title: MRL1

description: At the start of squaring stage


title: 5TTU_S8_L002

status: Public on May 08 2020

type: SRA

city: Portland

first: Kevin

last: Burfeind

state: OR

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health & Science University

library_source: transcriptomic

data_processing:
Raw reads were normalized and analyzed using the Bioconductor package DESeq2 (Love, Huber and Anders, 2014).  Only those genes that were expressed in at least one sample were included in differential expression analysis (28,762 out of 51,916 genes).
Genes were normalized taking into account the sample’s library size, which is the total number of reads mapping to a gene.  Raw p-values were adjusted for multiple comparisons using the Benjamani-Hochberg method (Benjamini and Hochberg, 1995)
Prior to performing Differential Expression Analysis, we performed Exploratory Data Analysis (EDA) to identify any issues with samples that would affect downstream analysis.  Issues such as samples not clustering with replicates or outlier samples could affect our ability to detect differentially expressed genes.
We defined down-regulated genes using the following criteria: statistical significance (Adjusted P-value < 0.05) and effect size (log2 Fold Change (log2fc) less than/equal to -2 ). Similarly, up-regulated genes were defined using same statistical significance and  effect size of log2fc greater than/equal to 2.  Independent filtering was performed to select a set of genes which will result in the most genes with adjusted p-values.  Tumor Brain was used as baseline for all Tumor related analyses (Tumor Blood vs Tumor Brain, Tumor Liver vs Tumor Brain, Tumor Tumor vs Tumor Brain).
We perform two enrichment analysis, Pathway (using Reactome) and Gene Ontology, using the Goseq Bioconductor R package (Young et al 2010), which takes into account gene length when performing enrichment analysis. Longer genes are more likely to be detected in sequencing and would therefore bias enrichment analysis.
Genome_build: mm10
Supplementary_files_format_and_content: see .xlsx files for processed and normalized reads

molecule: total RNA

organism: Mus musculus

source_name: Neutrophils from Tumor

extract_protocol:
Total RNA was isolated from FACS-sorted CD11bhighLy6Ghigh neutrophils using an RNAeasy Plus Micro kit (Qiagen). RNA integrity was verified by a Bioanalyzer (Agilent).
Sample cDNAs were prepared using the SMART-Seq v4 Ultra Low Input kit (Takara) using 250 pg of input total RNA followed by library preparation using a TruSeq DNA Nano kit (Illumina). Libraries were verified by Tapestation (Agilent). Library concentrations were determined by real-time PCR with a StepOnePlus Real Time PCR System (Thermo Fisher) and a Kapa Library Quantification Kit (Kapa Biosystems / Roche). Libraries were sequenced with a 100 cycle single read protocol on a Illumina HiSeq 2500 (Illumina) with four libraries per lane. Fastq files were assembled using Bcl2Fastq2 (Illumina).

tag: disease state

value: Tumor

tag: cell type

value: Neutrophils

tag: tissue

tag: strain

tag: chip antibody


title: WT EHEC with 10µM serotonin

city: Dallas

first: Aman

last: Kumar

state: Texas

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Our 6 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
Sequencing run: Our 6 RNA libraries were run on illumine NextSeq sequencer with SE-75.
Raw data was processed using DNAStar Lasergene software as per the instructions provided on the DNAStar website
Genome_build: sakai genome downloaded from ncbi was used as a reference genome
Supplementary_files_format_and_content: tab delimited text file includes the RKPM values for all samples under the conditions tested above.
Supplementary_files_format_and_content: .astar files can be accessed using DNAStar Lasergene software

organism: Escherichia coli

source_name: EHEC

growth_protocol: WT strains were grown in low gluocse DMEM  until late log phase with either water or 10µM serotonin hydrochloride in three biological replicates. Samples were checked for similar O.D and then samples were harvested by centrifugation. The RNA was extracted from the pellet fraction using Ribopure RNA extraction kit (Ambion).

extract_protocol:
RNA was extracted using Ribopure RNA extraction kit (Ambion)
6 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.

treatment_protocol: 10µM of serotonin hydrochloride or only water in a dilution ratio of 1:1000 was added to the low gluocse DMEM before starting the experiment

value: EHEC strain 86 24

tag: genotype

value: WT

tag: treatment

value: serotonin hydrochloride


title: DPAL2

city: Anyang

first: Jianyong

last: Wu

address: Huanghe Dadao 38#

country: China

institute: Institute of Cotton Research, CAAS

description: At the start of squaring stage

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Gossypium hirsutum

source_name: 1 day post anthesis ovule

growth_protocol: Field experiments

extract_protocol:
T.RNA with Sigma Spectrum Plant Total RNA kit (Sigma-  448 Aldrich, USA)
Accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA)

value: 1 day post anthesis ovule

tag: developmental stage

value: Squaring stage


title: 2TBR_S7_L002

source_name: Neutrophils from Brain

value: Brain


title: 3TTU_S20_L005


title: 1TLI_S18_L005

source_name: Neutrophils from Liver

value: Liver


title: 2SBL_S19_L005

source_name: Neutrophils from Blood

value: Sham

value: Blood


title: 4SBL_S6_L002


title: Pabpn1l-KO-2Cell-Rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the GV oocyte sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

growth_protocol: The oocytes are collected in vivo, and embyos are clutured in KSOM in vitro.

extract_protocol:
Oocytes/embryos were collected from indicated genotypes (10 embryos per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: Samples were collected with 0.2% BSA in DPBS at indicated time directly without extra treatment.

tag: strain background

tag: genotype/variation

value: 2Cell embryo


title: WT EHEC

value: water


title: MRL2

description: At the start of squaring stage

source_name: Leaf

value: Leaf


title: LF3

description: At the start of squaring stage

source_name: Flower buds

value: Flower buds


title: Pabpn1l-KO-2Cell-Rep1


title: 2TLI_S4_L001


title: Pabpn1l-KO-1Cell-Rep2

value: 1Cell embryo


title: LF2

description: At the start of squaring stage


title: Adult Peripheral Blood-Tconv-5

type: RNA

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Clariom_S_Human arrays according to ThermoFisher Scientific instructions, 16 hours at 45C at 60 rpm.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software

data_processing: Arrays were normalized using RMA as implemented in Partek

label: biotin

organism: Homo sapiens

source_name: Adult peripheral blood Tconv 14 days post expansion

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.

growth_protocol: Treg and Tconv were expanded as previously described in Seay et al 2017. In brief, sorted Treg and Tconv were incubated with anti-CD3 and anti-CD3 coated microbeads in the presence of exogenous IL-2 and expanded for 14 days following protocol 1.

extract_protocol: 300,000 CB Tregs, CB Tconv, APB Tregs, and APB Tconv were lysed in DNA/RNA lysis buffer (Zymo ResearchR) and stored at -80°C. RNA extraction was achieved using ZR-Duet™ DNA/RNA MiniPrep (Zymo Research, Catalog No. D7001), per the manufacturer’s instructions. Quality assessment of RNA was achieved by Experion™ Automated Electrophoresis System (BIO-RAD) using Experion RNA High Sensitivity Reagents and Experion Standard Sensitivity RNA chips following the manufacturer protocol. Only samples with a minimum RNA concentration of 10 ng/μL and RNA Quality Index (RQI) greater than or equal to 9.4 were used.

value: adult peripheral blood


title: Adult Peripheral Blood-Tconv-6


title: HSC-4 cells transfected control siRNA in suspension culture

city: Fukuoka

first: Kana

last: Hasegawa

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Faculty of Dental Science

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: suspension culture, control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using relia prep rna cell miniprep system (promega)  according to the manufacturer's instructions.

tag: transfection

value: control

value: squamous carcinoma cell line from tongue.

tag: cell line


title: 2TBL_S2_L001

value: Tumor

value: Neutrophils


title: Pabpn1l-KO-1Cell-Rep1


title: 3TLI_S5_L002


title: Adult Peripheral Blood-Tconv-3


title: LRL3

description: At the start of squaring stage


title: LF1

description: At the start of squaring stage


title: HSC-4 cells transfected LATS2 siRNA in suspension culture

source_name: suspension culture, siLATS2


title: HOC313 vehicle

city: Kumamoto-si

first: Akiyuki

last: Hirosue

state: Kumamoto

address: 1-1-1 Honjo,Chuo-ku

department: Faculty of Life Science

institute: Kumamoto University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: HOC313 cells, vehicle, 48h

growth_protocol: The cells were cultured in DMEM (Sigma) supplemented with 10% FBS (Corning), and maintained under a humidified 5% CO2 atmosphere at 37 ̊C.

extract_protocol: The total RNA was isolated and purified using miRNAeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: The cells were treated with JQ1 (1.0 μM for 48 h) or vehicle.

