title: F-HDAC-1.A05

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal


title: U937_72h_DAC_1

status: Public on Jun 30 2022

type: genomic

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

department: Div. Applied Bioinformatics

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: DNA methylation data  quality control and analysis were were performed using the Bioconductor package RnBeads (version 1.10.8). Sites that overlapped with SNPs and cross-reactive probes were filtered.  Furthermore, probes giving unreliable measurements, determined by the Greedycut algorithm, were excluded from analysis. The data were subjected to background subtraction using the methylumi package (method enmix.oob) and beta-mixture quantile normalization (BMIQ).

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: U-937 cells; treated with DAC after 0, 24 und 48 hours; harvested after 72 hours

label_protocol: Standard Illumina Protocol

extract_protocol: Cells were harvested after 72 and 120 hours of treatment. Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) for cell culture according to the manufacturer's protocol. Frozen cell pellets were thawed carefully and dissolved in PBS. Treatment with Proteinase K led to digestion of contaminating protein. By adding ethanol DNA was precipitated. After centrifugation the DNA was eluted in Tris-EDTA containing buffer.

treatment_protocol: U-937 cells were treated in triplicates with daily pulses of 200 nM DAC for three consecutive days. After 48 hours, simultaneously to the third DAC dose, 1 µM ATRA was administered.

tag: cell line

value: U-937; human AML cell line


title: F-HDAC-1.A03

type: SRA

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: C1 CAGE

library_source: transcriptomic

data_processing:
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of   alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set

molecule: total RNA

growth_protocol: Cells were cultured in DMEM high glucose medium supplemented with 10% inactivated fetal bovine serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 1 mM sodium pyruvate.

extract_protocol:
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).

treatment_protocol: Three treatment groups were made, with 1) untreated, 2) 1 uM TSA for 6 hours, and 3) 1 mM VPA for 6 hours.

tag: treatment

value: Control


title: WT, rep2, RNA-seq

city: Riverside

first: Xuemei

last: Chen

state: CALIFORNIA

address: 900 University AVe

country: USA

institute: University of California

data_processing:
Reads were mapped to the Arabidopsis genome Araport11 using STAT v2.6(47) with default settings. Mapped reads were counted using featureCounts v1.64(48) and differential expressed gene were analyzed using the R package DESeq2.
Assembly: TAIR 10
Supplementary files format and content: CSV file containing normalized read counts for all detected genes

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: 16 hr light and 8 hr dark on 1/2 MS medium

extract_protocol:
14-day-old seedlings were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent.
RNA library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB# E7770)
mRNAseq

tag: tissue

value: seedling

tag: genotype

value: Wild type


title: aar2-1, rep2, RNA-seq


title: F-HDAC-1.A04

description: C1 CAGE

value: VPA


title: WT, rep1, RNA-seq


title: S30

city: Manipal

first: Padmalatha

middle: S

last: Rai

state: Karnataka

address: Manipal

department: Biotechnology

country: India

institute: Manipal School of Life Sciences, Manipal Academy of Higher Education

data_processing:
Transcriptome sequencing data was analysed on Torrent Suite (Version 5.10.0) using the RNASeq Analysis plugin (5.2.0.5)
The STAR aligner was used to map reads to the hg19 version of the human genome. The unmapped reads in the first step were aligned using bowtie2.
Mapped reads from both the alignments were merged with Picard tools to obtain the read counts. The high-quality aligned reads were generated from the  filtered data and saved as ‘bam’ files.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file with absolute read counts for all samples

source_name: Whole Blood

extract_protocol:
Total RNA from whole blood was isolated using TRI reagent (MRC, Inc, USA). The integrity of the RNA was checked through agarose gel electrophoresis, and quantity was evaluated using Qubit fluorometer (Invitrogen, US). The isolated RNA samples were stored at −80°C until used. We performed whole transcriptome sequencing of total 30 RNA samples using poly(A) enrichment of the mRNA using dynabeads mRNA direct micro kit (Invitrogen, US; Thermo Fisher Scientific, Inc., US). Briefly, 1 µg of total RNA was subjected to mRNA enrichment using dynabeads oligo (dT) 25 (Thermo Fisher Scientific, Inc., US), and the eluted mRNA was used for library construction and sequencing.
Ion total RNA-seq kit v2 (Thermo Fisher Scientific, Inc., US) was used to construct whole transcriptome libraries from 1-500 ng of enriched poly(A) RNA according to manufacturer’s protocols.

value: Whole Blood

tag: age

tag: gender

value: MALE

tag: disease

value: healthy control

tag: group

value: control


title: U937_72h_DAC+ATRA_2

source_name: U-937 cells; treated with DAC after 0, 24 und 48 hours; treated with ATRA after 48 hours; harvested after 72 hours


title: U937_72h_ATRA_3

source_name: U-937 cells; treated with ATRA after 48 hours; harvested after 72 hours


title: F-HDAC-1.A01

description: C1 CAGE


title: U937_120h_untreated_2

source_name: U-937 cells; untreated; harvested after 120 hours


title: Drug_response_MCF7_bulk.BM-VPA-3

description: Bulk CAGE

source_name: MCF7 cell line


title: F-HDAC-1.A02

description: C1 CAGE


title: S28


title: U937_72h_DAC+ATRA_1


title: Drug_response_MCF7_bulk.BM-VPA-1

description: Bulk CAGE


title: Drug_response_MCF7_bulk.BM-VPA-2

description: Bulk CAGE


title: WT, rep3, RNA-seq


title: U937_72h_ATRA_2


title: U937_72h_ATRA_1


title: S29


title: Drug_response_MCF7_bulk.BM-TSA-2

description: Bulk CAGE

value: TSA


title: U937_72h_DAC+ATRA_3


title: S25

value: FEMALE


title: S27


title: S26


title: Drug_response_MCF7_bulk.BM-NR-3

description: Bulk CAGE


title: SAN_d

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
array detection: SA_Cy3
SA-d

hyb_protocol: A total of 750 ng biotinylated aRNA for each sample was hybridized overnight to Illumina Mouse Ref-8 v2  BeadChips. Following posthybridization rinses, arrays were incubated with streptavidin-conjugated Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.53 μm using an Illumina iScan scanner

data_processing: Hybridization intensity data extracted from the scanned images using Illumina BeadStudio GenomeStudio software, V2011.1.

label: Biotin

organism: Mus musculus

source_name: Sinoatrial node_replicate4

label_protocol: Total RNA quantity and quality was tested using the Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA). Five hundred ng total RNA was labeled according to the manufacturer’s instructions using the Illumina TotalPrepTM RNA amplification kit (Illumina, San Diego, CA).

growth_protocol: Mice were deeply anesthetized by 320 - 450 mg/kg pentobarbital sodium with 100 UI heparin. After checking suppression of the nociceptive reflex, the chest cavity was opened, and the heart and lung were excised in a block and then perfused sequentially with ice-cold, Ca2+ free, and heparinized external solution until most of the blood was washed out from the heart and lung. The composition of the external solution (mM) was: NaCl 136.9, KCl 5.4, NaH2PO4 0.33, HEPES 5.0, MgCl 0.5 and glucose 5.5 (pH 7.4 with NaOH). The heart-lung block was pinned to the tissue bath. Soft tissue containing the vagus nerve, adipose tissue was trimmed off under a stereomicroscope, then cardiopulmonary tissues were isolated one by one. Left atrium (LA) adjacent to the pulmonary vein (PV), a mass of left ventricle (LV), and free-wall of the right ventricle (RV) was isolated. Each LV mass was dissected into three pieces as samples. Because the SAN isolation procedure takes approximately 20 minutes, SA was isolated separately. The SA region was delimited by the borders of the crista terminalis, the interatrial septum, the superior vena cava, and right atrium (RA). Our SA-cutting technique was confirmed by quantitative PCR for mice. During tissue isolation, the external solution was perfused at a rate of 10 ml/min on ice. All cardiopulmonary tissues were isolated within 30 minutes after the heart was removed from the body. All tissue samples were fresh-frozen in liquid nitrogen and stored at - 80 °C for later RNA extraction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini columns (QIAGEN, Venlo, Netherland) using the manufacturers protocol.

tag: strain

value: Sinoatrial node

tag: Sex

value: Male

value: 5-10 weeks


title: S24


title: U937_120h_untreated_3


title: S23


title: U937_120h_DAC+ATRA_3

source_name: U-937 cells; treated with DAC after 0, 24 und 48 hours; treated with ATRA after 48 hours; harvested after 120 hours


title: Drug_response_MCF7_bulk.BM-NR-2

description: Bulk CAGE


title: SAN_a

description:
array detection: SA_Cy3
SA-a

source_name: Sinoatrial node_replicate1


title: U937_120h_DAC+ATRA_1


title: S22


title: U937_120h_DAC_3

source_name: U-937 cells; treated with DAC after 0, 24 und 48 hours; harvested after 120 hours


title: SAN_c

description:
array detection: SA_Cy3
SA-c

source_name: Sinoatrial node_replicate3


title: Drug_response_MCF7_bulk.BM-NR-1

description: Bulk CAGE


title: SAN_b

description:
array detection: SA_Cy3
SA-b

source_name: Sinoatrial node_replicate2


title: U937_120h_DAC_1


title: RV_9

description:
array detection: SA_Cy3
RV9

source_name: Right ventricle_replicate4

value: Right ventricle


title: Drug_response_HepG2_bulk.BH-VPA-3

description: Bulk CAGE

source_name: HepG2 cell line


title: U937_120h_ATRA_1

source_name: U-937 cells; treated with ATRA after 48 hours; harvested after 120 hours


