title: 6237_M0_DMSO


title: 6239_M0_uRBC

status: Public on May 13 2020

type: RNA

city: Barcelona

first: Gemma

last: Moncunill

state: Please Select

address: Carrer Rosselló 153 (CEK building)

country: Spain

institute: ISGlobal

hyb_protocol: Plates were processed using the GeneTitan Hybridization, Wash and Stain kit for WT arrays (Affymetrix) in a GeneTitan multichannel instrument.

scan_protocol: GeneChip Command Console (AGCC 3.2.4., Affymetrix) was used for instrument control, first quality analysis by image inspection and generate raw intensity data. Expression Console (EC 1.2, Affymetrix) was used for quality control analysis and normalization by RMA algorithm.

data_processing: R/bioconductor

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cultured PBMC

label_protocol: cDNA synthesis, fragmentation and labeling was performed starting with 125 to 200 ng total RNA, following Affymetrix protocol, using the WT Expression kit (Ambion), and WT Terminal Labeling kit (Affymetrix)

extract_protocol: Total RNA was extracted from cell pellets after RNAlater removal by centrifugation, using RNeasy Mini kits (Qiagen), either manually (batches of 24 samples) or using a QIAcube sample preparation workstation according to the manufacturer’s recommendations (batches of 12 samples). RNA concentration and quality were determined on a Nanodrop spectrophotometer (Thermo Scientific) in all samples and RNA integrity was assessed using a 2100 Bioanalyzer (Agilent) in 90% of CPS samples and 20% of the RTS,S samples.

treatment_protocol: CSP, DMSO, PfRBC or uRBC stimulations

tag: stimulation

value: uRBC

tag: subjectid

tag: vaccine

value: Control

tag: site

value: Lamba

tag: age

tag: immunization dose

tag: protection

value: protected

tag: timepoint

tag: Sex

value: M

tag: tissue

value: PBMC


title: 6237_M0_iRBC

value: iRBC

value: malaria


title: 6251_M0_CSP

value: CSP


title: 6448_M3_iRBC


title: 6239_M0_DMSO

value: DMSO


title: 6237_M0_CSP


title: first run_D18_C1

type: SRA

city: Durban

first: Alex

last: Sigal

state: -- SELECT --

address: 719 Umbilo Road, Congella

country: South Africa

institute: Africa Health Research Institute (AHRI)

description:
Reverse transcriptase region of HIV provirus
~ 300bp amplicon of the Reverse trancriptase region of HIV containing all the Efavirenz resistant mutants

library_source: genomic

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 (minimum mapping quality Q30), then mapped to HIV NL4-3 using Geneious v 11.1.4
For SNP detection in cell population experiments: minimum variant frequency of 0.01 and maximum variant p-value 0.0001
For SNP detection in single experiments: minimum variant frequency of 0.05 and maximum variant p-value 0.0001
Genome_build: AF324493.2
Supplementary_files_format_and_content: comma separated files (csv) containing the variant raw frequency of mutants, the quality score, coverage as wells as the unique identifiers for each read that has a SNP in it

molecule: genomic DNA

organism: Human immunodeficiency virus 1

source_name: RevCEM E7 cells infected with NL4-3

growth_protocol: Cell culture and experiments were performed in complete RPMI 1640 medium supplemented with L-Glutamine, sodium pyruvate, HEPES, non-essential amino acids (Lonza), and 10\% heat-inactivated FBS (Hyclone).

extract_protocol:
For infected single cells, the cells were lysed and DNA was kept suspended in the lysis buffer. For infected cell populations, genomic DNA was extracted using the QIAamp DNA mini kit (Qiagen)
Phusion hot start II DNA polymerase (New England Biolabs) PCR reaction mix (10$ul 5 x Phusion HF buffer, 1ul dNTPs, 2.5ul of the forward primer, 2.5ul of the reverse primer, 0.5ul Phusion hot start II DNA polymerase, 2.5ul of DMSO and molecular biology grade water to 50ul reaction volume) was added to the lysed single cells or extracted genomic DNA of cell populations. Two rounds of PCR were performed. The first-round reaction amplified a region of the RT gene in the proviral DNA using the forward primer 5’ tcgtcggcagcgtcagatgtgtataagagacagTTAATAAGAGAACTCAAGATTTC 3’ and reverse primer 5’ gtctcgtgggctcggagatgtgtataagagacagCCCCACCTCAACAGATGTTGTC 3’. Non-capitalized portion of the primers represent the Nextera XT Index Kit adaptors. Cycling program was 98C for 30 seconds, then 35 cycles of 98C for 10 seconds, 50C for 30 seconds and 72C for 15 seconds with a final extension of 72C for 5 minutes. 1$\mu l$ of the first round product was then transferred into a PCR mix as above, with second round Nextera XT Index Kit adaptor primers (forward 5’ tcgtcggcagcgtcagatgtgtataagagacag 3’, reverse 5’ gtctcgtgggctcggagatgtgtataagagacag 3’). The second round PCR amplified a 400bp product which was then visualized on a 1% agarose gel. The PCR amplicon was gel extracted using the QIAquick gel extraction kit (Qiagen). Illumina indices were attached to the amplicon with the Nextera XT Index Kit and deep sequenced using the Illumina Miseq. Fast-q files were analysed in Geneious.
amplicon sequencing using illumina MiSeq with adaptors from Nextera kit

treatment_protocol: Experiments were initiated with a cell-free infection, where 10^6 cells/ml RevCEM E7 were infected with 2 x 10^8 NL4-3 viral copies/ml (approximately 20ng p24 equivalent) for 2 days. Infected cells from the cell-free infection were used as the donors and cocultured with 10^6 cells/ml target cells. After two days of infection, 2% of the infected cells were added to uninfected target cells and cocultured for a 2-day cycle (day 0). Thereafter, 2% of resuspended infected cells were added to uninfected targets in the presence of EFV and co-cultured for each 2-day cycle.

tag: cell line

value: RevCEM E7 cells

tag: treatment

value: Cells treated every 2 days with Efavirenz

tag: time

value: First run_Day 18

tag: population/single cell

value: single cells


title: 6236_M0_DMSO

value: F


title: first run_D12_B4

value: First run_Day 12


title: first run_D12_B3


title: first run_D12_B2


title: 6236_M0_uRBC


title: 6236_M0_CSP


title: first run_D12_B11


title: 6232_M3_DMSO


title: first run_D12_B10


title: first run_D12_A9


title: 19508_M0_uRBC

value: Manhica


title: first run_D12_A8


title: first run_D12_B12


title: first run_D12_B1


title: first run_D12_A7


title: 6235_M3_CSP


title: 6232_M3_CSP


title: first run_D12_A3


title: first run_D12_A6


title: first run_D12_A5


title: first run_D12_A4


title: 6230_M3_uRBC

value: uRBC


title: 6230_M3_DMSO

value: Control


title: 6225_M0_iRBC

value: Lamba


title: 6230_M3_iRBC

value: protected


title: first run_D12_A1


title: first run_D12_A10


title: first run_D12_A11


title: 6228_M3_CSP


title: 6225_M0_CSP

value: M


title: first run_D12_A12


title: 6223_M0_uRBC

value: PBMC


title: first run_D10_C8

value: First run_Day 10


title: first run_D12_A2


title: 6223_M0_CSP


title: 6228_M3_DMSO

value: malaria


title: 6230_M3_CSP

value: CSP


title: 6235_M3_DMSO

value: DMSO


title: 6225_M0_uRBC


title: 6225_M0_DMSO


title: first run_D10_C7

value: RevCEM E7 cells


title: first run_D10_C5

value: Cells treated every 2 days with Efavirenz


title: first run_D10_C4


title: first run_D10_C3


title: first run_D10_C6


title: first run_D10_C2


title: first run_D18_C5

value: First run_Day 18


title: 6223_M0_DMSO


title: 6221_M0_uRBC


title: 6223_M0_iRBC

value: iRBC


title: first run_D10_B7

value: single cells


title: 6221_M0_iRBC

value: F


title: first run_D10_B6


title: first run_D10_B5


title: first run_D10_C1


title: 6214_M0_uRBC


title: 6221_M0_CSP


title: 6221_M0_DMSO


title: first run_D10_B9


title: 6214_M0_iRBC


title: first run_D10_B8


title: 6214_M0_CSP


title: 6214_M0_DMSO


title: first run_D10_B3


title: 6211_M0_DMSO


title: 6211_M0_CSP


title: first run_D10_B12


title: first run_D10_B4


title: 6191_M3_CSP


title: first run_D10_B11


title: first run_D10_B10


title: first run_D10_B2


title: 6200_M3_CSP


title: 6200_M3_uRBC


title: 6211_M0_uRBC


title: first run_D10_A9


title: 6211_M0_iRBC


title: 6200_M3_DMSO


title: 6200_M3_iRBC


title: first run_D10_B1


title: first run_D10_A8


title: 6191_M3_DMSO


title: first run_D10_A7


title: first run_D10_A6


title: first run_D10_A5


title: first run_D10_A2


title: first run_D10_A3


title: first run_D10_A12


title: first run_D10_A10


title: first run_D10_A11


title: 6148_M3_DMSO


title: 6148_M3_uRBC


title: 6148_M3_CSP


title: 6148_M3_iRBC


title: 6126_M3_uRBC


title: 6126_M3_iRBC


title: 6125_M3_CSP


title: 6125_M3_iRBC


title: 6126_M3_DMSO


title: first run_D10_A1


title: Population_Experiment #1_Day16

value: Day 16

value: population sequences


title: 5874_M3_DMSO


title: 6126_M3_CSP

value: Control


title: 6125_M3_uRBC

value: uRBC

value: Lamba


title: Population_Experiment #1_Day14

value: Day 14


title: Population_Experiment #1_Day18

value: Day 18


title: first run_D10_A4

value: First run_Day 10


title: first run_D12_B5

value: First run_Day 12


title: 3096_M3_iRBC

value: Bagamoyo

value: malaria

value: PBMC


title: 6125_M3_DMSO

value: DMSO

value: protected


title: 5874_M3_CSP

value: CSP

value: M


title: 3096_M3_uRBC

value: F


title: Population_Experiment #1_Day12

value: RevCEM E7 cells

value: Cells treated every 2 days with Efavirenz

value: Day 12


title: Population_Experiment #1_Day10

value: Day 10

value: population sequences


title: 3096_M3_CSP


title: 3096_M3_DMSO


title: 3089_M3_uRBC

value: uRBC


title: Population_Experiment #2_Day18

value: Day 18


title: Population_Experiment #1_Day8

value: Day 8


title: Population_Experiment #2_Day16

value: Day 16


title: Population_Experiment #2_Day14

value: Day 14


title: 3089_M3_DMSO

value: Bagamoyo


title: Population_Experiment #2_Day10


title: Population_Experiment #2_Day12


title: 3078_M0_CSP

value: PBMC


title: Population_Experiment #2_Day8


title: Population_Experiment #2_Day6

value: Day 6


title: 3078_M0_uRBC

value: protected


title: Population_Experiment #3_Day18


title: Population_Experiment #3_Day12


title: Population_Experiment #3_Day16


title: Population_Experiment #3_Day10


title: Population_Experiment #3_Day8


title: Population_Experiment #3_Day6


title: 3078_M0_iRBC

value: iRBC


title: 3089_M3_iRBC


title: 3076_M3_CSP

value: CSP

value: Control

value: M


title: 3074_M0_uRBC


title: 3074_M0_CSP


title: Population_Experiment #2_Day4

value: RevCEM E7 cells

value: Cells treated every 2 days with Efavirenz

value: Day 4


title: 3076_M3_uRBC


title: Population_Experiment #3_Day14

value: population sequences


title: 3076_M3_DMSO

value: DMSO


title: inplanta_Pf2_025

city: Bentley

first: Darcy

middle: Adam Bain

last: Jones

state: Western Australia

address: Kent Street

department: Centre for Crop and Disease Management

country: Australia

institute: Curtin University

description: RNA was extracted from sections of wheat leaves embedded in 75 mg/L benzimidazole agar, three days after inoculation with ~10^6 P. nodorum pycnidiospores in 0.02% Tween buffer.