value: tongue

value: vehicle, 48h

value: OSCC cell line


title: HSC-4 cells transfected control siRNA in 2D culture

source_name: 2D culture, control


title: Adult Peripheral Blood-Tconv-4


title: Adult Peripheral Blood-Tconv-2


title: 4TBL_S1_L001


title: HOC313 JQ1

source_name: HOC313 cells, JQ1,  1.0 μM, 48h


title: LRL2

description: At the start of squaring stage

value: Squaring stage


title: DPAL1

description: At the start of squaring stage

value: 1 day post anthesis ovule


title: Adult Peripheral Blood-Treg-5

source_name: Adult peripheral blood Treg 14 days post expansion


title: Pabpn1l-KO-GV-Rep1

value: GV oocyte


title: LRL1

description: At the start of squaring stage


title: Adult Peripheral Blood-Treg-4


title: Adult Peripheral Blood-Treg-6


title: Pabpn1l-WT-2Cell-Rep2


title: DPAH3

description: At the start of squaring stage


title: Pabpn1l-KO-GV-Rep2


title: DPAH2

description: At the start of squaring stage


title: Pabpn1l-WT-2Cell-Rep1


title: Adult Peripheral Blood-Tconv-1


title: NUP98-JARID1A_HA

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

library_source: genomic

data_processing:
RNA-seq processing:
Quality control with FastQC
Quality trimming, quality filtering and length filtering by PRINSEQ-lite
Alignment against the extended mouse reference genome (GRCm38/mm10 plus manually added sequences of eGFP, luciferase and the three fusions) with STAR
Processed with SAMtools
Counts per gene were obtained by featureCounts
Potential normalization strategies and the resemblance of replicates were visualized with NVT
Normalization and differential gene expression analysis where then done with DESeq2
ChIP-seq processing:
Quality control with FastQC
PRINSEQ-lite for quality trimming and filtering as well as length filtering
Alignment against the mouse reference genome (GRCm38/mm10) with bwa
Quality was assessed with deepTools
Peak calling was done with macs2
Called peaks were annotated with ChIPseeker
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample, bigwig files were generated using deepTools

molecule: genomic DNA

growth_protocol: transplantion-based, in vivo

extract_protocol:
bone marrow of moribund mice, DSG/Formaldehyde-crosslinked chromatin
NEBNext Ultra DNA Library Prep Kit for Illumina
RNA-seq: sorted GFP/CD45.2+ bone marrow cells, total RNA was extracted. ChIP-seq: bone marrow of moribund mice, DSG/Formaldehyde-crosslinked chromatin
RNA-seq: Facility (RNA/Lexogen, poly-A), stranded. ChIP-seq: NEBNext Ultra DNA Library Prep Kit for Illumina

treatment_protocol:
Transplanted mice untreated
RNA-seq: Transplanted mouse was treated with Doxycycline (4mg/ml) for 3 days, Transplanted mouse was treated with Doxycycline (4mg/ml) for 5 days, Transplanted mouse untreated. ChIP-seq: Transplanted mice untreated

value: regulatable expression of NUP98/JARID1A

value: none (untreated)

value: bone marrow

value: a-HA (Abcam, ab9110)


title: NUP98-CTRL_3

extract_protocol:
sorted GFP/CD45.2+ bone marrow cells, total RNA was extracted
Facility (RNA/Lexogen, poly-A), stranded
RNA-seq: sorted GFP/CD45.2+ bone marrow cells, total RNA was extracted. ChIP-seq: bone marrow of moribund mice, DSG/Formaldehyde-crosslinked chromatin
RNA-seq: Facility (RNA/Lexogen, poly-A), stranded. ChIP-seq: NEBNext Ultra DNA Library Prep Kit for Illumina

treatment_protocol:
Transplanted mouse untreated
RNA-seq: Transplanted mouse was treated with Doxycycline (4mg/ml) for 3 days, Transplanted mouse was treated with Doxycycline (4mg/ml) for 5 days, Transplanted mouse untreated. ChIP-seq: Transplanted mice untreated

value: regulatable expression of NUP98/NSD1, NUP98/JARID1A and NUP98/DDX42

value: sorted GFP/CD45.2+ bone marrow cells


title: NUP98-JARID1A_Input


title: DPAH1

description: At the start of squaring stage


title: NUP98-CTRL_2

value: regulatable expression of NUP98/NSD1, NUP98/JARID1A and NUP98/DDX41


title: NUP98-CTRL_1

value: regulatable expression of NUP98/NSD1, NUP98/JARID1A and NUP98/DDX40


title: Pabpn1l-WT-1Cell-Rep1

value: 1Cell embryo


title: HF3

description: At the start of squaring stage

value: Flower buds


title: Pabpn1l-WT-GV-Rep2


title: Adult Peripheral Blood-Treg-3

value: adult peripheral blood


title: NUP98-NSD1_Day5-OFF-DOX_3

value: regulatable expression of NUP98/NSD1


title: HF2

description: At the start of squaring stage


title: Pabpn1l-WT-GV-Rep1


title: Pabpn1l-WT-1Cell-Rep2


title: HF1

description: At the start of squaring stage


title: Adult Peripheral Blood-Treg-2


title: Adult Peripheral Blood-Treg-1


title: NUP98-NSD1_Day3-OFF-DOX_1


title: NUP98-NSD1_Day5-OFF-DOX_1


title: HRL2

description: At the start of squaring stage

value: Leaf


title: D9

city: Hamar

first: Maren

last: van Son

address: Storhamargata 44

country: Norway

institute: Norsvin

description: Low

data_processing:
Base calling were performed using Illumina’s RTA software v2.7.7.
Trimmomatic v.0.36 was used to trim reads by removing leading bases with Phred33 quality scores < 5, trailing bases with Phred33 quality scores < 3, using a sliding window of 4 bases and removing the 5’ terminal base if the average Phred33 score of the 4 bases was < 15, and completely discard trimmed reads with less than 36 remaining bases.
Mapping was done to the pig genome Sscrofa build 11.1 using the Star software v.2.5.2a and default parameters while simultaneously adding unique read groups to the files.
HTSeq was run with the reverse stranded option to calculate the number of reads mapped to each gene.
The differential expression analysis was conducted using the package edgeR v.3.12.1 in the R environment.
Genome_build: Sscrofa build 11.1
Supplementary_files_format_and_content: Tab delimited text file with HTSeq counts.

organism: Sus scrofa

source_name: Testis

extract_protocol:
The RNeasy Midi Kit (Qiagen) was used to extract total RNA from testis tissue.
Libraries were prepared using TruSeq mRNA stranded HT kit (Illumina) on a Sciclone NGSx liquid automation system (Perkin Elmer). Final library quality check was performed on Fragment Analyser (Advanced Analytical Technologies, Inc) and by qPCR (Kapa Biosciences).

tag: breed

value: Duroc


title: D7

description: Low


title: HRL1

description: At the start of squaring stage

value: Squaring stage


title: D6

description: Low


title: D5

description: High


title: DPAD3

description: At the start of squaring stage

value: 1 day post anthesis ovule


title: NUP98-NSD1_Day5-DOX_2

treatment_protocol:
Transplanted mouse was treated with Doxycycline (4mg/ml) for 5 days
RNA-seq: Transplanted mouse was treated with Doxycycline (4mg/ml) for 3 days, Transplanted mouse was treated with Doxycycline (4mg/ml) for 5 days, Transplanted mouse untreated. ChIP-seq: Transplanted mice untreated

value: Doxycycline (4mg/ml) for 5 days


title: NUP98-NSD1_Day5-DOX_1


title: D4

description: High


title: NUP98-NSD1_Day3-DOX_3

treatment_protocol:
Transplanted mouse was treated with Doxycycline (4mg/ml) for 3 days
RNA-seq: Transplanted mouse was treated with Doxycycline (4mg/ml) for 3 days, Transplanted mouse was treated with Doxycycline (4mg/ml) for 5 days, Transplanted mouse untreated. ChIP-seq: Transplanted mice untreated

value: Doxycycline (4mg/ml) for 3 days


title: D3

description: High


title: NUP98-NSD1_Day5-DOX_3


title: DPAD1

description: At the start of squaring stage


title: Cord Blood-Tconv-6

source_name: Cord blood Tconv 14 days post expansion

value: cord blood


title: DF3

description: At the start of squaring stage


title: NUP98-NSD1_Day3-DOX_2

value: bone marrow


title: Cord Blood-Tconv-5


title: Cord Blood-Tconv-7


title: D2

description: High


title: D1

description: High


title: DF2

description: At the start of squaring stage


title: NUP98-NSD1_Day3-DOX_1


title: Cord Blood-Tconv-1


title: DPAD2

description: At the start of squaring stage


title: Cord Blood-Treg-7


title: L15

value: Landrace


title: Cord Blood-Tconv-2


title: DF1

description: At the start of squaring stage


title: Cord Blood-Tconv-3


title: WT input

city: Ithaca

first: Rachel

middle: Leigh

last: Cosby

state: NY

address: 218 Biotechnology Bldg, 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Preprocessing: ChIP-seq reads were trimmed for adapter sequences and error-corrected by overlap analysis using fastp (Chen, et al. 2018).
Alignment: Reads were aligned to the Myoluc2.0 assembly with wild-type KRABINER transgene spiked in as an additional contig using bowtie2 (Langmead and Salzer 2012) with parameters --sensitive-local -I 0 -X 1500 and filtered for uniquely mapping (mapq > 1) concordantly aligned reads using samtools (Li, et al. 2009). Reads mapping to blacklisted high accessibility regions (contigs AAPE02059006, AAPE02072785, GL429886, GL429923, GL429927, GL429979, GL430411, GL430644, GL431357) were removed (samtools; Li, et al. 2009).
Peak calling: DNA binding peaks for each KRABINER variant (WT, mutDBD, and mutKRAB) were called relative to matched input samples using MACS2 with default parameters (Zhang, et al. 2008). Peaks called in all three genotypes were removed (bedtools intersect, >50% reciprocal overlap; Quinlan and Hall 2010).
bigWig score tracks for visualization and downstream analysis were generated using deepTools bamCoverage (Ramirez, et al. 2014); normalized bigWig score tracks produced in the same way but first normalized by library size and then normalized relative to the appropriate input sample ((deeptools bigwigCompare –operation ratio; Ramirez, et al. 2014)
Genome_build: Myoluc2
Supplementary_files_format_and_content: bigWig score tracks (*.bw) for visualization and downstream analysis were generated using deepTools bamCoverage (Ramirez, et al. 2014); normalized bigWig score tracks (*_norm.bw) produced in the same way but first normalized by library size and then normalized relative to the appropriate input sample ((deeptools bigwigCompare –operation ratio; Ramirez, et al. 2014); peaks called for each genotype relative to appropriate input using MACS2 (Zhang, et al. 2008) and filtered to remove peaks present in all genotypes

