title: Mouse pool 4 : cTEC knockout


title: Mouse pool 5 : mTEChi knockout

status: Public on Dec 21 2021

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Read-pairs were aligned to the mm10 genome using Rsubread version 1.24.1.
Read-pairs were counted for each Entrez Gene ID using Rsubread's featureCounts function and Rsubread's inbuilt mm10 gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with four columns. Columns give Entrez Gene ID, gene symbol, gene length and read count respectively. The supplementary file GenewiseCounts.txt.gz consolidates the read counts for all the samples into one file.

molecule: total RNA

organism: Mus musculus

source_name: Thymic epithelial cells

extract_protocol:
RNA from sorted TEC subsets was isolated using the microRNeasy Micro Kit (Qiagen) with on-column DNase digestion according to manufacturer’s instructions.
First strand cDNA synthesis and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) according to the manufacturer’s instructions. Complementary DNA (cDNA) libraries were prepared and indexed separately using the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s instructions. The indexed sample libraries were pooled and diluted to 1.5pM for 75 base paired-end sequencing on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per the manufacturer’s instructions.

tag: background mouse strain

tag: genotype

value: Kat7 knockout

tag: mouse pool

tag: anatomical location

value: medullary

tag: mhcii level

value: high


title: Mouse pool 2 : mTEChi wildtype

value: Wildtype


title: Mouse pool 2 : mTEClo wildtype

value: low


title: Mouse pool 3 : mTEChi wildtype


title: Mouse pool 2 : cTEC wildtype

value: cortical


title: eWATsaline rep1

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

data_processing:
Quality control, quality and adapter trimming of RNA-seq libraries were performed with Trim Galore version 0.6.4_dev (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were aligned with Rsubread version 2.6.2
Low counts genes were filtered with DEseq2 version 1.32.0
Differential expression analysis was performed with edgeR version 3.34.0
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file

source_name: mouse epididymal white adipose tissue

extract_protocol:
RNA was extracted using TRIzol (Invitrogen)
PolyA mRNA librairies were prepared from 200ng of total RNA using a NEB E6420 kit, according to the manufacturer's recommendations. Quality of the libraries was evaluated on a Bionalyzer DNA HS Chip (Agilent) and quantified using a Qubit fluorimeter (Invitrogen). The libraries were then pooled and sequenced on Illumina Nextseq500, PE40

treatment_protocol: mice were acclimated to 3 subcutaneous (s.c.) injections, distributed each 3 days, during 10 days of chow diet. For mice exposed to the GIP analogue, injections consisted of 2 pre-injections of saline followed by 1 sensitizer dose of (D-Ala2)GIP[Lys37PAL]. HFD was next introduced for 2 weeks during which mice received a total of 5 s.c. injections of saline or (D-Ala2)GIP[Lys37PAL] at 2 pmol/kg. Mice were then sacrificed and iWAT and eWAT dissected.

tag: tissue

value: eWAT

tag: treatment

value: saline

tag: strain

value: High Fat Diet introduced for 2 weeks


title: Mouse pool 1: mTEClo wildtype


title: Mouse pool 1: cTEC wildtype


title: Mouse pool 1: mTEChi wildtype


title: WM-3825 treated replicate 2

data_processing:
Read-pairs were aligned to the mm10 genome using Rsubread version 1.32.2.
Read-pairs were counted for each Entrez Gene ID using Rsubread's featureCounts function and Rsubread's inbuilt mm10 gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with four columns. Columns give Entrez Gene ID, gene symbol, gene length and read count respectively. The supplementary file GenewiseCounts.txt.gz consolidates the read counts for all the samples into one file.

source_name: Thymic epithelial cells from fetal thymic organ cultures

growth_protocol: Thymic lobes were harvested from E15.5 embryos and cultured in 1.35 mM 2’-deoxyguanosine (2dGuo) (Sigma-Aldrich) in FTOC medium for 4-5 days to deplete thymocytes. Thymic lobes were then transferred to fresh FTOC medium containing 10 micrograms/mL agonist anti-RANK antibody (R&D Systems) for 3 days to induce AIRE expression.

extract_protocol:
RNA from sorted TECs was isolated using the microRNeasy Micro Kit (Qiagen) with on column DNase digestion according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. The indexed sample libraries were pooled and diluted to 1.5pM for 75 base paired-end sequencing on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per the manufacturer’s instructions.

value: wildtype


title: WM-3825 treated replicate 3


title: slful_SFIM2

status: Public on Dec 22 2021

city: Wageningen

first: Xiaobing

last: Jiang

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

data_processing:
Barcoded libraries were pooled and sequenced on a NovaSeq platform (150 nt paired end reads).
Before mapping of the reads to the Solanum lycopersicum genome, raw reads were trimmed by removing adapter sequences.
Reads were mapped to the Solanum lycopersicum genome version 4.0 with RNA-Seq analysis package CLC Genomics Workbench 11 (www.clcbio.com).
Parameters mapping: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no.
Genome_build: Solanum lycopersicum genome version 4.0
Supplementary_files_format_and_content: xlsx (raw counts, flod change and p-value)

organism: Solanum lycopersicum

source_name: meristem

growth_protocol: Tomato plants were grown under normal greenhouse conditions.

extract_protocol:
Each sample (30-60 meristems) was disrupted with stainless steel beads and RNA was extracted using the InviTrap Spin Plant RNA Mini Kit (Stratec).
DNAse-treated RNA was used as template for RNA-seq library preparation (TruSeq RNA Library Prep Kit).

value: meristem

value: slful

tag: developmental stage

value: SFIM


title: MT1-CD43+CD34+CD38-Lin--3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing was done using the NextSeq 500/550 High Output Kit v2 (75 Cycles) (Illumina)
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 and Samtools --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.4a) and RSeQC (v2.6.4)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

organism: Homo sapiens

source_name: human iPSC derived CD43+CD34+CD38-Lin- hematopoietic progenitor cells

growth_protocol: For iPSCs, ReproCELL supplemented with bFGF at 37 ºC in a humidified incubator with 5% CO2. For hematopoietic differentiation, iPSCs were suspended in StemPro-34 media supplemented with glutamine, monothioglycerol, transferrin, and ascorbic acid. Cytokines and a chemical compound were utilized as follows during differentiation: on days 0-1, hBMP4 and Y27632; on days 1-4, hBMP4, hbFGF; on days 4-8, hVEGF, hbFGF, hIL-6, hIL-3, hIL-11, hSCF, and hFlt3L; and on days 8-15, hVEGF, hIL-6, hIL-3, hIL-11, hSCF, hFlt3L, hEPO; 4U/mL, and hTPO. For erythroid differentiation, FACS-sorted CD43+CD34+ iPSC-derived HPCs on day15 were plated onto OP9 cells and cultured and maintained with alpha-Minimum Essential Medium supplemented with 10% fetal calf serum, glutamine, monothioglycerol, transferrin, and ascorbic acid. The cytokines or chemical compound used during the differentiation were as follows: on days 15-20, hSCF, hFlt3L, hEPO, and hTPO; on days 20-27, hSCF and hEPO; and on days 27-34, hEPO and sodium ferrous citrate.

extract_protocol:
RNeasy Micro Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

tag: cell type

tag: differentiation stage

value: mutant type

tag: sorting method

value: FACS CD43+CD34+CD38-Lin- sorting


title: DMSO treated replicate 1

value: DMSO


title: WM-3825 treated replicate 1


title: DMSO treated replicate 2


title: DMSO treated replicate 3


title: Control replicate 3

value: control

value: tamoxifen


title: Kat7 knockout replicate 1

value: Kat7 knockout


title: Control replicate 1


title: Kat7 knockout replicate 3


title: Control replicate 2


title: Knockout replicate 1 (ko1)

data_processing:
Read pairs were aligned to the mm10 genome using Rsubread version 1.32.2.
Read-pairs were counted for each gene promoter region using Rsubread's featureCounts function. Promoter regions were defined using Rsubread's promoterRegions() function and Rsubread's inbuilt RefSeq annotation as 3kb upstream to 2kb downstream of each Entrez Gene transcription start site. Putative promoter regions were not extended past the end of the gene or outside the relevant chromosome, so for very short genes the promoter region can be less than 5kb in width.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with seven columns. Columns give Entrez Gene ID, chromosome, start and end genomic locations of the promoter region, strand, gene symbol and read count respectively. The supplementary file GenewiseCounts.txt.gz consolidates the read counts for all the samples into one file.

source_name: MHCII-high medullary thymic epithelial cells

extract_protocol:
DNA was prepared and extracted as described by  Corces et al "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues" (Nature methods 2017). DNA was cleaned using the Zymo DNA Clean and Concentrator-5 Kit (Zymo) according to the manufacturer’s instructions.
ATAC-seq libraries were prepared as described by Corces et al (2017).


title: Knockout replicate 3 (ko3)


title: Knockout replicate 2 (ko2)


title: Wildtype replicate 3 (wt3)


title: Wildtype replicate 1 (wt1)


title: Wildtype replicate 2 (wt2)


title: Tri-4-T_PD1-/KLRG1-

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

country: USA

institute: Pfizer

data_processing:
Sequencing alignment and gene expression quantification was performed using OmicSoft ArraySuite software. DESeq2 (v1.26.0) was used for differential gene analysis.
Supplementary_files_format_and_content: counts

source_name: tumor

extract_protocol: TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 106 cells were stained using viability dye and fluorescently labeled mouse anti-CD45, anti-CD3, anti-CD8, anti-PD-1, anti-KLRG1 antibodies to sort 4 different CD8+ T cells populations based on PD-1 and KLRG1 expression (+ or -)  using the FACSAria II cell sorter.

value: Tri

tag: facs sorted groups


title: Tri-5-T_PD1-/KLRG1-


title: Tri-3-T_PD1-/KLRG1-


title: Tri-2-T_PD1-/KLRG1-


title: Tri-4-T_PD1-/KLRG1+


title: Tri-2-T_PD1-/KLRG1+


title: Tri-3-T_PD1-/KLRG1+


title: Tri-1-T_PD1-/KLRG1-


title: Tri-1-T_PD1-/KLRG1+


title: Tri-2-T_PD1+/KLRG1-


title: Tri-3-T_PD1+/KLRG1-


title: Kat7 knockout replicate 2


title: Tri-1-T_PD1+/KLRG1-


title: Tri-3-T_PD1+/KLRG1+


title: Tri-4-T_PD1+/KLRG1+


title: Iso-3-T_PD1-/KLRG1-

value: Iso


title: Tri-4-T_PD1+/KLRG1-


title: Tri-1-T_PD1+/KLRG1+


title: Tri-2-T_PD1+/KLRG1+


title: Tri-5-T_PD1+/KLRG1+


title: Iso-2-T_PD1-/KLRG1+


title: Iso-3-T_PD1-/KLRG1+


title: Iso-1-T_PD1-/KLRG1-


title: Iso-4-T_PD1-/KLRG1+


title: Axin1/Trp53 mutant organoids sample 1

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 to produce 75bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Rsubread version 2.2.2.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation. At least 22 million read pairs were assigned for each sample. Read counts from the two batches of sequencing were summed together for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: mammary gland

growth_protocol: Organoids were cultured as described by Jamieson, P.R., Dekkers, J.F., Rios, A.C., Fu, N.Y., Lindeman, G.J., and Visvader, J.E. (2017). Derivation of a robust mouse mammary organoid system for studying tissue dynamics. Development 144, 1065-1071.