library_source: transcriptomic

data_processing:
Read adapters were trimmed using cutadapt v1.12 (https://cutadapt.readthedocs.io/), cutadapt --minimum-length 25 -a "AGATCGGcutadapt AAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" -g "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" -G ""GTTCGTCTTCTGCCGTATGCTCTANNNNNNCACTGACCTCAAGTCTGCACACGAGAAGGCTAG -n 3 -o trimmed_R1.fastq.gz -p trimmed_R2.fastq.gz reads1.fastq.gz reads2.fastq.gz
Fastq read quality was assessed before and after trimming using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Fungal reads were split from Wheat reads using BBSplit v36.67 (https://sourceforge.net/projects/bbmap) using the P. nodorum SN15 genome as bait (DOI: 10.1534/g3.112.004994). bbsplit.sh ambiguous=all path=index ref_SN15=genome.fasta out_SN15="split_R#.fastq.gz" outu="unaligned_R#.fastq.gz" in=reads1.fastq.gz in2=reads2.fastq.gz refstats=refstats.tsv scafstats=scafstats.tsv
Split fungal reads were aligned to the P. nodorum SN15 genome (DOI: 10.1534/g3.112.004994) using STAR v2.5.0a in 2 passes. The index was created including splice sites from existing annotations (DOI: 10.1371/journal.pone.0147221). STAR --runMode genomeGenerate --genomeDir mygenome  --genomeFastaFiles genome.fasta --sjdbGTFfile genes.gtf --sjdbOverhang 124 --genomeSAindexNbases 11
In the first STAR alignment pass, only splice junctions were retained. STAR --readFilesCommand zcat --genomeDir mygenome --outSAMtype None --outSAMmode None --outSJfilterReads All --outSJfilterOverhangMin 5 1 1 1 --outSJfilterCountUniqueMin 10 5 5 5 --outSJfilterDistToOtherSJmin 5 0 0 3 --outSJfilterIntronMaxVsReadN 0 1 500 5000 10000 20000 --alignIntronMin 5 --alignIntronMax 10000 --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --alignSoftClipAtReferenceEnds No --outFileNamePrefix mygenome reads1.fastq.gz reads2.fastq.gz
In the second STAR alignment pass, splice junctions from all first pass alignments were used as hints. STAR --readFilesCommand zcat --genomeDir mygenome --sjdbFileChrStartEnd *SJ.out.tab --outSAMtype BAM Unsorted --outBAMcompression 1 --outSJfilterReads All --outSJfilterCountUniqueMin 10 5 5 5 --outSJfilterIntronMaxVsReadN 0 1 500 5000 10000 20000 --alignIntronMin 5 --alignIntronMax 10000 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignSoftClipAtReferenceEnds No --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.2 --outMultimapperOrder Random --outSAMattributes All --outSAMstrandField intronMotif\ --outSAMattrIHstart 0 --outSAMmapqUnique 50 reads1.fastq.gz reads2.fastq.gz
BAM alignments were evaluated using samtools, RSeQC, and MultiQC.
Read counts were found using featureCounts v1.5.1 (http://subread.sourceforge.net/) using existing gene predictions (DOI: 10.1371/journal.pone.0147221). featureCounts -a genes.gtf -t exon -s 2 -p -B -C -o counts.tsv aligned.bam
Normalised fragment abundance was generated using DESeq2 v1.14.1 (DOI: 10.1186/s13059-014-0550-8) R package. The following sequence of functions/steps were used, with parameters affecting analysis indicated: `DESeqDataSetFromMatrix`; filter  genes with no fragments aligned; `estimateSizeFactors`; `DESeq(betaPrior=TRUE)` ; `rlog(blind = FALSE)`; `varianceStabilizingTransformation(blind = FALSE)`.
Genome_build: Parastagonospora nodorum SN15 genome, published but not in NCBI/INDSC [DOI: 10.1534/g3.112.004994,DOI:10.1371/journal.pone.0147221]. Available at: https://github.com/robsyme/Parastagonospora_nodorum_SN15
Supplementary_files_format_and_content: count_table.xlsx contains both the raw read counts from featureCounts and the DeSeq2 VST transformed counts for each of the 16 biological replicates, with gene location information.

molecule: polyA RNA

organism:
Triticum aestivum
Parastagonospora nodorum

source_name: Mixed wheat and mutant pf2-69 sample.

extract_protocol:
Total RNA was extracted using the Invitrogen TRIzol Plus RNA purification kit (cat: 12183A).
Libraries were constructed using an Illumina TruSeq stranded kit using poly-A pull down for mRNA enrichment, with a target insert size of 180 bp. Sequencing was performed on a HiSeq2500 v4 with 125bp PE reads. Both library construction and sequencing were performed by the Garvin Institute (Kinghorn Centre for Clinical Genomics/SCI Ramachiotti).

tag: cultivar

value: Halberd

tag: culture

value: in planta

tag: isolate


title: 3078_M0_DMSO

tag: stimulation


title: inplanta_Pf2_026


title: inplanta_Pf2_027


title: 3071_M3_CSP

tag: subjectid

value: malaria


title: 3071_M3_uRBC

value: uRBC

tag: vaccine


title: 3074_M0_iRBC

tag: site

value: Bagamoyo


title: 3074_M0_DMSO

tag: age

value: PBMC


title: 3076_M3_iRBC

tag: immunization dose


title: 3068_M0_iRBC

tag: protection

value: F


title: 3071_M3_iRBC

tag: timepoint


title: inplanta_SN15_018

source_name: Mixed wheat and wild type SN15 sample.


title: 3068_M0_DMSO

value: protected

tag: Sex


title: inplanta_SN15_019


title: inplanta_Pf2_024


title: inplanta_SN15_016


title: 3089_M3_CSP

tag: tissue


title: 3068_M0_CSP


title: inplanta_SN15_017


title: 3071_M3_DMSO


title: Bifidobacteria-treated Cerebellum P10B

city: Houston

first: Melinda

middle: Anne

last: Engevik

state: TX

address: 1 Baylor Plaza

department: Pathology & Immunology

country: USA

institute: Baylor College of Medicine

description:
Test group 2
SAMPLE 24

data_processing:
The array contained 84 pathway-focused genes, 5 housekeeping (reference) genes, and a panel of quality control targets to monitor genomic DNA contamination and efficiency of the first strand synthesis and PCR reactions. As defined by the manufacturer’s protocol, the CT value of the PCR efficiency control was within the range of 20 ± 2 for all arrays or samples across runs and between plates. The average values across all 27 samples and 7 plates used in our analysis was CTPPC = 20.37 (std dev ± 0.26). The samples also passed the tests controlling for genomic DNA contamination and first strand synthesis. Gene of Interest (GOI) CT values were normalized using the most stably expressed of the 5 reference genes, which was Gapdh on all panels (average gapdh CT across all panels =19.944 (std dev ± 0.33)). The CTs were then sorted into brain region and time point. The fold regulation was calculated using the 2−ΔCt relative quantification, with the threshold for biological significance set to 1.5. The data analysis web portal calculates Fold-change/regulation using ΔΔCT method, in which ΔCT is calculated between gene of interest (GOI) and reference gene (Gapdh), followed by delta-delta CT calculations (delta CT (Test Group)-delta CT (Control Group)). Fold Change was calculated using 2^ (-delta delta CT) formula. Fold-change values greater than one indicates a positive- or an up-regulation, and the fold-regulation is equal to the fold-change. Fold-change values less than one indicate a negative or down-regulation, and the fold-regulation is the negative inverse of the fold-change.
Fold Change worksheet reports test/control (i.e., CONV vs. GF ratios or BIF vs. GF ratios)

label: SYBR Green

organism: Mus musculus

source_name: Whole tissue homogenate from specified brain region at P10

label_protocol: Using the “Mouse Synaptic Plasticity RT² Profiler PCR Array” (PAMM-126Z; Qiagen), 96 genes (Supplementary Table S1) were profiled on the 27 samples (1 pooled sample as described above for each of the 3 brain regions, at each of the 3 time points, in each of the 3 treatment groups). The manufacturer’s protocol was followed for sample preparation. Briefly, 500 ng of each pooled sample was treated with DNase to eliminate genomic DNA contamination, followed by conversion to cDNA using the RT2 First Strand Kit. The cDNA was added to the kit mastermix on ice, and distributed to the 384-well plate containing 4 replicate primer assays for the 84 pathway-specific genes. Reactions using SYBR Green chemistry (Qiagen SYBR Green qPCR Mastermix, Cat. no. 330529) were performed in a 384 well block ViiATM 7 Real-Time PCR system (Applied Biosystems, Foster City, USA). The threshold values were set consistently across all runs in the same analysis (threshold manually set to 0.5 and lower limit of detection set to 35). The resulting table of CT values was uploaded to the data analysis web portal at http://www.qiagen.com/geneglobe. Samples were assigned to control (germ-free) and test groups (conventionalized vs. Bifidobacterium-treated), allowing for comparative analysis of gene expression at each time point.

growth_protocol: Germ-free (GF) Swiss Webster mice (Taconic) were bred in a germ-free facility at Baylor College of Medicine. The outbred colony of germ-free mice was maintained in a germ-free “colony isolator”. Swiss Webster mice are attractive as an outbred mouse model due to large litter sizes, nurturing instincts, and previous microbiome-gut-brain studies, making this strain useful for cross-study comparisons. Timed pregnancies were induced in adult female mice at approximately 6-8 weeks of age, in the germ-free colony isolators. Vaginal plugs were used to identify pregnant dams and time the pregnancy. Pregnant germ-free females were randomly assigned to an experimental group, and moved (under germ-free conditions) to the respective study isolator before the day of birth, which was considered as P0. Pregnant dams and their litters were maintained in separate cages within these 3 identical, but separate, flexible isolators fed with HEPA-filtered air. Each isolator housed only the dams and litters within a single experimental group in this study. Mice in each isolator were maintained under germ-free conditions or colonized with bacteria and maintained in “gnotobiotic conditions”. Offspring in each treatment group raised in these germ-free and gnotobiotic isolators were handled in the same manner. Dams and their respective litters in were kept together in filter-topped cages in the isolators pre-weaning, and in groups separated by sex, in filter-topped cages in the same isolators after weaning. All animals had access to irradiated food and water ad libitum. All animals were housed under 12 h light / dark cycle. Animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at Baylor College of Medicine, Houston, TX, in accordance with all guidelines set forth by the U.S. National Institutes of Health. Germ-free control mice received gavages of sterile 0.1 M phosphate buffered saline (PBS; Gibco) in the same manner as the experimental mice (described in section below). Germ-free status was monitored over the course of the experiment by plating fresh fecal pellets from the dams in each cage within the germ-free isolator on blood agar plates (Hardy Diagnostics) and incubating aerobically and anaerobically at 37°C.  Colonization of germ-free mice with bifidobacteria  Bifidobacteria were grown in culture conditions described above. Bacterial cultures grown overnight (approximately 12 h) were harvested in log phase. Cultures were combined in equal ratios based on OD600 readings (volume equal to approximately OD600 1.0 for each of the species), pelleted, then re-suspended in 3 mL sterile PBS. Colonization of males and females with bifidobacteria was achieved by administering 0.2 mL of this treatment directly to the stomach of each dam via oral gavage on alternating days post-partum. The treatment was also administered with the drinking water. Pups were administered 0.02 mL of the treatment mixture starting at P1, and on alternating days until P20. For pups between the ages of P1-P10, we administered the mixture orally via pipette tip. From P10 onwards, the oral gavage treatment was administered with an 18-gauge ball-tipped gavage needle. This persistent treatment ensured that all four human Bifidobacterium species were present during the postnatal window of interest in this study, irrespective of their ability to colonize the murine intestine in the absence of human milk oligosaccharides. Dilution plating of the treatment mixture on MRS plates at several timepoints during the experiment confirmed that the dams received approximately 1.1x1010 total CFUs (viable bacterial cells) per gavage. The pups received a smaller volume of the gavage mixture, approximate to 1.1x109 total CFUs per treatment. Colonization was monitored over the course of the experiment by plating fecal samples from the dam and pups on MRS agar plates and incubating at 37°C anaerobically. Growth on plates after 48 h was considered positive verification of successful colonization. All dams and pups showed consistently positive colonization after the first 2 d of treatment.  Colonization of germ-free mice with murine microbiota (conventionalization)  Conventionalized litters were colonized neonatally via indirect colonization of the dam and environment. Conventionalized males and females were derived by administering fecal slurries from specific pathogen free mice, which harbor a complex microbial community, via oral gavage to the dams on P1, and by adding used bedding (containing fecal pellets) to the cages on P1 and P3. A single cage of female, age-matched Swiss Webster mice were used as donors for each experimental cage and were the source of both the FMT and the dirty bedding transfer to avoid as much inter-individual variation as possible. Agar plating of intestinal contents from these pups on blood agar plates confirmed that this method effectively resulted in gut microbial colonization of the pups by P4. In order to maintain consistent handling throughout development between the groups, conventionalized pups (male and female) were also administered a sham gavage of sterile PBS in the same manner as described above. Colonization with conventional murine microbiota was monitored over the course of the experiment by plating fecal samples from the dam and pups on blood agar plates (Hardy Diagnostics) and incubating at 37°C aerobically and anaerobically. Growth on plates after 48 h confirmed presence of complex microbiota consisting of multiple species and was used as positive verification of successful colonization.

