title: Cadmium Treated Blueberry Root_rep2

status: Public on Aug 25 2021

city: JiLin

first: Chen

last: Shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

institute: Jilin Agricultural Science and Technology College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Vaccinium ashei

source_name: root

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: agent

value: Cadmium


title: sdlg-asil1-1-2-1-br1

status: Public on Aug 26 2021

type: SRA

city: Lancaster

first: Pablo

middle: D

last: Jenik

state: PA

address: PO Box 3003

department: Department of Biology

country: USA

institute: Franklin and Marshall College

library_source: transcriptomic

data_processing:
Libraries were sequenced on Illumina HiSeq 4000 sequencer.
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Arabidopsis thalian primary transcripts (TAIR10) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 40 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. TMM-normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including the raw counts for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis 14d seedlings

growth_protocol: Plants were germinated and grown on MS medium without sucrose, at 22°C with 16 hours of light in a Percival Scientic incubator for 14 days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Minikit (QIAGEN), per the manufacturer’s directions.
Illumina-complatible libraries were made starting with 5 ug of total RNA, using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, at the exception of the RNA and mRNA isolation: the polyA isolation from total RNA described in Supplementary Methods 2 was used and the NEXTflex ChIP-Seq Barcodes (BiooScientific) were used for Illumina-compatible adapters. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

treatment_protocol: Seedlings were collected 14d after germination and  flash-frozen in liquid nitrogen.

tag: tissue

value: 14d seedlings

tag: ecotype

tag: genotype

value: asil1-1 asil2-1


title: Non-Cadmium Treated Blueberry Root_rep2

country: China


title: Study1_DCN10

city: Philadelphia

first: Paul

middle: T

last: Ranum

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

data_processing:
Read Alignment with STAR_2.6.0c to the rhesus macaque genome (mmul10 from ensembl).
Feature counts values generated by STAR were used as the basis for differential expression analysis using DESeq2
Genome_build: mmul10
Supplementary_files_format_and_content: STAR generated tab delimited splice junction counts files "_SJ_out.tab"

organism: Macaca mulatta

source_name: Deep Cerebellar Nuclei

extract_protocol:
For RNA-Seq, total RNA (1 µg) was extracted from tissue using TRIzol (Ambion by Life Technologies) and treated to remove contaminating DNA using RNAeasy Plus Miniprep kit (QIAgen). For small RNA-Seq Small RNAs were extracted from tissue using miRNeasy Kit (QIAgen).
For RNA-Seq, RIN values were acquired using RNA Nano Chips (Agilent Technologies) in Agilent 2100 BioAnalyzer as per manufacturer’s protocol. Sequencing libraries were prepared using, NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). As no Rhesus specific ribosomal RNA (rRNA) depletion kit was available rRNA depletion was performed using combined Human, Mouse, and Rat species specific QIAseq FastSelect RNA Removal Kit (QIAgen). SPRIselect Beads (Beckman Coulter) were used for the purification steps. cDNA libraries were then indexed using the NEBNext Dual Index Kit (New England Biolabs).  Samples were analyzed on High Sensitivity DNA Chips (Agilent Technologies) with Agilent 2100 BioAnalyzer as per manufacturer’s protocol to determine library size, concentration and purity. For small RNA-Seq, RIN values were acquired using RNA Nano Chips (Agilent Technologies) in Agilent 2100 BioAnalyzer as per manufacturer’s protocol. Sequencing libraries were prepared using TruSeq Small RNA Library Prep Kit (Illumina) with the QIAquick Gel Extraction Kit DNA extraction supplement (QIAgen).  SPRIselect Beads (Beckman Coulter) were used for the purification steps. cDNA libraries were then indexed using the TruSeq Small RNA Library Prep Kit-Set A Indices (Illumina). Samples were analyzed on High Sensitivity DNA Chips (Agilent Technologies) with Agilent 2100 BioAnalyzer as per manufacturer’s protocol to determine library size, concentration and purity

treatment_protocol: The indicated treatments for each sample were administered by clearpoint MRI guided injection into the deep cerebellar nuclei of the the indicated Rhesus macaque.  A detailed protocol can be found in our publication Keiser et al., 2021 Nat Med.

tag: treatment

value: Vehicle

tag: ID

value: cerebellum


title: C1A

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

library_source: genomic

data_processing:
The quality check of raw reads was performed using the Genotypic FastQC tool.
The reads were aligned to the reference M. tuberculosis H37Rv genome using the Bowtie alignment tool
Peak detection was carried out using the Hypergeometric Optimization of Motif EnRichment (Homer) tool.
Genome_build: H37Rv

molecule: genomic DNA

organism: Mycobacterium tuberculosis

source_name: Mtb phosphate  limited (RegX3-IP) replicate (rep)1

growth_protocol: Mtb was  grown to log phase in Middle Brook 7H9 medium  containing 10% ADC

extract_protocol:
Mtb  grown in phosphate depleted medium  was crosslinked using 1% formaldehyde followed by quenching with 250mM glycine. The cells were  lysed and the DNA was sheared on Bioruptor plus (Diagenode) with 25 cycles of 30 sec/ 90 sec on/off, respectively, so as to generate fragment sizes of ~250 bp. Immune complexes were precipitated with  RegX3 antibody or control  IgG, and washed. DNA from total lysates (input) and immunoprecipitates (IP) were purified after decrosslinking with Proteinase K and samples were used immediately for next-generation sequencing (NGS).
ChIP-Seq libraries for sequencing were constructed at Genotypic Technology’s Genomics facility according to the NEXTflex ChIP-Seq library protocol outlined in the NEXTflex ChIP-Seq kit (cat nos102–1001)
The libraries were enriched using PCR followed by purification using Agencourt AMPURE XP beads (Beckman Coulter #A63881) and quality was checked on a High Sensitivity Bioanalyzer Chip (Agilent).Sequencing was performed at Genotypic Technology’s Genomics facility following certified protocols from Illumina on an Illumina Hi-seq platform using single-end 75 bp chemistry.

treatment_protocol: Log phase cells were harvested and resuspended in  phosphate limited medium and grown  for 72 hours under shaking at 37◦C

tag: media

value: phosphate limited

tag: chip antibody

value: anti-RegX3 (custom-made antibody of RegX3 was raised by Thermo Fisher Scientific, USA)

tag: molecule subtype

value: IP DNA


title: Non-Cadmium Treated Blueberry Root_rep3


title: Non-Cadmium Treated Blueberry Root_rep1


title: Non-Cadmium Treated Blueberry Leaf_rep1

source_name: Leaf

value: Leaf


title: Uninjured cord, biological rep1

type: RNA

city: Auckland

first: Connor

middle: Andrew

last: Clemett

state: Auckland

address: 85 Park Rd

department: Anatomy and Medical Imaging

country: New Zealand

institute: University of Auckland

description:
SD_Rat_Control_01
Rattus norvegicus domestica

hyb_protocol: Rat Clariom S arrays were incubated in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C / 60 RPM for 16-18 hours.

scan_protocol: GeneChips were scanned with the GeneChip™ Scanner 3000 (Applied Biosystems, #00-0186) according to manufacturer's instructions.

data_processing: Raw intensity CEL files were imported into Transcriptome Analysis Console (TAC software v4.0.2.15. Applied Biosystems), and gene level expression analysis was performed using the default ANOVA settings.

label: Biotin

organism: Rattus norvegicus

source_name: Uninjured cord

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

extract_protocol: Total RNA was extracted by mechanical tissue dissociation, TRIzol / chloroform extraction and phase separation. RNA extract quantified by Implen NP80 nanophotometer and quality assed by Agilent Bioanalyzer (RIN >8.80).

treatment_protocol: Adult female Sprague-Dawley rats (220-250 g) underwent surgical T10 laminectomy and moderate contusive injury (175 kDyn) by an Infinite Horizons impactor. Treatment groups were acutely administered the AAV5-GfaABC1D-dYFP reporter vector at the time of surgery by stereotaxic microinjection. Following recovery, at 7- and 28-days post-injury animals were euthanised, perfused with ice-cold saline and a 5 mm region centered on the spinal lesion excised to be snap frozen.

tag: strain

value: Sprague Dawley

tag: Sex

value: Female

tag: age

value: Adult

value: Spinal cord tissue

tag: injury

value: No Injury

tag: time post-injury


title: Non-Cadmium Treated Blueberry Leaf_rep3


title: sdlg-Ler-br3

value: Landsberg erecta

value: wild type


title: Cadmium Treated Blueberry Root_rep1

value: root


title: Cadmium Treated Blueberry Leaf_rep3

value: Cadmium


title: Cadmium Treated Blueberry Leaf_rep1


title: Non-Cadmium Treated Blueberry Fruit_rep3

source_name: Fruit

value: Fruit


title: Cadmium Treated Blueberry Leaf_rep2


title: Study1_DCN02


title: sdlg-asil1-1-2-1-br3

value: 14d seedlings

value: asil1-1 asil2-1


title: Cadmium Treated Blueberry Fruit_rep3


title: Cadmium Treated Blueberry Fruit_rep2


title: Non-Cadmium Treated Blueberry Fruit_rep2


title: Cadmium Treated Blueberry Fruit_rep1


title: Cadmium Treated Blueberry Root_rep3


title: Non-Cadmium Treated Blueberry Branch_rep2

source_name: Branch

value: Branch


title: Non-Cadmium Treated Blueberry Branch_rep1


title: Non-Cadmium Treated Blueberry Branch_rep3


title: Non-Cadmium Treated Blueberry Leaf_rep2


title: Cadmium Treated Blueberry Branch_rep3


title: Cadmium Treated Blueberry Branch_rep1


title: Non-Cadmium Treated Blueberry Fruit_rep1


title: PMY_Frac14

city: St. Louis

first: Chun-Kan

last: Chen

state: MO

address: 660 S Euclid Ave

department: Cell Biology and Physiology

institute: Washington University in St. Louis

description:
Total RNA
Polyribosome_enriched_oligos.xlsx

data_processing:
IRES screening and polysome profiling: Single-end reads in the length of 90-nt were trimmed to 37-nt containing the unique oligo variable region using fastx_trimmer module (-f 54). Trimmed reads were mapped to the synthetic library sequences using Bowtie2 with default settings. Multi-mappers were excluded from the subsequent analysis by excluding the reads with the "XS" flag in the .sam files (grep -v). The number of reads for each designed oligo was counted in each bin respectively using bedtools multiBamCov module.
M2-seq: Single-end reads in the length of 300-nt were trimmed to 174-nt containing the unique oligo sequence using fastx_trimmer module (-f 39 -l 212). ShapeMapper was used to align the trimmed reads to reference sequences and record mutations, and the results were converted to M2-seq data and mutation spectra using scripts available at https://github.com/ribokit/m2seq. The M2-net analysis, mutate-and-map visualization, RNA structural analysis, and RNA structure visualization were performed as described in Cheng et al. (PNAS, 2017).
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: IRES screening: .xlsx file that contains the synthetic oligo index, sequence, and cap-independnet translation activity.
Supplementary_files_format_and_content: Polysome profiling: .xlsx file that contains the number of (poly)ribosome-enriched oligos
Supplementary_files_format_and_content: M2-seq: .rdat file for 2nd structure determination

