title: ChiP-seq with HA-Upc2A G898D tag present + Fluconazole Challenge [MF-2]

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

data_processing:
Reads were mapped using Bowtie software and peaks assigned using MACS.  WIG output from MACS was visualized using IGV software.
Genome_build: s02-m07-r33 from Candida Genome Database on 2019 Feb 3
Supplementary_files_format_and_content: Wig files showing sequencing depth across the genome.

organism: Nakaseomyces glabratus CBS 138

growth_protocol: Overnight cultures were inoculated at 0.1 OD/ml in fresh YPD and allowed to grow to 0.4-0.5 OD/ml. Cells were treated with Fluconazole 20 µg/ml or ethanol for 2 hours.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma-Aldrich) for 15 min at room temperature with mild shaking [120-150 rpm]. The fixing reaction was stopped with 250 mM glycine (RPI) for 15 min at room temperature with mild shaking [120-150 rpm]. Cells were centrifuged and washed once with PBS. The cell pellet was resuspended in lysis buffer [50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, 1x protease inhibitor cocktail (Roche Applied Science, Penzberg, Germany). Cells were then lysed with 1 ml glass beads (Scientific Industries Inc, Bohemia, NY) at 4oC for 10 min. Both cell lysate and debris were collected and subsequently transferred to an AFA fiber pre-slit snap-cap [6 x 15mm] microtube (Covaris, Woburn, MA) for additional cellular lysis and DNA shearing.
Genomic DNA was sheared with E220 focused-ultrasonicator (Covaris) [peak incident power: 75 W, duty factor: 10%, cycles per burst: 200, treatment time: 16 min, temperature: 10oC max, sample volume: 130 µl.] The sheared sample was centrifuged and the clear lysate was collected. Upc2A was immunoprecipitated with Dyna beads-protein G magnetic beads (Invitrogen, Carlsbad, CA) and anti-HA antibody (Invitrogen) [1:50 dilution] overnight at 4oC. Beads were then washed twice with lysis buffer, once with lysis buffer+ 500mM NaCl, once with LiCl buffer [10 mM Tris pH 8, 250 mM LiCl, 0.5% P-40, 0.5% Sodiumdeoxycholate, and 1 mM EDTA], and once with Tris-EDTA buffer. Beads were resuspended in TE and treated with RNAse A (Thermo Fisher Scientific) at 37oC for 30 min. Beads were then washed once with Tris-EDTA buffer, resuspended in Tris-EDTA buffer with 1% SDS, and incubate at 65oC for at least 5 hours to reverse crosslink. Eluted DNA was subsequently purified with mini elite clean-up kit (Qiagen). Qubit fluorometric assay (Thermo Fisher Scientific) was used to analyze the yield quantity and Agilent Bioanalyzer (Agilent Technology, Santa Clara, CA) was used to determine the average sheared DNA size.
All ChIPed DNA libraries were generated with Accel-NGS plus DNA library kit (Swift Biosciences, Ann Arbor, MI) according to the manufacturer’s instructions.

tag: strain

tag: genotype/treatment

tag: chip antibody

value: Anti-HA


title: NHP_6_Hoti_Day1

status: Public on Sep 23 2021

type: RNA

city: Frederick

first: Catherine

middle: E

last: Arnold

state: MD

address: 1425 Porter St

department: Diagnostic Systems Division

country: USA

institute: US Army Medical Research Institute of Infectious Diseases

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample11_11

hyb_protocol: Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. Eight microliters of this master mixture was then incubated in separate tubes containing 50 ng of extracted host RNA and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 17 hours followed by 4°C until the samples were placed on NanoString Sprint Profiler analysis system.

data_processing: Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.

molecule: total RNA

organism: Macaca fascicularis

source_name: whole blood

extract_protocol: All whole blood samples were initially diluted 1:1 with purified molecular grade water prior to being vigorously mixed with a 3:1 ratio of TRIzol LS (ThermoFisher Scientific). All TRIzol LS mixtures and residual matrices were then frozen at -80°C until subsequent extraction and/or analysis. RNA for NanoString analysis was manually extracted using the miRNeasy kit (Qiagen) following manufacturer’s instructions with the modification that the initial TRIzol-LS/water/whole blood mixture was placed in a Phasemaker phase separation tube (ThermoFisher Scientific) prior to being centrifuged at 12,000 x g for 15 min at room temperature. The top aqueous layer was then transferred into a miRNeasy kit column.

treatment_protocol: Cynomolgus macaques were intravenously challenged with a target dose of 6 log10 plaque forming units of virus (either Kosava Hoti or Afghan09-2990).  Whole blood was collected on days 0, 1-7, 9, 12, 14, 21, and 28.

tag: virus

value: Kosava Hoti

tag: nhp no.

tag: tb status

value: No

tag: day post challenge

tag: tissue

value: whole blood


title: blood sample from donor 2134 3 days post vaccination [VIC008818]

type: SRA

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

description: processed data file: RV306_V5B_norm_expr.txt

library_source: transcriptomic

data_processing:
Libraries were sequenced and bases called with Illumina NovaSeq control software v1.4.0 and RTA v3.3.3
FASTQ files were generated from BCL files with Illumina bcl2fastq v2.20.0.422
fastp v0.19.7 was used to trim low-quality bases from both ends of each read with parameters --cut_front --cut_right --cut_mean_quality 20 --cut_window_size 15 --length_required 50
Trimmed reads were aligned to the human genome (GRCh38 build 92) using HISAT2 v2.1.0
Gene counts were generated from alignments using HTSeq (v0.9.1) with parameters -s yes -a 2 -t exon
Counts were filtered for protein coding genes and edgeR v3.28.0 was used to remove low-expressed genes and normalize counts with Trimmed mean of M-values (TMM) normalization method
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood_3 days after 4th immunization

extract_protocol:
Total RNA was extracted from whole blood collected in PAXgene Blood RNA tubes (cat# 762165) using Qiagen PAXgene Blood RNA kits (cat# 762164) and subjected to the ThermoFisher GlobinClear kit (cat# AM1980). cDNA was generated from 10 ng of RNA using the Takara Bio SMART-Seq v4 UltraLow Input RNA Prep kit (cat# 634891) per manufacturer’s suggestions, with control RNA spiked-in (Life Technologies ERCC Mix 1 cat# 4456740).
Sequencing libraries were generated using the Illumina Nextera XT DNA Sample Prep kit (cat# FC-131-1096) according to manufacturer's instructions and sequenced on Illumina NovaSeq 6000 with S2 Reagent Kit, 300 cycles (cat# 20012860)

tag: pid

value: high

tag: timepoint

value: 3 days after 4th immunization

tag: visit


title: NHP_6_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample09_09


title: NHP_1_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample07_07

value: Yes


title: ChiP-seq with HA-Upc2A tag present + Fluconazole Challenge [WTF-2]

library_source: genomic

molecule: genomic DNA


title: blood sample from donor 2106 3 days post vaccination [VIC008815]


title: NHP_8_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample10_10


title: Tachyzoite - 1

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

country: France

institute: CNRS

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Datasets were aligned with HiSAT2 v2.1.0  against the T. gondii ME49 genome from (ToxoDB-39)  and to the rat genome (Rattus norvegicus Rn6 (UCSC)). Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.

organism: Toxoplasma gondii

source_name: Purified T. gondii 76K tachyzoites grown in HFF cells

growth_protocol: Intracellular parasite were grown for 1, 2, 4, 7 and 14 days

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

value: Tachyzoite


title: Monocyte_25-V2

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.33.
Reads that passed the trimming step were aligned to human genome (Ensembl GRCh38 release 80) using the STAR aligner (version 2.4.2a).
Aligned reads were counted using HTSeq (version 0.6.1).
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

source_name: Blood Monocytes

extract_protocol:
RNA was extracted from sorted cells from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.
Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Next, libraries were validated by electrophoresis, quantified, pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq (2000/4000) using 2 x 75 base paired-end runs.