organism: Myotis velifer

source_name: Embryonic fibroblast

growth_protocol: Myotis velifer embryonic fibroblast cells of various genotypes were cultured at 37C, 5% CO2, with DMEM + 20% FBS, with passaging at ~80% confluency

extract_protocol:
For each KRABINER expression construct, 2 × 107 cells were pelleted at 500xg for 5 min at room temperature and washed once with 1 mL of PBS + 1X Pierce Protease Inhibitors [Thermo Fisher]. Cells were then fixed with 1% formaldehyde in PBS + inhibitors for 10 minutes at room temperature, with rocking. The fixation reaction was quenched with 0.125M glycine solution for 5 minutes at room temperature, with rocking.  Pellets were washed twice with ice cold PBS + inhibitors and stored at -80C until use. Frozen fixed cell pellets were then resuspended in 2 mL lysis buffer (1 % SDS, 10 mM EDTA, 10 mM Tris-Cl pH 8.0, and 1X Pierce Protease Inhibitors [Thermo Fisher]) and sonicated to average fragment size of ~500-800 bp using a Diagenode Bioruptor. Sonicated chromatin was diluted in 1X TBST+PI (25 mM Tris-Cl pH 8.0, 0.15 M NaCl, 0.05% Tween-20, and 1X Pierce Protease Inhibitors [Thermo Fisher]). For input libraries, 3.33% of total sonicated chromatin from each was pooled across genotypes of the same KRABINER variant for total input material of ~10% respective to each individual IP. For each IP, 100 µL Pierce c-Myc magnetic beads (Thermo Fisher) were washed twice in ice cold TBST+PI and then added to sonicated lysate and incubated for 16 h at 4 °C. Beads were washed three times with low salt wash buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-Cl pH 8.0), twice with high salt wash buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-Cl pH 8.0), once with lithium chloride wash buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 500 mM LiCl, 20 mM Tris pH 8.0), and three times with final wash buffer (2 mM EDTA, 10% glycerol, 20 mM Tris-Cl pH 8.0). Beads were the resuspended in TE buffer (10 mM Tris-Cl pH 8.0, 10 mM EDTA). Crosslinks were reversed at 65 °C for 16 h using 0.5% SDS and 0.4 µg/µl Proteinase K (Ambion) in a thermomixer. DNA was extracted twice with phenol:chloroform, once with chloroform, precipitated in ethanol
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to manufacturer's instructions with 4 cycles of PCR amplification

treatment_protocol: All samples are treated with 1ug/mL doxycycline for 24 hours prior to ChIP

value: Embryonic fibroblast

value: KRABINER KO

tag: transgene

value: WT KRABINER

value: doxycycline (induced)

tag: clone

value: pool of P4C11/P4B3/P4D7

tag: mark

value: input

tag: antibody beads


title: NUP98-NSD1_Day5-OFF-DOX_2

value: none (untreated)

value: sorted GFP/CD45.2+ bone marrow cells


title: L13


title: DRL3

description: At the start of squaring stage

value: Leaf


title: Cord Blood-Treg-5

source_name: Cord blood Treg 14 days post expansion


title: NUP98-JARID1A_Day5-OFF-DOX_1

value: regulatable expression of NUP98/JARID1A


title: Cord Blood-Tconv-4


title: 3TBR_S3_L001

tag: disease state

value: Tumor

value: Neutrophils

value: Brain


title: NUP98-JARID1A_Day5-OFF-DOX_2

tag: cell type


title: Cord Blood-Treg-2

tag: tissue


title: Cord Blood-Treg-3


title: Cord Blood-Treg-6


title: Cord Blood-Treg-4


title: DRL1

description: At the start of squaring stage

value: Squaring stage


title: NUP98-JARID1A_Day5-OFF-DOX_3

tag: strain


title: Cord Blood-Treg-1

value: cord blood


title: NUP98-JARID1A_Day3-OFF-DOX_1

value: bone marrow


title: L10

value: Landrace


title: NUP98-JARID1A_Day5-DOX_3

value: Doxycycline (4mg/ml) for 5 days


title: WT OE Rep3 ChIPseq

value: Embryonic fibroblast

value: KRABINER KO

value: myc

value: Pierce Anti c-Myc magnetic beads (cat #88842)


title: L9


title: DPAC3

description: At the start of squaring stage

source_name: 1 day post anthesis ovule

value: 1 day post anthesis ovule


title: WT OE Rep2 ChIPseq

value: WT KRABINER

value: doxycycline (induced)


title: L8


title: NUP98-JARID1A_Day5-DOX_2

value: sorted GFP/CD45.2+ bone marrow cells


title: WT OE Rep1 ChIPseq


title: DPAC1

description: At the start of squaring stage


title: mutKRAB input

value: mutKRAB KRABINER

value: pool of P3A8/P4D7/P4F4

value: input


title: L7

description: High_d0, High_d4_0


title: DRL2

description: At the start of squaring stage

value: Leaf


title: L12


title: L6


title: CF3

description: At the start of squaring stage

value: Flower buds

value: Squaring stage


title: CF2

description: At the start of squaring stage


title: mutKRAB OE Rep1 ChIPseq


title: L5


title: L4


title: NUP98-JARID1A_Day3-DOX_2

value: regulatable expression of NUP98/JARID1A

value: Doxycycline (4mg/ml) for 3 days

value: bone marrow


title: mutKRAB OE Rep2 ChIPseq

value: Embryonic fibroblast


title: NUP98-JARID1A_Day3-DOX_3


title: mutDBD OE Rep3 ChIPseq

value: KRABINER KO

value: mutDBD KRABINER


title: L3

value: Landrace


title: NUP98-DDX10_Day5-OFF-DOX_3

value: regulatable expression of NUP98/DDX10

value: none (untreated)


title: CF1

description: At the start of squaring stage


title: L2

description: Low_d0, Low_d4_0


title: CRL3

description: At the start of squaring stage


title: mutDBD OE Rep2 ChIPseq

value: doxycycline (induced)

value: myc

value: Pierce Anti c-Myc magnetic beads (cat #88842)


title: NUP98-DDX10_Day5-OFF-DOX_2

value: sorted GFP/CD45.2+ bone marrow cells


title: CRL2

description: At the start of squaring stage


title: DPAC2

description: At the start of squaring stage

value: 1 day post anthesis ovule


title: NUP98-JARID1A_Day5-DOX_1

value: Doxycycline (4mg/ml) for 5 days


title: NUP98-DDX10_Day5-OFF-DOX_1


title: CRL1

description: At the start of squaring stage

value: Leaf


title: mutDBD OE Rep1 ChIPseq


title: L1


title: mutKRAB OE Rep3 ChIPseq

value: mutKRAB KRABINER


title: Infected sample 32 hpi, Replicate 4

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Bos_taurus/UCSC/bosTau7
Supplementary_files_format_and_content: tad-delimited, raw counts

organism: Bos taurus

source_name: Primary bovine endothelial cells from bovine aorta

growth_protocol: primary bovine aortic endothelial cells (BAEC) were maintained in M200 medium  containing 20% of FBS, 100 IU/mL of penicillin, 100 mg/mL of streptomycin, 0.25 µg/mL amphotericin B and Large Vessel Endothelial Growth supplement

extract_protocol:
Confluent monolayers of BAECs were collected using a cell scraper, pelleted at 1350xg for 5 mins and harvested in RNAlater. Total RNA was extracted using QIAGEN miniRNeasy after homogeneization using a QIAShredder. Afterwards, Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, CA, USA) was used in the succeeding steps. Briefly, mRNA was enriched from total RNA samples (100-1000 ng) using poly-A selection and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc.,). The libraries were normalized to 10 nM in 10 mM Tris-Cl/0.1% Tween 20, pH8.5.

treatment_protocol: T25 flasks seeded with confluent BAEC monolayers (2x10^6 cells) were infected with purified tachyzoites of the BbSpain-1 isolate of Besnoitia besnoiti at a multiplicity of infection (MOI) of 10. Tachyzoites were allowed to invade host cells for 12 hours post-infection (12hpi) or 32 hpi.

value: Primary endothelial cells

value: Aorta

value: Treated for 32 h


title: NUP98-JARID1A_Day3-DOX_1

value: regulatable expression of NUP98/JARID1A

value: Doxycycline (4mg/ml) for 3 days

value: bone marrow


title: mutDBD input

value: Embryonic fibroblast

value: KRABINER KO

value: mutDBD KRABINER

value: pool of P1D7/P2B5/P2B7

value: input


title: NUP98-DDX10_Day5-DOX_3

value: regulatable expression of NUP98/DDX10


title: DPAB3

description: At the start of squaring stage

value: Squaring stage


title: Infected sample 32 hpi, Replicate 3


title: NUP98-DDX10_Day3-OFF-DOX_1

value: none (untreated)

value: sorted GFP/CD45.2+ bone marrow cells


title: DPAB2

description: At the start of squaring stage

value: 1 day post anthesis ovule


title: Infected sample 32 hpi, Replicate 2


title: NUP98-DDX10_Day5-DOX_2

value: Doxycycline (4mg/ml) for 5 days


title: NUP98-DDX10_Day5-DOX_1


title: Infected sample 32 hpi, Replicate 1

value: Primary endothelial cells


title: Infected sample 12 hpi, Replicate 4

value: Aorta

value: Treated for 12 h


title: Asthma patient 5

type: protein

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

hyb_protocol: The Human Cytokine Antibody Arrays kit (Raybiotech) was used according to the manufacturer’s instructions.