organism: synthetic construct

source_name: Designed oligonucleotides

extract_protocol:
IRES screening: Total DNA from each expression bin was extracted using Quick-DNA Microprep Plus Kit (Zymo Research).Synthesis (NEB BioLabs), and purified with DNase digestion (TURBO DNase; Thermo Fisher Scientific) and RNase R digestion (MACLAB; 20 U RNase R per 20 μg of RNA).
Polysome profiling: The total RNAs of each fraction were purified respectively using RNeasy Mini Kit (Qiagen) with DNase treatment (Qiagen). The RNAs were then treated with RNase R and purified using RNA Clean & Concentrator-25 (Zymo Research).
M2-seq: The circRNA of oligo of interest was produced with in vitro transcription using HiScribe™ T7 High Yield RNA
IRES screening: Three rounds of PCR using NEBNext Ultra II Q5 Master Mix (NEB BioLabs) were performed to generate the library for next-generation sequencing. For the first PCR, oligo library sequence was amplified using the following primer set – Fw: GGGATCACTCTCGGCATGGA; Rv: GCTCCTCGCCCTTGCTCAC. Each 50 μL PCR reaction contained 200 ng total DNA, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 24 cycles of 98°C for 30 s, 65°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the second PCR, adapter priming sequences were added to the oligo library using the following primer set – Fw: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGGATCACTCTCGGCATGGA; Rv: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTCCTCGCCCTTGCTCAC (underlined sequence represents the sequence for illumina adapters priming). Each 50 μL PCR reaction contained 1.25 μL of the first PCR product, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 18 cycles of 98°C for 30 s, 70°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the third PCR, custom barcodes adapters were used for the reaction. Each 50 μL PCR reaction contained 1 μL of 1:20 diluted second PCR product, 1 μM Ad1 adapter, and 1 μM Ad2 adapter. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 72°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. The PCR product was then separated on a 2% E-Gel™ EX Agarose Gel (Invitrogen) and the DNA fragments with expected size were purified using Zymoclean Gel DNA Recovery Kit (Zymo Research).
Polysome profiling: The oligo sequences from each sample were amplified by RT-PCR with SuperScript™ IV One-Step RT-PCR System (Thermo Fisher Scientific) using primers flanking the oligo sequence (Fw: GGGATCACTCTCGGCATGGA; Rv: GCTCCTCGCCCTTGCTCAC). cDNA libraries were generated and sequenced with HiSeq 4000 using the library generation method as for IRES screening.
M2-seq: The complimentary single-stranded DNA of the circRNA was generated by reverse transcription using SuperScript™ IV (Thermo Fisher Scientific) with oligo sequence specific primer (TCTTTTGTTGGAGTCTACTCGACTCCTTT) and purified with DNA Clean & Concentrator-5 (Zymo Research). Three rounds of PCR using NEBNext Ultra II Q5 Master Mix (NEB BioLabs) were performed to generate the cDNA library for next-generation sequencing. For the first PCR, oligo library sequence was amplified using the following primer set – Fw: GAACGACTCGAGTAGAGTCGAAAA; Rv: TCTTTTGTTGGAGTCTACTCGACTCCTTT. Each 50 μL PCR reaction contained 200 ng total DNA, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 67°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the second PCR, sequences for adapters priming were added to the oligo library using the following primer set – Fw: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGAACGACTCGAGTAGAGTCGAAAA; Rv: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTTTTGTTGGAGTCTACTCGACTCCTTT (underline represents the sequence for illumina adapters priming). Each 50 μL PCR reaction contained 1.25 μL of the first PCR product, 500 nM forward primer, and 500 nM reverse primer. The parameters for the PCR were 98°C for 1 min, 12 cycles of 98°C for 30 s, 67°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. For the third PCR, custom barcodes adapters were used for the reaction. Each 50 μL PCR reaction contained 1 μL of 1:20 diluted second PCR product, 1 μM Ad1 adapter, and 1 μM Ad2 adapter. The parameters for the PCR were 98°C for 1 min, 15 cycles of 98°C for 30 s, 72°C for 30 s, 72°C for 40 s, each, and finally one cycle of 72°C for 5 min. The PCR product was then separated on a 2% E-Gel™ EX Agarose Gel (Invitrogen) and the DNA fragments with expected size were purified using Zymoclean Gel DNA Recovery Kit (Zymo Research).
IRES screening: DNA-seq.
Polysome profiling: RNA-seq
M2-seq: RNA-seq

tag: functional assay

value: circRNA cap-independent translation

tag: cell line

tag: master plasmid

value: oligo-split-eGFP-circRNA


title: PMY_Frac13


title: PMY_Frac15


title: PMY_Frac12


title: PMY_Frac7


title: PMY_Frac8


title: PMY_Frac11


title: PMY_Frac9


title: PMY_Frac10


title: Cadmium Treated Blueberry Branch_rep2

tag: agent


title: CHX_Frac7


title: PMY_Frac5


title: PMY_Frac2


title: CHX_Frac14


title: CHX_Frac6


title: CHX_Frac9


title: CHX_Frac13


title: PMY_Frac3


title: CHX_Frac8


title: PMY_Frac6


title: CHX_Frac5


title: PMY_Frac4


title: CHX_Frac15


title: CHX_Frac4


title: CHX_Frac2


title: CHX_Frac1


title: CHX_Frac3


title: CHX_Frac10


title: CHX_Frac12


title: CHX_Frac11


title: OTI CD8+ T Palbo 24h_rep 1 [13_RNAseq_in_vitro_mouse]

city: Melbourne

first: Emily

middle: Jane

last: Lelliott

state: VIC

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the mouse reference genome (mm10) using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (from the Subread package, v1.5.0) prior to differential gene expression analysis using Voom/Limma.
Gene set enrichment analyses were performed using GSEA software (Broad Institute) and barcode plots were plotted using ReplotGSEA.R (part of the Rtoolbox R package).
Genome_build: GRCm38

organism: Mus musculus

source_name: OTI CD8+ T cells peptide-activated in vitro

growth_protocol: Splenocytes from C57BL/6.OT-I transgenic mice were cultured with 10 nM SIINFEKL plus 100 IU/mL IL-2 for 72 hrs in complete media (RPMI 1640 plus 20 mM HEPES containing 10% FBS, 1% GlutaMAX, 1 mM Sodium Pyruvate, 1 mM MEM Non-Essential Amino Acids, 0.1% 2-mercaptoethanol and Antibiotic-Antimitotic) at 37 °C in 5% CO2. Cells were then washed and maintained in complete media + 100IU/mL IL-2 at 37 °C in 5% CO2.

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions
Sequencing libraries were prepared using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria)
Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: 72h post-activation, cell cultures were treated with DMSO or 1uM palbociclib for 24h

tag: mouse strain

tag: culture & treatment protocol

value: T cells treated 72h post-activation and analysed 96h post-activation

tag: drug

value: Palbociclib 1uM

tag: cell type

value: OTI CD8+ T cells


title: CD8+ T Rb1-KO-DMSO 24h_rep 3 [12_RNAseq_in_vitro_mouse_rb_and_thy]

source_name: Mouse CD8+ T cells CD3/28-activated in vitro

growth_protocol: CD8+ T cells were isolated from C57BL/6 spleens and electroportated with CRISPR/sgRNA (control or RB1-targeting) and then activated with anti-CD3 (0.5 mg/mL) and anti-CD28 (0.5 mg/mL) in the presence of IL-2 (100 IU/mL) for 48 h at 37 °C in 5% CO2

treatment_protocol: 48h post-activation, cells were treated with DMSO, 2mM thymidine or 1uM palbociclib for 24h

value: T cells treated 48h post-activation and analysed 96h post-activation

value: Dimethyl Sulfoxide (DMSO) (Vehicle)

value: CD8+ T cells


title: OTI CD8+ T DMSO 24h_rep 3 [13_RNAseq_in_vitro_mouse]


title: OTI CD8+ T Palbo 24h_rep 3 [13_RNAseq_in_vitro_mouse]


title: CD8+ T Rb1-KO-Palbo 24h_rep 1 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T Rb1-KO-Palbo 24h_rep 3 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T Rb1-KO-Palbo 24h_rep 2 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: OTI CD8+ T Palbo 24h_rep 2 [13_RNAseq_in_vitro_mouse]


title: OTI CD8+ T DMSO 24h_rep 2 [13_RNAseq_in_vitro_mouse]


title: CD8+ T Rb1-KO-DMSO 24h_rep 2 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-Thy 24h_rep 1 [12_RNAseq_in_vitro_mouse_rb_and_thy]

value: Thymidine 2mM


title: CD8+ T WT-Palbo 24h_rep 3 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: OTI CD8+ T DMSO 24h_rep 1 [13_RNAseq_in_vitro_mouse]


title: CD8+ T WT-Thy 24h_rep 3 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-Palbo 24h_rep 1 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-Palbo 24h_rep 2 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-DMSO 24h_rep 2 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-Thy 24h_rep 2 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T Rb1-KO-DMSO 24h_rep 1 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-DMSO 24h_rep 3 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: CD8+ T WT-DMSO 24h_rep 1 [12_RNAseq_in_vitro_mouse_rb_and_thy]


title: HER2 CAR T DMSO 24h_rep 2 [11_RNAseq_in_vitro_mouse_HER2_CAR]

source_name: Mouse HER2 CAR T cells peptide-activated in vitro

growth_protocol: Splenocytes from C57BL/6 mice were activated with anti-CD3 (0.5 mg/mL) and anti-CD28 (0.5 mg/mL) in the presence of IL-2 (100 IU/mL) and IL-7 (2 ng/mL), followed by transduction with retrovirus encoding the CAR (comprised of an extracellular scFv specific for human HER2, a CD8 hinge region and transmembrane CD28 and CD3z domains)

