RNA-seq. Briefly, mice were terminally anesthetized with avertin (0.5 mg/g mouse, Sigma-Aldrich T48402-25G) in PBS (Corning 21-040-CV), then perfused transcardially with 15 ml of PBS + heparin (50 U/ml, Sigma-Aldrich H3149-50KU) to remove circulating blood cells. Brains were removed into PIPES buffer on ice and dissected in ice-cold PIPES buffer. The lateral wall of the SVZs from both hemispheres were carefully dissected under a dissecting microscope using forceps, scalpel with no.22 blade, and 22.5 degree stab knife. SVZs were minced, then digested in papain solution (14 U/ml, Worthington LS003119) for 10 min at 37oC. After centrifugation at 300g for 5 min at 4oC, liquid was removed and ovomucoid solution (0.7 mg/ml ovomucoid (Sigma-Aldrich T9253-1G), 0.5 mg/ml DNaseI (Sigma-Aldrich DN25-100MG), in DMEM/F12 (Gibco 11330057) was added. Tissue was triturated with a P1000 pipette to obtain single cell suspension. Cells were then layered onto 22% v/v Percoll (Sigma-Aldrich GE17-0891-01) in PBS and centrifuged at 700g for 10 min at 4oC without brakes to remove myelin debris. Supernatant, containing myelin and debris, was removed. Cell pellet was then resuspended in FACS buffer (1% BSA (Sigma A7979) + 0.1% glucose (Sigma G7021) in PBS) to wash and filtered through 40 um strainer. Cells were centrifuged at 300g for 5 min at 4oC, then resuspended in 70 ul of FACS buffer with DAPI (1 mg/ml, Thermo 62248). Live cells were isolated by FACS on a BD Aria sorter using a 100 um nozzle at 20 psi and collected in 750 ul FACS buffer in a protein low-bind microfuge tube (Eppendorf 0030108442). To allow multiplexing of multiple mice into a single 10x lane, cells were labeled with lipid-modified oligonucleotides at 4oC using a protocol (Buckley et al. 2022) adapted from MULTI-seq (McGinnis et al. 2019). The entirety of each sample was labeled and used. Cells from 2-6 mice were combined after labeling and loaded onto each lane of a 10x Genomics chip.
10x Genomics Chromium Next GEM Single Cell 3’ kits (v3.0 for whole-body reprogramming 1; v3.1 for all others) were used for library construction according to manufacturer's protocol.

treatment_protocol: To express rtTA specifically in the subventricular zone, AAV-Cre was delivered via stereotaxic injection into the lateral ventricle. SVZs were dissected for sequencing two weeks later.

value: subventricular zone (adult brain)

value: old control


title: A06h_Dox_old_rep1

value: Dox


title: D06h_untr_old_rep4

value: differentiation media


title: SVZ-targeted reprogramming, lane 4 (multiplexed scRNA-seq)

value: young control


title: C03_spegJY048_DNMT1_6GtoC_6U_rU_donor6_PEmax


title: SVZ-targeted reprogramming, lane 3 (multiplexed scRNA-seq)

treatment_protocol: To express rtTA specifically in the subventricular zone, AAV-Cre was delivered via stereotaxic injection into the lateral ventricle. Mice were allowed to recover for one week. To induce expression of the reprogramming factors in the subventricular zone, doxycycline (1 mg/ml) was given in the drinking water for one week.

value: old with SVZ-targeted reprogramming


title: A03_spegJY048_DNMT1_6GtoC_6U_rU_donor5_PEmax


title: B03_spegJY048_DNMT1_6GtoC_6U_rU_donor3_PE7_317


title: SVZ-targeted reprogramming, lane 6 (multiplexed scRNA-seq)


title: A03_spegJY048_DNMT1_6GtoC_6U_rU_donor3_PEmax


title: SVZ-targeted reprogramming, lane 2 (multiplexed scRNA-seq)


title: H09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor2_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY046_CXCR4_5GtoC_P191A_6U_rU


title: SVZ-targeted reprogramming, lane 1 (multiplexed scRNA-seq)


title: G09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor2_PEmax

value: T cells

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY046_CXCR4_5GtoC_P191A_6U_rU


title: G03_spegJY048_DNMT1_6GtoC_6U_rU_donor2_PEmax


title: F09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor1_PE7_317


title: E09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor1_PEmax


title: A18h_untr_young_rep5

value: adult brain (subventricular zone)