extract_protocol:
Total RNA was extracted.
Illumina TruSeq RNA v2 sample preparation protocol (100 ng RNA as input).

value: BALB/c

value: Axin1/Trp53 mutant


title: Prkar1a/Trp53 mutant organoids sample 2

value: Prkar1a/Trp53 mutant


title: Axin1/Trp53 mutant organoids sample 2


title: Tri-5-T_PD1+/KLRG1-


title: Axin1/Trp53 mutant organoids sample 3


title: Prkar1a/Trp53 mutant organoids sample 3


title: Trp53 mutant organoids sample 3

value: Trp53 mutant


title: Prkar1a/Trp53 mutant organoids sample 1


title: Trp53 mutant organoids sample 1


title: Iso-2-T_PD1-/KLRG1-


title: Iso-4-T_PD1-/KLRG1-


title: MDcell-LS+ACEidiet-rep2

city: Los Angeles

first: Janos

last: Peti-Peterdi

address: 1501 San Pablo Street

institute: University of Southern California

data_processing:
Raw sequencing reads were trimmed based on the quality score (Phred QC>=20, min read length=25 nt)
Trimmed reads were mapped to mouse genome build mm10 using Star 2.61 (Dobin et al. 2013) with default parameter settings and Gencode M21 mouse transcriptome annotation (Mudge JM and Harrow J 2015)
Gencode M21 was then used to quantify the aligned reads to genes using Partek E/M method
Gene level read counts in all samples were normalized using Upper Quartile normalization (Bullard et al. 2010) and subjected to differential expression analysis using Partek Gene Specific Analysis method (genes with fewer than 10 aligned reads in any sample among a data set were excluded)
Genome_build: MM10
Supplementary_files_format_and_content: raw gene counts in tab deliminated txt file with gene on rows and sample on columns.

source_name: kidney cortex-LS+ACEi diet

growth_protocol: C57BL6 nNos CreERT2-mTmG (MD-GFP) animals were raised in animal facilities according to protocol approved by the Institutional Animal Care and Use Committee at the University of Southern California.

extract_protocol:
MD cells (green) and control cells (intense red) were isolated by FACS. Cells were extracted using Qiagen miRNeasy purification kit following manufacturer's protocol for total RNA purification (Qiagen cat#217004)MD-GFP mice on C57BL6/J background were generated by intercrossing nNOS/CreERT2 and mTmG/fl mice resulting in membrane-targeted eGFP expression in MD cells (green), and membrane-targeted tdTomato expression in all other kidney cell types (red). The highest tdTomato expressing cells were collected as controls representing epithelial cells from distal tubule-collecting duct tubule segments.
Libraries were simultaneously prepared using Takara's SMARTer Stranded Total-RNA Pico v2 library preparation kit following manufacturer's protocol (Takara cat#634412).

treatment_protocol: Animals were given either control diet or low salt diet (TD 90228, Harlan Teklad, Madison, WI) combined with ACE inhibitor treatment using enalapril (150 mg/L via drinking water, purchased from Sigma, St. Louis, MO). After 14 days of treatment kidney cortex was digested, MD and control cells were FACS sorted based on their genetic fluorescent labeling for RNA extraction.

tag: genetic model

value: LS+ACEi diet


title: Controlcell-controdiet-rep4

source_name: kidney cortex-control diet

value: Control diet


title: MDcell-control-rep2


title: Controlcell-LS+ACEidiet-rep4


title: H113N_YFH1-off_Rep5

first: Siavash

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

data_processing:
FASTQ file quality check using FastQC. Read 1 of the paired-end reads used for downstream analyses.
Adapter sequences, and low quality reads trimmed using Cutadapt (very small percentage of total reads)
Genomic alignment using HISAT2. Strand-specific alignment.
Assignment to open reading frames and counting using featureCounts. Strand-specific assignment.
Differential expression analysis performed with DESeq2, with strain (WT, H113N, YFH1-off, H113N YFH1-off) and batch (rep2, rep3, rep4, rep5) as variables in the design formula.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Cell

growth_protocol: YFH1-off cells on YPG were inoculated into SC medium at OD600 = 1 and grown for 36 hours in a 30°C shaker, diluting to OD600 = 1 every 12 hours. After 36 hours, cells were diluted once more to OD600 = 1 in SC for a further 8 hours (44 hours total).

extract_protocol:
RNA was extracted from whole yeast cells using hot acid phenol, followed by a further phenol-cholorform extraction and ethanol precipitation.
Prior to preparing RNA-seq libraries for Illumina NovaSeq sequencing, contaminating DNA was digested using Turbo DNase (Thermo Fisher). RNA quality was then visually assessed by running on a 1% agarose gel to confirm that minimal degradation had occurred. RNA-sequencing libraries were prepared with the KAPA mRNA Hyper Prep kit (KAPA Biosystems), according to the manufacturer’s protocols. RNA-seq libraries were assessed for correct fragment size and the presence of adapter dimers buy running on a 1% agarose gel. Average library sizes of ~270 bp were generated. Libraries were pooled for multiplexed sequencing and further purified using KAPA Pure beads. Total DNA concentration was adjusted to 10 nM for Illumina sequencing.

value: H3H113N p(GAL1)-YFH1


title: Controlcell-controdiet-rep3


title: Controlcell-controdiet-rep2


title: H113N_YFH1-off_Rep3


title: MDcell-control-rep1


title: Iso-1-T_PD1-/KLRG1+


title: WT_YFH1-off_Rep5


title: Controlcell-LS+ACEidiet-rep2


title: H113N_YFH1-off_Rep2


title: H113N_YFH1-off_Rep4


title: Controlcell-LS+ACEidiet-rep1


title: MDcell-LS+ACEidiet-rep1


title: Controlcell-controdiet-rep1


title: WT_YFH1-off_Rep3


title: H113N_Rep5


title: Trp53 mutant organoids sample 2


title: WT_YFH1-off_Rep2


title: WT_YFH1-off_Rep4


title: H113N_Rep4


title: Untreated-1

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Paired-end reads were aligned against reference genome mm9 with STAR (version 2.6.1a), using default parameters and allowing maximum fragment length to be 2000bp. Only properly paired primary aligned pairs were retained for downstream analysis, which were filtered with SAMtools (version 1.7). Alignment BAM files were converted to BED files and mitochondria reads were removed with BEDtools (version 2.27.1). Bedgraph files were generated also with BEDtools and each library were normalized to 10 million reads for visualization.
Read count for each RefSeq gene was quantified with featureCounts (version 1.6.2) using default parameters. Differential expression analysis was performed with R (version 3.6.2) and packages DESeq2 (version 1.26.0). GO analysis of selected gene sets were performed with R package clusterProfiler (version 3.14.3).
Genome_build: mm9
Supplementary_files_format_and_content: Read count for each gene in each library

source_name: Mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were grown in standard MEF media: 2mM GlutaMAX, 10% fetal bovine serum (FBS). Reprogramming iPSCs were maintained on Mito-C feeder cells and cultured in DMEM supplemented with 15% heat-inactivated FBS, 2mM GlutaMAX, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, 1x Pen/Strep, and 1000U/mL ESGRO recombinant mouse LIF. Reprogramming iPSCs were supplemented with 1 µM PD0325901, 3 µM CHIR99021, and 2 µg/mL doxycycline. MEFs and reprogramming iPSCs were kept in a low (5%) oxygen 37˚C incubator for improved cell growth and survival.

extract_protocol:
Total RNA from untreated MEFs or reprogramming day 5 cells was extracted using the RNeasy Mini Kit (QIAGEN)
Total RNA (4 µg) extracted from reprogramming day 5 cells was processed for RNA-seq using a KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s protocol, with the following alterations. For step 3.1, mRNA was fragmented at 85˚C for 6 min to generate 301-400 bp fragments. For step 8, indexing was performed using a KAPA Single-Indexed Adaptor Kit (Roche), with 8 cycles of library amplification. All purification steps were completed using Ampure XP beads (Beckman). Sequencing libraries were prepped in two sets, with the RNA in each set randomized. Prior to sequencing, each library was analyzed with a Bioanalyzer High-Sensitivity DNA chip (Agilent) and KAPA Library Quantification Kit (Roche) to establish library quality. Libraries were sequenced on an Illumina NextSeq 500 using 75 bp paired-end sequencing (40 x 40 cycles).

treatment_protocol: Retroviral media was collected from PLAT-E cells 48 and 72 hrs after pMXs vector transfection and filtered through a 0.45-µm PES filter. Primary Tet2-/- OKSM; rtTA MEFs (seeded 48 hrs prior at a density of 5 x 104 cells / well on 6-well plates) were incubated for 24 hrs with 200 µL of retroviral solution and 1.8 mL MEF media, supplemented with 4 µg/mL polybrene (American Bio). Following two rounds of infection, cells were seeded on Mito-C-treated MEF feeder cells at a density of 5 x 103 cells / well on 6-well plates. After 24 hrs, the retrovirus-transduced MEFs were moved into iPSC media (2i/LIF+Dox) to initiate reprogramming. Cell media was changed every day for the duration of reprogramming.

tag: strain background

tag: age

value: embryonic day 12.5 (e12.5)

tag: isolation

tag: genotype/variation

value: MEF-control


title: Untreated-2


title: Untreated-100


title: H113N_Rep3

tag: genotype


title: H113N_Rep2


title: Controlcell-LS+ACEidiet-rep3


title: WT_Rep5

value: Wild type


title: WT_Rep4


title: Tet2-WT-2


title: Tet2-WT-1


title: Tet2-WT-250


title: WT_Rep2


title: Tet2-E-2


title: WT_Rep3


title: Tet2-E-250


title: Uninjected

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

data_processing:
Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0
Alignment, filtering, barcode counting, and UMI counting was done using cellranger count; version 4.0.0
Samples were aggregated and normalized using cellranger aggr; version 4.0.0
Genome_build: custom_GRCz11_reporters
Supplementary_files_format_and_content: Filtered feature barcode matrix

organism: Danio rerio

source_name: Endothelial Cells, HSPCs

growth_protocol: Embryos were maintained in E3 embryo medium until 52 hpf

extract_protocol:
Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin-EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized, dissociation was stopped with addition of 800 ml of DMEM-10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL.
Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions
scRNA-seq

treatment_protocol: Control samples were not injected (uninjected) and treated samples were injected with 4 ng of vegfc MO at the one-cell stage

value: Uninjected

value: 52 hours post fertilization


title: Tet2-E-1


title: Tet2-E-100


title: pMXs-2


title: pMXs-250


title: Vegfc MO

value: Vegfc MO


title: T4

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

country: China

institute: The Second Hospital of Shandong University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: LncRNA_Expression_Profiling.xlsx: Excel file includes counts and FPKMs; number of raw junction reads.