extract_protocol: For preparation of RNA for gene expression analysis, the mice were individually anesthetized using isoflurane until no reflex was observed. The mice were rapidly decapitated, and the brains were dissected to isolate the cerebellum, hippocampus, and cortex. The tissues were flash frozen and stored separately at -80°C until RNA isolation. RNA was isolated from the cerebellum, cortex, and hippocampus of male mice from each developmental timepoint via Trizol. The 260/280 ratio was measured for each sample using a Nanodrop spectrophotometer, and after this step ranged between 1.8 and 2.0. RNA samples were stored at −80°C until use. Two µg of RNA from 5 samples (male mice only) were pooled into one representative sample per treatment, time point, and brain region (27 pooled samples total, n=5 mice per pooled sample). Pooled RNA was purified with the Zymo RNA clean and concentrate kit according to the manufacture’s protocol with one modification. Zymo-Spin IIICG columns were used instead of Zymo-Spin IC Columns in order to purify larger quantities of RNA (~100 µg of RNA). A Bioanalyzer (Agilent) was used to verify that the purity and concentration of pooled and cleaned RNA was of sufficient quality and quantity prior to use with the synaptic plasticity qPCR array.

tag: developmental stage

tag: tissue type

value: Cerebellum

value: Bifidobacterium-treated

tag: plate #

value: Plate 3

tag: sample code


title: Germ-free Cerebellum P20G

description:
Control
SAMPLE 25

source_name: Whole tissue homogenate from specified brain region at P20

tag: treatment

value: Germ-free

value: Plate 6


title: Bifidobacteria-treated Cerebellum P20B

description:
Test group 2
SAMPLE 27


title: Conventionalized Cerebellum P10X

description:
Test group 1
SAMPLE 23

value: Conventionalized


title: Bifidobacteria-treated Cerebellum P4B

description:
Test group 2
SAMPLE 21

source_name: Whole tissue homogenate from specified brain region at P4

value: Plate 7


title: Germ-free Cerebellum P10G

description:
Control
SAMPLE 22


title: Conventionalized Cerebellum P4X

description:
Test group 1
SAMPLE 20


title: 3065_M3_DMSO


title: Conventionalized Cerebellum P20X

description:
Test group 1
SAMPLE 26


title: Bifidobacteria-treated Cortex P20B

description:
Test group 2
SAMPLE 18

value: Cortex

value: Plate 5


title: 3065_M3_uRBC


title: Germ-free Cerebellum P4G

description:
Control
SAMPLE 19


title: 3057_M3_DMSO

value: DMSO

value: Control

value: M


title: 3065_M3_iRBC

value: iRBC


title: 3065_M3_CSP

value: CSP

value: Bagamoyo


title: 3068_M0_uRBC

value: uRBC

value: F

value: PBMC


title: 3053_M3_iRBC

value: protected


title: 3056_M3_DMSO


title: 3053_M3_DMSO


title: 3052_M3_CSP


title: 3053_M3_uRBC


title: 3057_M3_CSP


title: 3052_M3_uRBC


title: Conventionalized Cortex P20X

description:
Test group 1
SAMPLE 17


title: Germ-free Cortex P20G

description:
Control
SAMPLE 16


title: Bifidobacteria-treated Cortex P4B

description:
Test group 2
SAMPLE 12

value: Bifidobacterium-treated


title: Conventionalized Cortex P4X

description:
Test group 1
SAMPLE 11


title: 3052_M3_iRBC


title: Conventionalized Cortex P10X

description:
Test group 1
SAMPLE 14

value: Plate 2


title: Bifidobacteria-treated Hippocampus P20B

description:
Test group 2
SAMPLE 9

value: Hippocampus

value: Plate 4


title: Germ-free Cortex P10G

description:
Control
SAMPLE 13

value: Germ-free


title: Germ-free Cortex P4G

description:
Control
SAMPLE 10

value: Cortex


title: Conventionalized Hippocampus P20X

description:
Test group 1
SAMPLE 8

value: Conventionalized


title: Germ-free Hippocampus P20G

description:
Control
SAMPLE 7


title: Bifidobacteria-treated Cortex P10B

description:
Test group 2
SAMPLE 15


title: 3053_M3_CSP


title: 3049_M3_iRBC


title: 3056_M3_CSP


title: Germ-free Hippocampus P10G

description:
Control
SAMPLE 4

value: Plate 1


title: Conventionalized Hippocampus P10X

description:
Test group 1
SAMPLE 5


title: Bifidobacteria-treated Hippocampus P4B

description:
Test group 2
SAMPLE 3

value: Plate 3


title: Bifidobacteria-treated Hippocampus P10B

description:
Test group 2
SAMPLE 6


title: 3049_M0_uRBC

value: Control

value: M


title: 3049_M3_uRBC


title: Conventionalized Hippocampus P4X

description:
Test group 1
SAMPLE 2


title: 3049_M3_CSP

value: CSP


title: 3049_M0_iRBC

value: iRBC

value: Bagamoyo


title: Germ-free Hippocampus P4G

description:
Control
SAMPLE 1


title: 3049_M3_DMSO

value: DMSO


title: lckgfp_s458

city: Chicago

first: Elizabeth

last: Jerison

state: IL

address: 529 E 57th St

department: Physics

institute: University of Chicago

data_processing:
STAR (2.5)
Htseq (0.8.0) htseq-count -m intersection-nonempty --nonunique all
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw counts of numbers of reads aligned to each feature for each cell, in tab-separated format (lckgfp_counts.txt)

organism: Danio rerio

source_name: Danio rerio tail

extract_protocol:
Lysis was performed as described in Schaum et al., Nature 2018
A Smart-Seq2 based protocol was used for reverse transcription and cDNA amplification, and a Nextera based protocol was used for library preparation, as described in Schaum et al., Nature 2018

treatment_protocol: Liberase TL (100 ug/mL) and manual trituration was used to dissociate tail tissue. Cells were FACS sorted (FITC+)