value: HER2 CAR T cells


title: HER2 CAR T Palbo 24h_rep 3 [11_RNAseq_in_vitro_mouse_HER2_CAR]


title: HER2 CAR T DMSO 24h_rep 3 [11_RNAseq_in_vitro_mouse_HER2_CAR]


title: HER2 CAR T Palbo 24h_rep 2 [11_RNAseq_in_vitro_mouse_HER2_CAR]


title: HER2 CAR T DMSO 24h_rep 1 [11_RNAseq_in_vitro_mouse_HER2_CAR]


title: HER2 CAR T Palbo 24h_rep 1 [11_RNAseq_in_vitro_mouse_HER2_CAR]


title: MC38-OVA Vehicle_rep 3 [8_RNAseq_ex_vivo_mouse]

source_name: Tumor-infiltrating CD8+ T cells

growth_protocol: MC38-OVA cells were grown subcutaneously in C57BL/6 mice

extract_protocol:
Tumors were harvested, processed and FAC sorted for CD8+ T cells. Cells were sorted directly into TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions
Sequencing libraries were prepared using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria)
Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Mice were treated with palbociclib or corresponding vehicles for 7 days, administered daily by oral gavage, starting 3 days post-tumour inoculation

tag: tumor type

value: MC38-OVA subcut

tag: treatment

value: 50mM sodium lactate (vehicle) - 7 days

value: Tumor-infiltrating CD8+ T cells


title: OT-I CD8+ T cells Input [7_ChIPseq_in_vitro_mouse]

data_processing:
Bcl2fastq v2.17.1.14 was used for demultiplexing. The Fastq files generated by sequencing were aligned to the mouse reference genome (GRCm38/mm10) using bowtie (v2.2.3)
Samtools (v1.8) was used for manipulation of SAM and BAM files, after which MACS (v2.0.10) was used for peak calling.
Browser viewable TDF files were generated using IGVTools (v2.3.72) and ChIP-Seq tracks were visualized using IGV (v2.3.55)
Differentially accessible regions were quantitative analyzed using Rsubread featureCounts on merged reference bed file containing all peaks identified across treatment conditions after which the limma-voom package was used for statistical analysis of differentially accessible regions. Subsequently, = HOMER (v4.8.3) was used for motif analysis on MACS2 peak summits using FindMotifGenome.pl for differentially accessible regions using all summits as a background set with the -bg option.
ChIP-seq peaks were annotated to genes using the AnnotatePeaks.pl function after which R was used for visualization.
Genome_build: GRCm38

extract_protocol:
T cells were cross-linked with 2% formaldehyde for 10 minutes at room temperature and quenched with addition of 1.25M glycine. Cells were washed twice (5% BSA, 800g, 5min, 4˚C) and lysed in nuclear extraction buffer three times. Nuclei resuspended in sonication buffer and sonicated with a Covaris S220 sonicator (peak power, 105; duty factor, 20; cycle/burst, 200; duration, 600s). Samples were cleared by centrifugation at 12,000g for 20 min, and one volume of dilution buffer was added to cleared chromatin. 1% chromatin was taken as input. Immunoprecipitation was performed overnight at 4°C with rotation with 2µg anti-H3K27ac antibody (Abcam). Immunoprecipitated samples were captured by incubation with 20µl Dynabeads Protein G (Life Technologies) blocked with 0.1% BSA for 2 hours. Beads were then washed twice each with wash buffer 1, wash buffer 2, wash buffer 3 and TE buffer. DNA was eluted with 100µL elution buffer for 30 minutes twice and reverse crosslinked. DNA product was purified using Zymo ChIP DNA Clean and Concentrator Kit.
Libraries were generated using the NEBNext Ultra II DNA library prep kit from NEB. For sequencing, libraries were pooled and sequenced on a NextSeq 500 (Illumina) and 15 to 20 million single-end 50 bp reads were generated per sample.

treatment_protocol: 72h post-activation, cell cultures were treated with DMSO or 1uM palbociclib for 6h

value: T cells treated 72h post-activation and analysed 78h post-activation

tag: chip antibody


title: MC38-OVA Palbo_rep 1 [8_RNAseq_ex_vivo_mouse]

value: palbociclib 80mg/kg daily - 7 days


title: MC38-OVA Vehicle_rep 2 [8_RNAseq_ex_vivo_mouse]


title: MC38-OVA Vehicle_rep 1 [8_RNAseq_ex_vivo_mouse]


title: OT-I CD8+ T cells DMSO 6h_rep 1 [7_ChIPseq_in_vitro_mouse]


title: OTI CD8+ T cells Palbo 24h_rep 2 [6_ATACseq_in_vitro_mouse]

data_processing:
Bcl2fastq v2.17.1.14 was used for demultiplexing. The Fastq files generated by sequencing were aligned to the mouse reference genome (GRCm38/mm10) using bowtie (v2.2.3)
Samtools (v1.8) was used for manipulation of SAM and BAM files, after which MACS (v2.0.10) was used for peak calling.
Browser viewable TDF files were generated using IGVTools (v2.3.72)
Differentially accessible regions were quantitative analyzed using Rsubread featureCounts on merged reference bed file containing all peaks identified across treatment conditions after which the limma-voom package was used for statistical analysis of differentially accessible regions. Subsequently, = HOMER (v4.8.3) was used for motif analysis on MACS2 peak summits using FindMotifGenome.pl for differentially accessible regions using all summits as a background set with the -bg option.
ATAC-seq peaks were annotated to genes using the AnnotatePeaks.pl function after which R was used for visualization.
Genome_build: GRCm38

extract_protocol:
Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4).
Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C. Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an Ilumina NextSeq 500 with 75 bp single-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 700 bp using a Pippin Prep system (Sage Science).


title: OTI CD8+ T cells Palbo 24h_rep 1 [6_ATACseq_in_vitro_mouse]


title: OTI CD8+ T cells Palbo 24h_rep 3 [6_ATACseq_in_vitro_mouse]


title: MC38-OVA Palbo_rep 3 [8_RNAseq_ex_vivo_mouse]


title: OTI CD8+ T cells DMSO 24h_rep 2 [6_ATACseq_in_vitro_mouse]


title: OTI CD8+ T cells DMSO 24h_rep 3 [6_ATACseq_in_vitro_mouse]


title: OTI CD8+ T cells DMSO 24h_rep 1 [6_ATACseq_in_vitro_mouse]


title: MC38-OVA Palbo_rep 2 [5_ATACseq_ex_vivo_mouse]

extract_protocol:
Tumors were harvested, processed and FAC sorted for CD8+ T cells. Sorted cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4).
Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C. Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an Ilumina NextSeq 500 with 75 bp single-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 700 bp using a Pippin Prep system (Sage Science).


title: MC38-OVA Vehicle_rep 1 [5_ATACseq_ex_vivo_mouse]


title: MC38-OVA Palbo_rep 1 [5_ATACseq_ex_vivo_mouse]


title: MC38-OVA Vehicle_rep 2 [5_ATACseq_ex_vivo_mouse]


title: OTI CD8+ T cells sc-seq - HTO [04_in_vitro]

data_processing:
Cell Ranger: Reads were aligned to the Mm10 reference genome, cellular barcodes were de-multiplexed and unique molecular identifiers (UMI) and Hashtag oligos (HTO)) were quantified using 10x Genomics' Cell Ranger software (version 3.1.0). Cell barcodes containing RNA or antibody counts from cells from more than one sample (inter-sample doublets) were identified using Seurat's HTODemux function. Barcodes containing counts from more than one cell within the same sample (intra-sample doublets) were identified using the Scrublet python package (version 0.2.1) . A cutoff of more than one median absolute deviation (MAD) value above the median Scrublet score was chosen. Cells identified as either type of doublet were removed from the analysis. Relative transcription factor activity in each cell was estimated using the Single-Cell Regulatory Network Inference And Clustering (SCENIC) method. Area-under-curve (AUC) scores for transcription factors were calculated based on inferred gene regulatory networks using the pyscenic python package (version 0.9.19). Gene expression and antibody count matrices were processed in R (version 3.6.1) using the Seurat R package (version 3.1.0) . RNA transcript counts for barcodes identified as cells by Cell Ranger were normalized using sctransform via Seurat's SCTransform function. The counts were first transformed with no covariates in the sctransform model then cell cycle phase scores were estimated using Seurat's CellCycleScoring function with mouse homologues of the cell cycle gene sets provided by Seurat. The sctransform normalization was then rerun with the cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell as variables to be regressed out in the model. Principal component analysis (PCA) was then performed on the sctransform scaled RNA expression values for genes with residual variance in the sctransform model greater than 1.3. A shared-nearest-neighbours (SNN) network was calculated using the top 10 principal components using the FindNeighbors function with k-nearest neighbors set to 50 and cosine distance metric. The SNN network was then used to identify cell populations using the FindClusters function using the Louvain algorithm with resolution parameter 0.6. Uniform Manifold Approximation and Projection (UMAP) values were also calculated using the RunUMAP function with the top 10 principal components as input and parameters n.neighbors=50 and metric="cosine".
Genome_build: mm10

growth_protocol: Splenocytes from C57BL/6.OT-I transgenic mice were cultured with 10 nM SIINFEKL plus 100 IU/mL IL-2 for 72 hrs in complete media (RPMI 1640 plus 20 mM HEPES containing 10% FBS, 1% GlutaMAX, 1 mM Sodium Pyruvate, 1 mM MEM Non-Essential Amino Acids, 0.1% 2-mercaptoethanol and Antibiotic-Antimitotic) at 37 °C in 5% CO2. Cells were then washed and maintained in complete media + 100IU/mL IL-2 at 37oC in 5% CO2.

extract_protocol:
Cells were labelled with HTO, followed by droplet encapsulation for single cell sequencing using 10xGenomics platform
All samples were prepared using the 10x Genomics Single Cell 3′ v3 protocol according to the manufacturer’s instructions up until the cDNA amplification step (10x Genomics, USA). Two picomoles of HTO additive oligonucleotides were spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3 protocol (10x Genomics, USA). Following cDNA amplification, 0.6X SPRI was used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from Cell Hashtag (HTO)-containing fraction (in supernatant). The cDNA fraction was processed according to the 10x Genomics Single Cell 3′ v3 protocol to generate the transcriptome library; indexing was done using Chromium i7 Multiplex Kit. An additional 1.4X reaction volume of SPRI beads was added to the HTO fraction to bring the ratio up to 2.0X. The beads were washed with 80% ethanol, eluted in water, and an additional round of 2.0X SPRI performed to remove excess single-stranded oligonucleotides from cDNA amplification. After final elution, separate PCRs were set up to generate the HTO library (SI-PCR and D7xx_s).