source_name: Lung adenocarcinoma patients

extract_protocol:
Serum isolated from coagulation‐promoting vacuum tubes within 2 hours was immediately transferred to a 1.5 mL Eppendorf tube and immediately centrifuged at 1500 g for 5 minutes and then 13800 g for 5 minutes at 4°C to eliminate cell sediments. ExoQuick™ solution (EXOQ5A‐1; SBI System Biosciences, USA) was mixed evenly with supernatant according to the manufacturer's instructions. Subsequently, incubate at 4°C for 30 minutes, followed by centrifuged twice at 4°C (1500g, 30 minutes and 1500g, 5 minutes), supernatants were discarded, and the exosome pellets were resuspended in 250 μL PBS and stored at −80°C for further analysis. Total exosomal RNA was extracted from miRNeasyMicro Kit (Qiagen) according to the manufacturer’s instructions.
Briefly, rRNAs were removed from total RNA using Ribo-Zero rRNA Removal Kits (Illumina, USA) according to the manufacturer’s instructions. Subsequently, rRNA-depleted RNAs were used to constructed RNA libraries with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA). BioAnalyzer 2100 system (Agilent Technologies, USA) was performed to control the quality and quantified.
Libraries mentioned above were denatured as single-stranded DNA molecules, after captured on Illumina flow cells, amplified as clusters and finally sequenced on Illumina HiSeq Sequencer for 150 cycles.

tag: diagnosis

value: Lung adenocarcinoma

tag: sample type

value: Serum exosomes


title: T1


title: T2Dd5wt3

library_source: genomic

data_processing:
ATAC-seq reads were aligned using Bowtie2 (Langmead and Salzberg 2012) (default parameters, paired-end mode). Duplicate reads were removed using SAMTools (Li et al. 2009) (function: rmdup), along with mitochondrial reads and reads in blacklist regions. Bedgraph files normalized to reads per million (RPM) were prepared using BEDTools (Quinlan and Hall 2010) (function: genomecov; parameters: -bg -scale 1000000/READ_COUNT), and then converted to Bigwig tracks for UCSC browser visualization (Kent et al. 2010; http://genome.ucsc.edu).
Peak calling was performed using macs2 (Zhang et al. 2008) (function: callpeak; parameters: -f bed -g mm --qvalue 0.01 --bdg --SPMR) (function: bdgcmp -c control_lambda -m subtract).
Genome_build: mm9
Supplementary_files_format_and_content: Narrow peak files called by macs2.

molecule: genomic DNA

extract_protocol:
Post-FACS cells were applied directly to the Fast-ATAC optimized ATAC-seq workflow (Corces et al. 2016), with the following modifications. Cells were washed 1x in MEF media, and then 75,000 cells were resuspended in 1 mL warm RPMI media (Gibco). Following a 5 min spin at 4˚C (500 x g), cells were washed with 1 mL ATAC-RSB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 + 0.1% Tween), and then resuspended in TDE1 transposase solution (Illumina) + 0.01% digitonin. The transposase mix was incubated at 37˚C with shaking for 30 mins, after which the transposed DNA was purified using a MinElute Reaction Cleanup Kit (QIAGEN).
Transposed fragments were amplified for 8 cycles using indexed primers according to Buenostro et al 2015, and then purified by AMPure XP bead selection (Beckman Coulter). ATAC libraries were quantified using the NEBNext Library Quant Kit (NEB) and assayed using a Bioanalyzer High Sensitivity DNA chip (Agilent) to establish library quality. Pooled libraries were sequenced on an Illumina NextSeq 500 using a High Output Kit v2.5 (75 cycles) (Illumina).

value: SSEA1-RFP flow sorting

value: Mouse embryonic fibroblasts

value: Tet2-WT transduced (iPSC Day 5)


title: T3


title: T2Dd5wt4


title: T2


title: H5

source_name: Healthy controls

value: Healthy


title: T2Dd5wt2


title: H4


title: T2Dd5wt1


title: H1


title: H2


title: H3


title: T2Dd5pmxs4

value: Empty vector transduced (iPSC Day 5)


title: T2Dd5pmxs3


title: T2Dd5pmxs1


title: T5


title: T2Dd5pmxs2


title: pMXs-100


title: MLNVenus_neg_2

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Human duodenal organoids MLN-Venus-, sample 2

data_processing:
Sequenced reads were trimmed for adapter sequence using cutadapt, mapped to the primary human genome (GRCh38) using STAR, and raw counts generated with featureCounts.
Differential gene expression modelling and normalised counts per million were generated using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for all samples.

source_name: Duodenal organoids

growth_protocol: Organoids were routinely replated into BME domes (~20 ul) on uncoated plastic, and grown in IF medium supplemented with 50 ng/ml EGF. EGF was removed from culture medium, with the addition of Notch and MEK inhibitors in 5% Wnt IF media (termed IF*) where necessary, to encourage M-cell differentiation.

extract_protocol:
hMLN-Venus organoid samples showing Venus expression were dissociated to single cells, and stained with DAPI and DRAQ5. Live cells (DAPI-, and DRAQ5+) were FACS sorted into 2x populations (Venus+, and Venus-). RNA extraction and isolation were performed using RNAeasy Micro Plus kit (Qiagen). RNA concentration and quality (RIN 7-9) were assessed using RNA6000 Pico Kit and Bioanalyser 2000 (Agilent).
The library was constructed with using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara Bio).

tag: population

value: Venus-

tag: replicate


title: MLNVenus_neg_3

description: Human duodenal organoids MLN-Venus-, sample 3


title: MLNVenus_pos_3

description: Human duodenal organoids MLN-Venus+, sample 3

value: Venus+


title: T2Dd5e4

value: Tet2-E transduced (iPSC Day 5)


title: T2Dd5e2


title: T2Dd5e1


title: MLNVenus_pos_2

description: Human duodenal organoids MLN-Venus+, sample 2


title: T2Dd10wt3

value: Tet2-WT transduced (iPSC Day 10)


title: MLNVenus_neg_1

description: Human duodenal organoids MLN-Venus-, sample 1


title: MLNVenus_pos_1

description: Human duodenal organoids MLN-Venus+, sample 1


title: T2Dd10wt4

value: embryonic day 12.5 (e12.5)


title: T2Dd10wt1


title: T2Dd10pmxs4

value: Empty vector transduced (iPSC Day 10)


title: mhCO+Aβ [CROP-seq]

city: NEW HAVEN

first: Bilal

last: Cakir

state: Connecticut

address: 10 Amistad Street, Ste 214J

institute: Yale University

description: Cortical organoid differentiated from hESCs

data_processing:
Library strategy: CROP-seq
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
The cell ranger output was processed in R using Seurat (v3.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format. Metadata file was provided as  tab-separated format. gRNA sequences used in this study are shown as fasta format.

source_name: Microglia-containing cortical organoid with Aβ treatment

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits

value: mhCO

tag: sort

tag: treatment


title: T2Dd10pmxs1


title: T2Dd10pmxs2


title: MLNVenus_pos_4

description: Human duodenal organoids MLN-Venus+, sample 4


title: mhCO [CROP-seq]

source_name: Microglia-containing cortical organoid

value: ABeta


title: MLNVenus_neg_4

description: Human duodenal organoids MLN-Venus-, sample 4


title: T2Dd5e3


title: mhCO_v2_GFP-

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
The cell ranger output was processed in R using Seurat (v3.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format. Metadata file was provided as  tab-separated format.

source_name: GFP- cells from microglia-containing organoid

extract_protocol:
Chromium™ Single Cell 3’ Reagent Kits
Single-cell RNA-seq

value: GFP-


title: T2Dd10pmxs3


title: T2Dd10e4

value: Tet2-E transduced (iPSC Day 10)


title: mhCO_v2_GFP+

source_name: GFP+ cells from microglia-containing organoid

value: GFP+


title: mhCO+Aβ


title: T2Dd10e2


title: mhCO


title: hCO+Aβ

source_name: Human cortical organoid with Aβ treatment

value: hCO


title: T2Dd10e3

value: SSEA1-RFP flow sorting


title: T2Dd10e1

value: Mouse embryonic fibroblasts


title: T2DMEF3

value: control untreated MEFs


title: T2DMEF2


title: T2DMEF1


title: mCtx_Nuc_rep 3_polyA

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

description: Nucleoplasmic polyA(+) RNA im mCtx biological replicate 3

data_processing:
Sequenced reads were mapped to mm10 genome using STAR.
TPM values obtained from Kallisto (version 0.43.0)
Read counts obtained from FeatureCount.

source_name: mouse primary cortical neuron  (mCtx)

growth_protocol: E14 mESC line was cultured on 0.1 % gelatin-coated dishes in mESC media supplemented with LIF. mNPC line were  were grown in DMEM/F12 supplemented with B27 (without vitamin A), 1 mM GlutaMax, and antibiotics. EGF and FGF were added every day at 10 ng/ml concentration. Primary cortical neurons (mCtx) were plated on 0.1 mg/ml poly-L-lysine coated dishes and culture media for 5 days.

extract_protocol:
Total RNA was collected with the Trizol LE regent for cytoplasmic RNAs, and Trizol reagent for soluble nucleoplasmic and chromatin-associated RNAs. Long RNA over 200 nt was selected using RNeasy MinElute Cleanup Kit (Qiagen). Polyadenylated RNA was selected using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit. A final library of 250-400 bp was size selection with an agarose gel.
The libraries were subjected to 100 bp paired-end sequencing (Illumina HiSeq4000).