title: RV_8

description:
array detection: SA_Cy3
RV8

source_name: Right ventricle_replicate3


title: S19

value: Type 2 Diabetes


title: aar2-2, rep1, RNA-seq


title: RA_7

description:
array detection: SA_Cy3
RV7

source_name: Right ventricle_replicate2


title: U937_120h_untreated_1


title: U937_120h_DAC+ATRA_2


title: S21


title: S16


title: Drug_response_HepG2_bulk.BH-TSA-2

description: Bulk CAGE


title: S20


title: Drug_response_HepG2_bulk.BH-TSA-1

description: Bulk CAGE


title: RV_2

description:
array detection: SA_Cy3
RV2

source_name: Right ventricle_replicate1


title: S18

source_name: Whole Blood


title: U937_120h_DAC_2


title: Drug_response_HepG2_bulk.BH-VPA-2

description: Bulk CAGE


title: U937_120h_ATRA_3


title: Drug_response_HepG2_bulk.BH-VPA-1

description: Bulk CAGE


title: S17


title: Drug_response_HepG2_bulk.BH-TSA-3

description: Bulk CAGE


title: S14


title: S15


title: Drug_response_HepG2_bulk.BH-NR-2

description: Bulk CAGE


title: RA_3

description:
array detection: SA_Cy3
RA3

source_name: Right atrium_replicate3

value: Right atrium


title: RA_4

description:
array detection: SA_Cy3
RA4

source_name: Right atrium_replicate4


title: RA_2

description:
array detection: SA_Cy3
RA2

source_name: Right atrium_replicate2


title: Drug_response_MCF7_bulk.BM-TSA-1

description: Bulk CAGE

source_name: MCF7 cell line


title: Drug_response_HepG2_bulk.BH-NR-1

description: Bulk CAGE


title: Drug_response_HepG2_bulk.BH-NR-3

description: Bulk CAGE


title: S11


title: Drug_response_fibroblasts_bulk.BF-VPA-2

description: Bulk CAGE

source_name: Dermal fibroblasts, neonatal


title: S12


title: LV-7

description:
array detection: SA_Cy3
LV7

source_name: Left ventricle_replicate2

value: Left ventricle


title: Drug_response_fibroblasts_bulk.BF-VPA-3

description: Bulk CAGE


title: RA_1

description:
array detection: SA_Cy3
RA1

source_name: Right atrium_replicate1


title: S10


title: U937_120h_ATRA_2

value: U-937; human AML cell line


title: S13


title: Drug_response_fibroblasts_bulk.BF-TSA-3

description: Bulk CAGE


title: LV-8

description:
array detection: SA_Cy3
LV8

source_name: Left ventricle_replicate3


title: S8


title: LV-9

description:
array detection: SA_Cy3
LV9

source_name: Left ventricle_replicate4


title: Drug_response_fibroblasts_bulk.BF-TSA-1

description: Bulk CAGE


title: S9


title: LA_4

description:
array detection: SA_Cy3
LA4

source_name: Left atrium_replicate4

value: Left atrium


title: LA_3

description:
array detection: SA_Cy3
LA3

source_name: Left atrium_replicate3


title: Drug_response_MCF7_bulk.BM-TSA-3

description: Bulk CAGE


title: LV-2

description:
array detection: SA_Cy3
LV2

source_name: Left ventricle_replicate1


title: Drug_response_fibroblasts_bulk.BF-TSA-2

description: Bulk CAGE


title: S6


title: LA_1

description:
array detection: SA_Cy3
LA1

source_name: Left atrium_replicate1


title: Drug_response_fibroblasts_bulk.BF-VPA-1

description: Bulk CAGE


title: S7


title: S5


title: Drug_response_fibroblasts_bulk.BF-NR-3

description: Bulk CAGE

value: Control


title: S4


title: Drug_response_fibroblasts_bulk.BF-NR-2

description: Bulk CAGE


title: LA_2

description:
array detection: SA_Cy3
LA2

source_name: Left atrium_replicate2


title: S3


title: S2


title: human MPCs PTF1A KO – rep2

city: BArcelona

first: Irene

last: Miguel-Escalada

address: Dr Aiguader 88

country: Spain

institute: CRG

library_source: genomic

data_processing:
Adaptors were trimmed from ChIP-Seq raw reads using cutadapt v1.9.1 (options -m 20)
Trimmed ChIP-Seq reads were aligned to hg19 using bowtie2 v2.1.0 (options –no-unal)
ChIP-Seq peaks were called using MACS2 using options –bw=300 –keep-dup all -q 0.01 (H3K27ac) and -q 0.05 (PTF1A and MED1).
Consistent peaks between 2 biological samples were defined by overlapping MACS2 called peaks from each replicate with bedtools intersectBed v2.27.1
Genome_build: hg19
Supplementary_files_format_and_content: peak text files are broadPeak or narrowPeak text files outputs from MACS2
Supplementary_files_format_and_content: Bigwig files  were created using bedGraphToBigWig from UCSC tools.

source_name: human pancreatic MPCs

growth_protocol: Human embryonic stem cell line H1 (Wicell) was cultured in E8 medium (Thermo Fisher). Differentiation to pancreatic progenitors was performed following protocols published by Balboa et al 2018 and Rezania et al 2014.

extract_protocol:
MPCs were crosslinked with 1% PFA, lysed and sonicated with Covaris S220. DNA-protein complexes were isolated with antibodies, as described in Miguel-Escalada et al 2019.
NEBNext Ultra II DNA library Prep Kit (New England Biolabs)

tag: cell type

value: HPSCs-derived MPCs (stage 4)

tag: antibody

value: PTF1A (gift from Bertrand Blondeau)


title: human MPCs PTF1A KO – rep1


title: human MPCs PTF1A WT – rep1


title: B1b_WT_3

city: Charlottesville

first: Tanyaporn

last: Pattarabanjird

state: Virginia

address: 345 Crispell Dr. MR6

department: Carter Immunology Center

institute: University of Virginia

data_processing:
HISAT 2 for read alignment and was mapped to GrCM38/mm10
StringTie for assembling and merging transcript
Ballgown for plots and differential expression tables
Assembly: GrCM38/mm10

source_name: Peritoneal Cavity

extract_protocol:
Extraction and purification of RNA were performed using RNeasy kit (Qiagen). Total amount of ~200ng for each sample was used to construct sequencing libraries.
All of the library preperation steps were performed by Novogene. In brief, mRNA was enriched with poly A capture following by RNA fragmentation using enzyme digestion and cDNA generation using reverse transcription.

value: Peritoneal Cavity

value: WT


title: B1b_WT_2


title: human MPCs Med1 KO – rep2

value: MED1 (Bethyl laboratories, A300-793A)


title: Drug_response_fibroblasts_bulk.BF-NR-1

description: Bulk CAGE


title: human MPCs Med1 KO – rep1


title: S1

source_name: Whole Blood

value: Whole Blood

value: MALE


title: human MPCs Med1 WT – rep2


title: B1a_WT_3


title: LPS3

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

country: South Korea

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

description: Replicate3:negative control for drug

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref8 expression v.2 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Probes signal value was transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using LPE test and Fold change in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.   Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/).   All data analysis and visualization of differentially expressed genes was conducted using R 2.15.0 (www.r-project.org).

label: biotin

source_name: MACS-sorted GR1+ cells from spleen

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: female C57BL/6 mice were injected with LPS (or PBS) i.p. at time 0, and were injected with HY209 (or PBS) 30 min later.

extract_protocol: Gr1+ cells were MACS-soreted from 10-15 spleens of C57BL/6 mice in each group and were pooled together. It was repeated three times to make 3 seperate bilogical samples for microaray. Two to three biological replicates each containing Gr1+ cells (More than 95 % of Gr1+ cells were CD11b+) were amplified using Ambion Illumina TotalPrep RNA Amplification kit. Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Spleens were extracted from the mice at 48h after the LPS injection. Gr1+ cells were MACS purified.

tag: lps injection

value: yes

tag: hy209 injection

value: Spleen

value: 6~8 week


title: B1a_WT_2


title: B1b_WT_1


title: human MPCs PTF1A WT – rep2


title: LPS2

description: Replicate2:negative control for drug


title: human MPCs Med1 WT – rep1


title: LT3

description: Replicate3:test group


title: mice after intracerebral hemorrhage model operation [V3]

city: Hangzhou

first: Yonghe

last: Zheng

state: Zhejiang

address: Jiefang Road 88th

country: China

institute: department of neurosurgery, Zhejiang University School of Medicine Second Affiliated Hospital

data_processing:
cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam).
The mapped reads of each sample were assembled using stringtie-1.3.4(ccb.jhu.edu/software/stringtie/) with default parameters (command line: stringtie -p 2 -G genome.gtf -o output.gtf -l mapped.bam). Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kb)]).
Transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Assembly: musculus norvegicus.musculus_norvegicus.Rnor_6.0.96
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: time

value: wildtype

value: basal ganglia

value: The vehicle group was treated with the vehicle used for Laminaria after ICH


title: mice after intracerebral hemorrhage model operation treated with Laminaria [La2]

value: The La group was treated with Laminaria after ICH


title: mice after intracerebral hemorrhage model operation treated with Laminaria [La3]


title: PBS1

description: Replicate1:negative control for sepsis and drug


title: LT1

description: Replicate1:test group


title: mice after intracerebral hemorrhage model operation treated with Laminaria [La1]


title: B1a_WT_1


title: human MPCs H3K27ac KO – rep1

value: H3K27ac (Abcam, ab4729)


title: mice after intracerebral hemorrhage model operation [V2]


title: LPS1

description: Replicate1:negative control for drug


title: PBS3

description: Replicate2:negative control for sepsis and drug


title: LT2

description: Replicate2:test group


title: mice after intracerebral hemorrhage model operation [V1]


title: human MPCs H3K27ac WT – rep2


title: human MPCs H3K27ac KO – rep2


title: wt thymus xray rep 2  [single-end]

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Alignment of raw sequence reads to the murine transcriptome (mm10) was performed via Rsubread and transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline.
Assembly: mm10
Supplementary files format and content: RNA.invivo.d24.wt.p53.xray.csv
Supplementary files format and content: p53.Null.WT.xray.RNA.invivo.cpm.csv

source_name: thymus

extract_protocol: Expression profiling by high throughput sequencing of spleen, liver and thymus in wt p53 mice and mice with a deletion of the C-terminus of p53. Organ pieces are immediately placed in RNAlater during dissection and stored at 4oC until RNA is extracted using RNeasy Mini Kit (Qiagen) and following manufacturer’s instructions.  The isolated RNA is quantitated and either stored at -80o in preparation for RNA-seq. Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

value: thymus

value: tissue

value: xray 2Gy 3h


title: wt spleen xray rep 3 [single-end]

source_name: spleen

value: spleen

value: control


title: mice after shame operation [s2]

value: The sham mice received the same treatment, including needle insertion, but without whole blood  injection


title: mice after shame operation [s1]


title: human MPCs H3K27ac WT – rep1

value: HPSCs-derived MPCs (stage 4)


title: Met_7

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: polyA RNA

source_name: primary pancreatic neuroendocrine tumor tissue, diagnosed and prepapared by pathologists

extract_protocol:
Total RNAs were extracted from flash-frozen tumor tissues.Total RNA was used for TruSeq stranded library generation, and paired end clustering with 51x2 cycles of sequencing were performed on HiSeq 2500/4000 (Illumina) at the WCM genomics core facility
TotalScript RNA-Seq Kit (Epicentre)

value: Metastatic Pancreatic Neuroendocrine Tumors

tag: diagnosis

value: Well-differentiated pancreatic neuroendocrine neoplasm

value: F


title: wt thymus xray rep 1 [single-end]

value: WT


title: wt liver xray rep 3 [single-end]

source_name: liver

value: liver


title: Met_5

value: M


title: Met_4

value: Well-differentiated pancreatic neuroendocrine neoplasm, low grade

value: Unknown


title: wt spleen xray rep 1 [single-end]


title: Met_6


title: wt liver xray rep 1 [single-end]


title: Met_2

value: Carcinoma of the pancreas with both acinar and neuroendocrine differentiation


title: Met_3

value: Well-differentiated pancreatic neuroendocrine neoplasm, invading duodenum


title: d24 thymus xray rep 3 [single-end]

value: thymus


title: wt liver xray rep 2  [single-end]