tag: cell type

value: Blood Monocytes

tag: participant id

tag: visit id

value: pre-vaccination

tag: treatment

value: Vaccine

tag: hiv-1 acquisition


title: ChiP-seq with HA-Upc2A G898D tag present [M-2]

value: HA-Upc2A G898D tag present


title: Monocyte_25-V7

value: month 7


title: blood sample from donor 2109 3 days post vaccination [VIC008816]


title: NHP_8_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample08_08


title: Monocyte_21-V2


title: blood sample from donor 1033 2 weeks post vaccination [VIC008824]

description: processed data file: RV306_V6_norm_expr.txt

source_name: whole blood_2 weeks after 4th immunization

value: low

value: 2 weeks after 4th immunization


title: ChiP-seq with HA-Upc2A tag present [WT-2]

source_name: ChiP-seq with HA-Upc2A tag present

value: HA-Upc2A tag present


title: ChIP-seq with no HA tag present [C-2]

source_name: ChIP-seq with no HA tag present

value: no HA tag present


title: Monocyte_19-V7


title: NHP_11_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample05_05


title: blood sample from donor 2098 3 days post vaccination [VIC008811]


title: NHP_8_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample06_06


title: Monocyte_21-V9

value: month 12


title: ChiP-seq with HA-Upc2A G898D tag present [M-1]

value: Anti-HA


title: Monocyte_19-V2


title: ChiP-seq with HA-Upc2A tag present + Fluconazole Challenge [WTF-1]


title: blood sample from donor 2099 3 days post vaccination [VIC008812]


title: NHP_7_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample03_03


title: NHP_4_Hoti_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample02_02

value: Kosava Hoti

value: No


title: Monocyte_21-V7


title: Monocyte_19-V9


title: NHP_3_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample01_01

value: whole blood


title: NHP_3_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200109_30102365920321-01_Sample09_09


title: Monocyte_18-V7


title: ChiP-seq with HA-Upc2A G898D tag present + Fluconazole Challenge [MF-1]


title: blood sample from donor 2074 3 days post vaccination [VIC008810]

value: high

value: 3 days after 4th immunization


title: Monocyte_18-V2

value: Yes


title: blood sample from donor 1125 3 days post vaccination [VIC008801]


title: blood sample from donor 2055 3 days post vaccination [VIC008809]


title: ChiP-seq with HA-Upc2A tag present [WT-1]


title: NHP_10_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample10_10


title: Monocyte_17-V2

value: Blood Monocytes


title: NHP_10_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200108_30102420200621-01_Sample04_04


title: blood sample from donor 1132 3 days post vaccination [VIC008802]


title: NHP_1_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample12_12


title: Monocyte_16-V7


title: NHP_5_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample11_11


title: ChIP-seq with no HA tag present [C-1]


title: Monocyte_17-V7


title: NHP_2_Hoti_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample08_08


title: blood sample from donor 1109 3 days post vaccination [VIC008795]

description: processed data file: RV306_V5B_norm_expr.txt


title: blood sample from donor 1123 3 days post vaccination [VIC008800]


title: Zax3_+P_Sh_24hr

city: Thuwal

first: Jian You

last: Wang

state: Not Specified

address: 4700 King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia

country: Saudi Arabia

institute: KAUST

description: Zax

data_processing:
RNA‐Seq reads were aligned to the O. sativa genome v7.0 downloaded from Phytozome v12.1 (http://phytozome.jgi.doe.gov/).
Data processing and analysis were performed using the LSTrAP workflow. Adapter sequences were removed from fastq files by Trimmomatic, and aligned to the genome using HISAT2.
Read counts aligned to each annotated gene were computed with HTSeq. The results were passed through LSTrAP quality control and TPM normalized. The mean data were used to cluster and resistance level was visualized as a heatmap using a hierarchical clustering R script. Principal component analysis (PCA), a multivariate statistical technique, was further conducted to examine links between samples.
All analyses were performed using R statistical package. For differential gene expression, read counts from HTSeq were analyzed using the R package DESeq2. Genes were considered differentially expressed based on a P‐value adjusted by the Benjamini–Hochberg procedure below 0.05.
Supplementary_files_format_and_content: Differential gene expression analysis

organism: Oryza sativa

source_name: rice seedling

growth_protocol: Nipponbare background WT rice plants were grown under controlled conditions (a 12 h photoperiod, 200-µmol photons m-2 s-1 and day/night temperature of 27/25 oC). Rice seeds were surface-sterilized in a 50 % sodium hypochlorite solution with 0.01 % Tween-20 for 15 min. The seeds were rinsed with sterile water and germinated in the dark overnight. The pre-germinated seeds were transferred to petri dishes containing half-strength liquid Murashige and Skoog (MS) medium and incubated in a growth-chamber for 7 days. Thereafter, the seedlings were transferred into black falcon tubes filled with half-strength modified Hoagland nutrient solution with adjusted pH to 5.8. The nutrient solution consisted of 5.6 mM NH4NO3, 0.8 mM MgSO4.7H2O, 0.8 mM K2SO4, 0.18 mM FeSO4.7H2O, 0.18 mM Na2EDTA.2H2O, 1.6 mM CaCl2.2H2O, 0.8 mM KNO3, 0.023 mM H3BO3, 0.0045 mM MnCl2.4H2O, 0.0003 mM CuSO4.5H2O, 0.0015 mM ZnCl2, 0.0001 mM Na2MoO4.2H2O and 0.4 mM K2HPO4.2H2O.

extract_protocol:
Total rice root RNA was extracted with TRIzol (Invitrogen, https://www.thermofisher.com/de/de/home.htmL) using a Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA).
The cDNA libraries were constructed following standard Illumina protocols and paired‐end sequenced on an Illumina HiSeq 4000 machine by the Bioscience core lab of KAUST.

treatment_protocol: three-week-old seedlings were grown hydroponically in half-strength modified Hoagland nutrient solution. Seedlings were further treated with 5 µM zaxinone for 2 h, 6 h, or 24 h and tissues were collected.

value: Shoot

value: Zaxinone


title: Zax2_+P_Sh_24hr

description: Zax


title: blood sample from donor 1076 3 days post vaccination [VIC008789]


title: blood sample from donor 1117 3 days post vaccination [VIC008799]


title: Zax1_+P_Sh_24hr

description: Zax


title: blood sample from donor 2015 3 days post vaccination [VIC008807]


title: blood sample from donor 1110 3 days post vaccination [VIC008796]


title: NHP_10_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample09_09


title: Zax3_+P_Sh_6hr

description: Zax


title: Monocyte_15-V2

value: pre-vaccination

value: Vaccine


title: Mock1_+P_Sh_24hr

description: Mock

value: Mock


title: Monocyte_17-V9


title: NHP_8_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample04_04


title: NHP_11_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample05_05


title: Mock3_+P_Sh_24hr

description: Mock


title: Monocyte_11-V7

value: month 7


title: NHP_4_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample07_07


title: blood sample from donor 1049 3 days post vaccination [VIC008783]


title: NHP_7_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample03_03


title: Mock2_+P_Sh_24hr

description: Mock


title: blood sample from donor 1033 3 days post vaccination [VIC008780]

value: low


title: Zax2_+P_Sh_6hr

description: Zax


title: NHP_11_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample06_06


title: Monocyte_08-V7


title: Monocyte_15-V7


title: blood sample from donor 1073 3 days post vaccination [VIC008787]


title: blood sample from donor 1069 3 days post vaccination [VIC008786]


title: Zax1_+P_Sh_6hr

description: Zax


title: Monocyte_11-V2


title: blood sample from donor 1028 3 days post vaccination [VIC008778]


title: blood sample from donor 1003 3 days post vaccination [VIC008776]


title: Monocyte_15-V9


title: Mock3_+P_Sh_6hr

description: Mock


title: NHP_9_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample01_01


title: NHP_9_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20200107_30102420190621-01_Sample02_02


title: blood sample from donor 3039 2 weeks post vaccination [VIC008774]

description: processed data file: RV306_V6_norm_expr.txt

value: 2 weeks after 4th immunization


title: NHP_6_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample11_11


title: Monocyte_07-V9

value: month 12


title: Monocyte_07-V7


title: Monocyte_07-V2


title: Mock2_+P_Sh_6hr

description: Mock


title: NHP_4_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample12_12


title: Human PCNSL tumor sample

city: Hong Kong

first: Zhe

last: LIU

address: Tat Chee Avenue

department: computer science

country: China

institute: city university of hong kong

data_processing:
The Cell Ranger software pipeline (version 4.0, http://support.10Xgenomics.com/single-cell-gene-expression/software/overview/welcome) provided by 10x Genomics was used to demultiplex cellular barcodes. Unique molecular identifier (UMI) counts were obtained by mapping reads to the human reference genome (GRCH38 3.1.0) genome and align transcriptomes using the STAR aligner and down-sample reads as required to generate normalized aggregate data across samples.
We processed the UMI count matrix using the Seurat R package (version 4.0.2), resulting in 34,851 cells with 36,601 genes for PCNSL samples.
We first removed the likely multiplet captures which is a major concern in microdroplet-base experiments through doubletfinder. We filtered cells at the cell and gene levels to obtain the reliability results of PCNSL scRNA-seq data, respectively. We removed the low qualify cells with the following criteria: (i) The number of expressed genes was <200 or >2,000; (ii) The number of total counts was > 20,000. (iii) The percentage of mitochondrial counts > 10%. We only kept the genes detected in at least 20 cells. After applying these quality control criteria, we obtained 20,307 cells with 12,229 genes in total, which were used for downstream analysis.
Genome_build: human reference genome hg38

source_name: PCNSL patient brain tissue

extract_protocol: scRNA-seq libraries were prepared using a Chromium Single cell 3’ Reagent kit, version 2. Amplified cDNA and final libraries were evaluated using a High Sensitivity DNA Kit (Agilent Technologies).