title: mCtx_Cyto_rep 2_polyA

description: Cytoplasmic polyA(+) RNA im mCtx biological replicate 2


title: mCtx_Nuc_rep 2_polyA

description: Nucleoplasmic polyA(+) RNA im mCtx biological replicate 2


title: T2Dd10wt2


title: mCtx_Chr_rep 3_polyA

description: Chromatin-associated polyA(+) RNA im mCtx biological replicate 3


title: mCtx_Cyto_rep 1_polyA

description: Cytoplasmic polyA(+) RNA im mCtx biological replicate 1


title: mCtx_Chr_rep 1_polyA

description: Chromatin-associated polyA(+) RNA im mCtx biological replicate 1


title: mCtx_Nuc_rep 1_polyA

description: Nucleoplasmic polyA(+) RNA im mCtx biological replicate 1


title: mNPC_Cyto_rep 3_polyA

description: Cytoplasmic polyA(+) RNA im mNPC biological replicate 3

source_name: mouse neuronal progenitor cell (mNPC)


title: STI1: dTPR/dTPR Animal 4

city: Jerusalem

first: Hermona

last: Soreq

state: Israel

address: The Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Base calling, QC and fasq file generation by the illumina Basespace platform
Alignment to mouse genome GRCm38.p5 using TopHat
counts processing using HTSeq-counts
Normalization and Differencial expression using Deseq2
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: txt. File per sample with alligned counts

extract_protocol:
Brain was extracted and dissected on ice. Cortex separated from other brain regions and frozen on dry ice in Eppendorf tube before transferred to -80°C. Small piece (~3 mm) was isolated for RNA extraction).  RNA harvested in TRIzol. Sequencing-compatible poly(A)-terminated single-end libraries were generated using an RNA Library prep kit (SENSE Total RNA-Seq Library Prep Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dTPR-/dTPR-

tag: age (days)

tag: tissue

value: Cortical brain tissue (part of 1 hemisphere)


title: STI1: dTPR/dTPR Animal 2


title: STI1: dTPR/dTPR Animal 3


title: STI1: dTPR/dTPR Animal 5


title: mNPC_Nuc_rep 3_polyA

description: Nucleoplasmic polyA(+) RNA im mNPC biological replicate 3


title: mCtx_Cyto_rep 3_polyA

description: Cytoplasmic polyA(+) RNA im mCtx biological replicate 3


title: hCO

source_name: Human cortical organoid

tag: cell type


title: STI1: dTPR/dTPR Animal 1


title: STI1: wt/wt Animal 5

value: WT


title: mNPC_Nuc_rep 2_polyA

description: Nucleoplasmic polyA(+) RNA im mNPC biological replicate 2


title: mNPC_Chr_rep 3_polyA

description: Chromatin-associated polyA(+) RNA im mNPC biological replicate 3


title: mNPC_Cyto_rep 2_polyA

description: Cytoplasmic polyA(+) RNA im mNPC biological replicate 2


title: T2DMEF4


title: STI1: wt/wt Animal 4


title: STI1: wt/wt Animal 3


title: STI1: wt/wt Animal 2


title: mNPC_Chr_rep 2_polyA

description: Chromatin-associated polyA(+) RNA im mNPC biological replicate 2


title: mCtx_Chr_rep 2_polyA

description: Chromatin-associated polyA(+) RNA im mCtx biological replicate 2


title: mNPC_Chr_rep 1_polyA

description: Chromatin-associated polyA(+) RNA im mNPC biological replicate 1


title: mNPC_Nuc_rep 1_polyA

description: Nucleoplasmic polyA(+) RNA im mNPC biological replicate 1


title: 24hr_KO_ov207

city: Taipei

first: Wei-Ling

last: Tu

state: Beitou

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The RNA-seq libraries were sequenced on a HiSeq2500 (Illumina, Inc., CA, USA) by single end sequencing with 100 bp read length to a depth of 18 to 22 million reads for each library.
After trimming of low quality of bases (< Q20), the first 12 bases and adapters, the trimmed reads, were mapped to Genome Reference Consortium Mouse Build 38 (GRCm38/mm10) and run RNA-seq analysis by CLC Genomics Workbench v 11.0 (QIAGEN, Germany).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tissue

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The RNA sequencing libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kit (Illumina Inc., USA), which produced directional RNA-seq libraries starting from 4 µg of total RNA according to manufacturer’s instruction. The RNA libraries were quantified by qPCR and quality assessed with the 2100 Bioanalyzer HS DNA Kit.

value: Liver

tag: strain

value: Dph1 KO

value: Diethylnitrosamine (DEN)


title: 24hr_CT_op379

value: Control


title: mESC_Cyto_rep 3_polyA

description: Cytoplasmic polyA(+) RNA im mESC biological replicate 3

source_name: mouse embryonic stem cell (mESC)


title: 24hr_CT_op378


title: mESC_Chr_rep 3_polyA

description: Chromatin-associated polyA(+) RNA im mESC biological replicate 3


title: mESC_Nuc_rep 3_polyA

description: Nucleoplasmic polyA(+) RNA im mESC biological replicate 3


title: mESC_Cyto_rep 2_polyA

description: Cytoplasmic polyA(+) RNA im mESC biological replicate 2


title: mNPC_Cyto_rep 1_polyA

description: Cytoplasmic polyA(+) RNA im mNPC biological replicate 1


title: mESC_Cyto_rep 1_polyA

description: Cytoplasmic polyA(+) RNA im mESC biological replicate 1


title: mESC_Nuc_rep 2_polyA

description: Nucleoplasmic polyA(+) RNA im mESC biological replicate 2


title: LUM0524 YAC128 mouse on FVN/B strain 7262580

city: Leiden

first: Elsa

last: Kuijper

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

data_processing:
Primary processing and base calling was performed with Illumina’s HCS and RTA. Demultiplexing and generation of FASTQ files was done with Illumina scripts (bcl2fastq v1.8).
Analysis of sequencing data was performed using the BIOPET Gentrap in-house pipeline (http://biopet-docs.readthedocs.io/en/v0.7.0/pipelines/gentrap/) The fastqc toolkit (v0.11.2) was used to evaluate sequencing quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sickle (v1.33 with default settings) and Cutadapt (v1.10, with default settings except for “-m 20”) were used to clean up reads.
Cleaned reads were aligned to the mouse reference genome build 10 (GRCm38/mm10) using STAR aligner version 2.3.0e
The non-default settings used by STAR are “--outFilterMultimapNmax 1 –outFilterMismatchNmax 10 –outSJfilterReads Unique”.
Gene raw read counts are generated using HTSeq (v0.6.1) with the Refseq gene annotation extracted from UCSC on 11-09-2015. The non-default settings used by HTSeq are “--format bam –stranded no”. Gene expression analysis was performed using edgeR (v 3.14.0). GC-content correction was first performed using the conditional quantile normalization (CQN) package as previously described (Hansen KD, Irizarry RA, Wu Z: Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (Oxford, England) 2012, 13:204-216.)
Genome_build: GRCm38/mm10

source_name: cortex

growth_protocol: YAC128 transgenic HD mice maintained on the FVB/N strain and wild-type FVB/N mice (WT) were obtained from Jackson Laboratories (Bar Harbor, Maine, USA) and bred at the Leiden University Medical Center. Only male mice were used. Mice were group housed in individually ventilated cages with food and drinking water available ad libitum. At the start of the study, the age of both the wild-type and YAC128 group ranged between 6 and 10 months with an average of about 7 months of age. At 14 months from the start of the study, the mice were sacrificed.

extract_protocol:
Brains were isolated directly after sacrifice and brainstem, cerebellum, cortex and striatum were dissected and snapfrozen in liquid nitrogen. Approximately 30mg of tissue was used for RNA isolation, using Trizol and the PureLink RNA mini column kit (Thermo Fisher Scientific) according to manufacturers instruction. RNA was treated with DNAse to remove contamination of genomic DNA. Isolated RNA was shipped to DeCode Genetics (Reykjavik, Iceland) for RNA sequencing.
Quality of RNA was assessed with the LabChip GX using the 96-well RNA kit (Perkin Elmer). Non strand-specific sample preparation was performed using the TruSeq Poly-A v2 kit (Illumina, San Diego, USA) following manufacturer’s instructions. In brief, mRNA was captured using magnetic poly-T oligo-attached magnetic beads, RNA molecules were fragmented, and cDNA synthesis was performed using SuperScript II (Invitrogen, Carlsbad CA, USA) with random hexamer primers. Subsequently, 2nd strand cDNA synthesis was performed in conjunction with RNAse-H treatment. End repair was performed to generate blunt ends and 3′ adenylation was performed, followed by ligation of indexing adapters to the ds-cDNA. PCR was performed to amplify the fragments. Quality of sequencing libraries was determined through pool sequencing on a MiSeq instrument (Illumina) to assess insert size, sample diversity and optimize cluster densities. Pooled samples (4 samples/pool) were clustered on paired-end (PE) flowcells (1 pool per lane) using a cBot instrument (Illumina). The sequencing was performed using a HiSeq 2500 with v4 SBS sequencing kits (read lengths 2x125 cycles).

treatment_protocol: Mice were not treated in this study but aged naturally. All mice were exposed to behavioral tests: rotarod (0, 2, 4, 6, 8 and 12 months from the start) and beamwalk (2, 4, 6 and 8 months from the start).

tag: genotype/strain

value: YAC128 mouse on FVN/B strain

tag: age (weeks)

value: cortex

tag: rin


title: STI1: wt/wt Animal 1

tag: strain background


title: LUM0523 YAC128 mouse on FVN/B strain 7262580

source_name: striatum

value: striatum


title: mESC_Chr_rep 2_polyA

description: Chromatin-associated polyA(+) RNA im mESC biological replicate 2


title: mCtx_Cyto_rep 3_Total

description: Cytoplasmic total RNA im mCtx biological replicate 3

data_processing:
Sequenced reads were mapped to mm10 genome using STAR.
Gene expression values, TPM were calculated using Kallisto program
read counts were calculated using Featurecount
Genome_build: mm10
Supplementary_files_format_and_content: Text files include exon expression values for each sample.

extract_protocol:
Total RNA was collected with the Trizol LE regent for cytoplasmic RNAs, and Trizol reagent for soluble nucleoplasmic and chromatin-associated RNAs. Long RNA over 200 nt was selected using RNeasy MinElute Cleanup Kit (Qiagen). RNA was processed with Ribo-minus kit to remove ribosomal RNA.
Libraries were constructed with the Illumina TruSeq stranded kit by skipping oligo-dT bead incubation step. A final library of 250-400 bp was size selection with an agarose gel.
The libraries were subjected to 100 bp paired-end sequencing (Illumina HiSeq4000).