value: tissue


title: Met_1


title: Myd88 Ctrl WT

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

library_source: transcriptomic single cell

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: GRChm8 V2.1.0
Supplementary files format and content: Seurat V4 R Objects

source_name: Myd88 Ctrl WT

extract_protocol:
Transmural tissue samples were removed from the left ventricle apex during LVAD implantation or after whole heart explantation. Samples for single cell were processed fresh by enzymatic digestion while samples for single nuclei were frozen in liquid nitrogen and stored at -80C until use and processed by mechanical homogenization. All single cell/nuclei suspensions were sorted by FACS to remove debris and dead cells.
10X Genomics Chromium Single Cell 5’ Reagent V1.1

tag: storage condition

value: Used fresh/not stored

tag: technology

value: Single Cell


title: Day 7 Recipient

source_name: Day 7 Recipient


title: Day 14 Recipient

source_name: Day 14 Recipient


title: Day 1 Recipient

source_name: Day 1 Recipient


title: Day 1 Donor

source_name: Day 1 Donor


title: wt spleen xray rep 2  [single-end]

value: spleen

tag: cell line

tag: treatment

value: control


title: wt thymus xray rep 3 [single-end]

tag: tissue

value: xray 2Gy 3h


title: d24 thymus xray rep 2  [single-end]


title: Baseline Donor

source_name: Baseline Donor


title: mice after shame operation [s3]

value: brain

tag: genotype

value: wildtype

value: basal ganglia

value: The sham mice received the same treatment, including needle insertion, but without whole blood  injection


title: Loc_9

value: Localized Pancreatic Neuroendocrine Tumors

value: Well-differentiated pancreatic neuroendocrine neoplasm


title: Loc_8

value: M


title: d24 spleen xray rep 3 [single-end]

value: WT


title: d24 spleen xray rep 1 [single-end]


title: Loc_6

value: Pancreatic endocrine neoplasm

value: F


title: Day 7 Donor

source_name: Day 7 Donor


title: Challenged Vegfr3iLECko rep3

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing was performed on the Illumina HiSeq platform.
Raw reads were aligned to the mouse genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) and Bowtie2.
Batch effects were corrected using DESeq2. Very low abundant genes (transcripts per million value < 2 in all sequencing samples) were removed.
Normalized data were subjected to differentially expressed gene (DEG, fold change > 2; p<0.05) analysis using the DESeq2 algorithm.
DEGs between the indicated groups were then used for generation of the Volcano plot and Venn diagram and for KEGG and GO functional enrichment analyses. Gene set enrichment analysis (GSEA) was also performed using DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: conjunctiva

growth_protocol: Mice were breeding on a C57BL/6j background and housed in a specific pathogen free animal facility with a 12h/12h light-dark cycle.

extract_protocol:
Total RNA was extracted from freshly dissected conjunctiva using the Qiagen RNeasy Plus Kit. To obtain sufficient quantitation of RNA, conjunctival tissue from three mice with identical genotyping and treatment condition was combined and used as one sequencing sample, and a total of three relicate experiments (3x3mice in each group) were performed.
RNA quality was evaluated via Agilent 2100 Bioanalyzer. One microgram of qualified RNA was used to construct mRNA sequencing libraries.

treatment_protocol:
Vegfr3fl/fl;Prox1CreERT2 and littermate Vegfr3fl/fl mice recieved five intraperitoneal (i.p.) injections of tamoxifen (75 mg/kg body weight) at week 5.
Mice at week 6 were immunized with i.p. injection of 5μL HBSS containing 250μg OVA and 0.3μg PTX as well as 5mg of aluminum hydroxide. After 14 days, mice were challenged by instillation of OVA eye drops (250μg/5μL) once daily for 28 days in the right eye, while the contralateral eye was treated with saline.

value: conjunctiva

value: Tamoxifen admin, OVA/PTX immunized, OVA challenged daily for 28 days


title: d24 spleen xray rep 2  [single-end]

value: tissue


title: Challenged Vegfr3iLECko rep2


title: Loc_5


title: Challenged Vegfr3iLECko rep1


title: d24 liver xray rep 2  [single-end]

value: liver


title: d24 liver xray rep 1 [single-end]


title: Loc_3


title: Challenged Ctrl rep2

value: Vegfr3 fl/f (Ctrl)


title: d24 liver xray rep 3 [single-end]

value: control


title: Challenged Ctrl rep1


title: Loc_4


title: d24 thymus xray rep 1 [single-end]

value: thymus


title: wt thymus xray rep 2  [paired-end]

value: xray 2Gy 3h


title: Myd88 KO

source_name: Myd88 KO

value: Used fresh/not stored

value: Single Cell


title: Challenged Ctrl rep3


title: Loc_1

value: Well-differntiated pancreatic endocrine neoplasm


title: wt thymus xray rep 1 [paired-end]


title: wt thymus xray rep 3 [paired-end]


title: Loc_2

value: Localized Pancreatic Neuroendocrine Tumors


title: Loc_15

value: Well-differentiated


title: Loc_13

value: Well-differentiated pancreatic neuroendocrine neoplasm

value: M


title: Loc_10


title: NeutsBld40

city: La Jolla

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
Read count was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: read_count.txt: tab-delimited text files includes read count for each samples (Column names: Gene ID, 30 samples as described in the SAMPLES section)

source_name: Blood

extract_protocol:
Neutrophil subpopulations were FACS sorted from human fresh bone marrow and melanoma blood
Cells will be sorted directly in TriZOL LS and frozen at -80 immediately. Sorted bone marrow cells and melanome blood in TRIzol LS Reagent were thawed on ice. RNA isolation was performed using the Direct-zolTMRNA MiniPrep (Zymo Research) according to manufacturer’s instructions. RNA concentration was measured on a Agilent 2200 TapeStation using the Agilent High Sensitivity RNA ScreenTape System (Agilent Technologies). Library preparation and sequencing will be performed according to the Smart-Seq2 protocol in the La Jolla Institute for Immunology sequencing core.

tag: disease state

value: Melanoma patient


title: GC, KO1, day14

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

data_processing:
RNA-seq fastq files were aligned to the Mus Musculus Reference Genome (version GRCm38) and raw gene read counts (Refgene) were generated using the Omicsoft Aligner (OSA).
Raw read counts were normalized and analyzed for differential expression using DESeq2

source_name: Primary lymph node cells

growth_protocol: SCAP(fl/fl), AID-Cre(+/-), R26-YFP(+/+) mice and SCAP(+/+), AID-Cre(+/-), R26-YFP(+/+) controls were immunized subcutaneously with 25μg NP-OVA adjuvanted with RIBI.

extract_protocol:
Cells were lysed in 350μL of Buffer RLT with β-ME (Qiagen). RNA was extracted using the RNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a Fragment Analyzer (Agilent) and 10ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding an average of 30 million reads per sample.

treatment_protocol:
At day 14 post immunization, inguinal lymph nodes were collected, processed into single cell suspensions, and stained with a panel of fluorochrome-conjugated antibodies.
8,000 YFP+ germinal center B cells (CD3-CD19+CD44-CD138-CD38-CD95+) were purified using the Aria II fluorescence activated cell sorter (BD Bioscience)

value: Primary lymph node cells

value: Germinal center B cells

value: NP-OVA+RIBI sc immunization

value: Day 14


title: GC, KO4, day14


title: Unchallenged Ctrl rep2

value: conjunctiva

value: Tamoxifen admin, OVA/PTX immunized


title: Loc_12


title: wt spleen no treatment rep 3 [paired-end]

value: spleen

value: tissue

value: WT

value: control


title: Loc_14


title: Unchallenged Ctrl rep1

value: Vegfr3 fl/f (Ctrl)


title: Unchallenged Ctrl rep3


title: wt spleen no treatment rep 2 [paired-end]


title: wt thymus no treatment rep 3 [paired-end]

value: thymus


title: Loc_11

value: Localized Pancreatic Neuroendocrine Tumors


title: wt spleen xray rep 3 [paired-end]

value: xray 2Gy 3h


title: NeutsBld36


title: GC, KO3, day14


title: wt spleen xray rep 2  [paired-end]


title: KO aIgM 24h_2

data_processing:
RNA-seq fastq files were aligned to the Mus Musculus Reference Genome (version GRCm38) and raw gene read counts (Refgene) were generated using the Omicsoft Aligner (OSA).
Raw read counts were normalized and analyzed for differential expression using DESeq2
Enrichment analysis was performed using hypergeometric distribution to identify the biological significance of the DE genes.

source_name: Spleenic B cells

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent)

treatment_protocol: B cells were beads-purified and stimulated

value: Spleenic B cells

value: B cell

value: SCAPfl/fl CD19Cre/+ (KO)

value: anti-IgM stimulation for 24 hrs


title: wt spleen no treatment rep 1 [paired-end]


title: wt spleen xray rep 1 [paired-end]


title: wt thymus no treatment rep 1 [paired-end]


title: GC, C4, day14

value: Primary lymph node cells

value: Germinal center B cells


title: NeutsBld34

value: Melanoma patient


title: wt liver xray rep 3 [paired-end]

value: liver


title: GC, KO2, day14

value: NP-OVA+RIBI sc immunization

value: Day 14


title: NeutsBld28


title: NeutsBld20


title: NeutsBld22


title: wt thymus no treatment rep 2 [paired-end]

value: tissue


title: NeutsBld26


title: BcellsBldS45

value: Bcells


title: WT aIgM 24h_2

value: SCAP+/+CD19Cre/+ (WT)


title: KO aCD40 24h_2

value: anti-CD40 stimulation for 24 hrs


title: KO aIgM 24h_1


title: GC, C3, day14


title: wt liver xray rep 2  [paired-end]

value: WT


title: GC, C1, day14


title: KO aCD40 24h_1


title: WT aIgM 24h_1


title: wt liver xray rep 1 [paired-end]


title: WT aCD40 24h_1


title: WT aCD40 24h_2


title: BcellsBldS44


title: BNeutsBld39

value: BNeuts


title: wt liver no treatment rep 1 [paired-end]

value: control


title: KO LPS 24h_1

value: Spleenic B cells

value: LPS stimulation for 24 hrs


title: NeutsBld18


title: KO LPS 24h_2

value: B cell

value: SCAPfl/fl CD19Cre/+ (KO)


title: WT LPS 24h_2


title: BcellsBldS41


title: wt liver no treatment rep 3 [paired-end]


title: BcellsBldS42


title: wt thymus no treatment rep 1

description: clusters.Thymus.irrad.IgG.bed

data_processing:
Alignment of raw sequence reads to the murine transcriptome (mm10) was performed via Rsubread.The p53 cistrome was analyzed with Rsubread/csaw.  A sliding window was used to identify capture read counts between the tissue-specific p53 signal and the relevant input, using a window width of 50 bp. To define significant p53 peaks a feature count matrix was filtered, globally normalized and dispersions calculated, following which a generalized linear model function applied to estimate significant differences. To minimize the penalties for false discovery, immediately adjacent significant windows were merged (to a maximum width of 5 kb) and the final peak pValue calculated on the merged and weighted windows. A significant peak was one with an FDR adjusted pValue < 0.2. The ChIPpeakAnno (Zhu et al., 2010) package was used to calculate the number of significant overlaps (minimum of 1 bp shared) of significant peaks across tissues,
Assembly: mm10
Supplementary files format and content: peak bed

extract_protocol: Dissected mouse organs are placed in 6-well plates contain chilled PBS. The DNA fragments are purified the following day using the Qiagen Qiaquick PCR purification Kit Protocol. The sample and input DNA can be used for PCR or measured using the Qubit reader and used for ChIP-seq.