value: brain

tag: type

value: PCNSL


title: Zax3_+P_Sh_2hr

description: Zax


title: Monocyte_05-V7


title: Zax1_+P_Sh_2hr

description: Zax


title: Mock1_+P_Sh_6hr

description: Mock


title: Mock3_+P_Sh_2hr

description: Mock


title: Monocyte_04-V7


title: Mock2_+P_Sh_2hr

description: Mock


title: Monocyte_04-V2


title: Monocyte_05-V2


title: NHP_1_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample08_08

value: Kosava Hoti


title: Zax3_+P_R_24hr

description: Zax

value: Root


title: Monocyte_04-V9


title: Mock1_+P_Sh_2hr

description: Mock


title: Monocyte_03-V7

value: No


title: Monocyte_03-V2


title: NHP_6_Hoti_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample06_06

value: whole blood


title: NHP_4_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample10_10


title: Monocyte_02-V7


title: NHP_12_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample09_09


title: Zax1_+P_R_24hr

description: Zax


title: NHP_2_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample04_04

value: Yes


title: NHP_8_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample05_05


title: Mock2_+P_R_24hr

description: Mock


title: NHP_3_Hoti_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample02_02


title: Zax2_+P_R_24hr

description: Zax


title: NHP_6_Hoti_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample03_03


title: Monocyte_02-V2

value: Blood Monocytes


title: Monocyte_01-V7


title: NHP_9_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample12_12


title: NHP_8_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample07_07


title: Zax2_+P_R_6 hr

description: Zax


title: NHP_2_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190614_30102365870321-01_Sample01_01


title: Zax3_+P_R_6 hr

description: Zax


title: Mock1_+P_R_24hr

description: Mock


title: Zax1_+P_R_6 hr

description: Zax


title: Mock3_+P_R_24hr

description: Mock


title: Mock2_+P_R_6 hr

description: Mock


title: Mock1_+P_R_6 hr

description: Mock


title: Mock3_+P_R_6 hr

description: Mock


title: NHP_8_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample10_10


title: NHP_11_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample11_11


title: Zax3_+P_R_2 hr

description: Zax


title: NHP_7_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample08_08


title: FF_GC_rep2

city: Ithaca

first: Pat

last: Johnson

state: New York

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

data_processing:
FastQ files were first processed through trim-galore (Barbraham Institute, Cambridge UK) as a quality control step to trim adaptors and filter for low quality reads.
Sample files were then aligned to the Galgal6 genome using the RNA-seq aligner, STAR.
Differential expression analysis was conducted using DeSEQ2.
Genome_build: Galgal6
Supplementary_files_format_and_content: normalized count table for each gene and sample

organism: Gallus gallus

extract_protocol:
5-6 recently selected follicles (6-8 mm) per bird were removed and granulosa cells were collected and pooled. Total RNA was extracted from granulosa cells using a RNeasy Mini kit with optional on-column DNase treatment (Qiagen Inc., Valencia CA). Quantity and purity of the samples was analyzed using spectrophotometry. RNA integrity was then determined by Fragment Analyzer (Advanced Analytical, Ames IA). All samples had a RQN of >9.9.
Samples were enriched by PolyA+ RNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich MA). Libraries were then generated using the NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs, Ipswich MA).

treatment_protocol: Starting at 28 weeks of age, hens were given a dietary treatment of either ad libitum (FF) or restricted (RF) feed allowance for 6 weeks.

value: FF

value: Granulosa cells of 6-8 mm follicles


title: FF_GC_rep1


title: Zax1_+P_R_2 hr

description: Zax

value: Zaxinone


title: Zax2_+P_R_2 hr

description: Zax


title: RF_GC_rep2

value: RF


title: NHP_10_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample09_09


title: NHP_12_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample07_07


title: Mock2_+P_R_2 hr

description: Mock

value: Mock


title: Zax2_+P_Sh_2hr

description: Zax

value: Shoot


title: Mock1_+P_R_2 hr

description: Mock


title: NHP_5_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample03_03


title: RF_GC_rep1


title: NHP_12_Afghan_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample04_04


title: Recurrent pregnancy loss 5

city: Southampton

first: Jennifer

middle: Elizabeth

last: Pearson-Farr

address: MP887, Southampton General Hospital

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

data_processing:
Gene expression analysis: Raw FASTQ reads were aligned to the human genome via STAR 2.7.3a alignment using human genome 38 and trimmed with trimmomatic. QC was assessed by FastQC (version 0.11.3). Gene count data were normalised, and differential gene expression analysis was carried out in RStudio R-4.0.3 package DESeq2 (version 1.30.1).
Splicing and gene transcript expression analysis: Raw FASTQ reads were trimmed for the adapter sequence and quality filtering (reads containing N > 10%, reads where >50% of read has Qscore<= 5). Paired FASTQ files were aligned to GRCh38 human genome reference using GENCODE v29 gene annotations and  STAR v2.6.0a splice aware aligner, using ENCODE recommend options. The two-pass alignment method was used, with soft clipping activated. BAM files sorted by chromosomal coordinates were assessed for saturation of known splice junctions were calculated using RSeqQC v3.0.1. Salmon tool was used to perform transcript abundance estimates from raw FASTQ files using selective alignment with a decoy-aware transcriptome built from GRCh38. rMATs v4.0.2 (rMATS turbo ) was used to statistically measure differences in splicing between replicates of wild-type and mutant sequence. BAM files aligned with STAR v2.6.0a two-pass method with soft clipping suppressed were used as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Data table with transcripts per million for every gene transcript and every sample

source_name: Endometrial gland

extract_protocol:
Qiagen miRNeasy extraction kit protocol
Library preparation was performed using the TruSeq® Stranded mRNA Library Prep kit (Illumina). The final library was quantified by a Roche KAPA library quantification kit (Illumina) and by the Agilent 2100 Bioanalyser.

treatment_protocol: Endometrial gland isolation was performed by enzyme digestion within 1 h of tissue collection. Endometrial tissue pieces were digested with 0.7 mg/ml type 1A collagenase in 50:50 DMEM/ Ham’s F12 nutrient mixture, containing 5% streptomycin at 37°C for 2 x 15 min intervals with gentle agitation. The endometrial gland fraction was purified and passed through a 50 µm sieve to remove other endometrial cell types. Endometrial glands were then stored in QIAol lysis reagent at -80°C until RNA extraction

tag: condition

value: Recurrent pregnancy loss

value: Endometrial gland

tag: stage of menstrual cycle

value: window of implantation


title: Recurrent pregnancy loss 4


title: RF_GC_rep3


title: salivary gland 24h_rep2

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: mm10

organism: Mus musculus

source_name: salivary gland

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: salivary gland

value: 5Gy  post irradiation 24h

tag: genotype

value: Wild type


title: salivary gland 6h_rep2

value: 5Gy  post irradiation 6h


title: NHP_2_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample06_06

tag: virus

value: Kosava Hoti

tag: nhp no.


title: salivary gland 24h_rep1


title: NHP_3_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample05_05

tag: tb status

value: No

tag: day post challenge

value: whole blood


title: Recurrent pregnancy loss 3

tag: tissue


title: Mock3_+P_R_2 hr

description: Mock

value: Root

tag: timepoint


title: salivary gland 6h_rep1


title: NHP_4_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample02_02


title: NHP_8_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190613_30102365720321-01_Sample01_01

value: Yes


title: salivary gland T0_rep2

value: Control


title: NHP_1_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample12_12


title: NHP_10_Afghan_Day9

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample11_11


title: NHP_12_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample10_10


title: salivary gland T0_rep1


title: WT_UNTREATED_3

city: St Louis

first: Matthew

middle: J

last: Walter

state: MISSOURI

address: 660 South Euclid Avenue

department: Oncology

institute: Washington University School of Medicine

data_processing:
Illumina Novaseq 6000 using paired reads extending 150 bases.
Reads were then aligned to the mouse genome (mm10/NCBI build 38) using Hisat2 version 2.0.86 with annotations provided by Ensembl version 92.
Gene counts were determined by processing the resulting reads using HTseq5 version 0.5.4p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: vav_dox.counts.original.filtered_20210907.tsv

source_name: adult bone marrow hematopoietic cells (Lin- cKit+ Sca1-)

extract_protocol:
Mouse E14.5 fetal liver cells or adult bone marrow were harvested and RNA was then isolated from sorted hematopoietic progenitor cells (Lin- cKit+ Sca1-) using the NucleoSpin RNA Plus XS kit (Macherey-Nagel), per manufacturer’s instructions.
The RNA-sequencing libraries were prepared using KAPA RNA Hyper Prep Kit with RiboErase, per manufacturer’s protocol. After amplification, ~300 bp fragments were sequenced on Illumina NovaSeq 6000, generating 2 x 150bp paired-end reads.