title: mESC_Chr_rep 1_polyA

description: Chromatin-associated polyA(+) RNA im mESC biological replicate 1


title: 24hr_KO_ov201


title: CD8 KO rep1

city: SAN FRANCISCO

first: SUJIT

last: KASHYAP

address: 513 Parnassus Ave

department: Pediatric Rheumatology

institute: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings)(Li and Durbin, 2009). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome
ChIP-seq reads were aligned to the mm10 genome assembly
The resulting histograms (genomic “signal maps”) were stored in bigWig files. H3K9me3 enriched regions were identified using the SICER algorithm(Zang et al., 2009) at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files and bigwig files

source_name: Spleenocyte, Lymph node

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer
ChIP-Seq and subsequent data analysis was performed by Active Motif. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Primary naïve CD8 T-cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

value: Spleen, lymph node

tag: age

value: 4-6 week

tag: chip antibody

value: H3K9ME3 (Active Motif, Cat. 39161, lot 14418003)


title: CD8 KO rep2

tag: genotype


title: mESC_Nuc_rep 1_polyA

description: Nucleoplasmic polyA(+) RNA im mESC biological replicate 1


title: CD8 Het rep1


title: Input DNA

value: Atf7ipfl/fl, Atf7ip+/fl


title: LUM0519 YAC128 mouse on FVN/B strain 7262577


title: CD8 Het rep2


title: mCtx_Chr_rep 3_Total

description: Chromatin-associated total RNA im mCtx biological replicate 3


title: LUM0521 YAC128 mouse on FVN/B strain 7262580

source_name: brainstem

value: brainstem


title: LUM0520 YAC128 mouse on FVN/B strain 7262577


title: LUM0518 YAC128 mouse on FVN/B strain 7262577

source_name: cerebellum

value: cerebellum


title: LUM0522 YAC128 mouse on FVN/B strain 7262580


title: mCtx_Nuc_rep 2_Total

description: Nucleoplasmic total RNA im mCtx biological replicate 2


title: LUM0516 YAC128 mouse on FVN/B strain 7261183


title: mCtx_Chr_rep 2_Total

description: Chromatin-associated total RNA im mCtx biological replicate 2


title: LUM0514 YAC128 mouse on FVN/B strain 7261183


title: mCtx_Nuc_rep 3_Total

description: Nucleoplasmic total RNA im mCtx biological replicate 3


title: mCtx_Nuc_rep 1_Total

description: Nucleoplasmic total RNA im mCtx biological replicate 1


title: mCtx_Cyto_rep 1_Total

description: Cytoplasmic total RNA im mCtx biological replicate 1


title: LUM0515 YAC128 mouse on FVN/B strain 7261183


title: mCtx_Chr_rep 1_Total

description: Chromatin-associated total RNA im mCtx biological replicate 1


title: LUM0513 YAC128 mouse on FVN/B strain 7261183


title: mNPC_Nuc_rep 3_Total

description: Nucleoplasmic total RNA im mNPC biological replicate 3


title: LUM0511 YAC128 mouse on FVN/B strain 7261182


title: LUM0512 YAC128 mouse on FVN/B strain 7261182


title: mNPC_Nuc_rep 2_Total

description: Nucleoplasmic total RNA im mNPC biological replicate 2


title: mNPC_Chr_rep 3_Total

description: Chromatin-associated total RNA im mNPC biological replicate 3


title: LUM0508 YAC128 mouse on FVN/B strain 7260444


title: LUM0510 YAC128 mouse on FVN/B strain 7261182


title: mNPC_Cyto_rep 2_Total

description: Cytoplasmic total RNA im mNPC biological replicate 2


title: LUM0509 YAC128 mouse on FVN/B strain 7261182


title: LUM0507 YAC128 mouse on FVN/B strain 7260444


title: mNPC_Nuc_rep 1_Total

description: Nucleoplasmic total RNA im mNPC biological replicate 1


title: mNPC_Cyto_rep 3_Total

description: Cytoplasmic total RNA im mNPC biological replicate 3


title: LUM0517 YAC128 mouse on FVN/B strain 7262577


title: LUM0506 YAC128 mouse on FVN/B strain 7260444


title: mNPC_Chr_rep 2_Total

description: Chromatin-associated total RNA im mNPC biological replicate 2


title: LUM0504 YAC128 mouse on FVN/B strain 7244889


title: LUM0505 YAC128 mouse on FVN/B strain 7260444


title: mCtx_Cyto_rep 2_Total

description: Cytoplasmic total RNA im mCtx biological replicate 2


title: LUM0503 YAC128 mouse on FVN/B strain 7244889


title: mNPC_Cyto_rep 1_Total

description: Cytoplasmic total RNA im mNPC biological replicate 1


title: mESC_Cyto_rep 3_Total

description: Cytoplasmic total RNA im mESC biological replicate 3


title: mNPC_Chr_rep 1_Total

description: Chromatin-associated total RNA im mNPC biological replicate 1


title: mESC_Cyto_rep 2_Total

description: Cytoplasmic total RNA im mESC biological replicate 2


title: LUM0501 YAC128 mouse on FVN/B strain 7244889


title: LUM0500   FVN/B wildtype mouse 7263461

value: FVN/B wild type


title: mESC_Nuc_rep 2_Total

description: Nucleoplasmic total RNA im mESC biological replicate 2


title: LUM0502 YAC128 mouse on FVN/B strain 7244889


title: mESC_Chr_rep 3_Total

description: Chromatin-associated total RNA im mESC biological replicate 3


title: LUM0498   FVN/B wildtype mouse 7263461


title: mESC_Chr_rep 2_Total

description: Chromatin-associated total RNA im mESC biological replicate 2


title: mESC_Cyto_rep 1_Total

description: Cytoplasmic total RNA im mESC biological replicate 1


title: LUM0499   FVN/B wildtype mouse 7263461


title: LUM0497   FVN/B wildtype mouse 7263461


title: mESC_Chr_rep 1_Total

description: Chromatin-associated total RNA im mESC biological replicate 1


title: LUM0495   FVN/B wildtype mouse 7263460


title: LUM0496   FVN/B wildtype mouse 7263460


title: LUM0492   FVN/B wildtype mouse 7263458


title: LUM0493   FVN/B wildtype mouse 7263460


title: mESC_Nuc_rep 1_Total

description: Nucleoplasmic total RNA im mESC biological replicate 1


title: LUM0494   FVN/B wildtype mouse 7263460


title: Ctrl2 RPE

city: New York

first: Ching-Hwa

last: Sung

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina HiSeq4000 or NovaSeq6000 sequencer with either single-read or paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The reads counts were conducted with HTSeq(Version 0.11.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read counts at gene level for each samples

source_name: RPE

extract_protocol:
The total RNAs of the loosened mouse RPE cell pellets were isolated using the Absolutely RNA Nanoprep kit (Agilent).
The messenger RNA was prepared using the TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: Retinal pigment epithelium


title: Cell 3 Bulk RNA Sequencing

city: Farmington

first: Dylan

last: Baker

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Fastq files were generated from BCL by bcl2fastq
Counts matrices were generated from Fastqs processed via Cellranger or Spaceranger with the mm10 reference
Bulk RNA mapped with star to mm10 subread featureCounts used to generate counts for each gene
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrices of single cell gene expression

source_name: Mouse Urinary Bladder

extract_protocol: Tissue Homogenization followed by Qiagen RNeasy isolation and Truseq II Library Prep; polyA selection

value: Dissociated Mouse Bladder

value: 12 Months

tag: sample group (sex/number)

value: 3X Female


title: KO1 RPE

value: Best1-Cre+/-; Clic4f/f


title: LUM0491   FVN/B wildtype mouse 7263458


title: KO2 RPE


title: Cell 2 Bulk RNA Sequencing


title: mESC_Nuc_rep 3_Total

description: Nucleoplasmic total RNA im mESC biological replicate 3

tag: sample type


title: LUM0489   FVN/B wildtype mouse 7263458


title: LUM0490   FVN/B wildtype mouse 7263458


title: LUM0488   FVN/B wildtype mouse 7263457


title: Cell 1 Bulk RNA Sequencing


title: LUM0487   FVN/B wildtype mouse 7263457


title: Tissue 3 Bulk RNA Sequencing

value: Whole Mouse Bladder


title: LUM0486   FVN/B wildtype mouse 7263457


title: LUM0485   FVN/B wildtype mouse 7263457


title: Tissue 2 Bulk RNA Sequencing


title: LUM0484   FVN/B wildtype mouse 7262576


title: Whole Bladder (Detrusor Enriched)

source_name: Mouse urinary bladder

extract_protocol: Standard 10X Chromium Single Cell Gene Expression

value: Whole Bladder

value: 14 Months

value: 2X  Female  + 2X  Male


title: LUM0483   FVN/B wildtype mouse 7262576

value: striatum


title: Detrusor Only

value: Detrusor layer of bladder

value: 3X  Female


title: Nuclei

value: Whole Bladder Nuclear Preparation


title: Ctrl1 RPE


title: Whole Bladder 5

value: 24 Months


title: LUM0482   FVN/B wildtype mouse 7262576


title: LUM0481   FVN/B wildtype mouse 7262576

value: brainstem


title: LUM0480   FVN/B wildtype mouse 7260443

value: cortex


title: Whole Bladder 1

value: 22 Months

value: 3X  Male


title: LUM0479   FVN/B wildtype mouse 7260443

value: FVN/B wild type


title: LUM0477   FVN/B wildtype mouse 7260443


title: LUM0476   FVN/B wildtype mouse 7252116


title: LUM0475   FVN/B wildtype mouse 7252116


title: Whole Bladder 2

value: 3 Months

value: 3X Male


title: Tissue 1 Bulk RNA Sequencing

value: 12 months

value: 3X Female


title: LUM0474   FVN/B wildtype mouse 7252116

value: cerebellum


title: P18_RNA-seq_Ino80cKO_rep5

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment to mm10 was performed by Tophat2 and read counts were obtained by Htseq-Count.
Differential expression analysis was performed by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with read counts per gene

source_name: spermatogenic cells from Testes

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were lysed in TRIzol reagent and total RNA was extracted by Zymo Direct-zol kit following manufacturers instruction.
Libraries were generated by Kapa stranded mRNA-seq kit library kit for Illumina sequencing isong 1µg RNA per sample.