value: primary

value: young

value: F

value: untr


title: OL-cKO

city: Xiamen

first: Yanchen

state: Fujian

address: Xiang'an south road

institute: Xiamen University

data_processing:
FASTQ data were processed with Trimmomatic v0.39 to remove low-quality reads.
Reads of ChIP-seq data were aligned to the mm10 genome using Bowtie v2.3.5.
Peak calling was performed using MACS2 with a p value cutoff of 0.01.
For the differential binding peaks of STAT3 ChIP-seq, MAnorm was used with cutoff P<0.05 and fold change>2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: bigwig files were generated using deepTools 3.1.3 and visualized by IGV 2.4.16.

source_name: Oligodendrocytes

growth_protocol: Mouse OPCs were cultured as described previously (Ou et al., 2019). Briefly, cortical tissues from P5 mice were diced thoroughly and digested by papain (20 units/ mL), cell suspension was subjected to immunopanning with antibodies against GalC and O4 sequentially. The enriched OPCs were then counted and seeded into poly-D-lysine coated culture plates. OPCs were maintained in OPC growth medium for 6 days, with a change of medium at day 3. For differentiation, the medium was changed to OPC differentiation medium containing triiodo-thyronine (40 ng/mL, Sigma Cat. T2877) for 1 day.

extract_protocol:
Lysates were clarified from sonicated nuclei and STAT3-DNA complexes were isolated with anti-STAT3 antibody.
The libraries were constructed following NEB’s Chip-seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from NEB with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are double-selected and purified. The library was amplified by 18 cycles of PCR.

value: Cortex-derived oligodendrocytes

tag: chip antibody

value: STAT3 (10253-2-AP, Proteintech)


title: OL-Ctrl


title: D12_spegJY040_CXCR4_5GtoC_standard_donor6_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY040_CXCR4_5GtoC_standard


title: D09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor6_PE7_317


title: cKO2

data_processing:
Differential expressed genes were identified using DESeq2 with fold change>1.5 and p<0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CtrlvscKO_deg_all.txt: Tab-delimited matrix table includes abundance measurements.

growth_protocol: Mouse OPCs were cultured as described previously (Ou et al., 2019). Briefly, cortical tissues from P5 mice were diced thoroughly and digested by papain (20 units/ mL), cell suspension was subjected to immunopanning with antibodies against GalC and O4 sequentially. The enriched OPCs were then counted and seeded into poly-D-lysine coated culture plates. OPCs were maintained in OPC growth medium for 6 days, with a change of medium at day 3. For differentiation, the medium was changed to OPC differentiation medium containing triiodo-thyronine (40 ng/mL, Sigma Cat. T2877) for 1-2 days.

extract_protocol:
After 24 h of differentiation, cells were washed by pre-chilled PBS and harvested in Trizol reagent (AG Biotech.)
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: OL-Input


title: cKO1


title: Ctrl2


title: Ctrl1


title: D09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor4_PE7_317


title: C12_spegJY040_CXCR4_5GtoC_standard_donor6_PEmax

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY040_CXCR4_5GtoC_standard


title: C09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor6_PEmax


title: B03_spegJY048_DNMT1_6GtoC_6U_rU_donor5_PE7_317

value: Electroporated with PE7 mRNA and synthetic pegRNA spegJY048_DNMT1_6GtoC_6U_rU


title: C09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor4_PEmax


title: B12_spegJY040_CXCR4_5GtoC_standard_donor5_PE7_317


title: B09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor5_PE7_317


title: Whole-body reprogramming, cohort 2, lane 1 (multiplexed scRNA-seq)

treatment_protocol: To induce expression of the reprogramming factors, mice were treated with doxycycline (1 mg/ml) in the drinking water. Reprogramming factors were turned on for two days, then off for five days. This cycle was repeated for a total of three pulses of reprogramming. Control mice were supplied with regular drinking water.

value: subventricular zone (adult brain)

value: ROSA26(rtTA-M2); Col1a1(tetO-OSKM)

value: young control, old control, and old with whole-body reprogramming


title: B09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor3_PE7_317


title: Whole-body reprogramming, cohort 2, lane 2 (multiplexed scRNA-seq)


title: A12_spegJY040_CXCR4_5GtoC_standard_donor5_PEmax


title: Minipigno.606APP/PS1 so2603P5-γinhibition (2uM)