value: thymus


title: BNeutsBld35


title: BcellsBldS43


title: wt thymus xray rep 2

description: clusters.Thymus.irrad.IgG.bed

value: xray 2Gy 3h


title: wt thymus xray rep 1

description: clusters.Thymus.irrad.IgG.bed


title: BNeutsBld33

value: Melanoma patient


title: wt spleen input

description: clusters.Spleen.irrad.IgG.bed

value: spleen

value: input


title: KO time 0_2

value: freshly isolated B cell, no treatment


title: wt thymus input

description: clusters.Thymus.irrad.IgG.bed

value: tissue


title: WT LPS 24h_1


title: wt liver no treatment rep 2 [paired-end]

value: liver


title: KO time 0_1


title: BNeutsBld27


title: wt spleen xray rep 2

description: clusters.Spleen.irrad.IgG.bed


title: BNeutsBld25


title: WT time 0_2

value: SCAP+/+CD19Cre/+ (WT)


title: wt spleen xray rep 1

description: clusters.Spleen.irrad.IgG.bed


title: BNeutsBld21


title: wt thymus no treatment rep 2

description: clusters.Thymus.irrad.IgG.bed


title: wt spleen no treatment rep 2

description: clusters.Spleen.irrad.IgG.bed


title: BNeutsBld17


title: NeutsBM58

source_name: Bone marrow

value: Healthy


title: WT time 0_1


title: CP_scRNAseq

city: Shanghai

first: Wenbin

last: Zou

address: No. 168, Changhai Road, Yangpu District, Shanghai

institute: Shanghai Institute of Pancreatic Diseases

description: BD

data_processing:
Basecalls performed using CASAVA version 1.8.
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
* MT% < 20%;
* Cell Gene Number < Median Gene Number * 2;
* Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10 (GRCm38)
Supplementary files format and content: *tsv: Tab-separated text files contain counts for each sample.

source_name: pancreas

extract_protocol:
Pancreata from one control mouse (sample 1) and two CP mice (sample 2) were enzymatically digested into a single-cell suspension, respectively. Freshly dissected tissue was laid placed on into a 10-cm tissue culture dish and cut into pieces using a sterile razor blade. After washing twice with PBS, each sample was moved to a 15-mL tube containing pre-warmed 37°C digestion buffer comprising 1% FBS, respectively. The tubes were incubated on a shaker at 37°C for 40 min at 37°C. Then, the cells were resuspended and washed three times in PBS before debris was filtered out with using a 30-μm mesh filter.
RNA libraries were generated by BD Rhapsody single cell RNA-seq and prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were randomly assigned to two groups (CP and control). To induce CP, mice were injected with caerulein (50 μg/kg/h) intraperitoneally 6 times a day at 1-hour intervals, 3 days per week, for a total of 6 weeks. The control group mice received injections of normal saline (NS) in lieu of caerulein.

value: pancreas

tag: age

value: 8 weeks

value: caerulein-induced CP


title: wt spleen no treatment rep 1

description: clusters.Spleen.irrad.IgG.bed

source_name: spleen

value: WT

value: control


title: wt liver no treatment rep 1

description: clusters.Liver.irrad.IgG.bed


title: wt liver xray rep 2

description: clusters.Liver.irrad.IgG.bed


title: BcellsBM54

value: Bcells


title: NeutsBM55


title: wt liver no treatment rep 2

description: clusters.Liver.irrad.IgG.bed


title: wt liver input

description: clusters.Liver.irrad.IgG.bed


title: wt liver xray rep 1

description: clusters.Liver.irrad.IgG.bed


title: BNeutsBld19

value: BNeuts


title: Fam69c WT

city: Beijing

first: Fan

last: Mei

address: 38 Xueyuan Road

institute: Peking University Health Science Center

description: 10x Genomics

data_processing:
Cell Ranger (v.4.0.0, 10× Genomics) was used for sample de-multiplexing, barcode processing and single-cell gene-UMI counting. Expression matrix was obtained and mapped to the Mus musculus reference genome mm10-2020-A, provided by 10× Genomics. Data processing was performed using the Seurat package (v.3.0) in R language (v4.0.3)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cortical tissue

extract_protocol:
The cortex from seven male mice at 4 months of age were pooled according to genotype and dissociated using gentleMACS Octo Dissociator with Heaters (Mitenyi Biotec no. 130-096-427) and Adult Brain Dissociation kit (Miltenyi Biotec no. 130-107-677). Cells were resuspended in 0.5% BSA in PBS and filtered through 70 μm filter. Cells were stained with 7-AAD (Invitrogen, 00-6993) and sorted using the BD FACS Aria III (100 μm nozzle).
Library construction was performed using Chromium Single Cell 3 Library and Gel Bead Kit v3.1 (10× Genomics, PN-1000121) with 13 or 12 indexing PCR cycles and sequencing on one high-output lane of the NovaSeq 6000 (Ilumina) with 28 bases for read 1, 150 bases for read 2 and 7or 8 bases for Index 1.

value: cortical tissue

value: brain cells

value: wildtype


title: BcellsBM56


title: BcellsBM50


title: NeutsBM52


title: WT CD8 T cell Post-transplant Day 7 Rep3

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

data_processing:
All data were processed and analyzed using the R programming language (Version 4.0.4), the RStudio interface (Version 1.4.1106), and Bioconductor
Transcript abundance of samples was computed by pseudoalignment with Kallisto (version 0.46.2). Transcript per million (TPM) values were then normalized for each pre and post transplant samples separately and fitted to a linear model by empirical Bayes method with the Voom and Limma R packages
Differential gene expression was defined as a FDR£10%; after controlling for multiple testing using the Benjamini-Hochberg method  were used for hierarchical clustering and heatmap generation in R.
Gene Ontology enrichment analysis was conducted using either the Function Annotation Chart tools using only GO BP and KEGG terms in the Database for Visualization and Integrative Discovery DAVID enrichment scores >1.3 are equivalent to a P value<0.05. For Gene set enrichment analysis (GSEA) we used Hallmark and C2 gene set collections of Molecular Signatures Database (MsigDB) and cluster Profiler package in R
Assembly: mm9
Supplementary files format and content: .tsv file

source_name: sorted CD8 T cell

extract_protocol: Total RNA was extracted with the Qiagen miRNeasy Mini kit. RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer. cDNA was prepared with the SMARTseq HT Kit (Takara Bio), using 1ng total RNA. Dual indexed sequencing libraries were prepared using the Nextera XT DNA Library Prep kit (Illumina), using 250pg cDNA.

tag: background strain

value: Wild type

tag: organ obtained

value: spleen

tag: day transplantation

value: Post transplanted Day 7


title: WT CD8 T cell Post-transplant Day 7 Rep2


title: Fam69c KO

description: 10x Genomics

tag: cell type

value: knockout


title: TCF-7 cKO CD8 Tcell Post-transplant Day 7 Rep3

value: TCF-7 cKO


title: BNeutsBM57


title: CONTROL_scRNAseq

description: BD

tag: strain


title: RNA-Seq PB Il-4 IL-21 biol rep 2

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Only reads that passed the Illumina quality filtering were further processed. Read 1 was trimmed 5' by 6 cycles, adapter were removed with cutadapt.
Reads were subsequently filtered against rDNA with the Bowtie.2. Sequences have then finally been aligned with tophat.1.4.1 against the mouse genome ncbi_37 (mm9).
Gene-wise read counts have been calculated with featureCounts.1.5.0., based on merged mouse gene as described in Revilla et al., 2012.
Associated TPMs have been calculated with a custom  R script.
Assembly: mm9
Supplementary files format and content: ASCII text file, comma separated: gene name and TPM value.

growth_protocol: Splenic B cells were grown on 40LB feeder cells with added IL4 (first 6 days) and IL21 (last 3 days, only samples 48159-48164

extract_protocol:
NebNext UltraII RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Plasmablast

value: iGB, IL-4 6 days, IL-21 3 days


title: RNA-Seq pre-PB Il-4 IL-21 biol rep 2

value: pre-Plasmablast


title: TCF-7 cKOCD8 Tcell Post-transplant Day 7  Rep2

source_name: sorted CD4 T cell


title: RNA-Seq Act B Il-4 IL-21 biol rep 2

value: Activated B-cell


title: WT CD8 T cell Post-transplant Day 7  Rep1


title: RNA-Seq PB Il-4 IL-21 biol rep 1


title: RNA-Seq Act B Il-4 IL-21 biol rep 1


title: RNA-Seq pre-PB Il-4 IL-21 biol rep 1


title: BNeutsBM51

value: Healthy


title: TCF-7 cKO CD8 Tcell Pre-transplant Rep3

value: Pre transplanted


title: C-rep7_rejected [st675]

first: Sophia

middle: C

last: Tintori

address: 29 Washington Pl - rm 951

institute: New York University

data_processing:
Identical reads were collapsed before analysis as in Tintori et al., 2016
Sets of samples from a single embryo were rejected if one or more library had an over-representation of ERCC spike in reads (if the number of ERCC spike in transcripts were more than one tenth the number of worm transcripts)
Transcripts were considered “detected” if their RPKM value was above a threshold of 25
All fold change calculations were done on adjusted RPKM values— raw RPKM values with 25 added to them— to avoid enriching for small differences between samples with low RPKM values
Assembly: ce10
Supplementary files format and content: fastq - raw reads from the Illumina HiSeq 2500
Supplementary files format and content: bed - genome alignments created by bedtools
Supplementary files format and content: rpkm - normalized trascript counts

organism: Caenorhabditis elegans

source_name: embryonic

growth_protocol: All worms were grown at 20°C and dissected at room temperature (21°C– 24°C)

extract_protocol:
Cells were lysed by flash freezing in 1 uL egg buffer. Libraries were generated directly from cell lysate - no RNA extraction method was used.
cDNA was generated using the SMARTer Ultra Low RNA Input for Illumina Sequencing Kit, and sequencing libraries were prepared using the Nextera XT kit, both according to manufacturers’ instructions.

treatment_protocol: Single embryos were selected at 10–20 min before the desired stage and dissected based on Edgar and Goldstein, 2012. Dissections were conducted by aspiration on a Yokogawa spinning disk confocal microscope under brightfield illumination, and cell types were identified by fluorescent markers.