tag: line

value: tail

tag: devlopmental stage

value: 15 dpf


title: lckgfp_s456


title: 3028_M3_CSP

tag: stimulation

value: protected

value: F

value: PBMC


title: lckgfp_s460


title: lckgfp_s457


title: lckgfp_s459


title: 3049_M0_DMSO

tag: subjectid


title: 3049_M0_CSP

tag: vaccine


title: 3043_M0_iRBC

tag: site


title: 3043_M0_uRBC

value: uRBC

tag: age


title: 3043_M0_CSP

tag: immunization dose


title: 3026_M3_uRBC

tag: protection


title: 3028_M3_DMSO

tag: timepoint


title: 3026_M3_CSP

tag: Sex


title: 3026_M3_DMSO

tag: tissue


title: 3028_M3_iRBC


title: lckgfp_s453


title: 3028_M3_uRBC


title: lckgfp_s452


title: lckgfp_s451


title: 3022_M3_CSP


title: 3022_M3_iRBC


title: 3026_M3_iRBC


title: lckgfp_s455


title: 3043_M0_DMSO


title: lckgfp_s450


title: lckgfp_s449


title: lckgfp_s454


title: lckgfp_s448


title: lckgfp_s446


title: lckgfp_s447


title: lckgfp_s442


title: lckgfp_s441


title: lckgfp_s440


title: 3019_M3_iRBC


title: 3019_M3_DMSO


title: 3022_M3_DMSO


title: 3022_M3_uRBC


title: lckgfp_s438


title: 3013_M3_CSP


title: lckgfp_s439


title: lckgfp_s437


title: lckgfp_s436


title: lckgfp_s435


title: 3013_M3_DMSO


title: lckgfp_s443


title: lckgfp_s434


title: 3019_M3_CSP


title: lckgfp_s432


title: 3012_M3_CSP


title: lckgfp_s429


title: lckgfp_s431


title: 3019_M3_uRBC


title: 3012_M3_iRBC


title: 2994_M0_CSP

value: malaria


title: lckgfp_s428


title: 3012_M3_uRBC


title: 2994_M3_iRBC


title: 2994_M3_DMSO


title: 3012_M3_DMSO


title: lckgfp_s433


title: 2994_M3_CSP


title: 2978_M0_uRBC


title: lckgfp_s426


title: lckgfp_s430


title: 2994_M3_uRBC


title: 2994_M0_iRBC


title: 2978_M0_iRBC


title: lckgfp_s425


title: 2960_M0_uRBC


title: 2994_M0_DMSO


title: lckgfp_s445


title: 2958_M3_DMSO


title: lckgfp_s424


title: 2978_M0_CSP


title: 2978_M0_DMSO


title: lckgfp_s444


title: lckgfp_s422


title: lckgfp_s420


title: lckgfp_s418


title: 2960_M0_CSP


title: 2960_M0_iRBC


title: lckgfp_s427


title: lckgfp_s423


title: lckgfp_s417


title: lckgfp_s415


title: lckgfp_s416


title: lckgfp_s421


title: 2958_M3_uRBC


title: lckgfp_s413


title: 2958_M3_iRBC


title: lckgfp_s412


title: lckgfp_s414


title: lckgfp_s411


title: 2958_M3_CSP


title: 2952_M3_iRBC


title: 2954_M0_DMSO


title: 2952_M3_uRBC


title: 2954_M0_uRBC


title: 2952_M3_DMSO


title: 2954_M0_iRBC


title: 2916_M0_DMSO


title: lckgfp_s409


title: lckgfp_s406


title: lckgfp_s407


title: lckgfp_s408


title: 2916_M0_uRBC


title: 2916_M0_iRBC


title: 2952_M3_CSP


title: lckgfp_s419


title: 2908_M3_uRBC


title: 2954_M0_CSP


title: 2908_M3_iRBC


title: 2903_M3_iRBC


title: 2916_M0_CSP


title: 2908_M3_CSP


title: 2908_M3_DMSO


title: lckgfp_s405


title: 2903_M3_CSP


title: lckgfp_s410


title: lckgfp_s404


title: lckgfp_s403


title: lckgfp_s401


title: 2903_M0_iRBC


title: lckgfp_s402


title: lckgfp_s400


title: lckgfp_s398


title: 2903_M0_DMSO


title: lckgfp_s399


title: lckgfp_s395


title: lckgfp_s397


title: lckgfp_s394


title: lckgfp_s396


title: lckgfp_s391


title: lckgfp_s390


title: 2903_M3_DMSO


title: 2903_M3_uRBC


title: 2903_M0_CSP


title: lckgfp_s388


title: lckgfp_s387


title: 2897_M0_iRBC


title: 2897_M0_uRBC


title: 2890_M3_CSP


title: lckgfp_s385


title: 2890_M3_uRBC


title: 2890_M3_iRBC


title: 2903_M0_uRBC


title: 2889_M3_CSP


title: 2888_M3_CSP


title: 2888_M3_DMSO


title: 2883_M3_iRBC


title: 2889_M3_DMSO


title: 2888_M3_uRBC


title: lckgfp_s393


title: lckgfp_s386


title: 2897_M0_CSP


title: lckgfp_s383


title: lckgfp_s389


title: lckgfp_s384


title: lckgfp_s382


title: 2889_M3_iRBC


title: lckgfp_s381


title: lckgfp_s379


title: lckgfp_s380


title: lckgfp_s378


title: lckgfp_s377


title: lckgfp_s376


title: lckgfp_s373


title: lckgfp_s374


title: 2883_M3_CSP


title: 2883_M3_uRBC


title: lckgfp_s375


title: 2888_M3_iRBC


title: 2878_M0_uRBC


title: 2878_M0_DMSO


title: 2883_M3_DMSO


title: lckgfp_s371


title: lckgfp_s372


title: 2878_M0_CSP


title: lckgfp_s370


title: 2878_M0_iRBC


title: lckgfp_s369


title: 2889_M3_uRBC


title: lckgfp_s368


title: 2861_M3_CSP


title: lckgfp_s367


title: 2853_M0_CSP


title: 2853_M0_uRBC


title: 2852_M3_uRBC


title: 2852_M3_DMSO


title: 2852_M3_iRBC


title: 2861_M3_DMSO


title: 2853_M0_iRBC


title: lckgfp_s365


title: lckgfp_s364


title: lckgfp_s362


title: lckgfp_s359


title: lckgfp_s358


title: 2852_M3_CSP


title: lckgfp_s366


title: lckgfp_s356


title: lckgfp_s361


title: lckgfp_s357


title: lckgfp_s360


title: lckgfp_s353


title: 2850_M0_CSP


title: 2830_M3_DMSO


title: 2850_M0_iRBC


title: lckgfp_s355


title: 2830_M0_iRBC


title: lckgfp_s351


title: 2830_M3_CSP


title: 2850_M0_DMSO


title: 2853_M0_DMSO


title: 2830_M0_CSP


title: lckgfp_s354


title: 2830_M3_uRBC


title: 2830_M0_uRBC


title: 2830_M0_DMSO


title: lckgfp_s349


title: lckgfp_s350


title: 2821_M3_iRBC


title: 2821_M3_uRBC


title: lckgfp_s348


title: 2821_M3_DMSO


title: lckgfp_s352


title: 2830_M3_iRBC


title: 2850_M0_uRBC


title: 2821_M3_CSP


title: 2820_M0_uRBC


title: 2820_M0_iRBC


title: lckgfp_s347


title: lckgfp_s345


title: lckgfp_s344


title: 2820_M0_DMSO


title: lckgfp_s342


title: lckgfp_s340


title: lckgfp_s346


title: 2820_M0_CSP


title: lckgfp_s337


title: lckgfp_s336


title: lckgfp_s343


title: lckgfp_s339


title: lckgfp_s338


title: lckgfp_s341


title: lckgfp_s334


title: lckgfp_s333


title: 2812_M0_iRBC


title: 2809_M3_DMSO


title: 2812_M0_CSP


title: lckgfp_s331


title: 2812_M0_uRBC


title: 2812_M0_DMSO


title: 2809_M3_CSP


title: 2800_M0_CSP


title: 2800_M0_uRBC


title: lckgfp_s330


title: lckgfp_s392


title: 2791_M3_CSP


title: lckgfp_s335


title: lckgfp_s329


title: lckgfp_s328


title: 2800_M0_DMSO


title: lckgfp_s332


title: 2809_M3_iRBC


title: 2800_M0_iRBC


title: 2802_M3_DMSO


title: 2802_M3_CSP


title: lckgfp_s327


title: 2791_M3_uRBC


title: 2809_M3_uRBC


title: 2787_M3_iRBC


title: lckgfp_s326


title: 2787_M3_DMSO


title: lckgfp_s324


title: lckgfp_s323


title: 2791_M3_iRBC


title: lckgfp_s322


title: lckgfp_s321


title: lckgfp_s320


title: 2762_M3_DMSO


title: 2762_M3_CSP


title: lckgfp_s319


title: 2787_M3_uRBC


title: lckgfp_s317


title: 2751_M3_DMSO


title: 2762_M3_uRBC


title: lckgfp_s316


title: lckgfp_s363


title: 2751_M3_uRBC


title: lckgfp_s315


title: lckgfp_s314


title: lckgfp_s318


title: 2750_M0_uRBC


title: lckgfp_s312


title: 2751_M3_CSP


title: lckgfp_s313


title: 2750_M0_iRBC


title: 2750_M0_DMSO


title: lckgfp_s308


title: lckgfp_s310


title: lckgfp_s307


title: 2762_M3_iRBC


title: 2751_M3_iRBC


title: lckgfp_s306


title: 2744_M0_CSP


title: 2750_M0_CSP


title: 2744_M0_DMSO


title: 2743_M3_iRBC


title: 2744_M0_iRBC


title: lckgfp_s309


title: lckgfp_s305


title: 2743_M3_CSP


title: 2743_M3_uRBC


title: lckgfp_s304


title: lckgfp_s303


title: 2787_M3_CSP


title: lckgfp_s301


title: lckgfp_s302


title: lckgfp_s299


title: lckgfp_s300


title: 2743_M0_DMSO


title: 2744_M0_uRBC


title: lckgfp_s297


title: 2743_M0_iRBC


title: 2743_M0_CSP


title: lckgfp_s298


title: 2743_M3_DMSO


title: lckgfp_s296


title: 2742_M3_uRBC


title: 2742_M3_CSP


title: 2742_M3_DMSO


title: lckgfp_s293


title: 2742_M0_CSP


title: lckgfp_s294


title: lckgfp_s292


title: lckgfp_s291


title: lckgfp_s290


title: lckgfp_s295


title: lckgfp_s289


title: lckgfp_s288


title: lckgfp_s287


title: lckgfp_s286


title: 2742_M0_DMSO


title: 2742_M3_iRBC


title: lckgfp_s284


title: 2729_M3_iRBC


title: lckgfp_s283


title: 2729_M3_uRBC


title: 2725_M3_CSP


title: 2721_M3_DMSO


title: lckgfp_s281


title: lckgfp_s282


title: 2729_M3_DMSO


title: lckgfp_s285


title: 2715_M3_CSP


title: 2725_M3_iRBC


title: 2713_M0_CSP


title: 2721_M3_CSP


title: lckgfp_s279


title: 2725_M3_DMSO


title: 2715_M3_iRBC


title: 2725_M3_uRBC


title: 2715_M3_uRBC


title: lckgfp_s325


title: lckgfp_s278


title: lckgfp_s277


title: 2689_M0_CSP


title: lckgfp_s276


title: lckgfp_s274


title: 2713_M0_DMSO


title: lckgfp_s275


title: 1351_57_I7_uRBC

value: CPS

value: Nijmegen

value: adults


title: lckgfp_s269


title: lckgfp_s280


title: lckgfp_s268


title: 2696_M0_DMSO


title: lckgfp_s270


title: 2689_M0_DMSO


title: lckgfp_s267


title: 1351_57_C1_uRBC


title: lckgfp_s266


title: 1351_57_I7_DMSO


title: 1351_57_C1_DMSO


title: 1351_57_C1_CSP


title: lckgfp_s265


title: lckgfp_s264


title: 1351_57_C1_PfRBC

value: PfRBC


title: 1351_57_I7_CSP


title: 1351_57_I7_PfRBC


title: 1331_67_C1_PfRBC


title: 1331_67_C1_uRBC


title: 1331_67_I7_uRBC


title: lckgfp_s263


title: 1331_67_I7_PfRBC


title: lckgfp_s262


title: 1331_67_I7_DMSO


title: lckgfp_s260


title: lckgfp_s259


title: 1331_67_I7_CSP


title: lckgfp_s258


title: 1331_67_C1_DMSO


title: lckgfp_s257


title: lckgfp_s256


title: lckgfp_s272


title: 1331_67_C1_CSP


title: 1322_43_I7_uRBC


title: lckgfp_s255


title: lckgfp_s253


title: lckgfp_s261


title: lckgfp_s252


title: 1322_43_I7_PfRBC


title: lckgfp_s251


title: 1322_43_C1_PfRBC


title: lckgfp_s249


title: 1322_43_C1_uRBC


title: lckgfp_s248


title: 1322_43_I7_DMSO


title: 1322_43_I7_CSP


title: 1322_43_C1_DMSO


title: lckgfp_s247


title: 1322_43_C1_CSP


title: 1320_45_C1_uRBC


title: lckgfp_s246


title: 1320_45_I7_DMSO


title: 1320_45_I7_PfRBC


title: lckgfp_s254


title: lckgfp_s245


title: lckgfp_s250


title: 1320_45_I7_uRBC


title: 1320_45_C1_CSP


title: 1301_55_I7_uRBC


title: lckgfp_s244


title: lckgfp_s243


title: 1320_45_C1_PfRBC


title: 1320_45_C1_DMSO


title: lckgfp_s242


title: 1301_55_C1_uRBC


title: lckgfp_s241


title: lckgfp_s240


title: lckgfp_s238


title: lckgfp_s237


title: 1301_55_C1_PfRBC


title: lckgfp_s311


title: lckgfp_s236


title: lckgfp_s235


title: lckgfp_s233


title: lckgfp_s232


title: 1301_55_I7_DMSO


title: lckgfp_s239


title: 1301_55_I7_CSP


title: lckgfp_s234


title: 1301_55_C1_DMSO


title: 24_p5424_K27ac

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

data_processing:
Unique reads were aligned to the reference build (GTCm387/mm9) using TopHat and Bowtie2.
duplicates were removed using Picard markDuplicates
RPKM values were obtained using Deeptools.
peaks were called using MACS2 findpeaks The reads were aligned to the mm9 build using Bowtie2 to map clean reads to reference gene
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values were determined using STAR aligner.

extract_protocol:
Cells were washed 1X with cut and run wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine), bound to activated ConA beads (Bangs Laboratories BP531), permeabilized in digi buffer (wash buffer + 0.002% digitonin), incubated with antibodies (1 g/CR in digi buffer), washed in digi buffer, incubated with pA-MN (gift from Heinkoff Laboratory, currently EpiCypher 15-1016), and washed in digi buffer. Following the final wash, cells were washed with ice-cold low salt wash buffer (20 mM HEPES, pH 7.5, 0.5 mM spermidine, 0.002% digitonin) and digested using MN-ase digestion buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.002% digitonin) for 25 minutes on ice. Solubilized chromatin was released using an isosmotic stop buffer (170 mM NaCl, 20 mM EGTA, 0.05% Digitonin, 20 µg/ml glycogen, 25 µg/ml RNase A, 2 pg/ml S. cerevisiae fragmented nucleosomal DNA) and was collected using a PCR clean up kit column (EZbioresearch M1001). All antibody incubations and digitonin washing steps were performed for 5 minutes at room temperature and included protease, phosphatase and deacetylase inhibitors (Roche).
For library preparation, DNA products were incubated with an end repair master mix (1 X T4 ligation buffer, dNTP, ATP, T4 PNK, T4 DNA Pol and TAQ DNA polymerase) and incubated as follows: 12’C 15 minutes (end polishing), 37’C 15 minutes (5’ end phosphorylation) and 58’C 1.5 hour (dA tailing). Polished libraries were purified using AmpureXP beads and ligated to either NEBNext Dual Index (NEB) or Illuminia TruSeq adaptors. Libraries were size selected and enriched by PCR.
Finished libraries were sequenced using Illumina HiSeq2500 (Genome Technology Access Center, Washington University).