treatment_protocol: Deletion of the U2af1 KO allele and expression of U2af1 (S34F) KI was achieved by six doses (300mg/mouse/dose) of polyinosinic-polycytidylic acid (Sigma) given every other day by intraperitoneal injection. The expression of transgenic U2AF1 (WT) or U2AF1 (S34F) was induced by Modified LabDiet® 5053 rodent chow with doxycycline at 1250 ppm, 2500 ppm or 10,000 ppm (TestDiet).

value: untreated

tag: developmental stage

value: adult

tag: tissue source

value: bone marrow

value: hematopoietic cells (Lin- cKit+ Sca1-)


title: Control 1

value: control


title: Recurrent pregnancy loss 1

value: Recurrent pregnancy loss

value: Endometrial gland


title: Control 4

value: window of implantation


title: in situ Hi-C sequencing lane 3

city: Berlin-Buch

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
ChIP-seq: UMIs were extracted from paired-end reads using UMI-tools (T. Smith, Heger, and Sudbery 2017) and mapped to the danRer11 genome assembly using Bowtie2 (Langmead and Salzberg 2012); -X 2000 --no-discordant --no-mixed). Mapped reads were filtered for MAPQ 30 and deduplicated using UMI-tools. Input-subtracted .bigwig for visualization (--operation subtract --binSize 50 --scaleFactorsMethod None --normalizeUsing CPM --smoothLength 250 --extendReads) and .bedgraph for HMM (--operation subtract --binSize 1 --scaleFactorsMethod None --normalizeUsing CPM --extendReads; see below) tracks were generated using deepTools (Ramírez et al. 2016). Reads were converted to bedpe files using bedtools (Quinlan and Hall 2010). Peaks were called using JAMM (Ibrahim, Lacadie, and Ohler 2015) considering both replicates separately (-r window -e 1 -b 250 -t paired).
chromatin RNA-seq: Unique molecular identifiers (UMIs) were extracted from .fastq files using UMI-tools (T. Smith, Heger, and Sudbery 2017) and reads trimmed using fastx_trimmer from the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads were then filtered for ERCC spike-in reads and rRNA by mapping to a custom index with Bowtie 1 (Langmead et al. 2009). Trimmed, filtered, reads were then mapped using STAR (Dobin et al. 2013). Mapped .bam files were then subjected to PCR deduplication using UMI-tools (T. Smith, Heger, and Sudbery 2017), followed by conversion to .fastq and remapping with STAR to generate final mapped files and normalized coverage tracks. For sci-ATAC-seq segment chromatin RNA quantification, coverage tracks were created for each genome strand using deepTools (Ramírez et al. 2016) and then summed within a 5kb window centered around the segment midpoint using bedtools map (Quinlan and Hall 2010).
Hi-C: In situ Hi-C reads were initially processed using the Juicer pipeline (Durand et al. 2016). TADs were called using the insulation method (Crane et al. 2015) after dumping valid interactions at 25kb binned resolution using juicer-tools and converting formats using HiTC (Servant et al. 2012). For scoring Hi-C interactions, valid interactions were dumped by juicer-tools at fragment resolution, filtered to remove interactions less than 20kb apart and format converted using custom scripts, and then subjected to shuffling and scoring using the SHAMAN method (Cohen et al. 2017).
Genome_build: danRer11
Supplementary_files_format_and_content: bigWigs for ChIP-seq contain input-subtracted, depth-normalized, signal and for RNA-seq contain depth signal; peak calls are in narrowPeak format.
Supplementary_files_format_and_content: cells.tsv and scregeseg_fi_regions.bed contain the region and barcode annotations, respectively, associated with the singleCellCountMatrix.mtx file.

organism: Danio rerio

source_name: whole embryo

extract_protocol: Embryos were collected 24hpf, dechorionated, fixed in 1% formaldehyde in PBS, quenched and washed as in (Bonn et al. 2012).  and nuclei were extracted according to (Bogdanović et al. 2013) using the cell lysis buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 0.5% IGEPAL (CA-630, Sigma, I8896) and a dounce homogeniser. Hi-C library preparation was performed as previously described (Rao et al. 2014) with modifications. In brief, isolated nuclei were divided in 5 aliquots and digested overnight with 1500U of HindIII per aliquot. After biotin-fill in, in each aliquot proximity ligation was carried with 100 units of T4 DNA ligase (Invitrogen) at 16°C overnight. DNA was purified by reverse crosslinking and DNA precipitation, and biotinylated nucleotides were removed from unligated fragments ends with 1U T4 DNA polymerase per µg DNA for 4 hours at 12°C. DNA was sonicated to 300 – 500 bp, using the Bioruptor Plus and size selected for fragments between 300 and 500 bp with AmPure XP beads. Biotinylated DNA fragments were pulled down with MyOne Streptavidin C1 beads (Invitrogen), end-repaired, a-tailed, and TruSeq sequencing adapters were ligated to the DNA fragments with 15U T4 DNA ligase (Invitrogen) overnight at 16°C, shaking at 750 rpm. Adapter-ligated DNA was amplified for 6-8 cycles using Herc II Fusion DNA polymerase (Agilent). PCR products were purified with AMPure XP beads and subjected to Illumina paired-end sequencing (2x 75 bp).