value: embryonic


title: WT CD8 T cell Pre-transplant Rep1


title: Loc_7

source_name: primary pancreatic neuroendocrine tumor tissue, diagnosed and prepapared by pathologists

value: Localized Pancreatic Neuroendocrine Tumors

value: Well-differentiated pancreatic neuroendocrine neoplasm

tag: Sex

value: F


title: Coutrep7_rejected [st673]


title: TCF-7 cKOCD8 Tcell Pre-transplant Rep2


title: TCF-7 cKO CD8 Tcell Pre-transplant Rep1


title: Cinrep6 [st671]


title: RNA-Seq Act B IL-4 biol rep 1

value: iGB, IL-4 6 days


title: Coutrep6 [st670]


title: Dab1_P0_KO_rep9 [95981]

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

data_processing:
Read processing, alignment and annotations are described elsewhere (Laukoter et al., 2020b). STAR alignment parameters: clip5pNbases 3, outFilterMultimapNmax 1, --outSAMtype BAM SortedByCoordinate and quantMode GeneCounts. Downstream analyses were performed in R (v3.6.1). Note that for Cdk5r1 samples were sequenced 3x (technical replicates) to increase read coverage. Read coverages of the deleted Cdk5r1 region (chr11:80477417-80478722, mm10) and the deleted Dab1 region (chr4:104605298-104605437, mm10) were calculated using bedtools intersect with the -split option on the aligned bam file produced by STAR. These read counts were added to the count tables produced by STAR with the gene name Cdk5r1_del and Dab1_del respectively.
Downstream analysis of read counts in genes as produced by STAR was performed in R.
We removed samples with a low percentage of uniquely aligned reads (<50%), and/or based on position in PCA plot. Two sets of samples were analysed, SetA contains control, mosaic and cKO of Cdk5r1 cells. SetB contains control and cKO samples from Cdk5r1 and Dab1. Detailed information on which samples were analysed in each set is given in Supplementary MS-Exel files.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text of read counts in genes as reported by STAR, xlsx file with alignment details and information on sample analyzed for the 2 sets (*.sample_details.xlsx) and results from differential expression analysis (DE_*.xlsx).

source_name: MADM-5 GT,Dab1/TG,Dab1;Emx1-Cre

growth_protocol: All mouse colonies were maintained in accordance with protocols approved by the institutional animal care and use committee, institutional ethics committee, and the preclinical core facility (PCF) at IST Austria. Experiments were performed under a license approved by the Austrian Federal Ministry of Science and Research following the Austrian and EU animal laws (license numbers: BMWF-66.018/0007-II/3b/2012 and BMWFW-66.018/0006-WF/V/3b/2017).

extract_protocol:
Preparation of cell suspension for cell sorting was prepared as previously described (Laukoter et al., 2020b) for E13, E16, and P0 time points for RNA-seq. From the MADM samples, GFP+ cells were collected for each genotype. For RNA-sequencing, 2000 cells were sorted directly into a custom-made lysis buffer (30nM TRIS pH 8, 10nM EDTA pH 8, 1% SDS and 200 μg/μL Proteinase K). Directly after cell sorting using FACS, samples were incubated for 30min at 37°C. Total volume was filled to 250μl using RNase-free H2O (Thermo Fisher Scientific) followed by the addition of 750μl Trizol LS (Thermo Fisher Scientific). Samples were mixed by inversion (5 times). After a 5min incubation step at RT, the entire solution was transferred into a MaXtract tube (QIAGEN). 200μl chloroform (Sigma-Aldrich) was added, followed by 3 times 5sec vortexing and 2min incubation at RT. Samples were centrifuged for 2min at 12000rpm at 18°C. The supernatant was transferred to a new tube and isopropanol (Sigma-Aldrich) was added in a 1:1 ratio. For better visibility of the RNA pellet 1μl GlycoBlue (Thermo Fisher Scientific) was added and the entire solution was mixed by vortexing (3x 5sec). Samples were left for precipitation o/n at −20°C. After precipitation samples were centrifuged for 20min with 14000rpm at 4°C. The supernatant was removed and the RNA pellet was washed with 70% ethanol, followed by a 5min centrifugation step (14000rpm at 4°C). The RNA pellet was resuspended in 12,5μl RNase-free H2O. RNA quality was analyzed using RNA 6000 Pico kit (Agilent) following the manufacturer’s instructions. The RNA samples were stored at −80°C until further use.
Library preparation (SMART-Seq v2) and RNA sequencing was performed by VBCF GmbH (Vienna, Austria).

treatment_protocol: Mice with specific pathogen-free status according to FELASA recommendations (Mähler (Convenor) et al., 2014) were bred and maintained in experimental rodent facilities (room temperature 21 ± 1°C [mean ± SEM]; relative humidity 40%–55%; photoperiod 12L:12D). Food (V1126, Ssniff Spezialitäten GmbH, Soest, Germany) and tap water were available ad libitum.

tag: target gene

tag: deletion type

value: KO

tag: color

value: green


title: Dab1_P0_KO_rep8 [95980]


title: TCF-7 cKO CD8 Tcell Post-transplant Day 7 Rep1

value: spleen


title: Dab1_P0_KO_rep6 [95978]


title: Dab1_P0_KO_rep7 [95979]


title: Cinrep5 [st668]


title: C-rep5 [st669]


title: BNeutsBM53

value: BNeuts


title: Dab1_P0_KO_rep5 [95977]


title: WT CD8 T cell Pre-transplant Rep2

value: Wild type


title: Cinrep7_rejected [st674]


title: WT CD8 T cell Pre-transplant Rep3


title: C-rep4 [st666]


title: Coutrep5 [st667]


title: Dab1_P0_KO_rep4 [95976]


title: Cinrep4 [st665]


title: Dab1_P0_KO_rep3 [95975]


title: RNA-Seq Act B IL-4 biol rep 2


title: Coutrep4 [st664]


title: Wildtype and Tag Control_CellPlex

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: RS-03675794_Pool1-controlsamples-CellPlex

data_processing:
Raw sequencing data were processed using Cellranger v6.0.0 software
Filtered gene-barcode matrices were used for further analyses with Seurat single cell data analysis R package.
Cells were annotated using SingleR package with ImmGen reference database
Assembly: mm10
Supplementary files format and content: gene expression count matrix

source_name: Peritoneal fluids

growth_protocol: intraperitoneal tumor growth

extract_protocol:
tissue dissociation to prepare single cell suspension
Single cell libraries are generated using the 10X Genomics Chromium Single Cell 3’ Reagent V3 Kit according to manufacturer’s protocol.  Cell suspensions are first assessed with Trypan Blue using a Countess FL automated cell counter (ThermoFisher), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells are loaded into the Chromium Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription is performed and the resulting cDNA is amplified.  The full-length amplified cDNA is used to generate gene expression libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. They are then pooled, denatured, and diluted to 300pM with 1% PhiX control library added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).
10X Genomics Chromium Single Cell 3’ Reagent V3 Kit

treatment_protocol: intratumoral treatment with OV.

value: Immune Cells

value: multiplexed sample:WT and Tag

value: MOVCAR 5009 tumor bearing

value: no treatment

tag: cmo

value: CMO301 = WT Control; CMO303 = Tag Control

value: Female


title: Wildtype and Tag OVV-treated_Cell Plex

description: RS-03675795_Pool2-OVV-CXCR4samples-CellPlex

value: CXCR4 antagonist-expressing Oncolytic virotherapy

value: CMO302 = WT_OV; CMO304 = Tag_OV


title: Wildtype and Tag OVV-treated_GEX


title: Dab1_P0_control_rep7 [95964]

source_name: MADM-5 GT/TG;Emx1-Cre

value: none/control


title: Pro-miR-148a_1_rep3

city: Nottingham

first: Mohammed

last: Ahmed

address: Clifton Lane

country: United Kingdom

institute: Nottingham Trent University

data_processing:
FastQ files were porcessed by Galaxy server (https://usegalaxy.org/)
Sequenced reads were aligned to mm9 mouse genome, followed by DESeq2 analysis
Genes with significant changes (p<0.05) were further analysed followed by Gene annotation, GO analysis and heat map generation
tab-delimited text files include over and under expressed gene transcripts after overexpression of miR-148a
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene names, counts, significant p value for gene that are under or overrepresented after overexpression of miR-148a

source_name: keratinocytes

growth_protocol: Primary mouse epidermal keratinocytes (PMEKs) were extracted from postnatal day 1-3 old pups and grown in EMEM (supplemeted with 0.05mM calcium) media until 60% confluent.

extract_protocol:
Using Trizol
Provided by Novogene

treatment_protocol: PMEKs were transfected with either miR-Control or pro-miR-148a (200nM); post 48hrs transfection collected for RNA extraction using Trizol.

value: Skin

value: keratinocytes

value: post natal day 1-3

value: wild type

value: overexpression of miR-148a


title: C-rep6 [st672]

value: embryonic


title: Pro-miR-148a_1_rep1


title: Wildtype and Tag Control_GEX


title: Dab1_P0_KO_rep2 [95974]

value: KO

value: green


title: Dab1_P0_KO_rep1 [95973]


title: Dab1_P0_control_rep5 [95962]


title: C-rep3_rejected [st663]


title: Dab1_P0_control_rep3 [95960]


title: Dab1_P0_control_rep6 [95963]


title: Coutrep2 [st658]


title: Pro-miR-148a_2_rep2


title: Cinrep2 [st659]


title: Cinrep3_rejected [st662]


title: Control_3 - miR-Control_rep3

value: control


title: Control_1 - miR-Control_rep1


title: Control_2 - miR-Control_rep2


title: Dab1_P0_control_rep4 [95961]


title: Dab1_P0_control_rep1 [95958]


title: C-rep1 [st657]


title: Dab1_P0_control_rep2 [95959]


title: Cinrep1 [st656]


title: Cdk5r1_P0_KO_rep10 [85075]

source_name: MADM-11 GT,Cdk5r1/TG,Cdk5r1;Emx1-Cre


title: Coutrep3_rejected [st661]


title: Cdk5r1_P0_KO_rep9 [85074]


title: C-rep2 [st660]


title: FFD+isoleucine [104216-001-039]

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Mus_musculus.GRCm38.gencode.vM19
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

growth_protocol: The animal experiment was performed according to standards of the Animal Care and Use Committee and ethical approved by an independent Animal Welfare Body (IVD TNO; approval number 20172064/TNO-439) and the ARRIVE guidelines were followed. Male Ldlr-/-.Leiden mice (genetic background 94% C57BL/6J and 6% 129S) obtained from the breeding stock at TNO Metabolic Health Research (Leiden, the Netherlands) were group-housed (four to five mice per cage) in Macrolon cages in clean-conventional animal rooms (relative humidity 50–60%, temperature ~21C, light cycle 7a.m. to 7 p.m.) in an animal facility accredited by the American Association for Accreditation of Laboratory Animal Care (AAALAC) at TNO Metabolic Health Research with ad libitum access to food and water. Mice were matched into three groups of 15 mice per group, based on body weight, plasma cholesterol and triglycerides and blood glucose. N=15 mice are required to detect statistical differences in NASH (at α=0.05 and power = 0.8), the main end-point.  During a 26 week run-in period, three groups of mice were fed a fast-food diet (FFD; 41 kcal% fat from milk fat, 44 kcal% from primarily fructose as carbohydrate, and 14 kcal% from mainly casein as protein source; Research Diets, new Brunswick, NJ,USA).