tag: tissue source

value: cell line - p5424 thymocyte

tag: genotype

value: CTCF Motif WT

tag: protocol

value: Cut and Run-seq

tag: rnp

value: No RNP

tag: chip antibody

value: H3K27ac ab Ab4729 1ug


title: 23_p5424_IgG_CR

value: IgG Invitrogen 31188


title: 1291_65_C1_PfRBC

value: M


title: 1291_65_I7_PfRBC


title: 1291_65_I7_CSP

value: CSP


title: 1291_65_I7_uRBC

value: protected


title: 22_p5424_CTCF_CR

value: Anti-CTCF Rockland 600-401-C42 1 ug


title: 1291_65_C1_DMSO

value: DMSO

value: PBMC


title: lckgfp_s231

tag: line

value: tail

value: 15 dpf


title: lckgfp_s230

tag: devlopmental stage


title: lckgfp_s273


title: 1291_65_I7_DMSO

tag: stimulation

value: CPS

value: Nijmegen


title: 2713_M0_iRBC

value: iRBC

tag: subjectid

value: Control

value: Bagamoyo

value: F


title: 1284_26_I7_uRBC

value: uRBC

tag: vaccine

value: adults


title: 2696_M0_CSP

tag: site


title: 1291_65_C1_CSP

tag: age


title: 1284_26_C1_uRBC

tag: immunization dose


title: 1284_26_I7_PfRBC

value: PfRBC

tag: protection


title: 1284_26_C1_PfRBC

tag: timepoint

value: M


title: 1301_55_C1_CSP

value: CSP

value: malaria

tag: Sex


title: 1284_26_I7_DMSO

value: protected

tag: tissue


title: 20_6312_IgG_CR

tag: tissue source

value: cell line - 63-12 pre B cell

value: CTCF Motif WT

value: Cut and Run-seq

value: No RNP

value: IgG Invitrogen 31188


title: lckgfp_s228

value: tail

value: 15 dpf


title: 19_6312_CTCF_CR

tag: genotype

value: Anti-CTCF Rockland 600-401-C42 1 ug


title: 21_6312_K27Ac

tag: protocol

value: H3K27ac ab Ab4729 1ug


title: 1284_26_C1_DMSO

value: DMSO

value: CPS

value: Nijmegen

value: PBMC


title: lckgfp_s229


title: lckgfp_s227


title: lckgfp_s226


title: 1169_18_I7_uRBC

value: uRBC

value: adults

value: M


title: lckgfp_s225


title: lckgfp_s224


title: 16_pH2Ax_6312_RNP-MycSE

tag: rnp

value: Myc Distal Super Enhancer

value: Anti-gammah2ax Millipore 05-636 1 ug


title: 1284_26_I7_CSP

value: CSP

value: protected


title: 1169_18_I7_PfRBC

value: PfRBC

value: malaria


title: lckgfp_s271

value: tail


title: 15_pH2Ax_6312_RNP-MycCTCF

value: cell line - 63-12 pre B cell

value: CTCF Motif WT

value: Cut and Run-seq

value: CTCF site 3 kb 3' of Myc

tag: chip antibody


title: 17_pH2Ax_6312-CTCFmotifKO_RNP-MycPro

source_name: 63-12 with Myc CTCF motif KO

value: CTCF Motif KO

value: Myc Promoter


title: 18_pH2Ax_6312-CTCFmotifKO_RNP-MycSE


title: lckgfp_s223

tag: line

value: 15 dpf


title: 1291_65_C1_uRBC

value: uRBC

value: CPS

value: Nijmegen

value: PBMC


title: lckgfp_s222

tag: devlopmental stage


title: 1169_18_I7_DMSO

tag: stimulation

value: DMSO

value: adults

value: M


title: 1169_18_C1_PfRBC

value: PfRBC

tag: subjectid


title: lckgfp_s221


title: 14_pH2Ax_6312_RNP-MycPro

value: Anti-gammah2ax Millipore 05-636 1 ug


title: 12_pH2Ax_6312_RNP-MycCTCF


title: 1320_45_I7_CSP

value: CSP

tag: vaccine

value: malaria


title: 1169_18_C1_uRBC

tag: site


title: 1169_18_C1_DMSO

tag: age


title: lckgfp_s220

value: tail


title: 1169_18_C1_CSP

tag: immunization dose


title: 11_pH2Ax_6312_RNP-MycPro

value: cell line - 63-12 pre B cell

value: CTCF Motif WT

value: Cut and Run-seq


title: lckgfp_s219


title: 1145_09_I7_uRBC

tag: protection

value: protected


title: 10_pH2Ax_6312-CTCFmotifKO_RNP-MycPro

value: CTCF Motif KO

value: Myc Promoter


title: 1145_09_C1_DMSO

value: CPS

tag: timepoint


title: 13_pH2Ax_6312-CTCFmotifKO_RNP-MycSE

value: Myc Distal Super Enhancer


title: 1145_09_C1_PfRBC

value: Nijmegen

tag: Sex

value: PBMC


title: lckgfp_s218

tag: tissue

value: 15 dpf


title: 1169_18_I7_CSP

value: adults

value: M


title: 1145_09_C1_uRBC

value: uRBC


title: 1145_09_I7_PfRBC

value: PfRBC


title: 1145_09_I7_DMSO

value: DMSO


title: 1145_09_I7_CSP

value: CSP


title: 1145_09_C1_CSP


title: 1355_61_I7_uRBC

value: F


title: lckgfp_s217

value: tail


title: 6_pH2Ax_6312_RNP-MycPro

tag: tissue source

value: cell line - 63-12 pre B cell

value: CTCF Motif WT

value: Cut and Run-seq

value: Anti-gammah2ax Millipore 05-636 1 ug


title: 1355_61_I7_PfRBC

value: CPS

value: protected


title: 1355_61_C1_PfRBC

value: Nijmegen


title: lckgfp_s216


title: 5_pH2Ax_6312_RNP-eB

tag: genotype

value: eBeta (eB)


title: 1355_61_I7_DMSO

value: PBMC


title: lckgfp_s215

value: 15 dpf


title: 1355_61_I7_CSP

value: adults


title: lckgfp_s213


title: 4_pH2Ax_p5424_RNP-MycPro

value: cell line - p5424 thymocyte

tag: protocol

value: Myc Promoter


title: 7_pH2Ax_6312-RNP-MycCTCF

tag: rnp

value: CTCF site 3 kb 3' of Myc


title: lckgfp_s212


title: 1_pH2Ax_6312_RNP-eB

tag: chip antibody


title: lckgfp_s214

tag: line


title: 3_pH2Ax_p5424_RNP-eB


title: 2_pH2Ax_6312_RNP-MycPro


title: lckgfp_s211

tag: devlopmental stage


title: KO_3b_2C45_MEFs_WGBS

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 108 bp, 2 X 109 bp, 2 X 110 bp, 2 X 101 bp or 2×100 bp paired-end reads, illumina) or Nextseq500 (75 bp or 86bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.15
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.18.2 with bowtie2 (version 2.3.0) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.18.2 with bowtie2 (version 2.3.0) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.

source_name: MEFs

growth_protocol: MEFs were isolated from E14.5 embryos and were cultured in DMEM (Nacalai tesque) with 2 mM L-glutamine (Nacalai tesque), 100× nonessential amino acids (NEAA) (Nacalai tesque), 100 U/ml penicillin, 100 mg/ml streptomycin (P/S) (Nacalai tesque) and 10% Fetal Bovine Serum (FBS) (GIBCO).

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.
methyl-seq, whole genome bisulfite sequencing and RNA-seq

tag: passage

tag: strains

value: F1 (129X1/SvJ and MSM/Ms)

tag: gender

value: Female

tag: analysis method

value: WGBS


title: lckgfp_s210

value: tail


title: KO_3a_2B16_MEFs_WGBS


title: 1355_61_C1_DMSO

tag: stimulation

value: DMSO

tag: subjectid

tag: vaccine

tag: site

tag: age

value: F


title: 1336_52_I7_uRBC

value: uRBC

tag: immunization dose

tag: protection

tag: timepoint

tag: Sex

tag: tissue


title: WT_B_2i_MEFs_WGBS


title: 1301_55_I7_PfRBC

value: PfRBC

value: CPS

value: malaria

value: M


title: 1326_49_I7_uRBC

value: Nijmegen

value: protected

value: PBMC


title: 1336_52_C1_CSP

value: CSP

value: adults


title: 1326_49_I7_PfRBC


title: 1336_52_C1_uRBC


title: 1355_61_C1_CSP


title: 1336_52_I7_DMSO


title: lckgfp_s208

value: 15 dpf


title: 1336_52_C1_PfRBC


title: 1336_52_C1_DMSO


title: 1336_52_I7_PfRBC


title: 1326_49_C1_PfRBC


title: 1326_49_C1_uRBC


title: 1355_61_C1_uRBC


title: 1336_52_I7_CSP


title: KO_3b_2C45_MEFs_MethylSeq

value: F1 (129X1/SvJ and MSM/Ms)

value: Methylseq


title: lckgfp_s207


title: lckgfp_s209


title: 1326_49_I7_CSP


title: KO_3a_2B16_MEFs_MethylSeq

value: Female


title: lckgfp_s206

value: tail


title: 1326_49_C1_DMSO

value: DMSO


title: 1326_49_I7_DMSO

value: F


title: 1326_49_C1_CSP


title: 1317_38_I7_PfRBC


title: lckgfp_s205


title: WT_A_2i_MEFs_MethylSeq


title: 1317_38_C1_uRBC

value: uRBC


title: lckgfp_s204


title: Macrophages exposed to cartilage fragments 3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

data_processing:
llumina HiSeq 2500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped by alignment to mice genome (mm10) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html). Low calculated fragments per kilobase of transcript per million mapped reads (FPKM) were removed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow

growth_protocol: Bone marrow cells (BMC) were isolated from the same mice sacrificed for cartilage fragments and added to Monocyte isolation kit BM (MACS; Miltenyi Biotec, Germany). Cells were then cultured in RPMI-1640 with 25 mg/l penicillin/streptomycin and 10% heat-inactivated fetal bovine serum (Sigma-Aldrich, St. Louis, USA) supplemented with 50 ng/ml mouse recombinant macrophage colony-stimulating factor (Mcsf; Peprotech, Rocky Hill, USA) for 7 days. Thereafter, differentiated macrophages were detached and seed onto 24-well-plates at 2×105 cells/well.

extract_protocol:
Differentiated macrophages cultured with or without cartilage fragments were lysed with TRIzol Reagent and harvested for RNA purification. RNA was purified using RNeasy Mini kit columns according to the manufacturer’s instructions, and integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer.
High-quality DNA-free RNA with integrity score > 9.0 was used to generate libraries using the TruSeq Stranded mRNA Sample Preparation Kit(Illumina, San Diego, USA) and their quality was examined by Bioanalyzer High sensitivity DNA kit (Agilent Technologies). The paired-end reads (100 bp) were further obtained by Illumina HiSeq 2500 (Illumina)

treatment_protocol: Cartilage fragments were resuspended in medium and added to macrophage cultures at ratio of 5:1 for cultivation period of 24 h.

tag: cell type

value: Bone marrow derived macrophage

tag: strain

value: Bone marrow

value: post natal day 28

tag: treatment

value: exposed to cartilage fragments


title: lckgfp_s203

tag: line

tag: devlopmental stage


title: Macrophages exposed to cartilage fragments 2


title: Macrophages exposed to cartilage fragments 1


title: Control macrophages 3

value: control


title: 1317_38_I7_uRBC

value: CPS

value: Nijmegen

value: protected


title: 1317_38_C1_PfRBC

value: PfRBC

value: adults

value: PBMC


title: 1317_38_I7_CSP

value: CSP


title: lckgfp_s201

value: 15 dpf


title: 1317_38_I7_DMSO


title: 1317_38_C1_CSP


title: 1317_38_C1_DMSO


title: lckgfp_s202

value: tail


title: 1316_66_I7_PfRBC


title: 1316_66_C1_uRBC


title: Control macrophages 1


title: 1284_26_C1_CSP

value: M


title: lckgfp_s200


title: lckgfp_s199


title: 1316_66_I7_uRBC

value: F


title: 1316_66_I7_CSP


title: 1316_66_C1_PfRBC


title: lckgfp_s198


title: 1316_66_I7_DMSO

value: DMSO


title: 1316_66_C1_DMSO


title: lckgfp_s197


title: Control macrophages 2

value: Bone marrow derived macrophage


title: lckgfp_s196


title: 2i-MEFs_WT_WGBS

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina) or Nextseq500 (75 bp or 86bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
Supplementary_files_format_and_content: ProcessedDataMatrixRPKM.txt:Tab-delimited text file includes RPKMs for each sample.