value: Mixed background

value: Spermatogenic cells

value: Testis


title: P18_RNA-seq_Ino80cKO_rep3


title: LUM0473   FVN/B wildtype mouse 7252116


title: P18_RNA-seq_Ino80cKO_rep4


title: LUM0472   FVN/B wildtype mouse 7248227


title: LUM0471   FVN/B wildtype mouse 7248227

value: striatum


title: P18_RNA-seq_Ino80cKO_rep2


title: Whole Bladder 4

value: Whole Bladder

value: 12 Months

value: 2X  Female  + 2X  Male


title: P18_RNA-seq_Ino80WT_rep4


title: LUM0470   FVN/B wildtype mouse 7248227


title: P18_RNA-seq_Ino80WT_rep5


title: P18_RNA-seq_Ino80cKO_rep1


title: LUM0469   FVN/B wildtype mouse 7248227

value: brainstem


title: P18_RNA-seq_Ino80WT_rep3


title: Whole Bladder 3


title: LUM0387 YAC128 mouse on FVN/B strain 7262577

data_processing:
Primary processing and base calling was performed with Illumina’s HCS and RTA. Demultiplexing and generation of FASTQ files was done with Illumina scripts (bcl2fastq v1.8).
Analysis of sequencing data was performed using the BIOPET Gentrap in-house pipeline (http://biopet-docs.readthedocs.io/en/v0.7.0/pipelines/gentrap/) The fastqc toolkit (v0.11.2) was used to evaluate sequencing quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sickle (v1.33 with default settings) and Cutadapt (v1.10, with default settings except for “-m 20”) were used to clean up reads.
Cleaned reads were aligned to the mouse reference genome build 10 (GRCm38/mm10) using STAR aligner version 2.3.0e
The non-default settings used by STAR are “--outFilterMultimapNmax 1 –outFilterMismatchNmax 10 –outSJfilterReads Unique”.
Gene raw read counts are generated using HTSeq (v0.6.1) with the Refseq gene annotation extracted from UCSC on 11-09-2015. The non-default settings used by HTSeq are “--format bam –stranded no”. Gene expression analysis was performed using edgeR (v 3.14.0). GC-content correction was first performed using the conditional quantile normalization (CQN) package as previously described (Hansen KD, Irizarry RA, Wu Z: Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (Oxford, England) 2012, 13:204-216.)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: fragment per gene counts

source_name: blood

extract_protocol:
For RNA sequencing, 200 µl of blood was obtained by tail cut at 40 and 75 weeks of age. Blood samples for RNA sequencing were collected in RNAprotect animal blood tubes (Qiagen) following manufacturer’s instructions, stored overnight at 4°C and subsequently frozen at -80°C until RNA isolation. After thawing, filled blood tubes were incubated for 4 hours at 25°C to ensure proper cell lysis. Isolation of RNA was subsequently performed using the RNeasy protect animal blood kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions for total RNA isolation including DNAse treatment, resulting in isolation of RNA molecules longer than approximately 200 nucleotides. Reduction of alpha and beta globin mRNA was performed on RNA samples using the GLOBINclear magnetic bead kit for mouse/rat (Qiagen) following manufacturer’s instructions. RNA was shipped to DeCode Genetics (Reykjavik, Iceland) for RNA sequencing.
Quality of RNA was assessed with the LabChip GX using the 96-well RNA kit (Perkin Elmer). Non strand-specific sample preparation was performed using the TruSeq Poly-A v2 kit (Illumina, San Diego, USA) following manufacturer’s instructions. In brief, mRNA was captured using magnetic poly-T oligo-attached magnetic beads, RNA molecules were fragmented, and cDNA synthesis was performed using SuperScript II (Invitrogen, Carlsbad CA, USA) with random hexamer primers. Subsequently, 2nd strand cDNA synthesis was performed in conjunction with RNAse-H treatment. End repair was performed to generate blunt ends and 3′ adenylation was performed, followed by ligation of indexing adapters to the ds-cDNA. PCR was performed to amplify the fragments. Quality of sequencing libraries was determined through pool sequencing on a MiSeq instrument (Illumina) to assess insert size, sample diversity and optimize cluster densities. Pooled samples (4 samples/pool) were clustered on paired-end (PE) flowcells (1 pool per lane) using a cBot instrument (Illumina). The sequencing was performed using a HiSeq 2500 with v4 SBS sequencing kits (read lengths 2x125 cycles).

value: YAC128 mouse on FVN/B strain

tag: rin value


title: P18_RNA-seq_Ino80WT_rep1


title: LUM0478   FVN/B wildtype mouse 7260443


title: P18_RNA-seq_Ino80WT_rep2


title: LUM0383 YAC128 mouse on FVN/B strain 7244889


title: LUM0385 YAC128 mouse on FVN/B strain 7261182


title: LUM0384 YAC128 mouse on FVN/B strain 7260444


title: P18_Input_DNA_Ino80cKO_rep2

data_processing:
Alignment to mm10 was performed by Bowtie2 and deduplicated and sorted bam files were created by Samtools.
Bam files were merged by samtools and bigwigs were generated by Deeptools with RPKM normatilization and also representing log2(ChIP/Input).
Peaks were called by macs2 callpeak using the options –extsize set to 147 and –nomodel.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic tracks, bed files for peaks.

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were fixed in 0.3% formaldehyde at 4˚C for 30 minutes. Nuclei were isolated and chromatin was digested with micrococcal nuclease before immunoprecipitation with antibody.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing

tag: antibody


title: LUM0382 FVN/B wildtype mouse 7263461

value: FVN/B wildtype mouse


title: P18_Input_DNA_Ino80WT_rep2


title: P18_Input_DNA_Ino80WT_rep1


title: P18_H2A.Z_ChIPseq_Ino80cKO_rep2

value: Rabbit anti-H2A.Z antibody (Abcam, ab4174)


title: LUM0381 FVN/B wildtype mouse 7263460


title: P18_H2A.Z_ChIPseq_Ino80cKO_rep1


title: P18_H2A.Z_ChIPseq_Ino80WT_rep2


title: LUM0380 FVN/B wildtype mouse 7263458


title: LUM0379 FVN/B wildtype mouse 7263457


title: LUM0378 FVN/B wildtype mouse 7262576


title: P18_H2A.Z_ChIPseq_Ino80WT_rep1


title: LUM0388 YAC128 mouse on FVN/B strain 7262580


title: P18_Input_DNA_rep2

value: Wild type


title: P18_Input_DNA_rep1


title: LUM0377 FVN/B wildtype mouse 7260443


title: LUM0376 FVN/B wildtype mouse 7252116


title: LUM0375 FVN/B wildtype mouse 7248227


title: RNAseq_Nvitripennis_uninjected_rep3

city: Wageningen

first: Julien

last: Rougeot

state: Gerlderland

address: Droevendaalsesteeg 1  Building 107

department: Plant Science Group

institute: Wageningen University and Research

data_processing:
Reads from whole embryos were mapped to Nvit_psr_1.1 N. vitripennis genome version with RefSeq annotation GCF_009193385.1 using STAR version 2.6.1b with --quantMode geneCounts
Genome_build: Nvit_psr_1.1
Supplementary_files_format_and_content: Raw gene counts (.tab)

organism: Nasonia vitripennis

source_name: whole white larvae

growth_protocol: The N. vitripennis lab strain AsymCX cured with Wolbachia infection (Werren et al., 2010) was used throughout the experiments. Wasps were reared on Calliphora sp. hosts and cultured at 25 °C at a L16:D8 cycle.

extract_protocol:
Total RNA of larvae pools was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol. RNA was resuspended in 10 µl DNase RNase free water and RNA concentration was measured on fluorometer (Qubit 2.0 – Life Technologies).
Absence of RNA degradation was checked on a bioanalyzer (Agilent 2000 - Agilent). Then, mRNA was enriched using ology (dT) primers and randomly fragmented using a fragmentation buffer. First strand cDNA synthesis was performed using random hexamers and followed by second strand synthesis by nick-translation using a customized synthesis buffer (containing dNTP, RNase H, Esccherichia coli DNA polymerase I). Double-stranded DNA was subsequently purified, end-repaired, A-tailed and ligated to Illumina sequencing adapters. Size selection was then performed and library was amplified by PCR. Library concentration was quantify on a fluorometer (Qubit 2.0 – Life Technologies) and insert size was analyzed on a bioanalyzer (Agilent 2100 – Agilent). Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovoSeq platform.  For more details, please contact Novogen (HK) company limited.on a bioanalyzer (Agilent 2000 - Agilent).

treatment_protocol: Larval RNAi knockdown was induced in AsymCX males in second instar larval stage (approximately 3 days after egg laying) (Werren, 2009, Cold Spring Harb Protoc). Gfp dsRNA was generated from the vector pOPINEneo-3C-GFP (Addgene plasmid # 53534; http://n2t.net/addgene: 53534; RRID: Addgene_53534, gift from Ray Owens).Full length GFP CDS was amplified by PCR with GFP_RNAi_F (5’-GTGACCACCTTGACCTACG-3’) and GFP_RNAi_R (5’-TCTCGTTGGGGTCTTTGCT-3’) primers. The 5′ and 3′ ends of those amplicons were provided with a T7 promotor sequence for dsRNA production using the MEGAscript RNAi kit (Ambion, Austin, Texas, USA) according to the manufacturer's protocol. Before injection, 2nd instar male larvae were placed on a petri-dish covered with 1% agarose in 1x PBS. Larvae were injected in the posterior part with 4 μg/μl GFP dsRNA diluted in milliQ water mixed with red food dye in the ratio 9:1, milliQ water with red food dye, or non-injected as control. Injections were performed using custom made needles and a IM300 Microinjecctor (Narishige). After injection, 2nd instar larvae were transferred back to host (6-8 per host) and sealed with the host shell. After 5 to 6 days post-injection, three samples (five individuals per sample) of white pupa stage males per category were collected, snap-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction.

value: AsymCX

value: whole larvae

value: white pupae

value: uninjected


title: P18_Input_DNA_Ino80cKO_rep1


title: RNAseq_Nvitripennis_uninjected_rep1


title: P18_INO80_ChIPseq_rep2

value: Rabbit anti-INO80 antibody (Abcam, ab105451)


title: RNAseq_Nvitripennis_water_rep3

value: water


title: LUM0360 YAC128 mouse on FVN/B strain 7262580


title: RNAseq_Nvitripennis_uninjected_rep2


title: RNAseq_Nvitripennis_water_rep2


title: P18_INO80_ChIPseq_rep1

value: Mixed background

value: Spermatogenic cells


title: MiR155 KI NKT KI_3 NK1.1+

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: 1 Ford Place

department: Department of Dermatology

institute: Henry Ford Health System

description: MiR 155KI KI NK1.1+ 3

data_processing:
bcl2fastq v2.17.1.14 conversion software used for basecalling.
The RNA-Seq reads were aligned to the mouse GRCm38/mm10 reference genome using Biomedical Genomics Workbench 5.0 (QIAGEN).
The expression levels for each sample were quantified and normalized usingBiomedical Genomics Workbench 5.0 (QIAGEN).
Genome_build: mm10
Supplementary_files_format_and_content: Raw_Counts.csv contains raw read counts for each gene in each sample. cpm.csv file contains counts per million reads mapped (CPM) for each gene in each sample. Excel files (Expression Browser NK1.1+.xlsx and Expression Browser NK1.1-.xlsx) contain gene expression level counts and statistics that include gene name, chromosome, region, identifier, KO vs. WT-Max group means, KO vs. WT-Fold change, KO vs. WT-Log fold change, KO vs. WT-P-value, KO vs. WT-FDR p-value, KO vs. WT- FDR-Bonferroni, Total counts and RPKM values for each sample.

source_name: Thymus

extract_protocol:
iNKT cells were sorted by FACS Aria II flow cytometer. Total RNA was extracted from the sorted cells with miRCURY RNA Isolation Kit - Cell & Plant (Exiqon). cDNA library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
cDNA was pre-amplified by a thermal cycler (Applied Biosystem) using 12-14 cycles and sheered into 150-400 bp fragments using Bioruptor Pico sonicator (Diagenode). The DNA ends were repaired using End-It™ DNA End-Repair Kit (Epicentre). The end repaired DNA fragments were ligated to adaptors by T4 ligase (NEB) after a single “A” was added at 3’ by Klenow Fragment (3’→5’ Exo-) (NEB). MinElute Reaction Cleanup Kit (Qiagen) was used for DNA cleanup after each step. Illumina P5 and P7 primers with individual adaptors were used for final library amplification. The 150-400 bp final product was purified on a 2% E-gel (Thermo Fisher Scientific).