scan_protocol: Scanning was conducted by the company

data_processing: To obtain relative expression, the signal intensity was subtracted from negative controls and normalized to internal positive with the RayBiotech analysis tool.

molecule: protein

source_name: asthma patient, exhaled breath condensate

label_protocol: biotin

extract_protocol: Exhaled breath condensate

tag: disease status

value: Asthma

value: exhaled breath condensate


title: Asthma patient 2


title: Asthma patient 3


title: Asthma patient 6


title: Infected sample 12 hpi, Replicate 3


title: BF1

description: At the start of squaring stage

tag: genotype

value: Flower buds


title: NUP98-DDX10_Day3-DOX_2

tag: treatment

value: Doxycycline (4mg/ml) for 3 days

value: bone marrow


title: BF3

description: At the start of squaring stage

tag: developmental stage


title: BF2

description: At the start of squaring stage


title: Asthma patient 1


title: BRL3

description: At the start of squaring stage

value: Leaf


title: Infected sample 12 hpi, Replicate 2


title: NUP98-DDX10_Day3-DOX_1


title: DPAB1

description: At the start of squaring stage


title: Mixed Sample Control and IL-17-/- Tag09-12

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing: Filtering, alignment, annotation of reads and cell calling were performed using the BD Rhapsody Analysis Pipeline v1.03

source_name: Spleenocytes

extract_protocol: Libraries were prepared using BD Rhapsody instrument according to "Single Cell Capture and cDNA Synthesis with BD Rhapsody Single-Cell Analysis System"( Doc ID: 210966 Rev. 1.0) using BD Rhapsody Cartridge Reagent Kit, BD Rhapsody Cartridge Kit, BD Rhapsody cDNA Kit, BD Rhapsody Targeted mRNA and AbSeq Amplification kit and the BD Immune Response Panel Mm. Sequencing was performed on a HiSeq2500 (Illumina)

value: Spleen

value: Control/IL-17a/f KO


title: Negative control, Replicate 4

value: Non-treated, Negative control


title: Infected sample 12 hpi, Replicate 1


title: BRAC1235.6h_MEMO

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) and STAR (2.5.2a) were used to align reads to the mouse Ensembl GRCm38 transcriptome.
Raw counts were normalised and differential expression analysis was performed with the DESeq2 package (version 1.18.1) within the R programming (version 3.4.3)
Genome_build: mouse Ensembl GRCm38
Supplementary_files_format_and_content: Transcripts per million (TPM) values. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: Myc WT mouse

extract_protocol:
Spleen were disrupted using a 70uM mesh strainer. Samples were then washed with FACS buffer (2% FBS and 2 mM EDTA in PBS), incubated for 30 min on ice  with antibodies and  CD43 MicroBeads (Cat# 130-049-801, Miltenyi Biotec). Red blood cells were then  lysed for 5 min at room temperature with 5mL of Gey's buffer. After a wash , samples were passed through a 70 um filter LS columns (Miltenyi) for magnetic separation and B cell enrichment. After washing,  single-cell suspension was  sorted by flow cytometry. Samples were collected in eppendorffs containing RTL Buffer Plus (Qiagen) with 1% beta-mercaptoethanol. Samples were purified with AllPrep DNA/RNA Mini and Micro Kits (Cat# 80204 and Cat# 80284, Qiagen) as per  manufacturer’s instructions.
Samples were prepared with Nugen cDNA kit and sequenced using Illumina HiSeq system

treatment_protocol: 8-12 week old female mice were intravenously immunised with 5x10^10 sheep red blood cells in 200uL of PBS and analysed 10 days after.

value: Spleen Memory B cells

tag: age

value: 8-12 week old

tag: Sex

value: female

value: 10 days after sheep red blood cells immunisation of mice

value: B220+ CD138Neg IgDneg CD38+ CD273+ cells


title: BRL2

description: At the start of squaring stage

source_name: Leaf

value: Squaring stage


title: Control patient 10

source_name: Healthy control patient, exhaled breath condensate

value: Healthy


title: Control patient 7


title: Control patient 9


title: BRL1

description: At the start of squaring stage


title: NUP98-DDX10_Day3-DOX_3

tag: genotype/variation

value: regulatable expression of NUP98/DDX10

value: sorted GFP/CD45.2+ bone marrow cells


title: Control patient 8

value: exhaled breath condensate


title: BRAC861.2g_MEMO


title: Negative control, Replicate 2

value: Primary endothelial cells

value: Aorta


title: Control patient 5


title: Negative control, Replicate 3


title: DPAA2

description: At the start of squaring stage

value: 1 day post anthesis ovule


title: Negative control, Replicate 1


title: DPAA1

description: At the start of squaring stage


title: Control patient 6


title: DCCT13.8l LZ

source_name: Myc V394D mouse

value: Spleen Light Zone GC B cells

value: B220+ CD138Neg  IgDneg CD38Neg Fas+ CD86High CXCR4Low cells


title: DCCT13.8j LZ


title: AF3

description: At the start of squaring stage

source_name: Flower buds

value: Flower buds


title: Control patient 4


title: Snf2- Mnase  5min

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

description: Snf2- Mnase  5min

data_processing:
Sequence were trimmed to remove adapters using TRIMMOMATIC
Mapping the reads to reference genome was done using Bowtie2
ChEC alignment and track visualization using bedgraph files were performed as previously described in Zentner  et al 2015.
Peaks were determined from the normalized ChEC ratio using MACS2 algorithm with a window size of 60 bp.
Analysis was done for data obtained using nomodel_extsize_200_keep-dup_all option. The assumption being removing duplicates will decrease the peak calling power of the MACS2 algorithm.
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/
Supplementary_files_format_and_content: peaks, bigwig

organism: Candida albicans

source_name: Yeast cells

growth_protocol: For each ChEC experiment, saturated overnight cultures of Mnase tagged and Mnase free strains were diluted to a starting OD600 of 0.1 in 50 ml YPD medium. Cells were grown at 30°C to an OD600 of 0.7–0.8

extract_protocol:
Nucleic acids were extracted using MasterPure yeast DNA purification kit (Epicentre, MPY80200) according the manufacturer’ instructions, and resuspended in 50 µl 0.1 X Tris-HCl buffer, pH 8.0. RNAs were digested with 10 µg RNase A at 37 °C for 20 min.
Libraries were prepared according to Illumina's instructions for Shotgun library preparation for ChIP samples (NEB Ultra II) Illumina Library QC
As Chip-Seq, A 50-bp paired-end sequencing of DNAs were performed using an Illumina HiSeq 4000 sequencing system.

treatment_protocol: Cells were pelleted at 3,000 g during 5 min and washed three times with 1 ml Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, one tablet Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF). Cells were then resuspended in 600 µl Buffer A containing 0.1% digitonin  and permeabilized for 10 min at 30 °C under shaking. MNase digestions were performed by adding CaCl2  at final concentration of 5 mM  and incubated at the indicated time at 30 °C. At each time point, a total of 200 µl aliquots of the ChEC digestions were transferred to a tube containing 50 µl of 250 mM EGTA to quench MNase digestions. For each factor analyzed, the timepoint “0” corresponds to a condition where MNase were not activated by CaCl2.

tag: fusion protein

value: Snf2- Mnase

tag: duration (min)


title: Snf2- Mnase  60min

description: Snf2- Mnase  60min


title: DCCT13.8k LZ


title: Snf2- Mnase  20min

description: Snf2- Mnase  20min


title: AF2

description: At the start of squaring stage


title: Control patient 2


title: DPAA3

description: At the start of squaring stage


title: BRAC1235.6h_LZ


title: BRAC861.2e_MEMO

value: Spleen Memory B cells


title: AF1

description: At the start of squaring stage


title: Nsi1- Mnase  60min

description: Nsi1- Mnase  60min

value: Nsi1- Mnase


title: ARL3

description: At the start of squaring stage

value: Leaf


title: DCCT13.8h LZ

value: 8-12 week old

value: female

value: 10 days after sheep red blood cells immunisation of mice


title: ARL2

description: At the start of squaring stage

value: Squaring stage


title: Control patient 1

value: Healthy


title: Sickle cell + asthma patient 4

source_name: Sickle cell + asthma patient, exhaled breath condensate

value: Sickle cell + asthma


title: BRAC861.2g_LZ


title: Nsi1- Mnase  20min

description: Nsi1- Mnase  20min


title: Control patient 3

value: exhaled breath condensate


title: BRAC861.2f_LZ


title: Sickle cell + asthma patient 3


title: Nsi1- Mnase  5min

description: Nsi1- Mnase  5min


title: ARL1

description: At the start of squaring stage


title: Sickle cell + asthma patient 2


title: Sickle cell + asthma patient 1


title: BRAC861.2e_LZ


title: Mnase Free 60min

description: Mnase Free 60min


title: MP Total-2

city: New York

first: Harold

middle: Kunal

last: Elias

state: New York

address: 417E 68th Street

department: Pathology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genomes (mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Primary hematopoietic cells

extract_protocol:
RNA was isolated using Trizol and precipitated with 100% isopropanol and linear acrylamide.
RNA libraries was generated using Illumina SMARTer amplification protocol

treatment_protocol: Primary mouse hematopoietic cells were incubated with cycloheximide at 100 ug/ml for 10 min at 37ºC. Cells were peltted and then washed with ice-cold PBS and resuspended in 250 ul of lysis buffer (300 mM NaCl, 15 mM Tris-HCl ph 7.5, 15 mM MgCl2, 1% TritonX-100, 100 ug/ml CHX, 200 U/ml Superase inhibitor). Prior to sucrose gradient, lysate was kept aisde for Total RNA isolation and cDNA preparation. Remaining lysate was layered over 4 ml 10-60% sucrose gradients.  The gradients were centrifuged at 37,000 rpm for 2 hr at 4º C in a SW60 Ti swinging bucket rotor (Beckman). Ten fractions of ~400 ul each were collected from the gradients and RNA was isolated. Fraction 7 was used for polysomal RNA isolation and cDNA preparation.