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: MEFs

tag: passage

value: F1 (129X1/SvJ and MSM/Ms)

tag: gender

value: Female

value: WGBS


title: Dnmt3a KO_Liver_methylseq

value: Liver

value: Male

tag: analysis method

value: Methylseq


title: 2i-MEFs_Dnmt3a KO_WGBS

source_name: 3a KO_2i-MEFs_WGBS


title: 1296_50_I7_uRBC

tag: stimulation

value: uRBC

tag: subjectid

value: CPS

value: Nijmegen

value: protected


title: lckgfp_s195

value: 15 dpf


title: 1316_66_C1_CSP

value: CSP

tag: vaccine

tag: site

value: adults

value: PBMC


title: 1296_50_I7_DMSO

value: DMSO

tag: age

tag: immunization dose

value: F


title: 1296_50_I7_CSP

tag: protection

tag: timepoint


title: 1296_50_C1_CSP

tag: Sex

tag: tissue


title: 1296_50_C1_DMSO


title: lckgfp_s194

value: tail


title: Dnmt3a KO_Heart_methylseq

value: Heart

tag: strain


title: Dnmt3a KO_Lung_methylseq

value: Lung


title: Dnmt3a KO_Limb_methylseq

value: Limb


title: lckgfp_s192


title: Dnmt3a KO_Brain_methylseq

value: Brain


title: lckgfp_s191


title: 1296_50_C1_uRBC


title: 2i-MEFs_Dnmt3b KO_methylseq

source_name: methylseq_3b MEF_methylseq

value: MEFs

value: F1 (129X1/SvJ and MSM/Ms)

value: Female


title: lckgfp_s190


title: 1296_50_C1_PfRBC

value: PfRBC

value: CPS


title: 1282_16_I7_PfRBC

value: Nijmegen

value: protected


title: 1282_16_I7_CSP

value: CSP


title: 1282_16_C1_uRBC

value: uRBC

value: adults


title: 1282_16_C1_PfRBC

value: PBMC


title: 1282_16_C1_DMSO

value: DMSO

value: F


title: 1269_46_I7_uRBC


title: 1282_16_C1_CSP


title: 2i-MEFs_Dnmt3a KO_methylseq

source_name: methylseq_3a MEF_methylseq

value: Methylseq


title: 1282_16_I7_uRBC


title: mRNA_ILC2_HDM_BAL2

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Reads were aligned using HISAT2 v2.0.4. (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
Sample scaling and statistical analysis were performed using the R package DESeq2 implementation in HOMER
Genome_build: mm10
Supplementary_files_format_and_content: RPKM expression values

source_name: bronchoalveolar lavage (BAL)

extract_protocol:
Murine ILC2s were obtained from Gata3-YFP/YFP (IL-33) or Gata3-YFP/WT mice (HDM) with airway inflammation. Cells were FACS-sorted using specific antibodies and YFP as described in detail in the manuscript.
RNA-Seq: Smart-seq2 library construction (as described in Picelli et al. Nature Methods (2013)

tag: cell type

value: FACS-purified lymphocytes

tag: population

value: chronic HDM (CD25Low)


title: lckgfp_s189

tag: line

value: tail

tag: devlopmental stage

value: 15 dpf


title: mRNA_ILC2_HDM_BAL1


title: lckgfp_s187


title: 1269_46_C1_DMSO


title: 1282_16_I7_DMSO


title: 1269_46_C1_PfRBC


title: 1269_46_I7_CSP


title: 1269_46_I7_DMSO


title: 1262_41_I7_uRBC


title: 1269_46_C1_CSP


title: mRNA_ILC2_IL33_BAL1

value: acute IL-33 (CD25High)


title: mRNA_ILC2_IL33_BAL2


title: lckgfp_s185


title: 1262_41_I7_PfRBC


title: lckgfp_s186


title: 1262_41_C1_uRBC


title: lckgfp_s184


title: 1296_50_I7_PfRBC


title: HUB-JP-037

city: Utrecht

first: Jens

last: Puschhof

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
Cells were sorted into a 384 well plate and processed for singel cell sequencing
EEC_atlas_raw.csv

data_processing:
Single cell data were demultiplexed, paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated, poisson corrected counts.

source_name: Human intestinal organoids

growth_protocol: Organoids were induced for Neurogenin 3 expression 5 days before sorting.

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Live cells  were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

tag: genotype

value: Neurogenin 3 overexpression

value: Intestine


title: 1262_41_C1_PfRBC

value: PfRBC

value: CPS


title: lckgfp_s183


title: 1262_41_C1_CSP

value: Nijmegen

value: protected


title: 1262_41_I7_CSP

value: CSP


title: 1262_41_C1_DMSO

value: adults


title: 1221_21_I7_uRBC

value: uRBC

value: PBMC


title: lckgfp_s182


title: HUB-JP-027


title: HUB-JP-035


title: HUB-JP-036


title: lckgfp_s180


title: HUB-JP-026


title: lckgfp_s181


title: HUB-JP-024


title: 1262_41_I7_DMSO

value: DMSO

value: F


title: lckgfp_s179


title: HUB-JP-022


title: lckgfp_s178


title: 1221_21_C1_PfRBC


title: 1221_21_C1_DMSO


title: 1221_21_C1_uRBC


title: 1221_21_I7_DMSO


title: 1209_11_C1_uRBC


title: 1209_11_I7_uRBC


title: 1221_21_C1_CSP


title: HUB-JB-033


title: 1209_11_I7_PfRBC


title: 1221_21_I7_PfRBC


title: 1221_21_I7_CSP


title: lckgfp_s177


title: lckgfp_s188


title: HUB-JB-032


title: 2i-MEFs_Dnmt3b KO_WGBS

source_name: 3b KO_2i-MEFs_WGBS

value: MEFs

tag: passage

value: F1 (129X1/SvJ and MSM/Ms)

tag: gender

value: Female

tag: analysis method

value: WGBS


title: lckgfp_s175

value: tail

value: 15 dpf


title: HUB-JB-027

value: Neurogenin 3 overexpression

value: Intestine


title: 1209_11_I7_CSP

source_name: Cultured PBMC

tag: stimulation

tag: subjectid

tag: vaccine

value: CPS


title: 1209_11_C1_DMSO

tag: site

value: Nijmegen

tag: age

tag: immunization dose


title: 1209_11_C1_PfRBC

value: PfRBC

tag: protection

value: protected

tag: timepoint

tag: Sex


title: HUB-JB-026

tag: tissue


title: 1173_13_I7_uRBC

value: adults

value: malaria


title: lckgfp_s174


title: 1209_11_C1_CSP

value: CSP

value: PBMC


title: HUB-JB-025


title: HUB-JB-024


title: 1209_11_I7_DMSO

value: DMSO

value: F


title: lckgfp_s172


title: lckgfp_s176


title: 1173_13_C1_uRBC

value: uRBC


title: lckgfp_s193


title: A549, infected with H7N9-2

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

country: China

institute: Zijingang Campus of Zhejiang University

description: control

data_processing:
Poly-N, adapter and low-quality were removed by Trim_Galore version 0.4.5 ，Quality control analysis was performed by Fast QC version 0.11.5
Clean reads were aligned to the Homo_sapiens.GRCh38.90 genome using STAR version 2.5.2b with the following configurations two passMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 24 --outSAMtype SAM --outSAMstrandField intronMotif.
LncRNAs were identified using four predicted tools including predictor of lncRNAs and mRNAs based on k-mer scheme (PLEK version1.2), Coding-Non-Coding-Index (CNCI version 2) and Coding Potential Calculator (CPC2-beta) ，Coding Potential Assessment Tool (CPAT version 1.2.2)
StringTie version 1.3.1c was used to calculate the FPKMs of both lncRNAs and mRNAs in each sample
Homo_sapiens.GRCh38.90
Supplementary_files_format_and_content: FPKMs

source_name: human lung epithelial cells

extract_protocol:
Total RNA was isolated from infected cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
RNA-seq was performed using an Illumina Hiseq 3000 (Illumina, United States) to get the raw data (raw reads). With the reads containing poly-N, adapter and low-quality being removed, clean data (clean reads) were obtained and the paired-end reads were aligned to human reference genome (version: Homo_sapiens.GRCh38)  . LncRNAs were identified using four predicted tools including predictor of lncRNAs and mRNAs based on k-mer scheme (PLEK) (Li et al., 2014), Coding-Non-Coding-Index (CNCI) (Sun et al., 2013) and Coding Potential Calculator (CPC) (Kong et al., 2007)，Coding Potential Assessment Tool (CPAT)(Wang L. et al., 2013). StringTie was used to calculate the FPKMs (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of both lncRNAs and mRNAs in each sample. RNA-seq and data analysis was completed by ShangHai Genergy Biotech (Shanghai, China)

treatment_protocol: A549 cells were infected with H3N2, and H7N9 at a multiplicity of infection (MOI) of 10 and harvested at 24 hour post infection or without, respectively.

tag: cell line

tag: infection

value: infected with H7N9

tag: strain


title: HUB-JB-022

tag: genotype


title: lckgfp_s171

tag: line

tag: devlopmental stage


title: lckgfp_s170


title: HUB-JB-020


title: lckgfp_s173


title: HUB-JB-023


title: lckgfp_s169


title: HUB-JB-019


title: A549, infected with H7N9-1

description: control


title: 1173_13_C1_PfRBC


title: lckgfp_s168


title: 1173_13_C1_DMSO


title: HUB-JB-018


title: 1173_13_I7_DMSO


title: 1173_13_C1_CSP


title: A549, infected with H3N2-1

description: infected at MOI=10 and harvested at 24 hour post infection

value: infected with H3N2


title: 1167_03_I7_uRBC


title: 1173_13_I7_CSP


title: 1167_03_I7_PfRBC


title: lckgfp_s167

value: tail


title: 1173_13_I7_PfRBC


title: 1167_03_C1_PfRBC


title: 1167_03_C1_uRBC


title: A549, uninfected-2

value: uninfected


title: HUB-JB-017

value: Neurogenin 3 overexpression


title: HUB-JB-003

value: Intestine


title: lckgfp_s166

value: 15 dpf


title: A549, uninfected-1


title: A549, infected with H3N2-2


title: lckgfp_s165


title: A88

city: Cambridge

first: Kathleen

middle: Marie

last: Smith

state: MA

address: 200 Sidney Street

department: Systems Computational Biology

institute: AbbVie

description:
Normal
processed data file: TPM93.Bissonnette.csv

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality.
Kallsito
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM93.Bissonnette.csv: Comma-separated text file includes TPM values.