tag: sample (oligo barcode)

value: DMSO (hash#3_CTTGCCGCATGTCAT); Palbociclib 1uM (hash#4_AAAGCATTCTTCACG)


title: OTI CD8+ T cells sc-seq - GEX [04_in_vitro]


title: OT-I CD8+ T cells Palbo 6h_rep 1 [7_ChIPseq_in_vitro_mouse]


title: OT-I CD8+ T cells DMSO 6h_rep 2 [7_ChIPseq_in_vitro_mouse]


title: OT-I CD8+ T cells Palbo 6h_rep 2 [7_ChIPseq_in_vitro_mouse]


title: OTI CD8+ T cells sc-seq - GEX [03_in_vivo]

growth_protocol: Splenocytes from C57BL/6-Ptprc.OT-I transgenic mice were cultured with 10 nM SIINFEKL plus 100 IU/mL IL-2 for 72 hrs in complete media (RPMI 1640 plus 20 mM HEPES containing 10% FBS, 1% GlutaMAX, 1 mM Sodium Pyruvate, 1 mM MEM Non-Essential Amino Acids, 0.1% 2-mercaptoethanol and Antibiotic-Antimitotic) at 37 °C in 5% CO2. Cells were then washed and maintained in complete media + 100IU/mL IL-2 at 37oC in 5% CO2 before transferring into congenic C57BL/6 mice.

extract_protocol:
30 days after transfer of DMSO- or palbociclib-pretreated OT-I T cells, spleens were harvested from recipient mice, processed and FAC sorted to isolate trasnferred cells. Isolated cells were then labelled with HTO, followed by droplet encapsulation for single cell sequencing using 10xGenomics platform
All samples were prepared using the 10x Genomics Single Cell 3′ v3 protocol according to the manufacturer’s instructions up until the cDNA amplification step (10x Genomics, USA). Two picomoles of HTO additive oligonucleotides were spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3 protocol (10x Genomics, USA). Following cDNA amplification, 0.6X SPRI was used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from Cell Hashtag (HTO)-containing fraction (in supernatant). The cDNA fraction was processed according to the 10x Genomics Single Cell 3′ v3 protocol to generate the transcriptome library; indexing was done using Chromium i7 Multiplex Kit. An additional 1.4X reaction volume of SPRI beads was added to the HTO fraction to bring the ratio up to 2.0X. The beads were washed with 80% ethanol, eluted in water, and an additional round of 2.0X SPRI performed to remove excess single-stranded oligonucleotides from cDNA amplification. After final elution, separate PCRs were set up to generate the HTO library (SI-PCR and D7xx_s).

treatment_protocol: 72h post-activation, cell cultures were treated with DMSO or 1uM palbociclib for 24h, immediately before transfer into congenic C57BL/6 mice


title: MC38-OVA sc-seq - HTO [01_mouse_TIL]

data_processing:
Cell Ranger: Reads were aligned to the Mm10 reference genome, cellular barcodes were de-multiplexed and unique molecular identifiers (UMI) and antibody capture (Antibody Derived Tags (ADT) and Hashtag oligos (HTO)) were quantified using 10x Genomics' Cell Ranger software (version 3.1.0). Cell barcodes containing RNA or antibody counts from cells from more than one sample (inter-sample doublets) were identified using Seurat's HTODemux function. Barcodes containing counts from more than one cell within the same sample (intra-sample doublets) were identified using the Scrublet python package (version 0.2.1) . A cutoff of more than one median absolute deviation (MAD) value above the median Scrublet score was chosen. Cells identified as either type of doublet were removed from the analysis. Relative transcription factor activity in each cell was estimated using the Single-Cell Regulatory Network Inference And Clustering (SCENIC) method. Area-under-curve (AUC) scores for transcription factors were calculated based on inferred gene regulatory networks using the pyscenic python package (version 0.9.19). Gene expression and antibody count matrices were processed in R (version 3.6.1) using the Seurat R package (version 3.1.0) . RNA transcript counts for barcodes identified as cells by Cell Ranger were normalized using sctransform via Seurat's SCTransform function. The counts were first transformed with no covariates in the sctransform model then cell cycle phase scores were estimated using Seurat's CellCycleScoring function with mouse homologues of the cell cycle gene sets provided by Seurat. The sctransform normalization was then rerun with the cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell as variables to be regressed out in the model. Principal component analysis (PCA) was then performed on the sctransform scaled RNA expression values for genes with residual variance in the sctransform model greater than 1.3. A shared-nearest-neighbours (SNN) network was calculated using the top 10 principal components using the FindNeighbors function with k-nearest neighbors set to 50 and cosine distance metric. The SNN network was then used to identify cell populations using the FindClusters function using the Louvain algorithm with resolution parameter 0.6. Uniform Manifold Approximation and Projection (UMAP) values were also calculated using the RunUMAP function with the top 10 principal components as input and parameters n.neighbors=50 and metric="cosine". Monocle3 was utilized for pseudotime analysis using default setting.
Genome_build: mm10

source_name: Tumor-infiltrating T cells

extract_protocol:
Tumors were harvested, processed and FAC sorted for TCRB+CD3+CD90.2+CD11b- cells followed by ADT and HTO tagging and droplet encapsulation for single cell sequencing using 10xGenomics platform
All samples were prepared using the 10x Genomics Single Cell 3′ v3 protocol according to the manufacturer’s instructions up until the cDNA amplification step (10x Genomics, USA). Two picomoles of HTO and ADT additive oligonucleotides were spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3 protocol (10x Genomics, USA). Following cDNA amplification, 0.6X SPRI was used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from the ADT- and Cell Hashtag (HTO)-containing fraction (in supernatant). The cDNA fraction was processed according to the 10x Genomics Single Cell 3′ v3 protocol to generate the transcriptome library; indexing was done using Chromium i7 Multiplex Kit. An additional 1.4X reaction volume of SPRI beads was added to the ADT/HTO fraction to bring the ratio up to 2.0X. The beads were washed with 80% ethanol, eluted in water, and an additional round of 2.0X SPRI performed to remove excess single-stranded oligonucleotides from cDNA amplification. After final elution, separate PCRs were set up to generate the CITE-seq ADT library (SI-PCR and RPI-x primers) and the HTO library (SI-PCR and D7xx_s).

treatment_protocol: Mice were treated with palbociclib or the corresponding vehicle for 7 days, administered daily by oral gavage

value: MC38-OVA subcutaneous

tag: target/sample (oligo barcode)

value: Vehicle_1 (ACCCACCAGTAAGAC); Vehicle_2 (GGTCGAGAGCATTCA); Palbociclib 80mg/kg_1(CTTGCCGCATGTCAT); Palbociclib 80mg/kg_2 (AAAGCATTCTTCACG)

value: Tumor-infiltrating T cells


title: MC38-OVA sc-seq - ADT [01_mouse_TIL]

value: PD1 (GAAAGTCAAAGCACT); Tim3 (ATTGGCACTCAGATG); CD4 (AACAAGACCCTTGAG ); CD8 (TACCCGTAATAGCGT )


title: Experiment2_sample11

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

description: Experiment 2

data_processing:
experiment1 and 2: 75bp single-end reads were generated on Illumina's NextSeq500 sequencer and checked for data quality using FastQC (Babraham Institute, Cambridge, UK). The samples were sequenced at ~20 million reads per sample.
experiment1: transcript abundance estimated by mapping the reads to mouse genome build mm10 using salmon v0.7.2, and were used in obtaining differentially expressed genes using Bioconductor package DESeq2.
experiment2: Reads were aligned to mouse genome build GRCm38 using STAR v2.5.2a and  gene abundance was estimated using HTSeq Count v0.11.0. Raw gene counts were then used to get differentially expressed genes using Bioconductor package DESeq2 v1.20.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: experiment1: transcripts per million values for each sample (comma-separated text file); differentially expressed genes from DESeq2 (Excel file)
Supplementary_files_format_and_content: experiment2: raw gene counts per sample (Excel file); transcripts per million values for each sample (comma-separated file); differentially expressed genes from DESeq2 (Excel file)

source_name: Liver tissue

extract_protocol:
Total RNA was isolated from liver tissue fragments in Trizol Reagent (Thermo) according to the manufacturer's instructions.
RNA was prepared into RNAseq libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Cat. #E7760) following the manufacturer’s recommended protocol. The libraries were then PCR amplified 15 cycles using barcoded PCR primers, purified and size selected using AMPure XP Beads before loading onto an Illumina NextSeq500 for 75 base single read sequencing. A total of >20 million "passed filter" reads were obtained for each of the samples.

value: 2 months

tag: tissue

value: liver

tag: genotype

value: Unc93b-3d/3d Pld3-/-Pld4-/- ("UNCPLD3PLD4 KO")


title: MC38-OVA sc-seq - GEX [01_mouse_TIL]


title: Experiment2_sample10

description: Experiment 2

tag: age


title: Experiment2_sample9

description: Experiment 2


title: Experiment2_sample12

description: Experiment 2


title: Experiment2_sample8

description: Experiment 2


title: Experiment2_sample7

description: Experiment 2


title: Experiment2_sample6

description: Experiment 2


title: Experiment2_sample5

description: Experiment 2


title: OTI CD8+ T cells sc-seq - HTO [03_in_vivo]

value: T cells treated 72h post-activation and analysed 96h post-activation

value: DMSO (hash#1_CCCACCAGTAAGAC); Palbociclib 1uM (hash#2_GGTCGAGAGCATTCA)

value: OTI CD8+ T cells


title: Experiment2_sample4

description: Experiment 2


title: Experiment1_sample12

description: Experiment 1

value: 2 weeks

value: Pld3-/-Pld4-/-  ("PLD3PLD4 KO")


title: Experiment2_sample3

description: Experiment 2


title: Experiment2_sample1

description: Experiment 2


title: Experiment2_sample2

description: Experiment 2


title: Experiment1_sample8

description: Experiment 1


title: Experiment1_sample6

description: Experiment 1


title: Experiment1_sample7

description: Experiment 1


title: Experiment1_sample9

description: Experiment 1


title: Experiment1_sample5

description: Experiment 1


title: Experiment1_sample4

description: Experiment 1


title: Experiment1_sample2

description: Experiment 1


title: Experiment1_sample3

description: Experiment 1


title: Experiment1_sample1

description: Experiment 1


title: Treated tumor draining LN mouse #1

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The raw reads in fastq format was processed using 10X genomics cellranger pipelines by mkfastq and output clusters with globally distinqushing genes by count per sample
Treatment and control samples were combined using cellranger aggr command.
The cellranger pipeline outputs containing the upregulated cell marker genes from the aggregated analysis were imported into Loupe Cell Browser to generate UMAP plots.
Genome_build: mm10

source_name: Single cells from tumor draining lymph node

growth_protocol: B16F10 tumors were implanted bilaterally in the upper anterior thigh.