value: 24 hpf

value: AB/TuLF


title: Control 2


title: WT_UNTREATED_2

tag: cell type


title: Recurrent pregnancy loss 2


title: NHP_2_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample12_12


title: single-cell combinatorial indexing ATAC-seq experiment 1

extract_protocol:
For wild type experiments the AB/TL strain was used. All zebrafish maintenance and procedures were conducted in accordance with standard laboratory conditions and animal procedures approved by the local authorities (LAGeSo, Berlin, Germany). Timed matings were set up between AB/TL adults and embryos were maintained at 28.5°C for 24 hpf from the time of fertilization. Staging and consistency within the clutch was confirmed by morphological criteria (Kimmel et al 1995). Chorions were removed by incubating in 15 ml pronase E at 1 mg/ml for 10 min with continuous shaking. Pronase was removed by five washes with 200 ml egg water (60 µg/ml  Ocean salt (Red Sea), 3 µM Methylene blue). For the first two wildtype experiments, embryo yolks were removed by placing 100 embryos in 500 µl de-yolking buffer (55mM NaCl, 1.8mM KCl, 1.25mM NaHCO3) and pipetting 10 times with a P100 pipette. Embryos were left to sink to the bottom, then de-yolking buffer was removed and 5 washes with egg water were performed. Batches of 25-50 embryos were distributed into 1.5ml eppendorf tubes, egg water removed and snap frozen in liquid nitrogen and maintain at -80°C. Embryos with mutated npas4l alleles were obtained from intercrosses of npas4lbns297 heterozygotes in a Tg(fli1a:nls-GFP)y7 background (Marass et al. 2019).  Homozygous cloche mutant (npas4lbns297/bns297) embryos were separated from heterozygous and homozygous wild type siblings (npas4lbns297/+, npas4l+/+) based on the loss of fli1a-GFP+ endothelial cells 24 hours after fertilization. Chorions were removed but yolks were left intact. Embryos were flash frozen in liquid nitrogen, stored at -80°C and transported on dry ice. Embryos were thawed in 2 ml of cold lysis buffer (CLB) (10 mM Tris-HCL, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) from (Buenrostro et al. 2013) supplemented with protease inhibitors (Complete Protease Inhibitor Cocktail, EDTA-free, Roche). Embryos were homogenised in a dounce homogeniser then incubated in cold lysis buffer at 4°C for 1 hour. Nuclei were then strained through 35 micron strainer caps of Corning Falcon test tubes (Thermo Fisher Scientific).
Tn5 was generated by the MDC Protein Production & Characterization Platform from Addgene plasmid #60240 according to (Picelli et al. 2014) at 1.95 mg/ml with the following minor modifications: in 50 mM Hepes-KOH pH 7.2, 0.8 M NaCl, 55 % Glycerin, 0.1 mM EDTA, 1 mM DTT and using buffers lacking Triton X-100 for the chitin column and dialysis. For each experiment 96 uniquely indexed transposon complexes were generated according to (Amini et al. 2014) with minor adaptations. Firstly, twenty uniquely indexed transposons were made by annealing a uniquely indexed oligonucleotide (Sigma-Aldrich) containing a Tn5 mosaic end sequence at its 3’ end, to complementary universal 5’-phosphorylated 19-bp mosaic end oligonucleotide. Oligonucleotides were mixed in a 1:1 molar ratio, giving a final concentration of 100 µm under the thermocycling conditions: 95°C for 5 minutes, cool to 65°C decreasing 0.1°C/second, 65°C for 5 minutes, cool to 4°C decreasing 0.1°C/second. Each annealed oligonucleotide transposon was mixed with Tn5 (1.95 mg/ml) [at a ratio of 0.143:1] and incubated for one hour at 25°C. Of the 20 indexed oligonucleotides, 8  contained an adaptor that could be bound by indexed Illumina P5 primers  (i5 oligonucleotides) and 12 contained an adaptor that could be bound by indexed Illumina P5 primers (oligonucleotide sequences were obtained from supplementary information of (Cusanovich, Reddington, et al. 2018)). To make 96 unique transposome complexes each i5 transposome could be mixed with each i7 transposome at a 1:1 ratio in columns 1-12 and rows A-H of a 96 well plate. Transposome complexes were stored at -20°C. Our protocol for generating sci-ATAC-seq data was largely following (Cusanovich, Reddington, et al. 2018; Cusanovich, Hill, et al. 2018), with some modifications. Purified  nuclei were stained with DAPI (4 µM) and 2500 were sorted into each well of a 96 well plate containing 19 µl of tagmentation buffer (10mM TAPS-NaOH, pH 8.8, 5 mM McCl2, 10% DMF, 6.6 mM Tris-HCl, 6.6 mM,  0.066 % IGEPAL CA-630) using a BD FACS Aria III. For tagmentation, 1 µl of uniquely barcoded Tn5 transposome was added to each well of the 96 well plate containing tagmentation buffer and nuclei. Plates were spun for 30 seconds at 500 x g and then incubated for 30 minutes at 37°C. Following tagmentation 40 µl of 40 mM EDTA supplemented with 0.3 mM spermidine was added to each well and the plate incubated for 15 minutes at 37°C. Nuclei and buffer from all wells were pooled in a reagent reservoir and passed through a 35 micron strainer into Corning Falcon test tubes (Thermo Fisher Scientific). DAPI was added and nuclei were sorted again with a  BD FACS Aria III. For the second sort, 25 nuclei were sorted into each well of 96-well plates (8-10 plates per experiment) containing 12 µl of nuclear lysis buffer (11 µl of EB buffer [Qiagen] supplemented with  0.5 µl of 100X BSA and 0.5 µl of 1% SDS). The 96-well plates from the second sort were stored at -20°C until ready for PCR amplification. Before PCR amplification, each plate was incubated at 55°C for 15 minute then 1 µl of 12.5% triton-X100 added per well to quench the SDS. To each well a unique combination of indexed P5 and P7 PCR primers (Cusanovich, Reddington, et al. 2018) was added (0.5 µM final concentration each), 10 µl of NEBNext Ultra II Q5 Master Mix (NEB) then immediately amplified in a thermocycler under the conditions: 72°C for 3 minutes, 98°C for 30 seconds, 18 cycles: 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute, hold at 4°C. Before amplifying a whole plate, the number of cycles was determined from several test wells that were sorted into a separate plate and monitored by qPCR with the addition of SYBR green to the PCR mix. In all experiments here 18 cycles were used. After PCR amplification, 96-wells of each plate were pooled cleaned up with DNA Clean & Concentrator-5 columns (Zymo) and then large fragments (above 1000 bp) removed with 1X Ampure beads (Agencourt). The concentration of libraries was measured with Qubit dsDNA HS Assay (Thermo Fisher Scientific) and quality checked with Bioanalyzer DNA High Sensitivity Kit (Agilent). Equimolar libraries from each 96 well plate were pools and sequenced with NextSeq500 (Illumina) High Output, 2x150 bp loading at a concentration of 1.6 pM. Custom primers (Cusanovich, Reddington, et al. 2018) and a custom sequencing recipe (Amini et al. 2014) were used to sequence the following read lengths: 110 bp + 45 bp + 110 bp + 39 bp (Read 1 + Index 1 + Read 2 + Index 2).


title: NHP_12_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample05_05


title: NHP_11_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample02_02


title: NHP_11_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample10_10


title: NHP_5_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample04_04


title: NHP_7_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample07_07


title: NHP_12_Afghan_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample06_06


title: NHP_12_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190612_30102367970321-01_Sample09_09


title: Control 3


title: single-cell combinatorial indexing ATAC-seq experiment 3

value: npas4lbns297; Tg(fli1a:nls-GFP)y7


title: single-cell combinatorial indexing ATAC-seq experiment 2


title: NHP_7_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample11_11


title: HEMI_2500_5

value: 2500 ppm Doxycycline and pIpC


title: Control 5


title: NHP_6_Hoti_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample07_07

value: Kosava Hoti

value: No


title: NHP_6_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample09_09

value: whole blood


title: Chromatin-associated RNA-seq replicate 1

extract_protocol: Embryos were collected 24hpf, dechorionated and homogenized on ice in buffer N (10 mM HEPES pH 7.5, 250 mM sucrose, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1X Complete Protease Inhibitor (Roche #11697498001) and 20 U/ml SUPERase-In RNase Inhibitor (Thermo Fisher Scientific #AM2696) using a dounce homogenizer. After allowing the debris to settle for 5 minutes on ice the supernatant was then washed in PBS, loaded on a sucrose cushion, centrifuged at 1000 g at 4°C and further fractionated according to (Conrad and Ørom 2017). RNA was extracted using Trizol (Thermo Fisher Scientific #15596018) and Direct-zol RNA MiniPrep Kit (Zymo Research #R2052) according to the manufacturer’s instructions. The library was prepared using NEXTflex Rapid Directional qRNA-Seq Kit (BiooScientific #NOVA-5130-01D) according to the manufacturer’s instructions and paired-end sequencing (2x75nt) was performed on a NextSeq 500/550 using a HighOutput v2 Kit for 150 cycles (Illumina #FC-404-2002, discontinued).


title: in situ Hi-C sequencing lane 1


title: Chromatin-associated RNA-seq replicate 2


title: HEMI_2500_6


title: HEMI_2500_2


title: in situ Hi-C sequencing lane 2


title: HEMI_2500_1


title: WTAP siRNA #1 rep1

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

country: Japan

institute: Institute for Advanced Medical Sciences, Nippon Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-complexity or low-quality sequence, then mapped to the human genome (GRCh38) using the aligner STAR (version 2.6.1c). The command-line parameters for STAR were: STAR --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000  --outFilterIntronMotifs RemoveNoncanonicalUnannotated .
Read count table was produced with RSEM(v1.3.1 ) using GENCODE database gene annotation (release 33).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: HUVECs

growth_protocol: HUVECs (Lonza) were cultured in EGM2 medium (culture medium supplemented with growth factors) (Lonza) and used within the first six passages.

extract_protocol:
siRNAs for each component of  WTAP complex, i.e. WTAP, Virilizer, BCLAF1, THRAP3, KIAA0853, CBLL1, RBM15, RBM15B,  METTL3, METTL14 (Ambion, s18433, s24832, s18875, s19360, s23010, s36537 and s224626, respectively) were transfected with lipofectamine 2000 RNAi MAX (Life Technologies) according to the manufacturer’s protocol. Forty-eight hours after siRNA transfection, cells were harvested and total RNA was extracted using the Maxwell RNAeasy kit (Promega) treating with DNaseI.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human Umbilical Vein Endothelial Cells(Lonza)  were treated with siRNAs of interest (WTAP, Virilizer, KIAA0853, CBLL1, RBM15/RBM15B, BCLAF1/THRAP3,  METTL3, METTL14)

tag: sirna

value: WTAP


title: NHP_5_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample06_06


title: NHP_5_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample08_08


title: HEMI_2500_3

tag: treatment


title: NHP_3_Hoti_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample04_04


title: METTL14 siRNA rep1


title: NHP_6_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample05_05


title: HEMI_1250_3

value: 1250 ppm Doxycycline and pIpC


title: HEMI_2500_4


title: NHP_5_Hoti_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample03_03


title: NHP_10_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample02_02


title: HEMI_1250_5


title: H3K36me3 ChIP-seq replicate 1

extract_protocol: Embryos were collected 24hpf and fixed in 0.5% formaldehyde (Carl Roth #4979.1) for 15 minutes as previously published for D. melanogaster (Bonn et al. 2012) with minor modifications: heptane was not added to the fixation buffer since unlike D. melanogaster zebrafish does not have a cuticula. Nuclei were extracted according to (Bogdanović et al. 2013) and sonicated for 16 cycles (30s ON, 30s OFF, on high setting) in a Bioruptor Plus (Diagenode) to achieve a DNA fragment size below 500bp. ChIP was performed using True MicroChIP Kit (Diagenode #C01010130) according to the manufacturer’s instructions with the following modifications: primary antibody was incubated at 4°C over-night and the reverse crosslinking was done over-night. The following antibodies were used: H3K4me1 (abcam #ab8895), H3K4me2 (abcam #ab32356), H3K4me3 (abcam #8580), H3K27ac (abcam #ab4729), H3K36me3 (abcam #ab9050). The library was prepared using NEXTflex qRNA-Seq Kit v2 (BiooScientific #5130-12, discontinued) according to the instructions for qChIP-Seq and paired-end sequencing (2x75nt) was performed on a NextSeq 500/550 using a HighOutput v2 Kit for 150 cycles (Illumina #FC-404-2002, discontinued).