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Reads were aligned to the porcine genome build Sscrofa11.1 (Ensemble release 92) using HISAT2 aligner (v2.1.0)
Transcript quantification was performed using htseq-count (v0.9.1)
Read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM)
Differentially expressed genes were determined from count tables using DEseq2 (v2.11.40.6)
Assembly: Sscrofa11.1 (Ensemble release 92)
Supplementary files format and content: tab-delimited file containing TPM values for each sample

organism: Sus scrofa

source_name: Ear biopsy

extract_protocol:
Porcine fibroblasts were obtained from ear biopsies from WT, PS1 and APP/PS1 Göttingen minipigs and cultured in porcine fibroblast medium (Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma Aldrich), 10% FBS (Life Technologies), 1% P/S (P/S, 10,000 units/mL and 10,000μg/mL; Life Technologies), 1% Gln (2.92g/100mL) and 6.667ng/mL Fibroblast Growth Factor-basic (bFGF; Life Technologies)) in 5% CO2 in a humidified chamber at 37oC. Established fibroblasts were split in a 1:3 ratio every 3 days using 0.05% trypsin EDTA (Life Technologies). All fibroblasts used in this study were tested negative for mycoplasma (MYCOPLASMACHECK, Eurofins Genomics).
Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Europe Genome Center. Total RNA was subjected to oligo dT based mRNA enrichment. 50 bp single-end read sequencing was performed on BGIseq-500 with DNBseq technology. More than 20 million clean reads were obtained per sample.

value: Ear biopsy

value: Fibroblasts

value: 2uML-685-458 (g-secretase inhibitor)


title: Minipigno.550APP/PS1 so2683P5-No inhibition

value: Vehicle


title: A09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor5_PEmax

value: T cells

value: Electroporated with PEmax mRNA and synthetic pegRNA spegJY046_CXCR4_5GtoC_P191A_6U_rU


title: Minipigno.550APP/PS1 so2683P5-γinhibition (2uM)


title: Minipigno.606APP/PS1 so2603P5-binhibition (15uM)

value: 15uM b-Secretase Inhibitor IV


title: A09_spegJY046_CXCR4_5GtoC_P191A_6U_rU_donor3_PEmax


title: Minipigno.512(A)RMCE F1 P9-γinhibition (2uM)

value: WT


title: Minipigno.606APP/PS1 so2603P5-No inhibition


title: WT cells, replicate 3

city: Helsinki

first: Mikko

last: Frilander

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
The STAR aligner was used for mapping the paired sequence reads to the genome (hg38/GRCh38). Transcript annotations were obtained from GENCODE (v29). The length of the genomic sequence flanking the annotated junctions (sjdbOverhang parameter) was set to 161. The Illumina adapter sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT were, respectively, clipped from the 3’ of the first and the second pairs in the read libraries (using clip3pAdapterSeq parameter).
Differential alternative splicing (AS) analysis was done using Whippet (v0.11) (Sterne-Weiler et al., 2018). Both merged aligned reads (bam files) and AS event annotations from GENCODE (v29) were used to build the index reference for AS events. To detect the significantly differential events, probability cutoff of Pr > 0.9 and Percentage Spliced In deviation cutoff of |ΔΨ| > 0.05 were used.
Differential intron retention was analyzed with  IRFinder-S using SUPPA2 wrapper (Lorenzi et al., 2021; Middleton et al., 2017).
Assembly: hg38/GRCh38
Supplementary files format and content: .xlsx table containing intron retention analysis (using IRFinder-S) and alternative splicing analysis (using Whippet)

growth_protocol: HEK293 cells were grown in DMEM, 10% FBS, 1% penicillin–streptomycin and 2 mM L-glutamine

extract_protocol:
Total RNA was isolated using Trizol extraction followed by an additional acidic phenol (pH 5.0) extraction. Total RNA prep was treated with DNase prior to library protocol.
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA kit (Illumina) Human Ribo-Zero rRNA depletion kit (Illumina) using manunfacturer's protocol