extract_protocol:
Two days after the day of cyclophosphamide, tumor-draining inguinal LNs were harvested from all mice, mechanically disaggregated, passed through 40 um mesh strainer, and washed 4 times with PBS + 1% BSA.  Cells were processed for scRNAseq libraries using the Chromium Controller (10X Genomics).
scRNAseq libraries were generated for approximately 2,000 cells per sample using 10X 3’ single cell mRNAseq V3 reagents.  The scRNAseq libraries were sequenced using Illumina NextSeq500 sequencer to collect approximately 80k reads per cell.  Each cell was tagged with a Unique Molecular Identifier (UMI) sequence, which represents the identity of each single cell throughput the analysis pipeline.

treatment_protocol: On day 9, the treatment group (2 mice) were begun on oral indoximod (2 mg/ml in drinking water) and daily ibrutinib (350 ug i.p).  On day 10, these mice received cyclophosphamide 150 mg/kg i.p.  The control group (2 mice) received no treatment.

value: Lymph node

tag: strain


title: Control tumor draining LN mouse #1

value: Control


title: epithelial cells of crypts from young mice

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

data_processing:
Fastq files quality check was performed using FastQC v0.11.5. The fastq files were mapped to the mm9 genome using TopHat v2.1.036 with the following parameters --bowtie1 --no-coverage-search -a 5. The number of reads covered by each gene is calculated by HTSeq-Count 0.11.237 with -s no -a 0 -t exon -m intersection-nonempty parameters. Before further analysis, all of the rRNA genes are removed from the count data. For calculating differentially expressed genes and normalized count, DESeq2 R package v1.20.038 was used with the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data is the expression matrix (raw counts) with genes in row (first column is the gene names) and samples in columns (first row is the sample id) normalized by DESeq2

source_name: Epithelial cells from small intestine of wild-type mice

growth_protocol: Young (10-15 weekw) and old (85-115 weeks) wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility. Organods were cultured for 2 weeks in vitro.

extract_protocol:
Small intestine crypts were isolated using the established protocol (Chazaud, B. & Mouchiroud, G. Inflamm-aging: STAT3 Signaling Pushes Muscle Stem Cells off Balance. Cell Stem Cell 15, 401–402 (2014).) with minor modifications. Briefly, mouse small intestine was dissected, washed in cold PBS and opened longitudinally. Villi were removed by scraping with a coverslip. The villi-free intestinal pieces (2 cm) were washed four times in cold PBS and transferred to 5mM EDTA/PBS, followed by two 30-min incubations at 4°C on a rotator. The tissue was transferred to fresh cold PBS and manually shaken for 30 sec. The crypt solution was filtered using a 70 μm cell strainer and centrifuged at 120xg for 5 min at 4°C. The crypts pellet was resuspended in 1 ml of cold PBS and evaluated for purity microscopically. Isolated crypts were aliquoted, snap frozen in liquid nitrogen and stored at -80°C for further experiments. For RNA isolation, the crypts were immediately resuspended in QIAzol Lysis Reagent (Qiagen) and stored at -80°C.
PolyA amplification was applied.  In brief, 50 to 500 ng of total RNA were depleted of ribosomal RNA using the Ribo-ZeroTM Gold Kit H/M/R Kit (illumina) following manufacturer’s instructions. Ribo-depleted RNA was resuspended in 17 μl of EFP buffer (illumina), heated to 94°C for 8 min, and used as input for first strand synthesis, using the TruSeqTM RNA Library Preparation Kit v2 (illumina) following manufacturer’s instructions.

treatment_protocol: For the Lgr5-eGFP ISCs isolation, the villi-free intestinal pieces (2 cm) were incubated in 5mM EDTA/PBS on ice for 45 min. The tissue was then shaken vigorously for 1 min, the crypt solution was filtered through a 100 μm cell strainer and centrifuged at 300xg for 5 min at 4°C. The crypts were dissociated with the mixture of 18 ml TrypLE Express, 2 ml of 10X DNase I Buffer (100 mM Tris HCl pH 7.5, 25 mM MgCl2, 5 mM CaCl2) and 1 ml DNase I (10 mg/ml) for 30 min at 37°C with brief vortexing every 10 min.

value: Epithelial cells

tag: sample type

value: Crypts

value: young


title: epithelial cells of crypts from old mice

value: old


title: Experiment1_sample11

description: Experiment 1


title: old_male_organoids_aboral_replication2

description: Processed_NormalizedCountsByDESeq2_bulkRNAseq.csv

value: Organoids

tag: gender

value: male


title: old_male_organoids_aboral_replication4


title: Experiment1_sample10

description: Experiment 1


title: old_male_organoids_aboral_replication1


title: old_male_organoids_inter_replication4


title: old_male_organoids_inter_replication3


title: old_male_organoids_oral_replication4


title: ckit_pos.2

data_processing:
Demultiplexing with Bcl2fastq2 were employed to generate the fastq file for each sample.
The RNAseq analysis was performed on Galaxy main server (usegalaxy.org). Adaptor and quality trimming of the raw sequencing reads was performed using Trim Glore! v0.6.3. Trimmed reads were aligned to mm10 reference genome using STAR v2.75.
Reads mapped to annotated features were counted using featureCounts (Galaxy v1.6.3).
The DEseq2 v1.18.1 implemented in Galaxy (v2.11.40.2) was used to normalize the raw accounts and identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count table in csv format

source_name: FACS-sorted Ly6c+c‑kit+ precursor cells

growth_protocol: B16F10 tumors were implanted bilaterally in the upper anterior thigh of C57BL/6 mice.

extract_protocol:
Cells were isolated by rapid mechanical disaggregation of TDLNs from established (day 14) untreated B16F10 tumors.  LNs were pooled and stained for CD11c, Ly6c and c kit, then the CD11cNEGLy6c+c kit+ precursor population was sorted and used for RNA-seq.Total RNA was isolated using TRIzol reagent.
The RNA-seq libraries were constructed using 8 ng of total RNA with SMARTer Stranded Total RNA-seq kit v2-Pico Input library preparation kit (TaKaRa Bio).

treatment_protocol: Mice received no treatment.

tag: surface markers

value: Tumor draining lymph node


title: ckit_pos.1


title: ckit_pos.3


title: old_male_organoids_inter_replication1


title: old_female_organoids_aboral_replication3

value: female


title: old_male_organoids_oral_replication1


title: old_male_organoids_oral_replication3


title: old_male_organoids_oral_replication2


title: Treated tumor draining LN mouse #2


title: old_female_organoids_aboral_replication2


title: Control tumor draining LN mouse #2


title: old_female_organoids_aboral_replication1


title: old_male_organoids_aboral_replication3


title: old_female_organoids_inter_replication2


title: old_female_organoids_inter_replication4


title: old_female_organoids_inter_replication1


title: old_female_organoids_inter_replication3


title: old_male_organoids_inter_replication2


title: old_female_organoids_oral_replication4


title: old_female_organoids_oral_replication3


title: old_female_organoids_oral_replication2


title: young_male_organoids_aboral_replication4


title: young_male_organoids_aboral_replication3


title: young_male_organoids_inter_replication1


title: young_male_organoids_inter_replication3


title: old_female_organoids_aboral_replication4


title: young_male_organoids_aboral_replication2


title: young_male_organoids_oral_replication4


title: old_female_organoids_oral_replication1


title: young_male_organoids_inter_replication4


title: young_male_organoids_oral_replication2


title: young_male_organoids_inter_replication2


title: young_male_organoids_oral_replication1


title: young_female_organoids_aboral_replication3


title: young_female_organoids_aboral_replication2


title: young_female_organoids_aboral_replication4


title: young_female_organoids_inter_replication4


title: young_female_organoids_aboral_replication1


title: young_female_organoids_inter_replication2


title: young_female_organoids_oral_replication3


title: young_female_organoids_oral_replication4


title: young_male_organoids_aboral_replication1


title: young_female_organoids_inter_replication3


title: young_female_organoids_oral_replication2


title: young_female_organoids_inter_replication1


title: old_male_crypts_aboral_replication4


title: young_female_organoids_oral_replication1


title: old_male_crypts_aboral_replication1


title: old_male_crypts_inter_replication3


title: old_male_crypts_aboral_replication2


title: old_male_crypts_inter_replication4


title: old_male_crypts_inter_replication1


title: old_male_crypts_oral_replication4


title: old_male_crypts_inter_replication2


title: old_female_crypts_aboral_replication2


title: old_male_crypts_oral_replication2


title: old_female_crypts_aboral_replication4


title: old_male_crypts_oral_replication3


title: old_female_crypts_inter_replication4


title: old_female_crypts_aboral_replication3


title: old_male_crypts_oral_replication1


title: old_female_crypts_inter_replication1


title: old_female_crypts_inter_replication3


title: old_female_crypts_inter_replication2


title: old_male_crypts_aboral_replication3


title: old_female_crypts_oral_replication2


title: old_female_crypts_oral_replication4


title: old_female_crypts_oral_replication1


title: old_female_crypts_oral_replication3


title: young_male_crypts_aboral_replication4


title: young_male_crypts_aboral_replication3


title: young_male_crypts_aboral_replication1


title: young_male_crypts_aboral_replication2


title: young_male_crypts_inter_replication4


title: young_male_crypts_oral_replication4


title: old_female_crypts_aboral_replication1


title: young_male_crypts_inter_replication1


title: young_male_crypts_inter_replication3


title: young_male_organoids_oral_replication3


title: MC38-OVA Palbo_rep 2 [8_RNAseq_ex_vivo_mouse]

value: MC38-OVA subcut

value: palbociclib 80mg/kg daily - 7 days

value: Tumor-infiltrating CD8+ T cells


title: young_male_crypts_oral_replication2


title: young_male_crypts_oral_replication3


title: young_male_crypts_oral_replication1


title: young_female_crypts_aboral_replication2


title: young_female_crypts_aboral_replication4


title: young_female_crypts_aboral_replication3


title: young_female_crypts_inter_replication4


title: young_female_crypts_oral_replication4


title: young_female_crypts_inter_replication2


title: young_female_crypts_aboral_replication1


title: young_female_crypts_inter_replication1


title: young_female_crypts_oral_replication2


title: young_female_crypts_oral_replication1


title: young_female_crypts_oral_replication3


title: low inoculum, day 3, dog 2

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
Gene-level expression quantification was performed using RSEM v1.3.0
Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <2 samples.
Standard differential expression was performed using the R package edgeR
Genome_build: CanFam3.1
Supplementary_files_format_and_content: raw expression (expected count generated from RSEM

organism: Canis lupus familiaris

source_name: whole venous blood

growth_protocol: Six purpose bred male beagles were born and raised in the Onderstepoort Veterinary Animal Research Unit. The animals were all microchipped, vaccinated and dewormed according to international guidelines and neutered at 6 months of age. Stringent ectoparasite control was applied by means of the isolation of the housing facility and 3 monthly dosing with an isooxazoline compound. All dogs were proven to be free of any blood borne parasites by PCR and reverse line blot. All dogs were housed communally in a play enriched environment and socialized with animal care givers each day. They were trained through a food reward system to become accustomed to being held for blood collection and blood pressure monitoring on a daily basis for several months before the beginning of the experiment.