tag: antibody

value: H3K36me3 ChIP-seq


title: ChIP-seq input for H3K36me3

value: ChIP-seq input for H3K36me3


title: H3K27ac ChIP-seq replicate 2

value: H3K27ac ChIP-seq


title: RBM15/RBM15B siRNAs rep1


title: BCLAF1/THRAP3 siRNAs rep1


title: H3K36me3 ChIP-seq replicate 2


title: HEMI_1250_4

value: adult

value: bone marrow

value: hematopoietic cells (Lin- cKit+ Sca1-)


title: NHP_11_Afghan_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190611_30102346650221-01_Sample01_01

value: Yes


title: NHP_7_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample12_12


title: METTL3 siRNA rep1


title: HEMI_1250_1


title: WT_UNTREATED_1

value: untreated


title: H3K4me3 ChIP-seq replicate 2

value: 24 hpf

value: H3K4me3 ChIP-seq


title: H3K27ac ChIP-seq replicate 1

value: AB/TuLF


title: CBLL1 siRNA rep2


title: H3K4me3 ChIP-seq replicate 1


title: HEMI_10K_1

value: 10,000 ppm Doxycycline and pIpC


title: NHP_1_Hoti_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample09_09

value: Kosava Hoti


title: NHP_7_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample10_10


title: NHP_5_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample07_07

value: No


title: KIAA0853 siRNA rep1


title: NHP_3_Hoti_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample08_08

value: whole blood


title: CBLL1 siRNA rep1


title: HEMI_10K_3


title: HEMI_10K_2


title: H3K4me2 ChIP-seq replicate 1

value: H3K4me2 ChIP-seq


title: H3K4me2 ChIP-seq replicate 2


title: NHP_9_Afghan_Day14

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample06_06


title: KIAA0853 siRNA rep2


title: H3K4me1 ChIP-seq replicate 1

value: H3K4me1 ChIP-seq


title: VAVS34F_2

description: Batch B

source_name: E14.5 fetal liver hematopoietic progenitor cells (Lin- cKit+ Sca1-)

value: fetal liver


title: VAVS34F_4

description: Batch B

value: hematopoietic progenitor cells (Lin- cKit+ Sca1-)


title: VIRMA siRNA rep2

value: Virilizer


title: VAVS34F_3

description: Batch B


title: H3K4me1 ChIP-seq replicate 2


title: WTAP siRNA rep2

value: WTAP


title: VAVONLY_3

description: Batch B


title: HEMI_10K_4

value: adult

value: bone marrow


title: NHP_10_Afghan_Day7

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample03_03


title: WTAP siRNA rep1


title: NHP_12_Afghan_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample04_04


title: ChIP-seq input for H3K4me1, H3K4me2, H3K4me3, and H3K27ac replicate 2


title: VIRMA siRNA rep1


title: VAVS34F_1

description: Batch B


title: control siRNA rep2

value: control


title: VAVHOMO_4

description: Batch A

value: untreated


title: VAVHOMO_3

description: Batch A


title: NHP_4_Hoti_Day4

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample12_12


title: VAVHOMO_2

description: Batch A


title: G898D UPC2A rep3

data_processing:
Read quality was confirmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Candida glabrata CBS138 genome using HISAT2 in paired-end read mode.  Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype .Nat Biotechnol 37, 907–915 (2019)
Sorted and indexed bam files of mapped reads were prepared using Samtools. Wig files were prepared using the NCBI Genome Workbench (https://www.ncbi.nlm.nih.gov/tools/gbench/).
Mapped reads were assembled onto annotated CBS138 genes with Stringtie using the -eB parameter. Raw gene count tables were generated using the prepDE.py script that is provided with Stringtie.  Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016).
Differential expression and statistical analysis was done from raw counts using the DESeq2 R package.  Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8
Genome_build: s02-m07-r33 from Candida Genome Database on 2019 Feb 3
Supplementary_files_format_and_content: Sequencing depth was represented by BigWig files for each sample.

organism: Nakaseomyces glabratus

source_name: G898D UPC2A

growth_protocol: A single colony of each C. glabrata strain was used to inoculate 2ml YPD, which was grown overnight at 30oC in an environmental shaking incubator.  Cell density was then adjusted to OD600=0.1 in 10 ml YPD, and cultures were grown as before for 6 hrs (mid-log phase).   Cells were collected by centrifugation, supernatants discarded, and cell pellets stored at -80 oC.  RNA was isolated from cell pellets via the hot phenol method as described previously (Schmitt ME, Brown TA, Trumpower BL Nucleic Acids Res. 1990 May 25; 18(10):3091-2).  The quantity and purity of RNA were determined by spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and verified using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Library prep, RNA sequencing, and analysis were performed as previously described (Whaley SG et al. mSphere. 2018 Jan-Feb; 3(1): e00466-17).

extract_protocol:
Whaley SG et al. mSphere. 2018 Jan-Feb; 3(1): e00466-17
RNA libraries were prepared for sequencing using standard  protocols

tag: strain background

value: G898D UPC2A


title: NHP_12_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample05_05


title: ChIP-seq input for H3K4me1, H3K4me2, H3K4me3, and H3K27ac replicate 1

value: 24 hpf


title: NHP_8_Afghan_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190607_30102346660221-01_Sample01_01

value: Yes


title: VAVHET_5

description: Batch A


title: VAVONLY_2

description: Batch A


title: G898D UPC2A rep2


title: NHP_7_Afghan_Day0

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample09_09


title: NHP_3_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample07_07


title: WT rep2

source_name: WT

value: wild type


title: NHP_3_Hoti_Day5

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample10_10

source_name: whole blood

value: Kosava Hoti


title: NHP_6_Hoti_Day6

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample11_11

value: No


title: 2_WT_hmC_mm10

city: Boston

last: Ramsey

state: MA

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq500) were mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
5´-ends of the aligned reads (= “tags”) were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library.  To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Methylated regions were identified using the MACS peak finding algorithm with our default cutoff of p-value = 1e-7
For Tag normalization, the tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
Overlapping intervals were grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals). In locations where only one sample has an Interval, this Interval defines the Merged Region.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files contain the histogram of fragment densities and genomic regions with local enrichments in tag numbers as determined by MACS

source_name: K14-CreER Tet2L/L epidermis, vehicle treated

growth_protocol: K14-CreER Tet2L/L mice were aged for ten weeks

extract_protocol:
Genomic DNA from murine epithelial preps was purified, sonicated, and then ligated to Illumina barcode adaptors.  Ligated DNA was denatured and incubated with a-5hmC antibody (#39769, 1:2,000; Active Motif, Carlsbad, CA) overnight at 4oC, and then immunoprecipitated DNA was purified
Immunoprecipitated DNA was sequenced using standard Illumina protocols. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: 100mg/kg tamoxifen or vehicle control was delivered daily by IP injection for 5 consecutive days.  Samples were collected 14 days after first injection

value: Isolated epidermal keratinocyes

tag: chip antibody


title: NHP_3_Hoti_Day1

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample08_08

extract_protocol: All whole blood samples were initially diluted 1:1 with purified molecular grade water prior to being vigorously mixed with a 3:1 ratio of TRIzol LS (ThermoFisher Scientific). All TRIzol LS mixtures and residual matrices were then frozen at -80°C until subsequent extraction and/or analysis. RNA for NanoString analysis was manually extracted using the miRNeasy kit (Qiagen) following manufacturer’s instructions with the modification that the initial TRIzol-LS/water/whole blood mixture was placed in a Phasemaker phase separation tube (ThermoFisher Scientific) prior to being centrifuged at 12,000 x g for 15 min at room temperature. The top aqueous layer was then transferred into a miRNeasy kit column.

value: whole blood


title: control siRNA rep1


title: WT rep3


title: G898D UPC2A rep1


title: VAVHET_4

description: Batch A


title: WT rep1


title: RORgt-RORa-KO_3

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

data_processing:
Reads were trimmed with TrimGalore v0.62 using default parameters
Trimmed reads were mapped to mouse GRCm38 using bowtie2 v2.3.5.1 using default paramters
Mapped reads were filtered using samtools to retain only primary mappings with MAPQ >=20
Peaks were called using MACS2 using options  --nomodel --extsize 200 --shift -100 --broad then merged in SeqMonk to produce consensus overlapping peak regions
Peaks were quantitated as size factor normalised log2 reads per million
Genome_build: Mus musclulus GRCm38
Supplementary_files_format_and_content: Tab delimited text file of peak positions and log2RPM values for all samples

source_name: Innate lymphoid cells

extract_protocol:
1) Small intestinal lamina propria cells were prepared and extracted via Collagenase VIII digestion.  2) Cells were MACS enriched (Miltenyi Biotec), then stained with antibodies targeting surface markers and submitted to high speed flow sorting (BD FACS Aria Fusion).  3) Sorted cells were lysed and their DNA was transposed in a reaction buffer containing Tagment DNA Buffer (ref 15027866, Nextera DNA Library Prep Kit, Illumina), Tagment DNA Enzyme 1  (ref 15027865, Nextera DNA Library Prep Kit, Illumina), digitonin (ref G944A, Promega).  4) Transposed DNA was purified using Qiagen MinElute Kit.
Libraries were prepared according to the protocol developped by Buenrostro et al. 2013 (Nature Methods, vol.10 no.12). Briefly, transposed DNA fragments were amplified by PCR, libraries were cleaned up using Ampure beads, checked using a Bioanalyser instrument and validated by qPCR. Their concentration was measured by a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms). ATAC-seq libraries were sequenced using a NextSeq 500/550 High Output Kit v2.5 (Illumina) using the Illumina NextSeq500 platform.