value: Human Embryonic Kidney


title: Participant 18: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 34

city: Leiden

first: Linda

last: Voogd

state: South-Holland

address: Albinusdreef 2

department: Infectious Diseases

country: Netherlands

institute: Leiden University Medical Center

description: sample 25

data_processing:
Single-end reads of 50 bps. in length were aligned against he human reference genome Homo sapiens GRCh38.91
Analysis of reads was performed in Rstudo v1.2 using the DESeq2 package
DESeq2 parameters were log2 fold change treshold 1, read count >4 per gene, adjusted p-value cut off= 0.05 and the DESeq2 multifactor design formula=‘~donor + cell population’
Assembly: GRCh38.91
Supplementary files format and content: .xlsx files contain the raw read counts for each sample for the identified gene
Supplementary files format and content: FG_All_mapped_reads Corrected.xlsx file contains the corrected read counts (according to the size factor) for each gene in each sample

source_name: CD8+ T-cell

extract_protocol:
RNA was extracted from lysed (QIAzol) sorted T-cells using an miRNeasy Mini Kit (Qiagen) and eluted into DNA Lobind Eppendorf Tubes
RNA was amplified to cDNA using the SMART-Seq version 4 Ultra Low Input RNA Kit for Sequencing (Takara Bio)

value: CD8+ T-cell

tag: hla-e genotype


title: WT cells, replicate 1


title: Particpant 15: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 34

description: sample 24


title: Minipigno.557APP/PS1 so2709P5-γ inhibition (2uM)


title: WT cells, replicate 2


title: Whole-body reprogramming, cohort 2, lane 3 (multiplexed scRNA-seq)


title: Participant 20: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 21


title: Participant 21: CD8+ HLA-E TM+  T-cells recognizing UL40-derived peptide from CMV

description: sample 22


title: RBM41 knockout cells, replicate 3


title: Participant 19: CD8+ HLA-E TM+  T-cells recognizing Mtb peptide 55

description: sample 20


title: Minipigno.512(A)RMCE F1 P9-No inhibition


title: Whole-body reprogramming, cohort 1 (multiplexed scRNA-seq)

value: old control and old with whole-body reprogramming


title: Minipigno.512(A)RMCE F1 P9-binhibition (15uM)


title: Participant 18: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 19


title: Participant 15: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 18


title: Minipigno.522(A)RMCE F1 far 3400P9-γinhibition (2uM)


title: RBM41 knockout cells, replicate 1


title: Participant 14: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 17


title: Participant 13: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 16


title: Minipigno.522(A)RMCE F1 far 3400P9-binhibition (15uM)


title: Participant 10: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 13


title: Participant 9: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55

description: sample 12


title: Minipigno.522(A)RMCE F1 far 3400P9-No inhibition


title: Participant 21: CD8+ TM- T-cells

description: sample 11


title: CHC23, tumor

city: Laval

first: Maya

last: Saleh

state: Qc

address: 531 Boulevard des Prairies

department: Armand Frappier Santé Biotechnologie

institute: INRS

data_processing:
Fastq raw sequencing data were processed using the 10x Genomics Space Ranger v1.3.0 pipeline with options indicated in supplementary file "Info_Supp_for_Visium.tsv"
Sequences were aligned to human GRCh38-2020 reference genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Downstream analyses were performed using Seurat software
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg.gz:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz:  list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5 : filtered feature file output from CellRanger, contains matrix, features and barcodes information
Library strategy: Spatial Transcriptomics

source_name: Hepatocellular Carcinoma

extract_protocol:
OCT-embedded tissue blocks were sectioned at 10 μm thickness using Cryostar NX70 (Leica) and tumoral tissues containing RNA with a RIN ≥ 6.8 were included in the Visium experiments. One section per patient was cut at 10 μm thickness and placed on Visium slide capture areas (10x Genomics). Slides were then processed following the 10x Genomics Visium Spatial protocol according to the manufacturer recommendations. The slides containing tissues were methanol-fixed at -20°C and processed for H&E staining and imaging.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Hepatocellular Carcinoma


title: Participant 20: CD8+ TM- T-cells

description: sample 10


title: Minipigno.500Master F2P5-γinhibition (2uM)


title: CHC20, tumor


title: patient 24, Adjacent non-tumoral

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
matrices generated by CellRanger were then processed using Seurat, followed by filtering and doublet removal steps
Normalization was done using SCTransform and rPCA Integration was performed in Seurat
Assembly: GRCh38
Supplementary files format and content: Giraud_Chalopin_innate_HCC_processed_count_data_mat.tsv.gz, raw count matrix after sample integration (rows are genes, columns are barcodes
Supplementary files format and content: Giraud_Chalopin_innate_HCC_metadata.tsv.gz, meta information corresponding to barcodes in the count matrix

source_name: Liver

extract_protocol:
15.000 single CD45+ panTCRαβ- CD19- innate immunity cells were loaded into a chip to form Gel Bead-in-Emulsion in the Chromium Controller. Single-cell libraries were generated using the Single Cell 3' reagent Kit v3.1 (10X Genomics) as per the manufacturer’s protocol.
cDNA was amplified by 12 PCR cycles and 12 cycles were also performed for library preparation (single index PCR). Libraries were pooled and sequenced on a NovaSeq 6000.