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit.
RNA was depleted of ribosomal RNA using the Ribo-Zero method (Illumina) and libraries prepared.

tag: subject id

tag: cohort

value: Skin

tag: response

tag: batch


title: HUB-JB-002


title: A86


title: A85


title: HUB-JB-001


title: A84


title: lckgfp_s162


title: A83


title: lckgfp_s161


title: lckgfp_s163


title: lckgfp_s164


title: lckgfp_s160


title: A82


title: A78

description:
Untreated_Les
processed data file: TPM93.Bissonnette.csv


title: A77

description:
NonLes
processed data file: TPM93.Bissonnette.csv


title: A76


title: A75


title: 1269_46_C1_uRBC

tag: stimulation

tag: subjectid

tag: vaccine

value: CPS

tag: site

value: Nijmegen


title: 1167_03_C1_DMSO

tag: age

value: adults

tag: immunization dose

tag: protection

tag: timepoint


title: 1269_46_I7_PfRBC

value: PfRBC

value: protected

tag: Sex

tag: tissue


title: lckgfp_s159


title: lckgfp_s157


title: lckgfp_s158


title: lckgfp_s156


title: lckgfp_s155


title: iPSdiff_1_S18

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

data_processing:
Raw reads were demultiplexed using bar code processing and aligned to the the human reference transcriptome (GRCH38) using STAR (version 2.5.1). Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 1.3.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
A total of 1705 and 1502 cells were selected respectively from each replicate post quality control filtering for further analysis.
Genome_build: GRCH38
Supplementary_files_format_and_content: h5

source_name: human iPSC-derived pulmonary neuroendocrine cells

growth_protocol: Human fibroblast-derived iPSCs were used. Briefly, differentiation to lung epithelium was carried out using Notch pathway inhibitor as previously described (Firth et al., 2014). After 91 days of differentiation iPSCs were dissociated to a single-cell suspension using Accutase (Stemcell Technologies, 7920) and used for RNA isolation and sequencing.

extract_protocol:
Day 91 differentiation cultures were dissociated for 30 mins at 37oC using Accutase (Stemcell Technologies, 7920) to obtain single-cell suspensions. Cells were stained with DAPI and sorted for live single cells followed by library preparation.
Single-cell RNA-seq libraries were prepared per the Single Cell3'  v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). After RT, GEMs were harvested and the cDNAs were amplified, cleaned up with SPRIselect Reagent Kit.  Indexed sequencing libraries were constructed using Chromium Single-Cell 3' Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA)  to obtain a sequencing depth of 200K~250K reads per sample.

tag: cell type

value: reprogrammed iPSCs


title: iPSdiff_2_S24


title: iPSdiff_2_S23


title: iPSdiff_2_S22


title: iPSdiff_2_S21


title: iPSdiff_1_S19


title: iPSdiff_1_S17


title: iPSdiff_1_S20


title: B20


title: MLN positive cells

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts.

source_name: MLN reporter organoids

extract_protocol:
RNeasy RNA extraction kit (Qiagen)
RNA was processed using the previously described CEL-seq2 technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Live cells  were sorted in Eppendorf tubes filled with 350 ul RLT reagent (Qiagen).

tag: genotype

tag: sorted cells

value: MLN positive


title: 1167_03_I7_CSP

value: CSP

value: malaria

value: F

value: PBMC


title: 1162_24_I7_uRBC

value: uRBC


title: 1162_24_C1_uRBC


title: lckgfp_s154

tag: line

value: tail

tag: devlopmental stage


title: B19

tag: subject id

tag: cohort

tag: response


title: lckgfp_s153


title: GCG positive cells

source_name: GCG reporter organoids

value: Neurogenin 3 overexpression

value: GCG positive


title: 1162_24_C1_CSP

tag: stimulation

tag: subjectid


title: 1162_24_I7_DMSO

value: DMSO

tag: vaccine

tag: site


title: 1162_24_C1_PfRBC

tag: age

tag: immunization dose


title: lckgfp_s152

value: 15 dpf


title: CHGA negative cells

source_name: CHGA reporter organoids

value: Intestine

value: CHGA negativity


title: 1162_24_C1_DMSO

value: CPS

value: Nijmegen

value: adults

tag: protection

tag: timepoint


title: lckgfp_s151

source_name: Danio rerio tail

tag: tissue


title: B17

value: Skin

tag: batch


title: B12

description:
SEC_Les
processed data file: TPM93.Bissonnette.csv

value: Inadequate responder


title: Neurogenin 3 positive cells

tag: genotype

value: Neurogenin 3 positive


title: B18


title: CHGA positive cells

tag: sorted cells

value: CHGA positive


title: 1167_03_I7_DMSO

value: malaria

tag: Sex

value: F


title: 1150_02_I7_uRBC

value: uRBC

value: protected

value: PBMC


title: 1167_03_C1_CSP

value: CSP


title: 1162_24_I7_PfRBC

value: PfRBC


title: 1162_24_I7_CSP


title: 1150_02_C1_uRBC


title: lckgfp_s150

tag: line

value: tail

tag: devlopmental stage

value: 15 dpf


title: B11

tag: subject id

tag: cohort


title: Tph1 positive cells

source_name: Tph1 reporter organoids

value: Neurogenin 3 overexpression

value: Intestine

value: Tph1 positive


title: lckgfp_s149


title: lckgfp_s148


title: WM7_R848

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating rLog transformed data.
Genome_build: GRCh38.p12 (Gencode release 28)
Supplementary_files_format_and_content: text file with DESeq2 rLog transformed data

source_name: Bone marrow aspirate

growth_protocol: culture conditions: Freshly isolated B-cells were cultured in 24- or 96-well plates at 2.5 × 105 cells/ml in IMDM + 10% heat-inactivated fetal bovine serum (HIFBS) (Invitrogen) with the addition of hIL-2 (20 U/ml), hIL-21 (50 ng/ml) and F(ab′)2 goat anti-human IgM and IgG (10 μg/ml) and Lipid Mixture 1, chemically defined (Sigma) and MEM amino acids solution (both at a final concentration of 1x). B-cells were stimulated with gamma-irradiated CD40L-expressing L cells (1 × 106/plate). Subsequent culture followed the protocol detailed in Cocco et al. 2012.18 Cells were harvested at day 6 of the culture which is equivalent to the plasmablast stage of differentiation.

extract_protocol:
isolation protocol: B-cells isolated by density centrifugation followed by negative selection with a memory B-cell isolation kit (Miltenyi) and subsequently depletion with CD3 and CD56 microbeads (Miltenyi). Alternatively, following density centrifugation, peripheral blood mononuclear cells (PBMCs) or bone marrow MNCs were initially depleted of cells expressing CD3 or CD56 with microbeads and then B-cells were positively selected with CD20 microbeads.
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).
RNA samples were quantified with a Qubit HS RNA assay kit (Thermo Fisher Scientific) and the quality was assessed by RNA HS assay using the TapeStation system (Agilent). Sequencing libraries were generated by using a TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina) according to the manufacturer’s protocol. Library performance was checked on the TapeStation followed by picogreen quantification. Equimolar pooling was performed across all the libraries and the final pool was sequenced on a NextSeq 500 platform (Illumina) using 76-bp single-end sequencing.

value: Bone marrow aspirate

tag: cell type

value: Plasmablast

tag: diagnosis

value: WM


title: WM6_R848


title: B9

value: Skin

tag: response

value: Inadequate responder


title: lckgfp_s146


title: B8


title: B7


title: lckgfp_s147


title: lckgfp_s145


title: B6

value: Responder


title: WM11_R848


title: WM15_R848


title: 1150_02_I7_PfRBC

tag: stimulation

tag: subjectid

tag: vaccine

value: CPS

tag: site

value: Nijmegen

value: adults

value: F


title: 1150_02_I7_DMSO

value: DMSO

tag: age

tag: immunization dose

tag: protection

value: protected

tag: timepoint

value: PBMC


title: 1150_02_C1_PfRBC

value: PfRBC

tag: tissue


title: lckgfp_s144

value: tail

value: 15 dpf


title: Healthy 3_R848

source_name: Peripheral blood

value: Peripheral blood

value: Healthy


title: B5

tag: batch


title: 1150_02_I7_CSP

value: CSP

tag: Sex


title: Healthy 2_R848

value: Plasmablast


title: Col-0 shoots, biological replicate 3

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS36 shoots Col-0

hyb_protocol: Labelled samples were hybridized to the Arabidopsis Gene 1.1. ST array Strips (Aﬀymetrix, Santa Clara, CA).

scan_protocol: Microarrays were scanned with Aﬀymetrix GeneAtlas System and saved to CEL ﬁles.

data_processing: The CEL ﬁles were analyzed by Transcriptome Analysis Console (TAC) Software (version 4.0.1, Applied Biosystems) following manufacturer's specifications. Microarrays were normalized and summarized using RMA method (Robust Multiarray Averaging), followed by Anova (ebayes) method to investigate differential expression among different treatment. The obserbved p-values were corrected by Benjamin-Hochberg procedure. Genome version: tair10; annotation version: AraGene-1_1-st-v1.na36.tair10.transcript.csv.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis ecotype Col-0, shoots

label_protocol: Samples containing 100 ng total RNA were reverse transcribed using the Ambion® WT Expression Kit and labelled with the Affymetrix GeneChip® WT Terminal Labelling Kit (ThermoScientific), according to the manufacturers’ protocols.

growth_protocol: Seeds were dry sterilised and placed on the solid medium with 0.8% Agargel (Sigma-Aldrich). Plants were grown in Araponic boxes (16 plants/box) kept in short day conditions (22 °C 8h day/18 °C 16h night) for about 4 weeks, with weekly changes of 0.5 x Hoagland medium. Individual plants were divided into shoot and root tissue and frozen in liquid nitrogen.

extract_protocol: Portions of plant material, drawn from at least 3 plants, were homogenised in TRI Reagent (Molecular Research Centre), and genomic DNA was removed with a RapidOut DNA removal kit (ThermoScientific). The quality, integrity and the concentration of RNA were evaluated using a Bioanalyzer 2100 (Agilent Technologies) and a Nano Drop ND-100 spectrophotometer.

tag: genotype/variation

value: Col-0 wild type

value: shoots

value: 4 weeks-old


title: 1150_02_C1_DMSO

data_processing: R/bioconductor

extract_protocol: Total RNA was extracted from cell pellets after RNAlater removal by centrifugation, using RNeasy Mini kits (Qiagen), either manually (batches of 24 samples) or using a QIAcube sample preparation workstation according to the manufacturer’s recommendations (batches of 12 samples). RNA concentration and quality were determined on a Nanodrop spectrophotometer (Thermo Scientific) in all samples and RNA integrity was assessed using a 2100 Bioanalyzer (Agilent) in 90% of CPS samples and 20% of the RTS,S samples.