extract_protocol:
Blood from each subject was collected into Tempus Blood RNA Tubes. RNA was isolated using Qiagen RNeasy Mini Kit.
Sequencing libraries were produced using the TruSeq Stranded mRNA kit

tag: breed

value: beagle

tag: Sex

tag: dose

value: low


title: low inoculum, day 8, dog 2


title: low inoculum, day 6, dog 2


title: low inoculum, day 4, dog 2


title: low inoculum, day 0, dog 2


title: young_male_crypts_inter_replication2


title: low inoculum, day 6, dog 1


title: low inoculum, day 1, dog 2


title: low inoculum, day 1, dog 1


title: low inoculum, day 0, dog 1


title: low inoculum, day 4, dog 1


title: low inoculum, day 3, dog 1


title: young_female_crypts_inter_replication3


title: high inoculum, day 3, dog 3

value: high


title: high inoculum, day 0, dog 3


title: low inoculum, day 0, dog 0


title: high inoculum, day 1, dog 3


title: high inoculum, day 8, dog 2


title: high inoculum, day 6, dog 2


title: high inoculum, day 4, dog 2


title: high inoculum, day 1, dog 2


title: high inoculum, day 0, dog 2


title: high inoculum, day 3, dog 2


title: high inoculum, day 6, dog 1


title: high inoculum, day 4, dog 1


title: low inoculum, day 8, dog 1


title: high inoculum, day 8, dog 1


title: patentalOf10umCadmiumReRep.Rep2

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

data_processing:
Fastq files were aligned to HG38 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged and the final file was turned into a bigwig
Genome_build: HG38
Supplementary_files_format_and_content: bigwig

organism: Homo sapiens

growth_protocol: MDA-MB-231 female breast cancer cell line were maintained at 37°C in Dulbecco’s Modified Essential Medium (DMEM) with 10% FB essence (VWR), 1% penicillin/streptomycin, and L-glutamine.

extract_protocol:
Rerep-seq was performed as described in . Briefly, In an 8 strip PCR tube 1 – 5 ug high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with a glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from Stratalinker followed by addition of 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37°C. The digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes; mixed with 10X loading dye then run on 0.8% agarose gel for 15 minutes. The fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System with the purified DNA eluted in 50uL nuclease free water.  Sequencing libraries were constructed using the Illumina Nextera DNA Flex Library Prep Kit (catalog number 20018704) following the manufacturers’ protocol and using 14 cycles of amplification for final library construction. Libraries were constructed using dual index barcodes from the Nextera DNA CD Indexes (catalog number 20018707).
Rerep-seq

treatment_protocol: Cadmium-resistant cell (MDA-MB-231cadR) cell lines were selected by passage in medium containing CdSO4. The CdSO4 concentration was increased by increments of 5-25 μM after 10 passages at the current concentration and when cell count increased at least 1.8 times average daily over at least four passages consistently. Cells used in this study were adapted to CdSO4 containing medium for 7 months up to 75 μM CdSO4.

tag: cell line

value: 10uM cadmium resistant


title: high inoculum, day 1, dog 1


title: high inoculum, day 0, dog 1


title: high inoculum, day 3, dog 1


title: 10umCadmium.ReRep.Rep1


title: patentalOf10umCadmiumReRep.Rep1


title: 10umCadmium.ReRep.Rep2


title: CSF-0823-B1-2_combined_TAACTCCG single cell from patient 3_1

city: Shanghai

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

description:
Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs)
P3_1.csv
CSF-0823-B1-2_TAACTCCG

data_processing:
Sequenced reads were mapped to hg38 using the STAR (version 2.7; https://github.com/alexdobin/STAR) with the default parameters
Genome_build: hg38
Supplementary_files_format_and_content: gene count

molecule: polyA RNA

source_name: cerebrospinal fluid

extract_protocol:
Antibody (CD45, CD3, CD19, BD Biosciences) and labeling dye for live cells (Calcein Blue AM, Life Technologies, CA) were used per manufacturer recommendations
Library for isolated single cell was generated by SMART-Seq2 method
SMART-Seq2 method

value: cerebrospinal fluid

tag: disease

value: CNSL-DLBCL


title: 121

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
Adapter sequences were removed using cutadapt (adapter sequence : AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Trimmed reads were aligned to the human genome (hg19) with bismark (using bowtie) (parameters :   -q --phred33-quals -n 1 -l 35 -k 2 --best --chunkmbs 1024)
Information on each citosine was extracted with bismark_methylation_extractor
Citosines in the top 1% most highly covered were removed to avoid including PCR duplicates in the calculations.
Citosines with a read coverage of less than 5 were removed as their signal is unreliable when calculating methylation percentages
Citosines on positions with SNPs were removed using BisSNP and dbsnp v.138 (-toCoverage 50000 -nt 8 -C CG,1 -C CHH,1 -C CHG,1 |  -C CG,1 -C CHH,1 -C CHG,1 -maxCov 50000 -minSNPinWind 2 -windSizeForSNPfilter 10)
Genome_build: hg19
Supplementary_files_format_and_content: tabulation separated table containing the methylation ratio and read coverage over each specified citosine. Only citosines with a coverage of 5 or more reads in at least one sample were kept.
The column headers for the processed data file are included in a separate file available on the series record.

source_name: Post-mortem nucleus accumbens

extract_protocol:
20 mg of frozen nucleus accumbens tissue was homogenized and DNA was extracted using Qiagen DNA MiniKits.
RRBS libraries were prepared from 1ug genomic DNA using MspI digestion, end-repair and adapter ligation before bisulfite conversion.

value: Brain

tag: group

value: Case

tag: ethnicity

value: HispanicCaucasian

tag: post mortem interval

tag: tissue ph

tag: smoker status

value: Non-smoker

tag: alcohol present at death

value: no


title: 122

tag: tissue

value: male


title: 120

tag: age


title: 115

value: Control


title: ARPKD2

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

description: Antibody Capture

data_processing:
The read count files were obtained by aligning fastq files to human transcriptome (Build GRCh38) using cellranger
For antibody captured experiment, assign cells to samples using cellranger
cell identities were demuxleted by demuxlet
The read count matrice and cell identities were feeded into Seurat to get seurat object
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat object contained all count data with full metadata annotation

source_name: control + ARPKD

growth_protocol: For production of primary HO, iPSCs were dissociated to single cells in buffer with 5 mM EDTA and 10 mM Y-27632 (Santa Cruz Biotechnology, Dallas, Texas), and were re-aggregated in low-cell-adhesion 60 mm dishes (Corning) in endoderm differentiation medium (105 cells/dish) containing 10 mM Y-27632. The endoderm differentiation medium consisted of DMEM/F12 + ITS (GIBCO) supplemented with 0.1 mM nonessential amino acids and 1 mM pyruvate. On days 0 to 3, Activin-A (100 ng/ml) and BMP4 (10 ng/ml) were added the definitive endoderm differentiation medium. For endoderm patterning and for the generation of foregut spheroids, Matrigel (BD Biosciences, GFR) was added to RPMI + B27 medium to a final v/v concentration of 2% from days 3 to 9. From days 3 to 6, 50 ng/ml FGF10 (Peprotech) was added to the medium. From days 6 to 9, 10 ng/ml FGF10 and 10 ng/ml BMP4 were added to the medium. After day 9, Matrigel (final 1% v/v concentration) was added to the organoid growth and differentiation medium (HCM, Lonza), which was supplemented with HGF (50 ng/ml), 50-ng/ml oncostatin M and 10 μM Dexamethasone (Sigma, St. Louis MO).  On day 20, the organoids were collected and re-seeded for further differentiation and characterization.

extract_protocol:
The HO cultures were placed in a 1 ml solution containing 1 mg/ml collagenase and 1 mg/mg dispase (Worthington-Biochem, Lakewood, NJ), and then incubated for 15 to 30 minutes at 37°C with shaking. The cells were further dispersed by gentle pipetting with a fire-polished glass pipette, and then filtered through a 40 μm cell strainer (PluriSelect, San Diego, CA). The single cell suspension was visually inspected under a microscope, cells were counted using a Scepter™ 2.0 Handheld Automated Cell Counter (EMD çMillipore, Burlington, MA), and then resuspended in PBS with 0.01% BSA. Single cells were captured in droplets with barcoded beads using the 10x Genomics Chromium system (Pleasanton, CA).
For comparison at  primary HO stage, Control and ARPKD Cellular suspensions (1x106/ml) were then loaded onto the  twon 10× Chromium instrument (10× Genomics); and were then sequenced according to the manufacturer’s instructions. 3 ARPKD and 3 control organoid samples were separately sequenced on two lanes of an Illumina HiSeq2500 Rapid Mode instrument, yielding 889M total reads (Contrl=C24 and ARPKD=P42). For compare differentiation trajectory between control and ARPKD, cells from 6 groups sampels including: iPSC (C1, C2 and C3), HB (C1, C2 and C3), HOs (C1, C2 and C3), iPSC (M1, M2 and M3), HB (M1, M2 and M3), HOs (M1, M2 and M3), were barcoded by total 6 cell hashing antibodies according to the manufacturer’s protocol (BioLegend TotalSeq™). Then, the pooled cells were captured using two 10x Single Cell 3' Reagent Kit v3 runs; and sequenced on two lanes of an Illumina HiSeq2500 instrument, which yielded 660 M total reads that covered 10,000 cells in total.