extract_protocol:
Blood samples were obtained from the tail vein in 5h-fasted mice, and body weight, food intake and body composition measurements were acquired at set time points during the study. After 38 weeks mice were sacrificed by gradual-fill CO2 exposure and liver tissues were collected for biochemical measurements and histopathology (snap frozen and formalin fixation, respectively).
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7420S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: After 26 weeks two FFD groups started with a 12-week intervention in which FFD was supplemented with 3% (w/w) valine (FFD+Val) or isoleucine (FFD+Iso) and these two treatment groups were compared to a FFD control group. Of note, in the BCAA intervention groups the casein content was lowered to make sure that the intake of total protein was comparable between the groups. In addition, levels of other essential amino acids were supplemented to bring them back up to the same level as in the FFD control group. During the whole study period of 26 weeks run-in plus 12 weeks of intervention, thus 38 weeks, a reference group (n=8) remained on a low-fat chow diet (chow; Sniff-R/M-V1530, Uden, the Netherlands).

tag: treatmentperiod

tag: mousenr

value: liver


title: FFD+isoleucine [104216-001-040]


title: Cdk5r1_P0_KO_rep8 [85073]


title: ABp-rep7 [st652]


title: Coutrep1 [st655]


title: D-rep8 [st654]


title: FFD+isoleucine [104216-001-038]


title: ABp+rep7 [st651]


title: FFD+isoleucine [104216-001-041]


title: D+rep8 [st653]


title: Cdk5r1_P0_KO_rep7 [85072]


title: FFD+isoleucine [104216-001-037]


title: Cdk5r1_P0_control_rep11 [85070]

source_name: MADM-11 GT/TG;Emx1-Cre


title: Cdk5r1_P0_control_rep12 [85071]


title: MS-rep7 [st650]


title: FFD+isoleucine [104216-001-035]


title: FFD+isoleucine [104216-001-034]


title: Cdk5r1_E16_KO_rep11 [85069]


title: Cdk5r1_E16_KO_rep10 [85068]


title: D-rep7 [st646]


title: MS+rep7 [st649]


title: FFD+isoleucine [104216-001-033]


title: Cdk5r1_E16_KO_rep9 [85067]


title: D+rep7 [st645]


title: Cdk5r1_P0_KO_rep6 [85066]


title: FFD+isoleucine [104216-001-036R]


title: Cdk5r1_P0_KO_rep4 [85064]


title: FFD+valine [104216-001-028]


title: ABp-rep6 [st642]


title: FFD+valine [104216-001-026]


title: FFD+valine [104216-001-027]


title: FFD+valine [104216-001-025]


title: Cdk5r1_P0_KO_rep5 [85065]


title: FFD+isoleucine [104216-001-032]


title: Cdk5r1_P0_KO_rep2 [85062]


title: D-rep6 [st638]


title: Cdk5r1_P0_KO_rep1 [85061]


title: Cdk5r1_P0_mosaic_rep6 [85060]

source_name: MADM-11 GT/TG,Cdk5r1;Emx1-Cre

value: mosaic


title: D+rep6 [st637]


title: Cdk5r1_P0_KO_rep3 [85063]


title: FFD+valine [104216-001-023R]


title: ABp-rep5 [st634]


title: FFD+valine [104216-001-024]


title: FFD+valine [104216-001-022RR]


title: ABp+rep6 [st641]


title: FFD+valine [104216-001-021]


title: Cdk5r1_P0_mosaic_rep3 [85057]


title: ABp+rep5 [st633]


title: Cdk5r1_P0_mosaic_rep5 [85059]


title: MS+rep6 [st639]


title: MS-rep5 [st630]


title: Cdk5r1_P0_mosaic_rep2 [85056]


title: FFD+valine [104216-001-020]


title: Cdk5r1_P0_control_rep10 [85054]


title: MS-rep6 [st640]


title: FFD [104216-001-015]


title: Cdk5r1_P0_mosaic_rep4 [85058]


title: Cdk5r1_P0_control_rep9 [85053]


title: FFD [104216-001-017]


title: FFD [104216-001-016]


title: MS-rep4 [st618]


title: FFD [104216-001-011]


title: FFD [104216-001-014]


title: MS+rep5 [st629]


title: Cdk5r1_P0_control_rep7 [85051]


title: Cdk5r1_P0_mosaic_rep1 [85055]


title: FFD [104216-001-010]


title: D+rep5_rejected [st627]


title: D+rep4 [st613]


title: D-rep4 [st614]


title: D-rep5_rejected [st628]


title: FFD [104216-001-009]


title: Cdk5r1_P0_control_rep8 [85052]


title: ABp+rep4 [st622]


title: ABp-rep4 [st624]


title: Cdk5r1_P0_control_rep4 [85048]


title: FFD [104216-001-008]


title: FFD [104216-001-012]


title: Cdk5r1_P0_control_rep6 [85050]


title: Cdk5r1_P0_control_rep3 [85047]


title: ABp-rep3 [st612]


title: FFD [104216-001-013]


title: chow [104216-001-005]


title: MS+rep4 [st617]


title: Cdk5r1_P0_control_rep5 [85049]


title: Cdk5r1_E16_KO_rep7 [85043]


title: Cdk5r1_E16_KO_rep8 [85044]


title: D-rep3 [st607]


title: Cdk5r1_P0_control_rep1 [85045]


title: chow [104216-001-004]


title: D+rep3 [st605]


title: Cdk5r1_E16_KO_rep6 [85042]


title: MS-rep3 [st610]


title: ABp+rep3 [st611]


title: chow [104216-001-002]


title: chow [104216-001-001]


title: MS-rep2 [st599]


title: ABp+rep2 [st601]


title: Pool 3 HTO

data_processing:
Raw sequencing data were processed using Cellranger v6.0.0 software
Filtered gene-barcode matrices were used for further analyses with Seurat single cell data analysis R package.  Each sample was demultiplexed with hashtag oligos (HTOs) using Seurat.
Cells were annotated using SingleR package with ImmGen reference database
Genome_build: mm10
Supplementary_files_format_and_content: gene expression count matrix
Supplementary_files_format_and_content: Antibody capture feature file

source_name: bone marrow

extract_protocol:
Bone marrow was harvested and enriched for cKit+ cells via magnetic bead isolation (Miltenyi Cat#130-091-224). Non-tumor-bearing samples, vehicle control tumor-bearing samples, and brequinar-treated tumor-bearing samples were stained with TotalSeq-B antibodies 0301, 0302, and 0303, respectively (Biolegend Cat#155831, 155833, 155835) and 1 sample from each group was pooled for a total of 3 experimental pools. Single cell libraries were generated using the 10X Genomics Platform and Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Feature Barcode technology for cell surface proteins.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cKit+ bone marrow progenitors

value: BALB/c

value: mixed sample (non-demultiplexed)

tag: treatment

value: 10 weeks at time of harvest


title: Cdk5r1_P0_control_rep2 [85046]


title: MS+rep3 [st609]

tag: tissue


title: Cdk5r1_E16_KO_rep3 [85039]


title: Cdk5r1_E16_KO_rep4 [85040]


title: Cdk5r1_E16_KO_rep5 [85041]


title: D-rep2 [st595]

tag: genotype


title: Cdk5r1_E16_mosaic_rep8 [85037]


title: Cdk5r1_E16_KO_rep2 [85038]


title: Control NE-4C cells

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

data_processing:
CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data, then mapped to GRCm39 whole genome using Hisat2 software.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCm39
Supplementary_files_format_and_content: Excel files including fpkm values for each sample

source_name: NE-4C cells infected with lentivirus carrying empty shRNA knockdown vector pLKO.1, and cultured for 5 days

growth_protocol: Control NE-4C cells and cells with Setdb1 knockdown were cultured in MEM supplemented with 1% MEM non-essential amino acids, 1% Glutamax and 10% FBS, at 37°C in 5% CO2 for 5 days

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
Libraries were contructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® using the protocol from the manufacturer.

tag: cell line

value: Neural stem cell line

tag: cell line source

value: E9 mouse embryo

tag: knockdown

value: empty vector


title: ABp-rep2 [st603]


title: Pool 2 HTO

tag: disease state

tag: age


title: NE-4C cell with Setdb1 knockdown

source_name: NE-4C cells infected with lentivirus carrying shRNA against Setdb1 (shSetdb1), and cultured for 5 days

tag: cell type

value: shRNA against Setdb1


title: Pool 1 HTO

tag: strain


title: Cdk5r1_E16_mosaic_rep7 [85036]


title: chow [104216-001-003]


title: Cdk5r1_E16_mosaic_rep6 [85035]


title: ABp-rep1 [st591]


title: Pool 3


title: Pool 2


title: MS-rep1 [st582]


title: MS+rep1 [st581]


title: ABp+rep1 [st589]


title: human - BL_3

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly: GRCh37

source_name: LN229 cell

growth_protocol: The cells were seeded on 6-well plate and cultured under 37°C with 5% CO2

extract_protocol:
Brain tissue samples were lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: The cells were treated with bortezomib+panobinostat (7.5 nM+15 nM) or DMSO for 48 h, respectively. The  all cells were collected and lysed to get total mRNAs.