value: 7 weeks

value: Thymus

value: NK1.1+ iNKT cells


title: RNAseq_Nvitripennis_water_rep1


title: RNAseq_Nvitripennis_dsGFP_RNA_rep3


title: RNAseq_Nvitripennis_dsGFP_RNA_rep2


title: MiR155 KI NKT KI_2 NK1.1+

description: MiR 155KI KI NK1.1+ 2


title: RNAseq_Nvitripennis_dsGFP_RNA_rep1


title: LUM0358 YAC128 mouse on FVN/B strain 7261183


title: LUM0359 YAC128 mouse on FVN/B strain 7262577


title: LUM0357 YAC128 mouse on FVN/B strain 7261182


title: MiR155 KI NKT KI_2 NK1.1-

description: MiR 155KI KI NK1.1- 2

value: NK1.1- iNKT cells


title: MiR155 KI NKT KI_3 NK1.1-

description: MiR 155KI KI NK1.1- 3


title: MiR155 KI NKT KI_1 NK1.1-

description: MiR 155KI KI NK1.1- 1


title: LUM0353 YAC128 mouse on FVN/B strain 7244889


title: MiR155 KI NKT KI_1 NK1.1+

description: MiR 155KI KI NK1.1+ 1


title: MiR155 KI NKT WT_3 NK1.1+

description: MiR 155KI WT NK1.1+ 3

value: WT


title: LUM0352 FVN/B wildtype mouse 7263461


title: LUM0351 FVN/B wildtype mouse 7263460


title: MiR155 KI NKT WT_2 NK1.1+

description: MiR 155KI WT NK1.1+ 2


title: MiR155 KI NKT WT_1 NK1.1+

description: MiR 155KI WT NK1.1+ 1


title: R.312_Spleen_GEX

city: Boston

first: Jim

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
Single-cell RNA – scRNA-Seq
Initial_10x_GEX_filtered_feature_bc_matrix.h5

data_processing:
Samples were aligned using the Cellranger multi pipeline (v6.0.2), with VDJ libraries listed as “vdj-t” to indicate T cell libraries. Samples were aggregated with the Cellranger aggr pipeline (v6.0.2) with normalize=none
We analyzed the total transcripts detected and total genes detected for each sample to determine appropriate thresholds and retained cells with 500 to 6,000 genes detected and 1,800 to 40,000 transcripts detected, and less than 5% of aligned reads originating from the mtDNA. We then applied SCTransform(52) to normalize the data, reduced the dimensionality of the dataset using PCA (retained 22 PC’s after check of ElbowPlot), clustered the data using Seurat’s FindClusters function with a resolution of 0.2, and subsetted the dataset to T cells by removing two clusters that were not enriched for the T cell genes CD3E, CD4, CD8A, or TRAC.
This resulted in a dataset with 28,646 cells by 15,904 genes. We then repeated the above procedure from SCTransform to clustering using 23 PC’s.
We then limited the dataset to samples from the PBMC, the MLR experiments, and the GVHD target organs. We then removed genes present in less than 5 cells, resulting in a dataset with 23,618 cells by 15,195 genes. This dataset was normalized using the same pipeline previously described, retaining 22 PC’s from the PCA.
Genome_build: MMul 10
Supplementary_files_format_and_content: h5 matrix of single-cell RNA-Seq

organism: Macaca mulatta

source_name: T Cells obtained from Spleen

extract_protocol:
Blood and MLR Samples: RM PBMCs were isolated from whole blood by Ficoll gradient centrifugation, and then used for MLR assays either immediately, or after liquid nitrogen cryopreservation in 10% dimethyl sulfoxide (DMSO)/90% fetal bovine serum (FBS). Frozen samples were thawed using RPMI-1640 media prior to resuspension in X-vivo-15 medium (BioWhitaker) supplemented with with 10% FBS (Irvine Scientific) for MLR incubation. At the time of the MLR, stimulator PBMCs were irradiated with 3500 cGy of (137Cs) radiation. Responder PBMCs were stained with cell trace violet (CTV, Invitrogen) as per manufacturer’s instructions. 2× 105 T cell-enriched responder PBMCs along with an equal number of stimulator PBMCs were added to each well in a 96-well plate (Corning) in X-vivo-15 medium supplemented with 10% FBS and incubated at 37°C for a total of 5 days. Cell culture media change was performed on day 3 of the culture. At the end of 5 days, cells were stained with an extracellular antibody for CD3 (clone SP34-2), CD20 (clone 2H7) and CD14 (clone M5E2, all antibodies from BD Bioscience) for 20min at 4°C, and high-, medium- and non-proliferating CD3+ T cells (identified based on the dilution of CTV) were sorted and processed for single cell sequencing using the Chromium Next GEM Single Cell 5’ Reagent Kit with optimized RM primers as described below.
GvHD Organ Samples: Viable LIVE/DEAD Violet-negative CD45-positive cells were sorted from two out of four GVHD-derived samples into host and donor fractions, based on MAMU-A001 expression.
10x Genomics Single Cell 5’ Reagent Kit for Single-cell RNA-Seq and with custom RM primers for single-cell TCR-Seq

tag: modality

value: GEX

tag: source

value: Spleen


title: R.279_MLR_VDJ_V2Primers

description:
Single-cell RNA – scRNA-Seq
V2_Primer_Contigs.tsv.gz

source_name: T Cells obtained from MLR

value: VDJ

value: MLR


title: R.319_Blood_GEX

source_name: T Cells obtained from Blood

value: Blood


title: R.319_MLR_GEX


title: R.319_CD3_GEX

source_name: T Cells obtained from CD3


title: MiR155 KI NKT WT_3 NK1.1-

description: MiR 155KI WT NK1.1- 3


title: LUM0350 FVN/B wildtype mouse 7263458

value: FVN/B wildtype mouse


title: R.279_Blood_GEX


title: R.279_MLR_GEX


title: MiR155 KI NKT WT_2 NK1.1-

description: MiR 155KI WT NK1.1- 2


title: R.279_CD3_GEX


title: LUM0355 YAC128 mouse on FVN/B strain 7260444

value: YAC128 mouse on FVN/B strain


title: LUM0356 YAC128 mouse on FVN/B strain 7261171


title: LUM0348 FVN/B wildtype mouse 7262576


title: LUM0347 FVN/B wildtype mouse 7260443


title: MiR155 KI NKT WT_1 NK1.1-

description: MiR 155KI WT NK1.1- 1


title: R.276_Blood_GEX


title: R.276_Liver_GEX

source_name: T Cells obtained from Liver

value: Liver


title: LUM0346 FVN/B wildtype mouse 7252116


title: R.276_MLR_GEX


title: R.328_Blood_VDJ

description:
Single-cell RNA - scTCR-Seq
V1_Primer_Contigs.tsv.gz


title: LUM0349 FVN/B wildtype mouse 7263457


title: PML-RARa/FLT3+_50195

city: Leuven

first: Zeynep

last: Kalender Atak

address: Herestraat 49

country: Belgium

institute: KULeuven

description: Sample 19

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters
Read counts per gene were obtained with the HTSeq package with htseq-count
The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.
Genome_build: GRCh37.61; GRCh37.p3
Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale

source_name: Bone Marrow

growth_protocol: none; primary patient sample

extract_protocol:
RNA extraction were performed using Trizol reagents (Invitrogen).
Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations  under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.

tag: diagnosis

value: acute myeloid leukemia (AML)

tag: aml type

value: Bone Marrow


title: Lib_FUN-55

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
hg38

source_name: Control Ileum HIBEC

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: disease state

value: Control

tag: tissue

value: Ileum

tag: cell type

value: HIBEC


title: Lib_FUN-56


title: Lib_FUN-54

source_name: Control Colon HIBEC

value: Colon


title: Lib_FUN-53


title: R.328_High_VDJ

source_name: T Cells obtained from MLR (CTV High)

value: MLR High


title: R.328_Low_VDJ

source_name: T Cells obtained from MLR (CTV Low)

value: MLR Low


title: R.328_Mid_VDJ

source_name: T Cells obtained from MLR (CTV Mid)

value: MLR Mid


title: R.327_Blood_VDJ


title: PML-RARa/FLT3+_45095

description: Sample 17


title: Lib_FUN-52


title: R.276_Spleen_GEX

value: GEX


title: PML-RARa/FLT3+_50536

description: Sample 18


title: Lib_FUN-51


title: NPM1+/FLT3-_49532

description: Sample 15


title: R.327_High_VDJ


title: R.330_Blood_VDJ


title: R.330_Mid_VDJ


title: Lib_FUN-50

source_name: UC Colon HIBEC

value: UC


title: R.330_Low_VDJ

value: VDJ


title: LUM0345 FVN/B wildtype mouse 7248227

tag: strain

tag: age (weeks)


title: R.327_Mid_VDJ


title: NPM1+/FLT3-_48899

description: Sample 14


title: PML-RARa/FLT3+_50569

description: Sample 16


title: R.330_High_VDJ


title: R.227_Liver_GEX


title: R.319_Blood_VDJ


title: Lib_FUN-49


title: Lib_FUN-48


title: R.319_CD3_VDJ


title: R.319_MLR_VDJ

value: MLR


title: NPM1+/FLT3-_49213


title: R.327_Low_VDJ


title: Lib_FUN-47


title: R.329_Blood_VDJ

value: Blood


title: NPM1+/FLT3-_48882

description: Sample 11


title: NPM1+/FLT3+_49305

description: Sample 10


title: Lib_FUN-46

source_name: CD Colon HIBEC

value: CD


title: Lib_FUN-45


title: R.329_Low_VDJ


title: R.329_Mid_VDJ


title: R.329_High_VDJ


title: R.279_Blood_VDJ


title: R.312_Spleen_VDJ

value: Spleen


title: Lib_FUN-44


title: R.279_MLR_VDJ


title: Lib_FUN-43


title: R.276_Spleen_VDJ


title: R.279_CD3_VDJ


title: NPM1+/FLT3+_48792

description: Sample 7


title: R.276_Blood_VDJ


title: NPM1+/FLT3-_48865

description: Sample 13


title: NPM1+/FLT3+_49666

description: Sample 8


title: Lib_FUN-42


title: Lib_FUN-41


title: R.276_MLR_VDJ


title: NPM1+/FLT3+_48758

description: Sample 6


title: R.227_Spleen_VDJ


title: R.276_Liver_VDJ

value: Liver


title: t(6;14)_390_11_pt.7

description: Sample 5

value: FLT3 positive mixed myeloid/T-cell lymphoid leukemias (MLPA)