treatment_protocol: Hepatic organoids were prepared from each of the control iPSC lines (C1, C2, and C3) and from the corresponding iPSC with the PKDH1 M36 mutation (M1, M2 and M3). Single cells from iPSC (day 0), day 9 HB and day 21 HO cultures were captured in droplets with barcoded beads using the 10x Genomics Chromium system (Pleasanton, CA).

tag: differentiation stage

value: iPSC+HB+HO

tag: cell id at each stage

tag: subject

tag: multiplex

value: hashing+demuxlet


title: P42

source_name: ARPKD

value: demuxlet


title: ARPKD1

description: Antibody Capture


title: 109

value: Caucasian

value: Smoker


title: 111


title: 113


title: 107


title: 105


title: 101


title: 103


title: AF

city: Linköping

first: Johan

last: Junker

state: Östergötland

address: KEF 09

department: Clinical and Experimental Medcine

country: Sweden

institute: Linköping University

hyb_protocol: according to Affymetrix protocols for U133 plus 2 (GPL570) using Affymetrix Hybridization Oven 640 and GeneChip Fluidics Station 450

scan_protocol: according to Affymetrix protocols for U133 plus 2 (GPL570) using Affymetrix GeneChip Scanner 3000

data_processing: RMA using CARMAWeb online, MvA analysis passing equivalent of |M|>1, A>3, comparing groupwise and saving genesets for enrichment/overrepresentation analysis in ENRICHr and WebGestalt online.

label: biotin

source_name: Primary keratinocytes pooled duplicate cultures

growth_protocol: Human primary keratinocytes expanded in KSFM with EGF and BPE to passage three (1:3 split per passage)

extract_protocol: Trypsinized cells, pooled duplicates, RNA isolation using RNeasy kit (Qiagen)

treatment_protocol: Starved in DMEM only for 12h, then given experimental media for another 24h before extraction (amniotic fluid 50% in DMEM, FCS 50% in DMEM, or DMEM alone)

tag: medium

value: Amniotic fluid, 50% in DMEM


title: 99

tag: Sex


title: 97


title: WT replicate 3 Raffinose

city: Toronto

first: Micheal

last: Tyers

state: Ontario

address: 555 University Avenue

institute: The Hospital for Sick Children

data_processing:
Reads were aligned using Bowtie2.2.5, with default parameters, to all Ensembl transcripts . Alignments with fewer than 2 inserted or deleted bases and a maximum edit distance of 5 (i.e. the sum of inserted, deleted, or mismatched bases) were counted to generate read counts per transcript.
Read counts from different sequencing lanes for the same sample were summed.
Genome_build: R64
Supplementary_files_format_and_content: Raw read counts per gene

organism: Saccharomyces cerevisiae

growth_protocol: WT and GAL-NRS1 strains were inoculated overnight in SC media with 2% raffinose and grown at 30oC with shaking. Cells were then diluted in SC raffinose to an OD600 of 0.07-0.1 incubated at 30oC till reaching an OD600 of 0.15-0.2.

extract_protocol:
Cells were pelleted at 3500 r.p.m and disrupted using glass beads. The RNA was phenol/chloroform extracted and ethanol precipitated. DNase treatment (Qiagen) was performed.
Total RNA was quantified using Qubit (Thermo Scientific) and RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the Kapa RNA HyperPrep (Roche) using a Poly-A selection (Thermo Scientific).

treatment_protocol: A sample was collected for RNA extraction prior to galactose induction. Cells are collected through centrifugation, resuspended in 20ml SC+2% raffinose, and added to 200ml SC+2% galactose, time zero was collected immediately, cells were incubated at 30oC with shaking, and samples were collected following galactose induction at 30min, 60min, 120min, 240min, and 360min.

tag: strain

value: WT


title: WT replicate 3 galactose 30 minutes


title: WT replicate 3 galactose 4 hours


title: WT replicate 3 galactose 6 hours


title: WT replicate 3 galactose 2 hours


title: FCS

label_protocol: according to Affymetrix protocols for U133 plus 2 (GPL570)

value: Fetal Calf Serum, 50% in DMEM


title: WT replicate 3 galactose 1 hour


title: DMEM

value: DMEM


title: WT replicate 2 Raffinose


title: WT replicate 3 galactose 0 minutes


title: 93


title: 91


title: WT replicate 2 galactose 6 hours


title: 87


title: WT replicate 2 galactose 4 hours


title: C24

source_name: control


title: WT replicate 2 galactose 30 minutes


title: 95


title: 89


title: WT replicate 2 galactose 2 hours


title: 85


title: WT replicate 2 galactose 1 hour


title: WT replicate 1 Raffinose


title: 79


title: WT replicate 1 galactose 6 hours


title: 77


title: WT replicate 1 galactose 30 minutes


title: 73


title: 71


title: HpyA_stat_low_WCE3

city: Durham

first: Amy

last: Schmid

state: NC

address: 3242 French Family Science Center

institute: Duke University

data_processing:
Gzipped FASTQ files were assessed for quality using FastQC and adapter sequences trimmed using Cutadapt/Trim Galore.
Trimmed fastq files were aligned to the Halobacterium salinarum NRC-1 genome (GCF_000006805.1_ASM680v1) using Bowtie2. Samtools was used to generate and sort BAM files. Sorted BAM files were used for further analysis.
Peak-calling was done using MACS2 software on individual samples (qval cutoff 0.01, nomodel parameter used) and narrowPeak files with peak locations, enrichment, and q-values were generated.
WIG files were generated using the samtools mpileup command. Per-base count files were generated using bedtools genomecov.
Genome_build: GCF_000006805.1_ASM680v1
Supplementary_files_format_and_content: WIG file

organism: Halobacterium salinarum

growth_protocol: Colonies of AKS134 (Empty vector negative control) and KAD128 (HpyA-HA; 4 biological replicates) were pre-cultured in rich media for ~120 hrs and diluted to OD~0.02. Paired replicates were grown in optimal and reduced salt rich media (4.2M and 3.4M NaCl respectively) supplemented with Mevinolin 0.1ug/mL for plasmid maintenance. At exponential phase (OD600 ~0.2-0.35;36-50 hrs) and stationary phase, (OD600~1.4-1.7, ~70-140  hrs.), 45 mL cell pellets were harvested, crosslinked with formaledhyde, and frozen for immunoprecipitation.

extract_protocol:
Cells were crrosslinked and immunoprecipitated with HA antibody (ab9110) as described in Wilbanks et al 2012 (doi: 10.1093/nar/gks063) with the following changes to the protocol: the cross-linking reaction was allowed to proceed for 20 minutes rather than 10, and cell pellets were resupended in 800 μL lysis buffer instead of 1.6mL.
Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent) . Samples were pooled and run on an Illumina HiSeq 4000 (Duke Sequencing and Genomics Technologies core) for single-end sequencing. 1st batch contained all stationary phase samples and 2nd batch contained all exponential phase samples.

tag: genotype

tag: growthphase

value: Stationary

tag: epitope tag

value: HA

tag: cell type

value: archaeal cells

tag: antibody


title: HpyA_stat_low_WCE4


title: 75

value: Brain

tag: group

tag: ethnicity

tag: post mortem interval

tag: tissue ph


title: HpyA_stat_opt_WCE4


title: HpyA_stat_opt_WCE1


title: HpyA_stat_low_WCE1


title: 81

tag: tissue

tag: age

tag: smoker status

value: Non-smoker

tag: alcohol present at death


title: 69

value: no


title: HpyA_stat_opt_WCE2


title: WT replicate 1 galactose 1 hour


title: HpyA_stat_low_WCE2


title: WT replicate 2 galactose 0 minutes


title: HpyA_exp_opt_WCE4

value: Exponential


title: 67

value: Case

value: male

value: HispanicCaucasian


title: HpyA_exp_opt_WCE3


title: HpyA_exp_opt_WCE2


title: 65


title: 83

value: Control


title: HpyA_exp_opt_WCE1


title: NRS1 replicate 3 Raffinose


title: HpyA_exp_low_WCE4


title: WT replicate 1 galactose 4 hours


title: HpyA_exp_low_WCE3


title: 63


title: WT replicate 1 galactose 2 hours


title: HpyA_stat_opt_WCE3


title: 59


title: HpyA_exp_opt_IP3


title: 57


title: WT replicate 1 galactose 0 minutes


title: NRS1 replicate 3 galactose 6 hours


title: NRS1 replicate 3 galactose 4 hours


title: NRS1 replicate 3 galactose 2 hours


title: 53


title: HpyA_exp_opt_IP2


title: HpyA_exp_low_WCE2


title: HpyA_stat_opt_IP3


title: HpyA_exp_opt_IP4


title: HpyA_exp_opt_IP1


title: NRS1 replicate 3 galactose 30 minutes


title: NRS1 replicate 3 galactose 1 hour


title: 55


title: NRS1 replicate 3 galactose 0 minutes


title: HpyA_stat_opt_IP4


title: HpyA_exp_low_WCE1


title: HpyA_stat_low_IP4


title: NRS1 replicate 2 Raffinose


title: HpyA_stat_low_IP3


title: HpyA_stat_opt_IP1


title: HpyA_stat_low_IP2


title: HpyA_stat_low_IP1


title: 47


title: NRS1 replicate 2 galactose 6 hours


title: HpyA_stat_opt_IP2


title: HpyA_exp_low_IP4


title: HpyA_exp_low_IP3


title: NRS1 replicate 2 galactose 4 hours


title: HpyA_exp_low_IP2


title: 51


title: 45


title: HA_stat_low_WCE

source_name: archaeal cells_Δura3ΔhpyA/HA_Stationary


title: 41

value: Caucasian


title: HpyA_exp_low_IP1


title: 43


title: NRS1 replicate 2 galactose 30 minutes


title: 49


title: NRS1 replicate 2 galactose 2 hours


title: NRS1 replicate 2 galactose 1 hour


title: HA_exp_opt_WCE


title: HA_stat_opt_WCE


title: 39

value: Smoker


title: HA_stat_low_IP


title: NRS1 replicate 2 galactose 0 minutes


title: HA_exp_low_IP


title: 35


title: HA_stat_opt_IP


title: HA_exp_opt_IP


title: 37


title: Ddx54KD_rep3

city: Worcester

first: Thomas

middle: G

last: Fazzio

state: Massachusetts

address: 364 Plantation Street, Lazare Research Building -560E

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts medical school

data_processing:
Libraries were sequenced on BGISEQ-500 using 100-base paired-end sequencing. Basecalling was performed by Zebra call.
Sequencing reads were trimmed for adaptor sequences, and mapped to mm10 genome using RSEM with parameters -p 16 --paired-end
Differential analysis was performed by EBSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Genome mapping results including gene and transcript id, their length, expected count, TPM, FPKM.
Supplementary_files_format_and_content: Differential analysis results by EBSeq, including PPEE, PPDE, PostFC, RealFC.