value: Glioblastoma (GBM)

value: treated with unit of  bortezomib and panobinostst under concentration of 7.5 nM and 15 nM


title: Cdk5r1_E16_mosaic_rep3 [85032]


title: human - DMSO_2

value: untreated


title: Cdk5r1_E16_mosaic_rep4 [85033]


title: Cdk5r1_E16_mosaic_rep5 [85034]


title: D-rep1 [st578]

value: embryonic


title: human - DMSO_3


title: human - BL_2


title: MS+rep2 [st597]


title: D+rep2 [st593]


title: Pool 1


title: Cdk5r1_E16_mosaic_rep2 [85031]


title: human - DMSO_4


title: LSK KO_batch2

city: Freiburg

first: Aurelie

last: Lenaerts

address: Stübeweg 51

department: Cellular and Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
scRNA-Seq data was analysed using the Scanpy package (Wolf et al., 2018). The UMI counts matrix (cell x genes) was obtained using the cellranger package (version 3.1.0) with default settings. Cells with <1200 detected genes and >10% of counts mapped to mitochondrial genes were excluded from further analysis. Count data was log-normalised and each cell was analysed for the expression of Xist and Y-chromosome genes. Cells with Xist expression but no Y-chromosome gene expression were assigned female and vice versa. The small minority of cells expressing both Xist and Y-chromosome genes were excluded from the analysis as suspected doublets, cells lacking expression of Xist and Y-chromosome genes were excluded.
Data for the remaining 59,505 cells were used to generate a common scRNA-Seq landscape as follows. 7000 top variable genes (excluding Ebf1, Xist, Y-chromosome genes and cell-cycle associated genes (as in (Dahlin et al., 2018)) were used to compute 50 principal components. Batch effects were removed using the Harmony method (Korsunsky et al., 2018). The corrected components were used to identify 8 nearest neighbours, which served as a basis for clustering (leiden algorithm) and UMAP (Traag et al., 2019) (https://github.com/TomKellyGenetics/leiden).
Genome_build: mm10
Supplementary_files_format_and_content: 10x Genomics filtered h5 files

growth_protocol: Primary cells

extract_protocol:
Mouse BM cells were isolated from pooled femora, tibiae and ilia bones, by crushing them in cold-PBS-0.04%BSA. For progenitor cell sorting, bone marrow cells were incubated with a biotin-antibody cocktail (CD3, B220, CD11b, Gr1, Ter119), followed by magnetic depletion with streptavidin-conjugated magnetic nanobeads (BioLegend). LK (Lin-cKit+) and LSK (Lin-Sca+cKit+) cells were sorted with a FACS Fusion II instrument (BD Biosciences). An equal number of FACS sorted LK (Lin-cKit+) and LSK (Lin-Sca1+cKit+) were combined from a female mouse and from a male mouse of each genotype, resulting in a pool of ~24,000 input cells. The cells was processed on a 10X Genomics Chromium controller to generate a cDNA library, according to manufacturer’s protocol.
Sequencing libraries were generated from cleaned, amplified cDNA using the Chromium Next GEM Single Cell 3’ Library kit (10X Genomics), with version 3.1 chemistry, including reagents for fragmentation, adaptor ligation, and sample index PCR. Single-cell RNA-seq paired-end 100 bp reads were generated using the Illumina NovaSeq 6000 system, at a depth of ~30,000 paired-reads per cell.

value: Ebf1fl/fl Tie2Cre +/cre

value: LSK

value: 10 weeks old


title: D+rep1 [st577]


title: LK KO_batch2

value: LK


title: LSK KO_batch1

value: 9 weeks old


title: human - BL_4


title: human - DMSO_1


title: Cdk5r1_E16_mosaic_rep1 [85030]

value: mosaic

value: green


title: YY348+350AA Tfb2 +Gal biological replicate 3

city: Boulder

first: Dylan

last: Taatjes

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

description: steady-state RNA (RNA-seq) from yeast cells

data_processing:
Sequenced reads were trimmed for adaptor sequences with cutadapt v1.16 and gene expression quantified using the psuedo-aligner salmon v0.10.2 with sacCer3 ensembl annotations. Differential gene expression analysis was performed using DESeq2, and differential genes called as padj. <0.05 and absolute (log2foldchange) >0.5.
Normalized bigwigs were generated by first aligning the trimmed fastqs to the SacCer3 reference genome using STAR to obtain .bams. The .bams were indexed using samtools, total read depth normalized bedgraphs were then generated with bedtools using these .bams, and the bedgraphs were converted to bigwigs using UCSC’s bedGraphtoBigWig function.
Genome_build: sacCer3
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary_files_format_and_content: Genome track (bigWig) and DESeq2 counts tables for metagene analysis

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells expressing WT Tfb2 as well as the RF369-370AA and YY348+350AA mutants were grown in CSM  raffinose

extract_protocol:
RNA was extracted using the hot acidic phenol method and DNAse I treated
RNA libraries were prepared with the KAPA mRNA hyperprep kit

treatment_protocol: Wild-type and mutant cells were shifted carbon sources from CSM raffinose to 2% galactose for 0min or 60min

value: YY348+50AA Tfb2

tag: plasmid

value: 60min 2% Gal


title: human - BL_1


title: LK KO_batch1


title: Cdk5r1_E16_KO_rep1 [85029]

tag: target gene

value: KO


title: LK WT_batch2

value: Ebf1wt//wt Tie2Cre +/cre


title: YY348+350AA Tfb2 -Gal biological replicate 3

value: 0min 2% Gal


title: LSK WT_batch1

value: Ebf1fl/fl Tie2Cre +/+


title: Cdk5r1_E16_control_rep11 [85027]

tag: deletion type

value: none/control


title: Kin_8m_rep1

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
RNAseq reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i) (Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR
Read counts for all genes annotated in GENCODE (hg19) were calculated using the read summarization program featureCounts (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: .txts with raw gene counts and RPKMs for each experimental group

source_name: Kin67 iPSC

growth_protocol: Cortical organoids were maintained in Neurobasal supplemented with 1% B27, 1% GlutaMax, 1% NEAA and 1% Penicillin/Strep and 20 ng/mL FGF2 (Life Technologies)  in humidified atmosphere with 5% CO2 at 37C

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

value: Kin67 iPSC

value: induced pluripotent stem cell

value: WT

tag: time

value: 8 months


title: YY348+350AA Tfb2 +Gal biological replicate 2


title: Cdk5r1_E16_control_rep10 [85026]

tag: color


title: Kin_8m_rep2


title: YY348+350AA Tfb2 -Gal biological replicate 2


title: Kin_4m_rep2

value: Day 120


title: Kin_4m_rep1


title: YY348+350AA Tfb2 +Gal biological replicate 1


title: YY348+350AA Tfb2 -Gal biological replicate 1


title: LSK WT_batch2

value: LSK

value: 10 weeks old


title: Cdk5r1_E16_control_rep8 [85024]


title: ATAC MPP4 Ebf1-KO rep 2

data_processing:
The Nextera transposase adapters were trimmed from the raw FASTQ using Cutadapt (version 2.10, (Martin, 2011)) using flags -A CTGTCTCTTATA -a CTGTCTCTTATA. Alignments against the mm10 reference genome (ensembl release 91) were created using the DNA-mapping module implemented in snakePipes (version 2.5.1, (Bhardwaj et al., 2019)) using the --dedup --mapq 5 flags. Data quality was assessed using FastQC (version 0.11.9, (Andrews, Simon, 2010), MultiQC (version 1.8, (Ewels et al., 2016)) and deepTools (version 3.3.2, (Ramírez et al., 2016)).
Analysis downstream was performed using a custom pipeline (github.com/WardDeb/ATACofthesnake) implemented in snakemake (version 6.0.0, (Koster and Rahmann, 2012)). Briefly, fragments mapping to read attracting regions (Amemiya et al., 2019) or exceeding 150 base pairs (to capture nucleosome-free regions) were filtered out using the alignmentSieve module in deepTools. Subsequently, peaks were called using MACS2 (version 2.2.7.1, (Zhang et al., 2008)) with the settings --nomodel, --shift -75, --extsize 150 -g 1.87e9 -q 0.01 and --keep-dup all, and a union of peaks per cell type (MPP3 and MPP4) was created using bedtools merge (version 2.30.0, (Quinlan and Hall, 2010)). Genes were annotated to the closest gene using Uropa (version 4.0.0, (Kondili et al., 2017)), allowing a 20kb distance upstream and 10kb distance downstream. Count matrices were created using the multiBamSummary module in deepTools, and differential accessible regions were called using the glmQLFit and glmQLFT functions from the edgeR package (version 3.32.0, (Robinson et al., 2010)) implemented in R (version 4.0.3, (R Core Team, 2020)). For peak calling and visualisation, replicates were merged per condition at the bam level.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were created using bamCoverage from deeptools (v3.3.1) with RPKM normalization. edgeR results files were generated using edgeR (v3.32.0).

extract_protocol:
Mouse BM cells were isolated from pooled femora, tibiae and ilia bones, by crushing them in cold-PBS-3%FCS. For progenitor cell sorting, bone marrow cells were incubated with a biotin-antibody cocktail (CD3, B220, CD11b, Gr1, Ter119), followed by magnetic depletion with streptavidin-conjugated magnetic nanobeads (BioLegend). MPP3 (LSK+ CD150- CD48+) and MPP4 (LSK+ CD150- CD48+ Flt3+) cells were sorted by a FACS Aria III or FACSymphony instrument (BD Biosciences). MPP3 and MPP4 cell pellets were resuspended in a lysis/transposition buffer (1 µl Tagmentase, 10 µl 2x TD buffer (Diagenode), 0.01% digitonin (Promega), 0.3x PBS) and incubated for 30 min at 37°C at 700 rpm. Reactions were cleaned up with Zymo DNA Clean and Concentrator -5 columns (Zymo Research).
ATAC-sequencing libraries were prepared as described in Buenrostro et al. 2015, using Nextera DNA UD Indexes (IDT); 10-12 PCR amplification cycles and double-sided size selection was performed. Paired-end 100 bp reads were generated using the Illumina NovaSeq 6000 system. Samples were first sequenced at shallow depth (~5 million reads) to assess the quality, prior to sequencing at a depth of 50 million reads. Reads from both flowcells were merged at the fastq level.

value: Ebf1fl/fl Tie2Cre +/cre

tag: Sex

value: female

value: 8 weeks old


title: Kin_2m_rep1

value: Day 60


title: RF369-370AA Tfb2 +Gal biological replicate 3

value: 60min 2% Gal


title: ATAC MPP4 Ebf1-KO rep 1


title: Cdk5r1_E16_control_rep9 [85025]

value: green


title: Cdk5r1_E16_control_rep7 [85023]


title: Kin_0m_rep2

value: Day 0


title: Cdk5r1_E16_control_rep12 [85028]


title: RF369-370AA Tfb2 -Gal biological replicate 3

value: 0min 2% Gal


title: ATAC MPP4 WT rep 2

value: Ebf1fl/fl Tie2Cre +/+

value: male

value: 9 weeks old


title: Cdk5r1_E16_control_rep6 [85022]

value: none/control


title: LK WT_batch1

value: Ebf1wt//wt Tie2Cre +/cre

value: LK


title: ATAC MPP4 WT rep 1


title: Kin_0m_rep1

value: Kin67 iPSC

value: induced pluripotent stem cell

value: WT


title: Kin_2m_rep2


title: Cdk5r1_E16_control_rep5 [85021]


title: RF369-370AA Tfb2 +Gal biological replicate 2


title: RF369-370AA Tfb2 +Gal biological replicate 1


title: Cdk5r1_E16_control_rep4 [85020]


title: DM600_4m_rep2

source_name: DM600 iPSC

value: DM600 iPSC

value: Myotonic Dystrophy

value: Day 120


title: Cdk5r1_E16_control_rep3 [85019]


title: ATAC MPP3 WT rep 1

value: female

value: 8 weeks old


title: ATAC MPP3 WT rep 2


title: DM600_4m_rep1


title: MPP4 Ebf1-KO rep 4

data_processing:
Raw FASTQ files were mapped against the mm10 reference genome using the mRNA-seq module implemented in snakePipes (version 2.5.1) (Bhardwaj et al., 2019), using the --trim flag. Briefly, reads were aligned using STAR (version 2.7.3a) (Dobin et al., 2013), followed by expression count quantification with featureCounts (version 2.0.0, (Liao et al., 2014)). Data quality was assessed using Deeptools QC (version 3.3.2, (Ramírez et al., 2016)).
Genes with an average expression higher than 100 counts in any condition were selected for further analysis. Differential expression analysis was performed using DESeq2 (version 1.28.1) (Love et al., 2014) implemented in R (version 4.0.0) and ashr was used for LogFoldChange (LFC) shrinkage of results (version 2.2.47)(Stephens, 2016). Genes were considered differentially expressed at a false discovery rate (FDR) < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix of samples were generated from featureCounts (version 2.0.0).
Supplementary_files_format_and_content: Normalized count matrix of samples were generated using DESeq2 (version 1.28.1)

extract_protocol:
Mouse BM cells were isolated from pooled femora, tibiae and ilia bones, by crushing them in cold-PBS-3%FCS. For progenitor cell sorting, bone marrow cells were incubated with a biotin-antibody cocktail (CD3, B220, CD11b, Gr1, Ter119), followed by magnetic depletion with streptavidin-conjugated magnetic nanobeads (BioLegend). MPP3 (LSK+ CD150- CD48+) and MPP4 (LSK+ CD150- CD48+ Flt3+) cells were sorted by a FACS Aria III or FACSymphony instrument (BD Biosciences), directly into RNA lysis buffer and harvested using Arcturus PicoPure RNA isolation kit.
RNA-seq libraries were prepared by the deep-sequencing facility (MPI-Freiburg) using NEBNext SingleCell/Low Input RNA library prep kit  (Cat#E6420), following manufacturer's recommendations. Paired-end 100 bp reads were generated using the Illumina NovaSeq 6000 system, at a depth of 50 million reads.