treatment_protocol: Mice were submitted to a tamoxifen-diet to induce Cre expression within innate lymphoid cells several weeks before purification and sorting.

value: Small intestinal lamina propria

value: Innate lymphoid cells

value: Id2creERT2+ x Rorcf/f x Roraf/f x tdRFP+


title: mLN cDC1s - Vps33B KO - HDM-treated - rep3

city: Dongguan

first: Gonghua

last: Huang

address: 1 Xincheng Avenue

institute: Guangdong Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly trimmed and filtered. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Sequenced reads were aligned to mm10 whole genome using hisat2 v2.0.5 with parameters -q -p 50 --qc-filter, where reference genome and gene splice sites files were downloaded from genome website directly.
HTSeq was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts for each gene of each sample

source_name: mLN cDC1s

extract_protocol:
mLNs were isolated and digested, then cDC1s were sorted by FACS, RNA was harvested using Trizol reagent.RNA-seq was performed by Illumina NovaSeq 6000 with 150-base paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were intranally immunized with 50 μg HDM, mLN cDC1s were sorted 24 h later.

value: HDM-sensitized


title: VAVHET_3

description: Batch A

value: fetal liver

value: hematopoietic progenitor cells (Lin- cKit+ Sca1-)


title: HOMOONLY_5

description: Batch A


title: NHP_9_Afghan_Day28

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample06_06


title: Pooled_Input_mm10

source_name: pooled input


title: mLN cDC1s - WT - HDM-treated - rep3


title: HOMOONLY_4

description: Batch A


title: Control_3

value: Id2creERT2+ x tdRFP+


title: 1_TET2-M_hmC_mm10

source_name: K14-CreER Tet2L/L epidermis, tamoxifen treated

value: #39769, 1:2,000; Active Motif, Carlsbad, CA


title: Isogenic upc2Δ cells plus fluconazole rep3

description: EFUNG_20180912_K00134_IL100106266_S13_L003

data_processing:
Read quality was confirmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Candida glabrata CBS138 genome using HISAT2 in paired-end read mode.  Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype .Nat Biotechnol 37, 907–915 (2019)
Sorted and indexed bam files of mapped reads were prepared using Samtools. Wig files were prepared using the NCBI Genome Workbench (https://www.ncbi.nlm.nih.gov/tools/gbench/).
Mapped reads were assembled onto annotated CBS138 genes with Stringtie using the -eB parameter. Raw gene count tables were generated using the prepDE.py script that is provided with Stringtie.  Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016).
Differential expression and statistical analysis was done from raw counts using the DESeq2 R package.  Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8
Genome_build: s02-m07-r33 from Candida Genome Database on 2019 Feb 3
Supplementary_files_format_and_content: Sequencing depth was represented by Wig files for each sample.

source_name: Isogenic upc2Δ cells plus fluconazole

growth_protocol: A single colony of each C. glabrata strain was used to inoculate 2ml YPD, which was grown overnight at 30oC in an environmental shaking incubator.  Cell density was then adjusted to OD600=0.1 in 10 ml YPD, and cultures were grown as before for 6 hrs (mid-log phase).  For the SBI-treated strains, either fluconazole (50 mg/ml final concentration) or DMSO (diluent control) was added to the 10 ml culture and grown as before for 6 hrs.  Cells were collected by centrifugation, supernatants discarded, and cell pellets stored at -80 oC.  RNA was isolated from cell pellets via the hot phenol method as described previously (Schmitt ME, Brown TA, Trumpower BL Nucleic Acids Res. 1990 May 25; 18(10):3091-2).  The quantity and purity of RNA were determined by spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and verified using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Library prep, RNA sequencing, and analysis were performed as previously described (Whaley SG et al. mSphere. 2018 Jan-Feb; 3(1): e00466-17).

tag: genotype/variation

value: 50 mg/l fluconazole for 6 hours


title: mLN cDC1s - WT - HDM-treated - rep2

tag: strain


title: RORgt-Tbet-KO_2

tag: genotype

value: Id2creERT2+ x Rorcf/f x Tbx21f/f x tdRFP+


title: HOMOONLY_3

description: Batch A

value: untreated


title: NHP_10_Afghan_Day2

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample03_03

data_processing: Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.

tag: virus


title: NHP_3_Hoti_Day3

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample04_04

tag: nhp no.


title: Isogenic upc2Δ cells plus fluconazole rep2

description: EFUNG_20180912_K00134_IL100106258_S5_L002


title: mLN cDC1s - Vps33B KO - HDM-treated - rep2


title: RORgt-KO_2

value: Id2creERT2+ x Rorcf/f x tdRFP+


title: mLN cDC1s - WT - HDM-treated - rep1

value: wild type


title: NHP_10_Afghan_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample02_02

tag: tb status


title: E. abortivum sporocarp biological rep 3, technical rep 3

city: Lincoln

first: Rachel

middle: Anne

last: Koch

state: NE

address: 1875 N 38th Street

department: Plant Pathology

institute: University of Nebraska

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent3_3

data_processing:
Sequencer: Illumina HiSeq 2500; Basecalling pipeline: HiSeq Control Software 2.2.38
Sequenced reads were trimmed for adaptors and sequencing contaminants were removed using bbduk (https://jgi.doe.gov/data-and-tools/bbtools/)
Reads were then mapped to the de novo E. abortivum or Armillaria assembled transcriptome using RSEM and Bowtie v 2, and only reads with a mapq score of q = or greater than 30 retained
The count data from RSEM was then normalized using TMM, implemented in edgeR
Genome_build: de novo transcriptome assembly of both E. abortivum and Armillaria mellea (will be submitted to the transcriptome assembly database on Genbank)
Supplementary_files_format_and_content: Entoloma.counts.genes.q30.matrix.txt: E. abortivum matrix table with raw gene counts for every gene and every sample for E. abortivum sporocarps and carpophoroids
Supplementary_files_format_and_content: Armillaria.counts.genes.q30.matrix.txt: Armillaria mellea matrix table with raw gene counts for every gene and every sample for Armillaria mellea sporocarps and carpophoroids
Supplementary_files_format_and_content: Ent.TMM.q30.csv: E. abortivum .csv file including TMM (normalized) values for each sample and gene for E. abortivum sporocarps and the carpophoroids
Supplementary_files_format_and_content: Arm.TMM.q30.csv: Armillaria mellea .csv file including TMM (normalized) values for each sample and gene for Armillaria mellea sporocarps and the carpophoroids

organism: Entoloma abortivum

source_name: E. abortivum sporocarp

extract_protocol:
Total RNA was extracted from the ground tissue using the Qiagen RNeasy kit (Qiagen Inc., Hilden, Germany) according to manufacturer’s protocol
Libraries were constructed with the TruSeq Standard Total RNA Library Preparation Kit with Ribo-Zero ribosomal reduction following the protocol developed by Schuierer et al (2017)

value: sporocarp


title: mLN cDC1s - Vps33B KO - HDM-treated - rep1


title: NHP_4_Hoti_Day21

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample01_01

value: Kosava Hoti

value: No

tag: day post challenge


title: NHP_11_Afghan_Day12

description:
50 ng extracted total RNA was hybridized to probes and read using the NanoString SPRINT
20190606_30102320400221-01_Sample05_05

value: Yes

tag: tissue

value: whole blood


title: RORgt-KO_1

value: Small intestinal lamina propria

value: Innate lymphoid cells


title: RORgt-RORa-KO_1

value: Id2creERT2+ x Rorcf/f x Roraf/f x tdRFP+


title: Isogenic upc2Δ cells plus fluconazole rep1

city: Iowa City

last: Moye-Rowley

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

institute: University of Iowa

description: EFUNG_20180802_K00134_IL100105479_S46_L004


title: Wild-type cells plus fluconazole rep3

description: EFUNG_20180912_K00134_IL100106262_S9_L003

source_name: Wild-type cells plus fluconazole


title: Gr-1+ CD11b+ cells stimulated with ATPgS

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: ATPgS

extract_protocol:
Total RNAs were extracted using RNeasy Mini kit (Qiagen) according to the  manufacturer’s instructions.
Full-length cDNA was generated with a SMART-Seq HT Kit (Takara Bio, Mountain View, CA). An Illumina library was prepared by using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA).