value: MP (progenitor cells)

tag: rna fraction

value: Total


title: Mnase Free 20min

description: Mnase Free 20min


title: MP polysomal-3

value: polysomal


title: MP Total-1


title: Mnase Free 5min

description: Mnase Free 5min


title: MP polysomal-2


title: Sickle cell patient 9

source_name: Sickle cell patient, exhaled breath condensate

value: Sickle cell


title: LH1

city: Guangzhou

first: Jinhuan

last: Song

state: Guangdong

address: Jinan University, No.601, West Huangpu Avenue

institute: Jinan University

description: processed data file: otu_table.txt

data_processing:
Library strategy: 16S rRNA sequencing
Sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Scientific) following manufacturer's recommendations. The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific). At last, the library was sequenced on an Ion S5TM XL platform and 400 bp/600 bp single-end reads were generated.
1. Single-end reads quality control:
1.1 Data split: Single-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence. 1.2 Data Filtration: Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean reads according to the Cutadapt (Martin M. , 2011) [1] (V1.9.1, http://cutadapt.readthedocs.io/en/stable/) quality controlled process. 1.3 Chimera removal: The reads were compared with the reference database (Silva database, https://www.arb-silva.de/) [2] using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) [3] to detect chimera sequences, and then the chimera sequences were removed [4]. Then the Clean Reads finally obtained.
2. OTU cluster and Species annotation:
2.1 OTU Production: Sequences analysis were performed by Uparse software (Uparse v7.0.1001, http://drive5.com/uparse/) [5]. Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation. 2.2 Species annotation: For each representative sequence, the Silva Database (https://www.arb-silva.de/) [2] was used based on Mothur algorithm to annotate taxonomic information. 2.3 Phylogenetic Relationship Construction: In order to study phylogenetic relationship of different OTUs, and the difference of the dominant species in different samples (groups), multiple sequence alignment were conducted using the MUSCLE software (Version 3.8.31, http://www.drive5.com/muscle/) [6]. 2.4 Data Normalization: OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences. Subsequent analysis of alpha diversity and beta diversity were all performed basing on this output normalized data.
Genome_build: Silva database, https://www.arb-silva.de/
Supplementary_files_format_and_content: otu_table.txt: Tab-delimited text file; relative proportions.

organism: mouse gut metagenome

source_name: feces

extract_protocol:
Total genome DNA from samples was extracted using CTAB/SDS method. DNA concentration and purity were monitored on 1% agarose gels. According to the concentration, DNA was diluted to 1 ng/µL using sterile water.
Sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Scientific) following manufacturer's recommendations.

tag: strain/background

value: Postnatal day 35

value: LH

value: Feces


title: LH2

description: processed data file: otu_table.txt


title: LH3

description: processed data file: otu_table.txt


title: DS8_RNAseq

city: Nashville

first: Corey

middle: Eduardo

last: Hayford

state: TN

address: 2220 Pierce Avenue

department: Chemical and Physical Biology

institute: Vanderbilt University

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling.
Reads were aligned using STAR (version 2.5.2b) with default parameters to the STAR hg38 reference genome.
Gene counts were obtained using the featureCounts package (version 1.6.4) within the Subread package.
Genome_build: hg38
Supplementary_files_format_and_content: Compressed single space-delimited text file with samples as column names and genes as row names. Numbers correspond to raw counts.

molecule: polyA RNA

source_name: Cancer Cell Line (single-cell derived subline of PC9-VU)

growth_protocol: All cells were grown in RPMI 1640 media with 10% FBS in T-75 flasks and passaged approximately every 3 days. Cells were passaged ~4-5 times from the time of frozen stock creation (VU/MGH - post labeling; BR1 - post dose escalation in afatinib; DSn - post expansion of single clone to T-75 flask). DS lines were single-cell cloned from PC9-VU after nuclear labeling. PC9-MGH was acquired separately and labeled. PC9-BR1 was created by dose-escalation treatment in EGFR inhibitor afatinib from the PC9-VU cell line.

extract_protocol:
RNA was extracted using a Trizole extraction (ThermoFisher), according to the manufacturer’s protocol.
RNASeq libraries were prepared using 200 ng of total RNA and the NEBNext rRNA Depletion Kit (NEB, Cat: E6310X), per manufacturer’s instructions. This kit employs an RNaseH-based method to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA). The mRNA was enriched via poly-A-selection using oligoDT beads and then the RNA was thermally fragmented and converted to cDNA. The cDNA was adenylated for adaptor ligation and PCR amplified.

treatment_protocol: All sequencing studies are reflective of untreated samples.

tag: cancer type

value: Non-small cell lung cancer

tag: egfr mutation status

value: EGFR exon 19 deletion

tag: egfr t790m mutation status

value: No T790M mutation

tag: population name

tag: passages


title: DS9_RNAseq


title: DS7_RNAseq


title: Sickle cell patient 10

tag: tissue


title: mRNA library

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling.
Gene counting, including alignment, filtering, barcode counting, and unique molecular identified (UMI) counting was performed using the count function in the 10X Genomics software Cell Ranger (version 3.0.2).
CITE-seq-Count (github.com/Hoohm/CITE-seq-Count) was used to count hashtags from the hashtag oligonucleotide (HTO) library. We then used the Demux function in the R package Seurat (satijalab.org/seurat) to demultiplex the HTO and mRNA libraries, and pair cells to their associated hashtag. Data was integrated into a count matrix with genes and cells, with hashtag identity as a metadata tag.
Genome_build: hg38
Supplementary_files_format_and_content: Both the mRNA and HTO libraries have compressed barcodes (cells, tab-separated), features (genes, tab-separated), and gene count (matrix, sparse-matrix) files in read_count and umi_count folders, respectively.

source_name: Cancer Cell Lines (cell line versions: PC9-VU, PC9-MGH, PC9-BR1; cell sublines: DS3, DS6, DS7, DS8, DS9)

extract_protocol:
RNA was extracted using the proprietary 10x genomics method.
scRNA-seq libraries were prepared using the 10x Genomics gene expression kit (version 2, 3’ counting) and cell hashing. Cells were prepared according to recommendations from the cell hashing protocol on the CITE-seq website (cite-seq.com/protocol). After cell preparation, 1 ng of eight different cell hashing antibodies (TotalSeq-A025(1-8) anti-human Hashtag, Biolegend) were used to label each of the eight samples (PC9-VU, PC9-MGH, PC9-BR1, DS3, DS6, DS7, DS8, DS9). Hashed single-cell samples were combined in approximately similar proportions and ‘super-loaded’ (aiming for ~20,000 cells; ~15,400 cells were obtained) onto the Chromium instrument. Cells were encapsulated according to 10X Genomics guidelines. Single-cell mRNA expression libraries were prepared according to manufacturer’s instructions. The leftover eluent of the mRNA expression library, containing the hashtag oligonucleotides (HTOs), was utilized to further size select the HTO library. The size-selected HTO library was PCR amplified to obtain higher quality reads.

value: Only PC9-BR1

value: mRNA


title: Hashtag Oligonucleotide (HTO) library

value: HTO


title: Sickle cell patient 7

tag: disease status


title: Sickle cell patient 8


title: DS6_RNAseq


title: MP polysomal-1

tag: strain


title: Control4

description: processed data file: otu_table.txt

tag: treatment

value: PBS


title: LSK Total-2

tag: developmental stage

value: LSK (stem cells)


title: DS3_RNAseq


title: Sickle cell patient 5


title: Control3

description: processed data file: otu_table.txt

tag: age


title: LSK Total-1


title: HRL3

description: At the start of squaring stage

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

extract_protocol:
T.RNA with Sigma Spectrum Plant Total RNA kit (Sigma-  448 Aldrich, USA)
Accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA)

tag: genotype

value: Leaf

value: Squaring stage


title: Sickle cell patient 4

value: exhaled breath condensate


title: PC9_BR1_RNAseq

source_name: Cancer Cell Line (derived from PC9-VU in EGFR inhibitor afatinib)

value: T790M mutation positive


title: Control2

description: processed data file: otu_table.txt


title: PC9_MGH_RNAseq

source_name: Cancer Cell Line (cultivated at Massachusetts General Hospital)

value: MGH


title: PC9_VU_RNAseq

source_name: Cancer Cell Line (cultivated at Vanderbilt University)

value: VU


title: Sickle cell patient 3

value: Sickle cell


title: LSK polysomal-2

value: polysomal


title: Sickle cell patient 2


title: LSK polysomal-1


title: Sickle cell patient 6


title: Control1

description: processed data file: otu_table.txt

value: Postnatal day 35

value: Feces


title: MCH-hM3Dq-IP-5 [tg3]

status: Public on May 07 2020

city: Cologne

first: Hong

last: Jiang

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description:
9845
A006200029_101058_S28_L001

data_processing:
Sequenced reads were aligned to the reference genome using hisat 2.1.0.
Transcript abundance was derived using stringtie 1.3.4d.
Differential gene expression analysis was carried out using a t-test on normalized FPKM values (IP / Input)
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheet containing mean expression levels per group, fold change and significance level for each annotated gene.