source_name: Embryonic stem cell

growth_protocol: mESCs were maintained in tissue culture plates coated with 0.2% gelatin, at 37°C in 5% CO2, passaged every 2-3 days.

extract_protocol:
RNA was extracted using an RNA Clean & Concentrator-25 Kit with on-column DNase I treatment for 1 hr.
Libraries were prepared by BGI Genomics Company using oligo-dT capturing to enrich mRNA.

treatment_protocol: Knockdown was performed by mixing 400 ng small interfering RNA with 4 µL Lipofectamine 2000 and 2.8E5 cells, incubated for 16 hr and replaced with fresh media. Cells were harvested at 48 hr.

tag: treatment

tag: replicate


title: NRS1 replicate 1 Raffinose


title: 33

tag: Sex


title: NRS1 replicate 1 galactose 6 hours

tag: strain


title: 31


title: HA_exp_low_WCE

tag: genotype


title: NRS1 replicate 1 galactose 4 hours


title: 29


title: Ddx27KD_rep3


title: Ddx54KD_rep1


title: 27


title: V8_HJ7M2BBXX

city: San Diego

first: Amin

last: Haghani

address: 5510 Morehouse Dr

institute: Altos labs

description:
gene counts.csv
gene map.csv

data_processing:
Raw sequencing reads were quality checked with FastQC
adapter sequences were trimmed from the reads using Trimmomatic
Reads were aligned to the mm10 genome using the HISAT2 splice-aware aligner
alignments overlapping genes were counted using featureCounts version 1.5.0-p3 relative to Gencode version M11
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv files count values for each gene

source_name: Blood

extract_protocol:
Samples were homogenized and disrupted with pestles, 22-gauge needles, pipetting and QIA shredders (Qiagen #79654).  DNA was extracted using QIAzol (Qiagen #79306) from the organic layer for genotyping. RNA was extracted following the QIAGEN RNeasy plus universal protocol (Qiagen #73404). Extracted RNA was used to determine sex of mouse pups by qPCR for the Y-chromosome Sry gene.
RNA (600ng) was made into RNA-seq libraries using the Illumina RiboZero Gold library preparation kit and sequenced on an Illumina HiSeq 3000 sequencer at the Lieber Institute for Brain Development

treatment_protocol:
Prenatal transcriptome changes of air pollution were examined by exposing pregnant C57BL/6 dams to 300 mg/m3 nano-sized particulate matter (nPM) for 5 hr/day, 3 days/weeks beginning at gestational day 2 until birth.
A random number of 3 pups per sex of each group were euthanized at day 5 age for collection of blood and cerebral cortex

value: M

value: Blood

value: Unexposed

tag: age (days)

value: 3 to 5

tag: rin

tag: lane


title: V7_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: Exposed


title: 25


title: Ddx27KD_rep2


title: Ddx27KD_rep1


title: Specific pathogen-free mice [miRNA]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Colonic lamina propria mononuclear cells

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: Balb/c

value: Male

value: Colon


title: Germ-free mice [miRNA]


title: NRS1 replicate 1 galactose 1 hour


title: 19

value: Brain


title: NRS1 replicate 1 galactose 0 minutes


title: NRS1 replicate 1 galactose 2 hours


title: V5_HJ7M2BBXX

description:
gene counts.csv
gene map.csv


title: 17

value: no


title: Ddx24KD_rep3


title: V4_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: F


title: Ddx54KD_rep2


title: Ddx24KD_rep2


title: V3_HJ7M2BBXX

description:
gene counts.csv
gene map.csv


title: NRS1 replicate 1 galactose 30 minutes


title: 15

value: Case

value: Non-smoker


title: Ddx24KD_rep1


title: 13

value: male


title: Ddx10KD_rep3


title: RNA_K562 cells-AAVS1-pg1-rep3

city: LA

first: Zhiheng

last: Liu

address: 610 Charles E Young Dr S

institute: UCLA

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 (2.0.4)
Read Counts were generated by StringTie (1.3.5)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw reads for each transcript

source_name: K562 cells

growth_protocol: K562 cells were cultured in in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Biological Industries) and 1% penicillin/streptomycin.

extract_protocol:
The total RNA was extracted using RNeasy Mini Kit (QIAGEN 79254), and three replicates were arranged. 2 μg of total RNA was further used for the construction of sequencing libraries.
The RNA-seq libraries were prepared using the NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490S), NEBNext RNA First Strand Synthesis Module (NEB E7525S), NEBNext mRNA Second Strand Synthesis Module (NEB E6111S) and NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7370L).

treatment_protocol: K562 cells were transduced with the pgRNA AAVS1-pg1 by lentiviral infection at an MOI of < 1, then 2 million pgRNA-infected K562 cells were FACS-sorted 8 days post infection.

tag: cell line

value: pgRNA targeting AAVS1


title: V24_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

source_name: Cortex

value: Cortex


title: V2_HJ7M2BBXX

description:
gene counts.csv
gene map.csv


title: V6_HJ7M2BBXX

description:
gene counts.csv
gene map.csv


title: RNA_K562 cells-AAVS1-pg1-rep2


title: 11

tag: group

value: HispanicCaucasian

value: Smoker


title: RNA_K562 cells-AAVS1-pg1-rep1


title: Ddx10KD_rep2


title: 9

value: Control

tag: ethnicity

value: Caucasian


title: Hub_22_7_knockout_scRNAseq

description: Drop-Seq

data_processing:
FASTQ files were aligned by STAR to hg19 genome
single cell RNA-seq gene expression raw counts were identified by Drop-Seq pipeline published by McCarroll Lab (https://github.com/broadinstitute/Drop-seq/releases)
Genome_build: hg19
Supplementary_files_format_and_content: gene expression raw counts in .txt format

source_name: K562 Cells

growth_protocol: cells are maintained in RPMI 1640 medium supplemented with FBS (10% v/v) and pen/strep (1% v/v, Sigma-Aldrich P4333)

extract_protocol:
cells are lysed as single cell in the droplet, and poly A+ RNA is captured by oligo-dT on the beads
poly A+ RNA is reverse transcribed using Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV RT), then the cDNA is tagmented and amplified following Illumina Nextera DNA preparation kit

treatment_protocol: lentivirus expressing pgRNA is used to infect the cells, and the cells are sorted at day 8 post infection

value: hub-22-7 KO


title: 7

tag: post mortem interval


title: V23_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: M

value: Exposed

value: 3 to 5


title: 5

tag: tissue ph


title: V21_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

tag: tissue

value: Blood


title: EGFPKD_rep3

value: EGFPKD


title: Ddx10KD_rep1


title: V22_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: Unexposed


title: Worm_EnNonGliaInf_4

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. Cells were sorted directly into Trizol. Total RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies). A total of 7 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies). The libraries were then normalized to 2,5 nM, pooled and loaded onto a HiSeq4000 (Illumina) to generate 75bp single-end reads.

treatment_protocol: All mice were injected with tamoxifen on two consecutive days 10 days prior cell isolation and some mice were infected with H. poly 7 days prior cell isolation.

value: Small intestine tunica muscularis

tag: cell type

value: Tunica muscularis minus Enteric Glia

tag: age

value: Adult

tag: disease state

value: H. poly


title: Worm_EnNonGliaInf_2


title: Worm_EnNonGliaInf_3


title: EGFPKD_rep2

tag: treatment


title: Worm_EnNonGliaInf_1


title: 3

value: Brain

value: male

tag: smoker status

tag: alcohol present at death

value: no


title: V20_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

tag: Sex

value: F

value: Cortex

tag: strain


title: 1

value: Control

value: HispanicCaucasian

value: Smoker


title: KO2-2

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

description: differentaited cells at day 7 (sample2)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

source_name: SOX10 KO2 hiPSC-derived cells at day 7 (sample2)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

tag: genotype

value: SOX10 KO


title: KO2-1

description: differentaited cells at day 7 (sample1)

source_name: SOX10 KO2 hiPSC-derived cells at day 7 (sample1)


title: Worm_EnNonGliaCtrl_2

value: Naive


title: Worm_EnNonGliaCtrl_3


title: V19_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

tag: age (days)

value: 3 to 5

tag: rin


title: KO1-2

description: differentaited cells at day 7 (sample2)

source_name: SOX10 KO1 hiPSC-derived cells at day 7 (sample2)


title: V17_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: Blood

tag: lane


title: Worm_EnNonGliaCtrl_1


title: V16_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: M

value: Unexposed


title: EGFPKD_rep1

value: EGFPKD

tag: replicate


title: V15_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: Exposed


title: Worm_EnGliaInf_3

value: Small intestine tunica muscularis

value: Enteric Glia

value: Adult

value: H. poly


title: Worm_EnNonGliaCtrl_4

value: Tunica muscularis minus Enteric Glia


title: WT1-1

description: differentaited cells at day 7 (sample1)

source_name: control hiPSC-derived cells at day 7 (sample1)

value: WT


title: V14_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: Cortex


title: Worm_EnGliaInf_2


title: V1_HJ7M2BBXX

description:
gene counts.csv
gene map.csv

value: F


title: V18_HJ7M2BBXX

description:
gene counts.csv
gene map.csv


title: WT1-2

description: differentaited cells at day 7 (sample2)

source_name: control hiPSC-derived cells at day 7 (sample2)


title: Worm_EnGliaInf_5


title: Jurkat RB1-KO-Palbo 72h_rep 3 [10_RNAseq_in_vitro_Jurkat]

city: Melbourne

first: Emily

last: Lelliott

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (from the Subread package, v1.5.0) prior to differential gene expression analysis using Voom/Limma.
Gene set enrichment analyses were performed using GSEA software (Broad Institute) and barcode plots were plotted using ReplotGSEA.R (part of the Rtoolbox R package).
Genome_build: Hg19

source_name: Jurkat cell line

growth_protocol: Jurkat cells were cultured in RPMI 1640 containing 10% FBS and 1% GlutaMAX

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions
Sequencing libraries were prepared using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria)
Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Cell cultures were treated with DMSO or 1uM palbociclib for 72h

tag: drug

value: Palbociclib 1uM

tag: treatment time

tag: cell line

value: Jurkat