tag: translocation


title: Lib_FUN-40

source_name: CD Ileum HIBEC


title: t(2;14)_176_10_pt.5

description: Sample 4

value: Bone Marrow


title: NPM1+/FLT3+_48604

description: Sample 9

value: acute myeloid leukemia (AML)


title: Platelets from Pf4Cre-Srsf3fl/fl mice, replicate 3

city: Clayton

first: Minna-Liisa

last: Anko

state: VIC

address: 15 Innovation Walk

department: Department of Anatomy and Developmental Biology

institute: Monash University

data_processing:
For megakaryocyte data, the raw read were trimmed using Trimmomatic with default parameters. The reads were aligned with STAR to Ensembl mm10 reference genome. The aligned files were deduplicated using the Picard MarkDuplicates function, ["Picard Toolkit." 2019 Broad Institute, Github Repository. http://broadinstitute.github.io/picard/; Broad Institute]. To obtain levels of gene expression, read counts were generated with the Subread function FeatureCounts. Genes with 1 count per million (CPM) in at least two samples were kept for further analysis.  Normalisation and differential gene expression was conducted with EdgeR.
For platelet data, Torrent Suite Software v5.6 (Thermo Fisher) was used for read processing, base calling, alignment to the reference transcriptome (mm10) and gene expression counts. Differential gene expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing log-fold change, p-value, FDR and read counts for DEGs

source_name: Platelets

extract_protocol:
Following fluorescence associated cell sorting based on CD41 and ploidy, low ploidy (8N only) and high ploidy (≥16N) megakaryocytes were pooled (52k±32k per sample) for RNA isolation using RNeasy Mini kit (Qiagen). RNA from washed platelets was isolated using TriReagent (Sigma-Aldrich).
Megakaryocyte RNA-seq libraries were prepared using SMARTer Stranded Total RNA Low Input Sample Prep kit (Clontech) and RNA-sequencing by Illumina HiSeq1500. Platelet RNA-seq libraries were prepared from 10ng of total RNA using an Ion AmpliSeq Transcriptome Mouse Gene Expression Kit and libraries were sequenced on an Ion Proton Sequencer (Thermo Fisher)

value: Platelets


title: R.227_Liver_VDJ


title: Platelets from Pf4Cre-Srsf3fl/fl mice, replicate 2


title: Lib_FUN-39

value: Ileum

value: HIBEC


title: t(2;14)_709_05_pt.4

description: Sample 3


title: Lib_FUN-38

value: Colon


title: Lib_FUN-37


title: t(2;14)_612-11_pt.1

description: Sample 1


title: Lib_FUN-36

value: Control


title: Platelets from Pf4Cre-Srsf3fl/fl mice, replicate 4


title: RNA-seq LPS Non-Cond rep3

city: Rishon LeZion

first: Tatiana

last: Kisliouk

address: 68 HaMaccabim Road

department: Animal Sciences

institute: ARO

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using Cutadapt. Resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome (galGal5.0, UCSD) according to Refseq annotations, using STAR.Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Read counts per gene were calculated using HTSeq-count, with the following parameters: 'htseq-count -s no --mode=union’. Normalization and differential expression analysis were performed using the DESeq2. Differentially expressed genes (DEG) were defined as genes that had a significant adjusted p value (padj) of less than 0.05 and at least 2-fold change. To elucidate gene alterations across all analyzed groups, the expression of all DEG was assessed. Respective heat maps were generated by custom R scripts and the Complexheatmap R package.
Genome_build: galGal5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Anterior hypothalamus

extract_protocol:
Total RNA was isolated with the RNA/DNA Purification Micro Kit (Norgen Biotek, Thorold, ON, Canada)
15 ng of purified RNA was used for library preparation with the bulk MARS-seq method (Jaitin et al. 2014 Science.343:776-9).100bp single reads were sequenced on a Novaseq 6000 sequencing system. The output was ~25 million reads per sample.

treatment_protocol: Chicks were heat‐conditioned on day 3 posthatch at 39°C for 24 h. One week later (day 10), LPS or saline was injected into the third ventricle. Chicks were sacrificed on day 11 and their AH dissected. Microglial cell population from hypothalamic cell pools of 10–12 chicks each was collected by FACS. Total RNA was isolated from each sample and subjected to RNA-Seq. DNA was extracted from microglia of 10-day-old heat-conditioned and non-conditioned chicks before LPS-challenge and subjected to RRBS.

value: microglia

tag: treatment

value: Non-Conditioned, LPS injected

tag: age

value: day 11 posthatch


title: RNA-seq LPS Cond rep2

value: Conditioned, LPS injected


title: RNA-seq LPS Cond rep1


title: mCtx_Cyto_rep 3_Small

institute: UCLA

description:
small RNA (ribominus)
Cytoplasmic small RNA im mCtx biological replicate 3

data_processing: none provided by the submitter

source_name: mouse primary cortical neuron  (mCtx)

extract_protocol:
Total RNA was collected with the Trizol LE regent for cytoplasmic RNAs, and Trizol reagent for soluble nucleoplasmic and chromatin-associated RNAs. Short RNA below 200 nt was selected using RNeasy MinElute Cleanup Kit (Qiagen). RNA was processed with Ribo-minus kit to remove ribosomal RNA.
Libraries were constructed with the Illumina TruSeq Small RNA sample Prep Kit. A final library of 120-160 bp was size selection with an TBE gel.
The libraries were subjected to 100 bp single-end sequencing (MiSeq).


title: Platelets from Cre-negative control mice, replicate 3

tag: genotype

value: Cre- control


title: Platelets from Cre-negative control mice, replicate 2


title: Platelets from Cre-negative control mice, replicate 1


title: mCtx_Nuc_rep 3_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mCtx biological replicate 3


title: RNA-seq LPS Non-Cond rep1


title: Lib_FUN-34


title: Lib_FUN-35


title: mCtx_Chr_rep 3_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mCtx biological replicate 3


title: RNA-seq LPS Cond rep3


title: Lib_FUN-33


title: R.312_Liver_VDJ

value: VDJ


title: mCtx_Cyto_rep 2_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mCtx biological replicate 2


title: RNA-seq Saline Cond rep3

value: Conditioned, saline injected


title: Platelets from wild type mice, replicate 2

value: wild type


title: Lib_FUN-30

value: CD


title: Platelets from Pf4Cre-Srsf3fl/fl mice, replicate 1


title: t(2;14)_81-07 _pt.2

description: Sample 2

source_name: Peripheral Blood

value: FLT3 positive mixed myeloid/T-cell lymphoid leukemias (MLPA)

value: Peripheral Blood


title: Platelets from wild type mice, replicate 1


title: Lib_FUN-29


title: RNA-seq Saline Cond rep2


title: RNA-seq LPS Non-Cond rep2


title: mCtx_Chr_rep 2_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mCtx biological replicate 2


title: Lib_FUN-28

value: UC


title: mCtx_Nuc_rep 1_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mCtx biological replicate 1


title: RNA-seq Saline Cond rep1


title: Platelets from wild type mice, replicate 3

value: Platelets


title: RNA-seq Saline Non-Cond rep1

value: Non-Conditioned, saline injected


title: mCtx_Cyto_rep 1_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mCtx biological replicate 1


title: RNA-seq Saline Non-Cond rep2


title: Lib_FUN-27

value: HIBEC


title: Stimulated Het rep3

data_processing:
Data Analysis : Downstream analysis was performed using a combination of programs including STAR, HTseq, dEseq2 and our wrapped scripts. Alignments were parsed using STAR program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to the reference genome : Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Correlations To allow for log adjustment, genes with 0 FPKM are assigned a value of 0.001. Correlation were determined using the cor test function in R with options set alternative =”greater” and method = “Spearman”.
GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). cluster Profiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Alternative splicing analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: tab-delimited xls files include count values for all samples along with the list of differentially expressed genes in the respective RNAseq expriment.

source_name: Spleenocyte, Lymph node

growth_protocol: Cells were grown in complete media when ever required using standard procedure

extract_protocol:
Briefly, spleen and lymph node from mice were extracted followed by isolation of CD8 T cells. RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Stimulated RNAseq was done after treatment of cells with CD3/CD28 for 48 hrs

value: Spleen, lymph node

value: 4-6 week


title: Stimulated Het rep2


title: Stimulated KO rep2


title: Stimulated KO rep3


title: mCtx_Chr_rep 1_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mCtx biological replicate 1


title: mNPC_Cyto_rep 3_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mNPC biological replicate 3

source_name: mouse neuronal progenitor cell (mNPC)


title: mCtx_Nuc_rep 2_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mCtx biological replicate 2


title: Lib_FUN-25

source_name: UC Colon HILEC

value: Colon

value: HILEC


title: mNPC_Nuc_rep 3_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mNPC biological replicate 3


title: Stimulated Het rep1


title: Lib_FUN-24


title: Stimulated KO rep1


title: RNA-seq Saline Non-Cond rep3

value: microglia

value: day 11 posthatch


title: Lib_FUN-26


title: Lib_FUN-22


title: Naive Het rep3


title: mNPC_Cyto_rep 2_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mNPC biological replicate 2


title: Naive Het rep2


title: mNPC_Nuc_rep 2_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mNPC biological replicate 2


title: Lib_FUN-20

source_name: Control Ileum HILEC

value: Control

value: Ileum


title: Lib_FUN-21


title: PERK_GSK_3

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: cDNA were hybridized for 16 h at 45°C on GeneChip ClariomS Human from Affymetrix GeneChips, washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v22 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a new matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples. We set a filter for those genes that displayed at least a ≥1,5 or ≤-1,5 fold difference in expression between groups and achieved an FDR of <0.05. Data were then interrogated for evidence of biologic pathway dysregulation using Gene set enrichment analysis (GSEA, Broad Institute). Enrichment rates were considered as significant for P-value <0.05 and FDR ≤0.1.

label: Biotin

source_name: MOLM-14 PERK KO cells incubated with GSK621

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript Sense Target labelling assay kit Affymetrix, Santa Clara, CA).

growth_protocol: AML cells were cultured in 10% fetal calf serum supplemented minimum essential medium Eagle (MEM, α-modification, Gibco, Lifetechnologies, Carlsbad, CA, USA, reference 41090028).

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), and 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit according to the manufacturer’s instructions (Affymetrix, Thermo Fischer Scientific).

treatment_protocol: PERK WT and PERK KO MOLM-14 cells were cultured 6h with vehicle (DMSO) or 30mM GSK621 before RNA extraction

value: hematopoietic

tag: cell line

value: acute myeloid leukemia

value: PERK KO

tag: treated with


title: Naïve KO rep3


title: mNPC_Chr_rep 2_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mNPC biological replicate 2

tag: sample type


title: PERK_GSK_2


title: Lib_FUN-19


title: SCR_GSK_3

source_name: MOLM-14 cells incubated with GSK621

value: SCR control