value: CPS


title: 1150_02_C1_CSP

value: Nijmegen


title: B10

tag: subject id

value: Skin

value: Inadequate responder


title: lckgfp_s143

tag: line

tag: devlopmental stage


title: B4

description:
UST_Les
processed data file: TPM93.Bissonnette.csv

tag: cohort

value: Responder


title: B3

tag: response


title: Col-0 shoots, biological replicate 2

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS35 shoots Col-0


title: lckgfp_s141


title: lckgfp_s142


title: B2


title: WM6_CD40L

value: Bone marrow aspirate

tag: cell type

tag: diagnosis

value: WM


title: B1


title: Healthy 1_R848


title: KO3 shoots, biological replicate 3

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS33 shoots KO3

source_name: Arabidopsis KO3 line, NBR1 deletion, shoots

value: NBR1 deletion


title: WM5_CD40L


title: B16

description:
ADA_Les
processed data file: TPM93.Bissonnette.csv


title: WM4_CD40L


title: KO3 shoots, biological replicate 2

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS32 shoots KO3


title: lckgfp_s138

value: tail


title: B15


title: lckgfp_s137

value: 15 dpf


title: B14


title: Healthy 3_CD40L

value: Peripheral blood


title: KO1 shoots, biological replicate 3

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS30 shoots KO1

source_name: Arabidopsis KO1 line, NBR1 deletion, shoots


title: Healthy 2_CD40L

value: Healthy


title: Col-0 shoots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS34 shoots Col-0


title: KO3 shoots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS31 shoots KO3


title: WM7_CD40L


title: Col-0 roots, biological replicate 3

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS27 roots Col-0

source_name: Arabidopsis ecotype Col-0, roots

value: roots


title: KO3 roots, biological replicate 3

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS24 roots KO3

source_name: Arabidopsis KO3 line, NBR1 deletion, roots


title: lckgfp_s140


title: lckgfp_s136


title: B13


title: KO1 shoots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS28 shoots KO1


title: lckgfp_s139


title: 90


title: Healthy 1_CD40L

value: Plasmablast


title: lckgfp_s135


title: lckgfp_s134


title: Standard, Human RUES2 Genomic DNA

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

description:
2 replicates
PCR Amplicon

data_processing:
Library strategy: Amplicon sequencing
Per-cycle basecall (BCL) were converted to per-read FASTQ files using bcl2fastq version 2.20.0.422 using default parameters.
Forward and reverse barcode attachment sites were trimmed using cutadapt version 1.16.
Forward and reverse read-pairs were merged using vsearch fastq_mergepairs and the merged reads with greater than one expected error were filter out.
Merged reads were then classified as either human or mouse using vsearch –usearch_global with the percent identity cutoff set at 99%.
The reference sequence used for human 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCTTCGCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCTCTCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCTTTGGTGACTCTAGA and the reference sequence used for mouse 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTGGTGACTCTAGA.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: An Excel file containing the number of reads mapped to human 18S or mouse 18S in each sample.

source_name: From RUES2 hESCs cultured with matrigel/mTeSR1

growth_protocol: Naïve hPSCs were maintained on mitomycin C-treated mouse embryonic fibroblast (MEF) feeders (5-6 × 104/cm2) in 2iLI medium (50% glucose-free DMEM/F12 and 50% glucose-free Neurobasal, 5 mM glucose, 1 mM glutamine, 1% NEAA, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 100 ug/ml streptomycin, 5 mg/mL bovine serum albumin to maintain osmolarity, 20 ng/mL recombinant human LIF, 18 µg/ml human insulin, 1 μM PD0325901, and 3 μM CHIR99021). Naïve hPSCs were passaged every 3 days with TrypLE. All naïve hPSCs were cultured in 5% O2 and 5% CO2.

extract_protocol:
Mouse embryos or human cells were homogenized in proteinase K solution (100 mM Tris-HCl pH8.0, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 250µg/ml Proteinase K) and incubated in the same solution at 55°C for 12-18 hours. Pheno/chloroform extraction was then used to extract genomic DNA.  The V3 regions of both human and mouse 18S ribosome genes were amplified from standard  samples or genomic DNA extracted from chimera using human/mouse universal primers containing barcode attachment sites on the 5’ ends (Forward: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCTAATACATGCCGACGGG; Reverse: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTAGAGTCACCAAAGCCGC; barcode attachment sites were underlined) and Hotstar plus kit (Qiagen) with an optimized PCR protocol (95°C, 5min; 94°C, 30s; 58°C, 30s; 72°C, 1min; 40 cycles; 72°C, 10min). PCR product from each sample was gel-extracted and purified with QIAquick Gel Extraction Kit (Qiagen)
Purified PCR products were barcoded and library prepared using PE150 kit (illumina)

treatment_protocol: Naive human PSCs were dissociated to single cells with TrypLE for 5-6 minutes and placed on 10 cm dishes for 45 minutes to remove MEF cells through attachment. The supernatant, which contained the hPSCs, was removed from the dish and centrifuged for 10 min at 2000 rpm. Cells in the pellet were resuspended in Mouse Blastocysts Injection Buffer (HEPES-buffered DMEM with 5% FBS). 10-12 naive hPSCs were injected to a C57BL/6J mouse blastocyst, which was obtained by superovulation from 3-4 week old C57BL/6J female mice. Injected blastocysts were transferred bilaterally to uterus of pseudopregnant CD-1 female mice at 7-9 weeks of age, with 14-18 blastocysts transferred per mouse. At Day 17.5, mouse embryos were retrieved and half of each mouse embryo cut sagittally were used in DNA extraction.

tag: sample type

value: Standard Sample


title: KO1 shoots, biological replicate 2

description:
Gene expression data from Arabidopsis thaliana shoots, 4 weeks old
AS29 shoots KO1

value: shoots


title: KO3 roots, biological replicate 2

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS23 roots KO3

value: 4 weeks-old


title: 89

description:
Normal
processed data file: TPM93.Bissonnette.csv


title: 88


title: 87


title: lckgfp_s132


title: lckgfp_s131


title: lckgfp_s130


title: lckgfp_s129


title: lckgfp_s128


title: KO3 roots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS22 roots KO3


title: Col-0 roots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS25 roots Col-0

value: Col-0 wild type


title: 83


title: lckgfp_s127


title: 85


title: 82


title: lckgfp_s126


title: 84


title: 81


title: lckgfp_s133


title: KO1 roots, biological replicate 3

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS21 roots KO1

source_name: Arabidopsis KO1 line, NBR1 deletion, roots


title: KO1 roots, biological replicate 2

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS20 roots KO1


title: KO1 roots, biological replicate 1

description:
Gene expression data from Arabidopsis thaliana roots, 4 weeks old
AS19 roots KO1


title: 86


title: Tbet_KO_bulkRNAseq_global

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

description: Tbet_RNAseq_count (Global KO).csv

data_processing:
For scRNAseq, raw Illumina sequencing data was demultiplexed and fastq files were generated using 10X Genomics Cellranger mkfastq v1.3.1
Fastq files were aligned to the mm10 genome and unique UMI sums per gene were calculated using 10X Genomics Cellranger count v1.3.1
For bulkRNAseq, fastq sequence data were pseudo-aligned and quantified using Salmon v0.12 48, with an index built on the mm10 reference transcriptome
Following pseudo-alignment, tximport and DESeq2 were used to analyze the differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: For scRNAseq, the three files per sample are 10X cellranger count output from non-empty droplets.  Valid cell barcodes and analyzed genes are present as tab-delimited files.  Unique UMI sums per gene per cell are recorded in market exchange format. For bulkRNAseq, the normalized gene count were summaried in excel file.

source_name: Bone marrow

extract_protocol:
For scRNAseq, cells were washed once with ice-cold PBS containing 10% FBS post-sorting and counted using hemocytometer. After that, the cells were loaded to 10X chromium machine (10X Genomics, Pleasanton, CA) and run through the library preparation procedures following guidance from the Chromium Single Cell 3’ Reagent Kits v2; For bulkRNAseq, after sorting, cells were lysed in Trizol. Bulk RNA was extracted and subject to library preparation using NEBNext® Ultra™ RNA Library Prep Kit.
scRNA libraries were prepared for sequencing using the guidance from the 10X Chromium Single Cell 3’ Reagent Kits v2; BulkRNAseq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit

value: NK cells

tag: sorting population


title: B6_WT_scRNAseq


title: Tbet_WT_bulkRNAseq_chimera

description: Tbet_RNAseq_count (Chimera).xlsx


title: Rictor_FoxO1_cDKO_scRNAseq


title: Tbet_KO_bulkRNAseq_chimera

description: Tbet_RNAseq_count (Chimera).xlsx


title: Tbet_WT_bulkRNAseq_global

description: Tbet_RNAseq_count (Global KO).csv


title: Raptor_cKO_scRNAseq


title: Rictor_cSKO_scRNAseq


title: 80

description:
Untreated_Les
processed data file: TPM93.Bissonnette.csv

source_name: Skin biopsy

value: Skin


title: Raptor_WT_scRNAseq


title: lckgfp_s124


title: 79

description:
NonLes
processed data file: TPM93.Bissonnette.csv


title: lckgfp_s123


title: Tbet_KO_scRNAseq


title: 78


title: lckgfp_s122


title: Rictor_cKO_scRNAseq


title: WBRT-MG (single cell RNA-Seq)

city: Freiburg

first: Michael

last: Schulz

address: Breisacher Straße 64

department: Institute for Neuropathology

country: Germany

institute: University Hospital Freiburg

data_processing:
R1 read: contains 8bp barcodes + 6 bp UMI + polyT
R2 read: contains the RNA sequence.
data generation and processing were performed according to Muraro et al., 2016
Data were analyzed with RaceID2 (Herman et al., 2018): FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Nature Methods 5(5): 379-386
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: .csv processed data file contains annotated gene IDs and all cells per plate.  Barcode details are in cel-seq2_barcodes.xls which is linked at the foot of the Series record.

source_name: mouse brain

extract_protocol:
Myeloid cells from tumor-bearing mice brain were FACS purified into 384 precaptured well plates, centrifuged and snap frozen on dry ice. Furtehr processing was performed by SingleCellDiscoveries (NL) according to description in Muraro et al. (2016; A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems. 3: 385 – 394.)
RNA libraries of single cells were prepared for sequencing using standard protocols

tag: strain

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)

value: microglia

tag: tumor stage

value: not stratified

tag: whole brain radiation therapy (wbrt)

value: d3/5x2 Gy


title: 77


title: lckgfp_s121

data_processing:
STAR (2.5)
Htseq (0.8.0) htseq-count -m intersection-nonempty --nonunique all
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw counts of numbers of reads aligned to each feature for each cell, in tab-separated format (lckgfp_counts.txt)

extract_protocol:
Lysis was performed as described in Schaum et al., Nature 2018
A Smart-Seq2 based protocol was used for reverse transcription and cDNA amplification, and a Nextera based protocol was used for library preparation, as described in Schaum et al., Nature 2018


title: lckgfp_s125


title: 76


title: Rictor_WT_scRNAseq


title: noWBRT-MG (single cell RNA-Seq)

value: small


title: WBRT-BMDM (single cell RNA-Seq)

value: BMDM


title: lckgfp_s119

value: tail

value: 15 dpf


title: 75


title: noWBRT-BMDM (single cell RNA-Seq)


title: lckgfp_s117


title: lckgfp_s118


title: MacTRAP_ub3

city: Marburg

first: Andreas

last: Hofmeister

state: Hessen

address: Baldingerstrasse 1

department: Zentrum für Innere Medizin

institute: Philipps-Universität Marburg

data_processing:
Basecalling was performed with RTA 1.18.64. Bcl conversion into Fastq were performed using bcl2fastq version 2.19.0.316. Illumina Sequencing kit V4 and Illumina HCS 2.2.58 Sequencing software was used for RNA-Seq.
The RNA-Seq. data were mapped against the mouse reference genome GRCm38 using Hisat2. The obtained SAM files were converted to BAM files using SAMtools "sort" command and subsequently made compatible for usage of the ".gtf" file of ENSEMBL (ftp://ftp.ensembl.org/pub/release-89/gff3/mus_musculus/). The resulting files were analyzed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: .txt

source_name: kidney macrophages

extract_protocol:
Grgic protocol: TRAP, modified (Based on published protocol: M Heiman, Cell 2008, 135 (4):738-48.)
RNA libraries were prepared at DKFZ Heidelberg according to SmarTer ultra low input protocol for RNA-sequencing using Illumina HiSeq2000 platform.

tag: age

value: 9 weeks

tag: immunopreciptate

value: unbound


title: MacTRAP_b1

value: bound


title: MacTRAP_b3


title: 74

tag: tissue

tag: batch


title: lckgfp_s116


title: 73


title: 71