extract_protocol:
Samples were transferred to a homogenization cylinder (Sartorius) with 1ml homogenization buffer (10 mM HEPES, 150 mM KCl, 5 mM MgCl2, 2.5 mM DTT, ¼ tablet/ml Protease inhibitors (EDTA free), 100 units/ml RNAsin, 250 μg/ml Cycloheximide, 1 tablet/10 ml PhosSTOP, 100 nM Calyculin A). Samples were homogenized 2 times at 250 rpm, and 9 times at 750 rpm. Homogenates were transferred to Eppendorf (Knigge and Joseph) tubes and clarified at 2,000 g for 10 min, at 4 °C.  Supernatants were transferred to a new EP tube on ice and 70 μl of 10% NP40 (Sigma Aldrich) and 70 μl of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC, Avanti) were added. This solution was mixed by inversion, incubated on ice for 2 min and clarified by centrifugation at 17,000g for 10 min at 4 °C. The harvested supernatant was transferred to a new EP tube, 50 μl was removed to another new EP tube, 950 μl Trizol and 50μl glycogen (5 mg/ml) were added. This sample was incubated on ice as input. 20 μl phospho-S6 244/247 antibody (44-923G, Invitrogen) were added to the remaining harvested supernatant and mixed well. Sample-antibody solution was incubated on ice for 1.5 hrs at 4 °C with gentle rotation. 100 μl Protein A Dynabeads per sample was washed 3 times with washing buffer 0.15M (10 mM HEPES, 150 mM KCl, 5 mM MgCl2, 1% NP40). The “sample-antibody” was added into the beads and incubated for 1 hr, at 4 C with gentle rotation. Sample-antibody solution was quick spinned for 2s and placed on the cold magnet for washing 4 times with washing buffer 0.35M (10 mM HEPES, 350 mM KCl, 5 mM MgCl2, 1%NP40, 1.25 mM DTT, 100 units/ml RNAsin, 125 μg/ml Cycloheximide, 50nM Calyculin A). Beads were collected by magnetic absorption. After the last wash, the supernatant was removed and 1 ml Trizol was added to the beads and gently resuspended by pipetting and incubated on ice for 5 min. Input and IP RNA were isolated and purified by the following steps. 200 μl CHCl3 was added to the samples, vortexed thoroughly and incubated in room temperature for 5 min. The samples were centrifuged at 12,200 g for 10 min at 4 °C. The aqueous phase was collected and added to 550 μl of ice cold isopropanol and incubated on ice for 15 min for RNA precipitation. The samples were centrifuged at speed of 12,200 g for 15 min at 4 °C. The precipitated RNA was washed by adding 1 ml of ice cold 80% ethanol and centrifuged at speed of 7,500 g for 15 min at 4 °C. Ethanol was discarded and the RNA was DNAsel digested (30 μl nuclease free water dissolved-RNA pellet, 3.7 μl DNAse 10X buffer, 2 μl RNAsin inhibitor and 2 μl DNAsel) for 30 min at 37 °C. DNAsel was deactivated by thorough vortexing. RNA concentrations were assessed employing the Invitrogen Qbit System and were stored in -80 °C until sending for RNA bulk sequencing.
Pre-amplification using the Ovation RNASeq System V2 was performed. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System) all 24 transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on a Illumna NovaSeq S2 flowcell with a PE100 protocol. The RNA sequencing pipeline utilizes the GRCm38 assembly of the mouse genome as gene sets from Ensembl release 96 (Yates et al., 2015).

treatment_protocol: All the mice were fasted for 12 hrs and i.p CNO treated for 1 hr.

tag: strain background

tag: genotype/variation

value: 10-13 weeks

value: Arcuate (ARC) and median eminence (ME)-hypothalamus

tag: ip antibody


title: Control-IP-4 [wt_3]

description:
9814
A006200029_101074_S36_L001

value: control

value: phospho-S6 244/247 antibody (44-923G, Invitrogen)


title: Control-Input-3 [wt_2]

description:
9892
A006200029_101068_S33_L001


title: Control-Input-6 [wt_5]

description:
9891
A006200029_101080_S39_L001


title: Control-IP-7 [wt_6]

description:
9902
A006200029_101086_S42_L001


title: MCH-hM3Dq-Input-4 [tg2]

description:
9844
A006200029_101052_S25_L001


title: Control-Input-4 [wt_3]

description:
9814
A006200029_101072_S35_L001


title: Control-Input-7 [wt_6]

description:
9902
A006200029_101084_S41_L001


title: Control-IP-2 [wt_1]

description:
9888
A006200029_101066_S32_L001


title: Control-IP-1 [wt_0]

description:
9803
A006200029_101062_S30_L001


title: Control-IP-5 [wt_4]

description:
9843
A006200029_101078_S38_L001


title: Control-Input-1 [wt_0]

description:
9803
A006200029_101060_S29_L001


title: MCH-hM3Dq-Input-3 [tg1]

description:
9813
A006200029_101048_S23_L001


title: MCH-ZsGreen

data_processing:
10x genomics cell ranger version 3.0.2
Cell clustering is carried out using R Seurat package version 3.1.1
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5: Cellranger output stored in hierarchical data format
Supplementary_files_format_and_content: cluster_markers.xlsx: Cluster markers derived by Seurat R package
Supplementary_files_format_and_content: count_matrix.csv.gz: Count matrix for each gene and cell as character separated value file

source_name: hypothalamus

extract_protocol:
Nuclear isolation for single cell sequencing  Nuclear isolation method was modified from (Habib et al., 2017). Hypothalami of ZsGreenMCH mice were dissected and collected into 1ml of ice-cold EZ PREP buffer (D8938, Sigma). The tissue was homogenized with a glass dounce, twice at 250 rpm and 12 times at 1000 rpm and incubated on ice for 5 min. Nuclei were centrifuged at 500g, 5 min after addition of 4 ml of nuclear lysis buffer and incubate on ice for 5 min. The supernatant was discarded and the pellet was resuspended in 4 ml nucleus suspension buffer (NSB, 1x PBS, 0.01% BSA, and 0.1% RNase inhibitor (352235, Clontech). Nuclei were centrifuged at 500g for 2 min. The supernatant was discarded and isolated nuclei were resuspended in 300 µl NSB and then filtered through a 30 μm cell strainer into sorting tubes for flow cytometry sorting on a BD FACSAria IIIu.
Single nucleus RNA sequencing: Upon dissolution of the Single Cell 3' Gel Bead in a GEM, primers containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 bp 10x Barcode, (iii) a 12 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Incubation of the GEMs produced barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, the GEMs were broken and the pooled fractions were recovered. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: 16-18 weeks

value: MCH-Cre dependent ZsGreen (fl/fl) reporter mice

value: Hypothalamus

tag: molecule subtype

value: nuclear RNA


title: Control-Input-2 [wt_1]

description:
9888
A006200029_101064_S31_L001


title: Control-IP-6 [wt_5]

description:
9891
A006200029_101082_S40_L001


title: MCH-hM3Dq-IP-4 [tg2]

description:
9844
A006200029_101054_S26_L001


title: MCH-hM3Dq-Input-1 [tg0]

description:
9989
A006200029_101040_S19_L001


title: MCH-hM3Dq-IP-3 [tg1]

description:
9813
A006200029_101050_S24_L001


title: Control-Input-5 [wt_4]

description:
9843
A006200029_101076_S37_L001


title: Sickle cell patient 1


title: Control-IP-3 [wt_2]

description:
9892
A006200029_101070_S34_L001


title: MCH-hM3Dq-Input-5 [tg3]

description:
9845
A006200029_101056_S27_L001


title: MCH-hM3Dq-IP-1 [tg0]

description:
9989
A006200029_101042_S20_L001


title: NR7_CTP_48h

city: Bonn

first: Abdul Karim

last: Barakat

address: Kurt-Georg-Kiesinger-Allee 3

institute: Federal Institute for Drugs and Medical Devices

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting for 8x60k array slides. Dye channel was set to Green.

data_processing: The scanned images were analyzed with GeneSpring Software (v.14.1.9, Agilent). Signal quality was maintained by filtering probes with compromised flags out. Differential gene expression was calculated in fold-change (FC) in sets of pairs: non-responders vs. responders (NR/RESP) or citalopram vs. control (CTP/ctrl., in both RESP and NR groups). Pathway analysis was done in pathway database imported from GenMAPP Pathway Markup Language15.

source_name: LCLs incubated with 3 µM citalopram for 48 h

label_protocol: RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies) according to the kit manual. Briefly, 100 ng RNA were reversely transcribed to cDNA, from which Cy3-labeled cRNA was transcribed, purified and hybridized to the expression microarray.