value: bone marrow

value: Ebf1fl/fl Tie2Cre +/cre

value: 11 weeks old


title: wild-type Tfb2 -Gal biological replicate 3

value: wild-type Tfb2

value: 0min 2% Gal


title: Cdk5r1_E16_control_rep2 [85018]

value: green


title: MPP4 Ebf1-KO rep 3


title: Cdk5r1_E13_KO_rep5 [85016]

value: KO


title: wild-type Tfb2 +Gal biological replicate 3

value: 60min 2% Gal


title: MPP4 Ebf1-KO rep 2

value: male

value: 9 weeks old


title: DM600_2m_rep1

value: induced pluripotent stem cell

value: Day 60


title: DM600_8m_rep2

value: DM600 iPSC

value: 8 months


title: ATAC MPP3 Ebf1-KO rep 2


title: Cdk5r1_E13_KO_rep4 [85015]


title: MPP4 Ebf1-KO rep 1

value: 10 weeks old


title: DM600_2m_rep2

value: Myotonic Dystrophy


title: DM600_0m_rep2

value: Day 0


title: Cdk5r1_E13_KO_rep3 [85014]


title: Cdk5r1_E16_control_rep1 [85017]

value: none/control


title: wild-type Tfb2 +Gal biological replicate 2


title: wild-type Tfb2 -Gal biological replicate 2


title: DM600_0m_rep1


title: RF369-370AA Tfb2 -Gal biological replicate 2


title: MPP4 WT rep 4

value: bone marrow

value: Ebf1fl/fl Tie2Cre+/+


title: Cdk5r1_E13_mosaic_rep8 [85013]

value: mosaic


title: DM1200_4m_rep2

source_name: DM1200 iPSC

value: DM1200 iPSC

value: Day 120


title: DM1200_8m_rep2


title: ATAC MPP3 Ebf1-KO rep 1

value: Ebf1fl/fl Tie2Cre +/cre

value: female

value: 8 weeks old


title: RF369-370AA Tfb2 -Gal biological replicate 1

value: 0min 2% Gal


title: MPP4 WT rep 3

value: male

value: 12 weeks old


title: DM600_8m_rep1

value: DM600 iPSC

value: induced pluripotent stem cell


title: wild-type Tfb2 -Gal biological replicate 1

value: wild-type Tfb2


title: DM1200_8m_rep1

value: Myotonic Dystrophy

value: 8 months


title: non-green photosynthetic seeds YC-rep3

city: Wuhan

first: Chinedu

middle: Charles

last: Nwafor

state: Hubei

address: No. 1 shizeshan street

department: College of Plant Science and Technology

institute: Huazhong Agricultural University Wuhan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 using bowtie v0.12.2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: Table contain raw gene counts for every gene and every sample

source_name: Chlorophyll synthase mutant

growth_protocol: All plants were grown at 22 °C with 16 h light (120 µ E m−2 s−1)/8 h dark).

extract_protocol:
Seed were carefully removed from siliques and non-photosynthetic seeds were seperated from photosynthetic seeds. both seed were frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: yellow seeds


title: Cdk5r1_E13_mosaic_rep7 [85012]

value: green


title: MPP4 WT rep 1

value: bone marrow

value: Ebf1fl/fl Tie2Cre+/+


title: wild-type Tfb2 +Gal biological replicate 1

value: 60min 2% Gal


title: DM1200_4m_rep1

value: DM1200 iPSC

value: Day 120


title: non-green photosynthetic seeds AY-rep1


title: Cdk5r1_E13_mosaic_rep6 [85011]

value: mosaic


title: MPP4 WT rep 2

value: female

value: 11 weeks old


title: Cdk5r1_E13_mosaic_rep5 [85010]


title: MPP3 Ebf1-KO rep 4

value: Ebf1fl/fl Tie2Cre +/cre


title: DM1200_2m_rep2

value: Day 60


title: Cdk5r1_E13_control_rep9 [85009]

value: none/control


title: DM1200_2m_rep1

value: induced pluripotent stem cell


title: MPP3 Ebf1-KO rep 2

value: male

value: 9 weeks old


title: non-green photosynthetic seeds YB-rep2


title: green photosynthetic seeds GE-rep2

value: green seeds


title: green photosynthetic seeds GF-rep-3


title: Cdk5r1_E13_control_rep8 [85008]


title: DM1200_0m_rep2

value: Myotonic Dystrophy

value: Day 0


title: MPP3 Ebf1-KO rep 3

value: bone marrow


title: MPP3 WT rep 3

value: Ebf1fl/fl Tie2Cre+/+

value: 12 weeks old


title: DM1200_0m_rep1

value: DM1200 iPSC


title: Cdk5r1_E13_mosaic_rep3 [85003]

value: green


title: MPP3 Ebf1-KO rep 1

value: 10 weeks old


title: Cdk5r1_E13_mosaic_rep4 [85004]

value: mosaic


title: Mature Tregs [43-4]

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

data_processing:
fastq files were trimmed to remove the first 3 bases from both R1 and R2 reads using trimmomatic (v0.33)
trimmed fastq files were aligned to the GRCm38 reference genome using HiSat2 (v2.1.0)
subread featureCounts (v1.4.6) was used to quantify gene expression counts using the Ensembl GTF v97 GRCm38 gtf
Assembly: GRCm38
Supplementary files format and content: subread_counts.txt is a tab delimited text file containing gene expression counts produced by subread featureCounts

organism: Mus

source_name: Thymocytes

extract_protocol:
Mechanically dissociated thymus, depleted of CD8 via negative magnetic enrichment, was sorted via flow cytometry of a BD FACSAria II to isolate each input cell population. Cells were sorted into RLT buffer with 2-mercaptoethanol.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit

value: C57Bl/6 x Foxp3-GFP

value: Thymus

value: Thymocytes

tag: cell population

value: female

value: 6 week old


title: Bst2+, CD25+ and/or FOXP3+ [43-5]


title: green photosynthetic seeds GD-rep 1


title: MPP3 WT rep 4

value: male

value: 11 weeks old


title: Cdk5r1_E13_mosaic_rep2 [85002]


title: CD25+ Treg progenitor [43-2]


title: CVB_4m_rep2

source_name: CVB24 iPSC

value: CVB24 iPSC

value: induced pluripotent stem cell

value: WT

tag: treatment

value: Day 120


title: Cdk5r1_E13_KO_rep1 [85005]

value: KO


title: CVB_8m_rep1

value: 8 months


title: CVB_2m_rep1

value: Day 60


title: Cdk5r1_E13_mosaic_rep1 [85001]

value: green


title: Cdk5r1_E13_control_rep7 [85007]

value: none/control


title: CVB_4m_rep1


title: CVB_2m_rep2


title: CVB_8m_rep2


title: MPP3 WT rep 2

tag: tissue

value: bone marrow

value: Ebf1fl/fl Tie2Cre+/+


title: FOXP3lo Treg progenitor [43-3]

value: C57Bl/6 x Foxp3-GFP

value: Thymus


title: Bst2+, CD25+ and/or FOXP3+ [42-5]

value: Thymocytes

value: female


title: Cdk5r1_E13_control_rep6 [85000]


title: Mature Tregs [42-4]

value: 6 week old


title: Cdk5r1_E13_control_rep2 [84996]


title: Cdk5r1_E13_KO_rep2 [85006]


title: Microglia from naïve mice 5

city: Charlottesville

first: Tajie

last: Harris

state: VA

address: 200 Jeanette Lancaster Way

department: Neuroscience

institute: University of Virginia

description: matrix column 5

data_processing:
Fastq files were processed with Trimmomatic (Bolger et al., 2014)  to trim adapters and filter reads with a minimum quality score of 15, leading and trailing quality scores of 3, and a minimum fragment length of 36.
Quality of the reads were evaluated using FastQC, and after passing quality control (QC), were aligned to the mm10 genome (Harrow et al., 2012).
The number of reads aligning to each gene was quantified with HTSeq (Anders et al., 2015)
Raw and  normalized counts were generated in DESeq2 (Love et al., 2014), alongside a larger set of samples based on a broader experiment.
Assembly: GENCODE M13
Supplementary files format and content: .csv file containing raw counts for gene abundances

source_name: brain

growth_protocol: Age- and sex-matched mice were maintained in accordance with standard protocols of the Institutional Animal Care and Use Committee at the University of Virginia.

extract_protocol:
Immediately after sacrifice mice were perfused with 30 mL of cold 1X PBS. Brains were harvested and put into cold complete RPMI media. For serum, blood from the heart was collected and allowed to clot at 4°C overnight. Brains were minced and homogenized, digested with 0.227 mg/mL collagenase/dispase and 50 U/mL DNase (Roche) at 37°C for 45 minutes. Homogenate was passed through a 70 µm filter (Corning) and washed with cRPMI. Filtered brain homogenate was then resuspended with 20 mL of 40% Percoll and spun at 650 x g for 25 minutes. Myelin was aspirated, samples were washed with cRPMI, and then resuspended in cRPMI.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intraperitoneally administered tamoxifen (4 mg per 20 g body weight, Sigma-Aldrich) between 4-7 weeks of age for 5 consecutive days to induce ZsGreen expression in microglia. Four weeks following tamoxifen treatment, brains were harvested for analysis.

value: brain

value: Microglia

tag: genotype

value: CX3CR1creERT2/+ :ROSA26ZsGreen/ZsGreen

value: Tamoxifen