value: Liver

value: innate immune cells


title: Participant 19: CD8+ TM- T-cells

description: sample 9


title: Minipigno.500Master F2P5-binhibition (15uM)


title: patient 20, Adjacent non-tumoral


title: Minipigno.500Master F2P5-No inhibition


title: Participant 18: CD8+ TM- T-cells

description: sample 8


title: ILCs - ABX+PBS

city: CHARLOTTESVILLE

first: Md Jashim

last: Uddin

state: VA

address: 257 COLONNADE DR APT 12

institute: University of Virginia

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing and gene counting were done using Cell ranger software v6.0.1 provided by the 10x genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon Innate lymphoid cells (ILCs)

extract_protocol:
The whole colon from mice was dissected and opened longitudinally, followed by washing with PBS. Tissues were then left in buffer 1 (HBSS with 25 mM HEPES and 5% FBS) until harvesting all the mice. Colon tissues were incubated at 37°C temperature with gentle shaking for 40 min to remove the epithelial layer into 40 ml Buffer 2 (HBSS with 15 mM HEPES, 5 mM EDTA, 10% FBS, and 1 mM DTT). Tissue sections were cut into small pieces with a fine scissor and incubated into 5 ml digestion buffer (RPMI 1640 containing 0.17 mg/ml liberase, 30 mg/ml DNase) for 30-35 minutes at 37°C temperature with gentle shaking. Solutions were then passed through 100-micron and 40-micron cell strainers to collect single-cell suspensions. Suspensions were centrifuged at 500g for 5 minutes to pellet cells, followed by resuspension into 300 ml FACS buffer (2% FBS in PBS). From the cell suspensions, ILCs were enriched using a mouse Lineage cell depletion kit (Milteny Biotec) following the manufacturer's protocol.
Library was prepared using manufaturer's protocol (10x genomics, single cell 3' protocol)).In brief, cells were passed through Chromium Next GEM chip G with barcoded gel beads to generate GEM (Gel Beads-in-emulsion). After that, barcoded cDNA was generated in GEMs. GEMs were then broken, and cDNA was cleaned up and amplified for the library preparation. Sequencing was performed using the P3-100 cycle kit.

treatment_protocol: Here, samples were mouse colon ILCs. Mice were kept untreated or administered ABX or ABX+IL-33 before collecting ILCs from colon. Conditions were -No Abx (Baseline), Abx (mice were administered an antibiotic cocktail -45 mg/L Vancomycin, 35 mg/L Colistin, 35 mg/L Gentamycin, and 215 mg/L Metronidazole, in drinking water for three days and followed by ip injection of Clindamycin, 0.016mg/g of body weight),and  Abx+IL-33

value: Colon Innate lymphoid cells (ILCs)

value: Abx+PBS


title: patient 23, Adjacent non-tumoral


title: RBM41 knockout cells, replicate 2


title: AR.12, trachea, WT

city: Edinburgh

first: Daniel

middle: Oliver

last: Dodd

address: Western General Hospital  Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequence files were processed using the nf-core/rnaseq workflow version 2.3 (https://github.com/nf-core/rnaseq) running Nextflow (nextflow 22.04.5, build 5708 (15-07-2022 16:09 UTC) for all rna-seq data, with default parameters.
reads were aligned to mm10 using star 2.6.1d and read counts produced by salmon 1.5.2
Assembly: mm10
Supplementary files format and content: salmon.merged.gene_counts_length_scaled.tsv, salmon.merged.gene_tpm.tsv

source_name: trachea

extract_protocol:
RNAeasy Micro Kit ws used to extract RNA, gDNA was removed using an eliminator column.
Libraries were prepared from 500ng of each total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the provided protocol. Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification the mRNA was fragmented using divalent cations under elevated temperature and primed with random hexamers. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification as the polymerase used in the assay is not incorporated past this nucleotide. AMPure XP beads (Beckman Coulter, #A63881) were then used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to another during the subsequent adapter ligation reaction, and a corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. Multiple indexing adapters were then ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 10 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing. After amplification libraries were purified using AMPure XP beads.