growth_protocol: LCLs were grown in RPMI medium supplemented with 15% fetal bovine serum, antibiotics (100 µg/ml penicillin, 100 µg/ml streptomycin) and a final concentration of 2 mM L-glutamine. Medium exchanging was done every second day.

extract_protocol: RNA was extracted using the NucleoSpin® RNA Kit (Macherey-Nagel, Germany) according to the manufacturer instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: LCLs were treated with 3 µM citalopram (dissolved in ethanol) for 24 and 48 hours days. Control cultures received the equal volume of the vehicle and were grown in parallel.

tag: response status

value: non-responder

value: Lymphoblastoid Cell Lines (LCLs)


title: NR6_CTRL_48h

source_name: LCLs incubated with 0.03% EtOH for 48 h


title: NR8_CTRL_48h


title: NR6_CTP_48h


title: NR5_CTRL_48h


title: NR2_CTRL_48h


title: NR1_CTP_48h


title: NR7_CTRL_48h


title: NR2_CTP_48h


title: NR1_CTRL_48h


title: RESP8_CTP_48h

value: responder


title: NR8_CTP_48h


title: NR4_CTRL_48h


title: RESP5_CTRL_48h


title: NR3_CTRL_48h


title: NR4_CTP_48h


title: NR5_CTP_48h


title: RESP5_CTP_48h


title: RESP6_CTP_48h


title: RESP7_CTP_48h


title: RESP6_CTRL_48h


title: NR3_CTP_48h


title: RESP9_CTRL_48h


title: RESP7_CTRL_48h


title: RESP8_CTRL_48h


title: RESP9_CTP_48h


title: RESP3_CTRL_48h


title: RESP4_CTP_48h


title: RESP3_CTP_48h


title: RESP4_CTRL_48h


title: RESP1_CTP_48h


title: RESP2_CTP_48h


title: RESP1_CTRL_48h


title: NR4_CTP_24h

source_name: LCLs incubated with 3 µM citalopram for 24 h


title: NR1_CTRL_24h

source_name: LCLs incubated with 0.03% EtOH for 24 h


title: NR3_CTP_24h


title: RESP2_CTRL_48h


title: NR5_CTRL_24h


title: NR5_CTP_24h


title: RESP6_CTP_24h


title: NR4_CTRL_24h


title: RESP7_CTP_24h


title: NR6_CTP_24h


title: NR1_CTP_24h


title: NR8_CTP_24h


title: RESP5_CTRL_24h


title: RESP5_CTP_24h


title: NR7_CTRL_24h


title: RESP9_CTRL_24h


title: NR2_CTP_24h


title: RESP6_CTRL_24h


title: NR6_CTRL_24h


title: RESP8_CTRL_24h


title: RESP7_CTRL_24h


title: RESP8_CTP_24h


title: NR2_CTRL_24h


title: NR8_CTRL_24h


title: RESP9_CTP_24h


title: NR3_CTRL_24h


title: RESP4_CTRL_24h


title: RESP3_CTRL_24h


title: RESP2_CTRL_24h


title: RESP1_CTRL_24h


title: RESP4_CTP_24h


title: RESP3_CTP_24h


title: RESP1_CTP_24h


title: RESP2_CTP_24h


title: RNAseq from stem tissue, biological replicate 2

city: JAEN

first: Jorge

middle: Antolín

last: Ramirez

state: --- Select a state ---

address: Campus Las Lagunillas s/n 23071

department: Experimental Biology

country: Spain

institute: University of Jaen

description: PolyA RNAseq

data_processing:
Raw Illumina RNAseq reads were first preprocessed using Fastqmcf by discarding primers and reads with adaptors, unknown nucleotides, and poor-quality or short-length reads, increasing the Q score to more than 30 for all the libraries and filtering for lengths greater than 50 bp (Q30L50)
Quality control of sequencing was performed using NGS_QC software
Trimming and cleaning of the obtained reads was performed using the software Trimgalore
The gene-expression study was made with the DNAStar (ArrayStar 15) Qseq software for RNAseq analysis (www.dnastar.com). Reads were mapped to Olea europaea cv. Picual genome as the reference Oleur061. We undertook mapping using parameters k-mer = 63 and 95% of matches and used the default normalization method of ‘reads per kilobase per million mapped reads’, RPKM. The number of replicates per sample for expression average calculation was two. A basal expression level of log2 RPKM = -2 was considered, so only genes with expression values above this threshold level were considered as expressed, and those with values equal or below the threshold level were considered as not expressed.
Genome_build: Oleur061 assembled genome from Olea europaea cv. Picual (PRJNA556567)
Supplementary_files_format_and_content: Matrix table with gene’s IDs and their linear RPKM counts

organism: Olea europaea

source_name: Stem

extract_protocol:
Spectrum Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) used according to the manufacturer’s instructions
A pool of the cDNA libraries was sequenced by paired-end sequencing (101 x 2) with an Illumina HiSeq 2000 sequencer. Two biological replicates per sample were sequenced, and each replicate was loaded twice on two different lanes in the flow cell.

value: Adult

tag: cultivar

value: Picual

value: Stem


title: RNAseq from root tissue, biological replicate 2

description: PolyA RNAseq

source_name: Root

value: Root


title: NR7_CTP_24h


title: RNAseq from root tissue, biological replicate 1

description: PolyA RNAseq


title: RNAseq from meristem tissue, biological replicate 1

description: PolyA RNAseq

source_name: Meristem

value: Meristem


title: 200397870078_R04C02

type: genomic

city: Shanghai

first: Yao

last: Zhu

address: No.270 Dong'an Rd.

department: Urological Oncology

institute: Fudan Universitty Shanghai Cancer Center

description: primary tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing:
RnBeads version 1.3.4 in the R software 3.2
Unmethylated and methylated signal intensities

label: Cy5 and Cy6

source_name: penile cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from RNA-later preserved frozen tissue using the QIAmap DNA mini Kit (Qiagen) according to standard instructions

tag: sample type

value: Frozen sample

tag: hpv infection

value: Negative


title: 200400320044_R04C02

description: primary tumor

label: Cy5 and Cy5

value: Positive


title: 200400320126_R04C01

description: primary tumor

label: Cy5 and Cy3


title: RNAseq from leaf tissue, biological replicate 2

description: PolyA RNAseq

source_name: Whole leaf

value: Whole leaf


title: RNAseq from meristem tissue, biological replicate 2

description: PolyA RNAseq


title: 200397870078_R05C01

description: primary tumor


title: RNAseq from stem tissue, biological replicate 1

description: PolyA RNAseq


title: 200397870078_R06C02

description: primary tumor


title: 200397870078_R03C02

description: primary tumor


title: RNAseq from leaf tissue, biological replicate 1

description: PolyA RNAseq


title: 200397870078_R01C01

description: primary tumor


title: 200400320126_R02C01

description: primary tumor


title: 200397870078_R05C02

description: primary tumor


title: 200400320126_R02C02

description: primary tumor


title: 200397870078_R02C02

description: primary tumor

label: Cy5 and Cy4


title: RNAseq from flower tissue, biological replicate 2

description: PolyA RNAseq

source_name: Whole open mature flower

value: Whole open mature flower


title: 200400320044_R01C02

description: primary tumor


title: 200400320126_R03C02

description: primary tumor


title: RNAseq from flower tissue, biological replicate 1

description: PolyA RNAseq


title: 200400320126_R04C02

description: primary tumor


title: RNAseq from fruit tissue, biological replicate 2

description: PolyA RNAseq

source_name: Epicarp and mesocarp from mature fruit

value: Epicarp and mesocarp from mature fruit


title: RNAseq from fruit tissue, biological replicate 1

description: PolyA RNAseq


title: 200400320044_R02C02

description: primary tumor


title: 200400320044_R06C01

description: primary tumor


title: 200397870078_R06C01

description: primary tumor


title: E17.B1p.00024

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

data_processing:
BGI-seq basecalling software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample

organism: Macaca fascicularis

source_name: embryo

extract_protocol:
After washing with phosphate buffered saline (PBS) (MA0008, meilunbio), the embryo was digested with 0.1% trypsin (25200-072, Gibco) at 37°C for 5 to 10 min. Then the trypsin was neutralized with 2% FBS (04-002-1A, Biological Industries) and FBS was washed off with cold PBS with 0.1 to 1% bovine serum albumin (BSA). Finally, individual cells were picked into a lysis medium on ice with a mouth pipette. All procedures were performed under stereomicroscope
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for BGISEQ-500

value: embryo


title: E17.B1p.00015


title: E17.B1p.00018


title: E17.B1p.00027


title: E17.B1p.00017


title: E17.B1p.00016


title: E17.B1p.00023


title: E17.B1p.00026


title: E17.B1p.00012


title: E17.B1p.00014


title: E17.B1p.00022


title: E17.B1p.00021


title: E17.B1p.00010


title: E17.B1p.00020


title: E17.B1p.00011


title: E17.B1p.00025


title: E17.B1p.00002


title: E17.B1p.00028


title: 200400320044_R05C02

description: primary tumor


title: 200400320044_R06C02

description: primary tumor


title: 200400320126_R03C01

description: primary tumor


title: 200400320126_R06C01

description: primary tumor


title: 200397870078_R02C01

description: primary tumor


title: 200400320126_R01C01

description: primary tumor


title: E17.B1p.00003


title: E17.B1p.00040


title: E17.B1p.00041


title: E17.B1p.00037


title: E17.B1p.00030


title: E17.B1p.00043


title: E17.B1p.00038


title: E17.B1p.00031


title: E17.B1p.00039


title: E17.B1p.00013


title: E17.B1p.00036


title: E17.B1p.00035


title: E17.B1p.00042


title: E17.B1p.00004


title: E17.B1p.00044


title: E17.B1p.00045


title: E17.B1p.00032


title: E17.B1p.00047


title: E17.B1p.00046


title: 200397870078_R03C01

description: primary tumor


title: E17.B1p.00005


title: E17.B1p.00033


title: 200400320126_R01C02

description: primary tumor


title: E17.B1p.00006


title: E17.B1p.00019


title: E15_B1_10


title: E17.B1p.00009


title: E15_B1_12


title: E15_B1_15


title: E15_B1_11


title: E15_B1_13


title: E15_B1_16


title: E15_B1_02


title: E15_B1_21


title: E15_B1_22


title: E15_B1_19


title: E17.B1p.00007


title: E17.B1p.00048


title: E15_B1_25


title: E15_B1_23


title: E15_B1_27


title: E15_B1_01


title: E15_B1_26


title: E15_B1_17


title: E15_B1_29


title: E17.B1p.00008


title: E15_B1_28


title: E15_B1_03


title: E15_B1_18


title: E15_B1_32


title: E15_B1_30


title: E15_B1_14


title: E15_B1_35


title: E15_B1_33


title: E15_B1_31


title: E17.B1p.00034


title: E15_B1_39


title: E15_B1_04


title: E15_B1_34


title: E15_B1_36


title: E15_B1_38


title: E15_B1_24


title: E15_B1_40


title: E15_B1_37


title: E15_B1_41


title: E15_B1_43


title: E15_B1_46


title: E15_B1_44


title: E15_B1_47


title: E15_B1_48


title: E15_B1_49


title: E15_B1_45


title: E15_B1_50


title: E15_B1_05


title: E15_B1_51


title: E15_B1_52


title: E15_B1_53


title: E15_B1_56


title: E15_B1_58


title: E15_B1_57


title: E15_B1_54


title: E15_B1_55


title: E15_B1_63


title: E15_B1_60


title: E15_B1_06


title: E15_B1_59


title: E15_B1_65


title: E15_B1_66


title: E15_B1_61


title: E15_B1_62


title: E15_B1_42


title: E15_B1_67


title: E15_B1_68


title: E15_B1_69


title: E15_B1_70


title: E15_B1_07


title: E15_B1_71


title: E15_B1_74


title: E15_B1_73


title: E15_B1_75


title: E15_B1_76


title: E15_B1_77


title: E15_B1_79


title: E15_B1_20


title: E15_B1_84


title: E15_B1_78


title: E15_B1_83


title: E15_B1_82


title: E15_B1_81


title: E15_B1_85


title: E15_B1_87


title: E15_B1_86


title: E15_B1_93


title: E15_B1_89


title: E15_B1_09


title: E15_B1_94


title: E15_B1_95


title: E13.B1pe.00001


title: E13.B1pe.00010


title: E13.B1pe.00011


title: E13.B1pe.00014


title: E13.B1pe.00012


title: E13.B1pe.00016


title: E13.B1pe.00013


title: E13.B1pe.00017


title: E17.B1p.00001


title: E15_B1_08


title: E13.B1pe.00018


title: E13.B1pe.00021


title: E15_B1_91


title: E13.B1pe.00022


title: E15_B1_90


title: E13.B1pe.00019


title: E13.B1pe.00023


title: E13.B1pe.00026


title: E13.B1pe.00024


title: E13.B1pe.00027


title: E13.B1pe.00025


title: E13.B1pe.00028


title: E13.B1pe.00003


title: E13.B1pe.00029


title: E15_B1_92


title: E13.B1pe.00030


title: E13.B1pe.00032


title: E13.B1pe.00015


title: E13.B1pe.00031


title: E13.B1pe.00033


title: E13.B1pe.00035


title: E13.B1pe.00020


title: E13.B1pe.00034


title: E13.B1pe.00039


title: E13.B1pe.00038


title: E13.B1pe.00037


title: E13.B1pe.00036


title: E13.B1pe.00040


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title: E19_B2_17


title: E19_B2_15


title: E19_B2_16


title: E19_B2_18


title: E19_B2_12


title: E19_B2_02


title: E19_B2_19


title: E17_B5_86


title: E19_B2_20


title: E19_B2_22


title: E19_B2_26


title: E19_B2_23


title: E19_B2_21


title: E19_B2_25


title: E19_B2_24


title: E19_B2_27


title: E19_B2_03


title: E19_B2_33


title: E19_B2_32


title: E19_B2_28


title: E19_B2_30


title: E19_B2_34


title: E19_B2_31


title: E19_B2_35


title: E19_B2_44


title: E19_B2_04


title: E19_B2_39


title: E19_B2_45


title: E19_B2_43


title: E19_B2_41


title: E19_B2_47


title: E19_B2_46


title: E19_B2_38


title: E19_B2_37


title: E19_B2_29


title: E19_B2_49


title: E19_B2_51


title: E19_B2_05


title: E19_B2_50


title: E19_B2_52


title: E19_B2_36


title: E19_B2_53


title: E19_B2_54


title: E19_B2_40


title: E19_B2_55


title: E19_B2_42


title: 3e-KO-LP

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Adapters trimmed using Cutadapt
Reads were aligned to the mouse reference genome Mm10 using STAR
Gene feature counting was performed with RSEM
Transcripts with expression counts of 0 across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: gene filtered RSEM counts (txt, tab delimited)

source_name: FACS sorted mammary epithelial cells

growth_protocol: 10-12 week old female FVB/N mice at estrus. Mice generated described in Yun et al. 2004. Development

extract_protocol:
Qiagen miRNease micro kit (Qiagen)
Ovation RNA-seq System V2 kit (NuGEN) was used to synthesise cDNA with RNA inputs ranging from 0.5-2 ng as per the manufacturers protocol. The Ovation Ultralow System V2 kit was then used to prepare libraries from the cDNA.

tag: replicate

value: FVB/N

tag: cell type

value: mammary epithelial

tag: subpopulation

value: Luminal Progenitor

value: ID4 KO


title: 3f-KO-ML

value: Mature Luminal


title: 3b-WT-LP

value: WT


title: 4f-KO-ML


title: E19_B2_56

tag: tissue


title: 4c-WT-ML

tag: strain


title: 3c-WT-ML


title: 3d-KO-basal

value: Basal


title: E19_B2_48


title: 4b-WT-LP


title: E19_B2_59


title: E19_B2_58


title: 3a-WT-basal


title: E19_B2_06


title: 2f-KO-ML


title: 2e-KO-LP


title: E19_B2_62


title: 2c-WT-ML


title: E19_B2_60


title: 2d-KO-basal


title: E19_B2_61


title: 2a-WT-basal


title: E19_B2_63


title: E19_B2_64


title: E19_B2_65


title: E19_B2_57


title: 4e-KO-LP


title: 4a-WT-basal


title: 4d-KO-basal


title: 1f-KO-ML


title: 1a-WT-basal


title: E19_B2_66


title: 1c-WT-ML


title: E19_B2_67


title: E19_B2_07


title: E19_B2_68


title: E19_B2_71


title: 1d-KO-basal


title: E19_B2_70


title: 1e-KO-LP


title: E19_B2_72


title: E19_B2_73


title: 2b-WT-LP


title: E19_B2_75


title: E19_B2_74


title: E19_B2_76


title: E19_B2_77


title: E19_B2_78


title: 1b-WT-LP


title: E19_B2_69


title: pDC_WT_rep3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10

source_name: Dendritic cells

growth_protocol: Itgax-cre Stk11 fl/fl (LKB1) (17591855; 12226664) and WT male and female mice, all on a C57BL/6 background, were purchased from The Jackson Laboratory and crossed, housed and bred at the LUMC, Leiden, The Netherlands, under SPF conditions.

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
cDNA synthesis was carrid out using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: To expand the number of Thymic DCs in mice, Flt3L-secreting B16 melanoma cells were harvested and washed using phenol red-free HBSS (Gibco) before subcutaneous injection of 2 × 106 cells in 100 µL of HBSS into the flank of 8 to 12 week old mice. Nine to twelve days later, thymi were harvested, placed in 500 µL medium (with Ca2+), mechanically disrupted, digested by addition of 50 µL medium (with Ca2+) supplemented with Collagenase D (Roche, Woerden, The Netherlands, end concentration of 1 mg/mL) and DNase I (Sigma, end concentration of 2000 U/mL) and incubation for 20 min at 37 °C. Upon completion of digestion, single-cell suspensions were subjected to red blood cell lysis (inhouse; 0.15 M NH4Cl, 1 mM KHCO3, 0.1 mM EDTA [Sigma] in ddH2O) and filtered with a 100 µm sterile filter before counting. From these suspensions, DC populations were further enriched by positive isolation with CD11c-Microbeads (Miltenyi, Leiden, The Netherlands) and sorting in cDC1 (CD8a+CD11c+MHCII+), cDC2 (CD11b+CD11c+MHCII+) and pDC (Siglec-H+CD11cint) subsets on a BD FACSAria using a 85 μm nozzle at 45 PSI.

tag: cell subtype

value: pDC


title: E19_B2_79


title: pDC_KO_rep2

value: KO


title: cDC1_WT_rep1


title: E19_B2_08


title: cDC1_WT_rep2


title: pDC_WT_rep1


title: pDC_WT_rep2