value: trachea

value: 4 days

value: male


title: Minipigno.498Master F2P5-γinhibition (2uM)

value: Ear biopsy

value: Fibroblasts

value: 2uML-685-458 (g-secretase inhibitor)


title: AR.11, trachea, WT


title: ILCs - ABX+IL-33

description: 10X Genomics


title: ILCs - No Abx

description: 10X Genomics

value: No treatment


title: patient 19, Adjacent non-tumoral


title: Participant 15: CD8+ TM- T-cells

description: sample 7


title: Minipigno.498Master F2P5-binhibition (15uM)

value: 15uM b-Secretase Inhibitor IV


title: Participant 14: CD8+ TM- T-cells

description: sample 6


title: patient 18, Adjacent non-tumoral


title: AR.10, trachea, WT

value: female

value: WT


title: Minipigno.557APP/PS1 so2709P5-binhibition (15uM)


title: Participant 13: CD8+ TM- T-cells

description: sample 5

value: CD8+ T-cell


title: Participant 10: CD8+ TM- T-cells

description: sample 2


title: AR.9, trachea, WT


title: patient 16, Adjacent non-tumoral


title: AR.7, trachea, Het

value: Het


title: Minipigno.499Master F2P5-γinhibition (2uM)


title: Participant 9: CD8+ TM- T-cells

description: sample 1


title: patient 14, Adjacent non-tumoral


title: AR.6, trachea, Het


title: Minipigno.499Master F2P5-binhibition (15uM)


title: Particpant 4: CD8+ HLA-E TM+  T-cells recognizing UL40-derived peptide from CMV


title: patient 13, Adjacent non-tumoral


title: patient 12, Adjacent non-tumoral


title: Participant 8: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: Minipigno.499Master F2 P5-No inhibition

value: Vehicle


title: AR.4, trachea, Het


title: Minipigno.558APP/PS1 so2709P5-γinhibition (2uM)


title: AR.5, trachea, WT


title: AR.3, trachea, Hom

value: Hom


title: Participant 6: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: AR.2, trachea, Het


title: Participant 7: CD8+ HLA-E TM+  T-cells recognizing Mtb peptide 55


title: Minipigno.558APP/PS1 so2709P5-binhibition (15uM)


title: patient 17, Adjacent non-tumoral

value: Liver

value: innate immune cells


title: Minipigno.498Master F2P5-No inhibition


title: Minipigno.558APP/PS1 so2709P5-No inhibition


title: AR.1, trachea, Hom


title: Minipigno.607APP/PS1 so2603P5-γinhibition (2uM)


title: patient 20, tumor

value: Hepatocellular Carcinoma


title: patient 19, tumor


title: AI.4, trachea, Hom

value: trachea

value: 5 days


title: Minipigno.607APP/PS1 so2603P5-binhibition (15uM)


title: patient 18, tumor


title: Participant 3: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: Participant 2: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: Minipigno.607APP/PS1 so2603P5-No inhibition


title: patient 24, tumor


title: patient 17, tumor


title: Participant 1: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: patient 23, tumor


title: KO77_T354M_Rep4

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: -77KO expressing Gata2 T354M mutant replicate 4

data_processing:
Sequencing reads were aligned by STAR (version 2.5.2b) to mouse genome (mm10, chromosomes 1 to 19, X, Y, and M) with GENCODE comprehensive gene annotation (version M16) on the reference chromosomes only. Command line options for STAR followed ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh)
Gene expression levels were quantified by RSEM (version 1.3.0) with command line options following ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh).
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

source_name: Lin- hematopoietic progenitor cells

extract_protocol:
total RNA
standard NuGEN Ovation protocol

value: Lin- hematopoietic progenitor cells

value: T354M rescue

value: Cells were infected with MSCV vector coding GATA2 T354M mutant. Cells were cultured for 3 days and RNA was harvested.


title: KO77_T354M_Rep3

description: -77KO expressing Gata2 T354M mutant replicate 3


title: Participant 5: CD8+ HLA-E TM+ T-cells recognizing Mtb peptide 55


title: Participant 8: CD8+ TM- T-cells


title: patient 16, tumor


title: KO77_T354M_Rep2

description: -77KO expressing Gata2 T354M mutant replicate 2