treatment_protocol: Gr-1+ CD11b+ cells were isolated from BALB/c mice administered 3% DSS for 6 days and stimulated with 100 M ATPS for 2.5 hours.

value: BALB/c

value: Gr-1+ CD11b+ cells

value: stimulated with ATPgS


title: Gr-1+ CD11b+ cells stimulated without ATPgS

source_name: control

value: stimulated without ATPgS


title: E. abortivum sporocarp biological rep 3, technical rep 1

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent3_1


title: Isogenic upc2Δ cells rep3

description: EFUNG_20180912_K00134_IL100106269_S16_L003

source_name: Isogenic upc2Δ cells


title: E. abortivum sporocarp biological rep 2, technical rep 1

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent2_1


title: Control_1

value: Id2creERT2+ x tdRFP+


title: E. abortivum sporocarp biological rep 3, technical rep 2

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent3_2


title: Wild-type cells plus fluconazole rep1

description: EFUNG_20180802_K00134_IL100105475_S42_L004

value: 50 mg/l fluconazole for 6 hours


title: E. abortivum sporocarp biological rep 2, technical rep 2

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent2_2


title: E. abortivum sporocarp biological rep 1, technical rep 3

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent1_3


title: E. abortivum sporocarp biological rep 2, technical rep 3

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent2_3


title: Wild-type cells plus fluconazole rep2

description: EFUNG_20180912_K00134_IL100106254_S1_L002


title: Wild-type cells rep2

description: EFUNG_20180912_K00134_IL100106257_S4_L002

source_name: Wild-type cells


title: RORgt-RORa-KO_2


title: Control_2


title: Isogenic upc2Δ cells rep1

description: EFUNG_20180802_K00134_IL100105482_S49_L004


title: Gr-1+ CD11b+

treatment_protocol: Myeloid cells, such as CD64- DCs, CD64+ MΦ, and Gr-1+ CD11b+ cells, were isolated from the colon of healthy BALB/c mice.

value: colon

tag: cell subtype


title: Wild-type cells rep3

description: EFUNG_20180912_K00134_IL100106265_S12_L003


title: CD64- DCs

value: CD64- DCs


title: Isogenic upc2Δ cells rep2

description: EFUNG_20180912_K00134_IL100106261_S8_L002


title: E. abortivum sporocarp biological rep 1, technical rep 1

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent1_1


title: RyhB_2

status: Public on Sep 22 2021

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

data_processing:
Conversion of data generated on Illumina sequencing systems using bcl2fastq Conversion Software v1.8.4
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized (FPKM)
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: Excel file including normalized reads (FPKM) for each sample and the enrichment ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: The bacterial strains were grown in 100mL of LB medium to an OD600nm of 0.5

extract_protocol:
Cells were resuspended in 2 mL of buffer A and lysed using a French Press (430 psi, three times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 75 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 100 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-RyhB during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 delta-hfq delta-ryhB

tag: growth phase

value: exponential phase

tag: repeat

value: Repeat 2


title: MS2-RyhB_2


title: Wild-type cells rep1

first: Scott

description: EFUNG_20180802_K00134_IL100105478_S45_L004

value: wild type


title: CD64+ MΦ

source_name: macrophage

tag: cell type

value: macrophage

value: CD64+ MΦ


title: RybB_2

data_processing:
Conversion of data generated on Illumina sequencing systems using bcl2fastq Conversion Software v1.8.4
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized (FPKM)
Supplementary_files_format_and_content: Excel file including normalized reads (FPKM) for each sample and the enrichment ratio

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-RybB during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 delta-hfq delta-rybB


title: MS2-RybB_2


title: RybB_1

value: Repeat 1


title: MS2-RyhB_1


title: DsrA_2

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-DsrA during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 delta-hfq delta-dsrA


title: MS2-DsrA_2


title: MS2-RybB_1


title: MS2-DsrA_1


title: RORgt-Tbet-KO_1

value: Small intestinal lamina propria

value: Innate lymphoid cells

value: Id2creERT2+ x Rorcf/f x Tbx21f/f x tdRFP+


title: lem2iss10_RNA-seq_rep3

city: Planegg

first: Sigurd

last: Braun

address: Großhaderner Str. 9

department: BMC

institute: LMU

description: RNA sequencing of lem2∆iss10∆ cells

data_processing:
Raw read were de-multiplexed. Adapter-trimmed reads were aligned to the S. pombe reference genome (ASM294v2.27) and a custom GTF file using STAR (v2.7.3a) and processed using RSEM (v1.3.3).
Differential expression was analysed using the DESeq2 (v1.22.2) and tximport (v1.10.1) R libraries.
Bedgraph coverage files were generated using genomecov (bedtools v2.29.1).
Genome_build: ASM294v2.27
Supplementary_files_format_and_content: Bedgraph files of coverage

organism: Schizosaccharomyces pombe

source_name: logarithmically growing lem2-deltaiss10-delta cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YES).

extract_protocol:
RNA was extracted using TRIzol
Library was constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB#E7420), according to manufacturer's recommendation.

tag: batch

value: h


title: lem2iss10_RNA-seq_rep2

description: RNA sequencing of lem2∆iss10∆ cells


title: iss10_RNA-seq_rep3

description: RNA sequencing of iss10∆ cells

source_name: logarithmically growing iss10-delta cells


title: lem2iss10_RNA-seq_rep1

description: RNA sequencing of lem2∆iss10∆ cells


title: RyhB_1


title: lem2_RNA-seq_rep9

description: RNA sequencing of lem2∆ cells

source_name: logarithmically growing lem2-delta cells


title: wt_RNA-seq_rep16

description: RNA sequencing of WT cells

source_name: logarithmically growing WT cells

value: WT


title: lem2_RNA-seq_rep8

description: RNA sequencing of lem2∆ cells


title: iss10_RNA-seq_rep2

description: RNA sequencing of iss10∆ cells


title: E. abortivum sporocarp biological rep 1, technical rep 2

description:
"pure" tissue containing only E. abortivum
Entoloma.counts.genes.q30.matrix.txt
Ent.TMM.q30.csv
Ent1_2

value: sporocarp


title: wt_RNA-seq_rep15

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep14

description: RNA sequencing of WT cells


title: iss10_RNA-seq_rep1

description: RNA sequencing of iss10∆ cells


title: lem2_RNA-seq_rep7

description: RNA sequencing of lem2∆ cells


title: ChIPseq_Input_TT2_GLN_KO_C43_P7_paied_end

city: HONG KONG

first: Danny

last: Leung

state: HONG KONG

address: Clear Water Bay

institute: HONG KONG UNIV OF SCIENCE & TECHNOLOGY

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie 2 with parameters -q -N 1 -L 25 -X 500 --no-discordant --no-mixed
Duplicates were then removed by Picard MarkDuplicates v2.9.0
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2013).
supplementary_files_format_and_content:BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

source_name: Embryonic stem cell

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 83% confluency.

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with sonication. The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using KAPA Hyper Prep Kit (Roche) according to manufacturer protocol

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 13minutes at room temperature then quenched with glycine.

tag: chip-seq antibody

tag: cell line

value: GLN KO


title: ChIPseq_Input_J1_PB1_paired_end

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie 2 with parameters -q -N 1 -L 25 -X 500 --no-discordant --no-mixed
Duplicates were then removed by Picard MarkDuplicates v2.9.0
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2012).
supplementary_files_format_and_content:BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 82% confluency.

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 12minutes at room temperature then quenched with glycine.

value: GLN KI with PiggyBac


title: ChIPseq_Input_TT2_paired_end

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie 2 with parameters -q -N 1 -L 25 -X 500 --no-discordant --no-mixed
Duplicates were then removed by Picard MarkDuplicates v2.9.0
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2011).
supplementary_files_format_and_content:BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 81% confluency.

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 11minutes at room temperature then quenched with glycine.


title: DsrA_1


title: ChIPseq_Input_J1_paired_end

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie 2 with parameters -q -N 1 -L 25 -X 500 --no-discordant --no-mixed
Duplicates were then removed by Picard MarkDuplicates v2.9.0
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
supplementary_files_format_and_content:BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 80% confluency.

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.


title: ChIPseq_Input_J1_PB14_paired_end


title: ChIPseq_H3K27ac_TT2_GLN_KO_C43_P7_paied_end

value: H3K27ac (Active Motif:39133)


title: ChIPseq_H3K27ac_J1_paired_end


title: ChIPseq_H3K27ac_J1_PB1_paired_end


title: ChIPseq_H3K27ac_J1_PB14_paired_end


title: RNAseq_TT2_Klhdc4_KD_scramble_shRNA_2

data_processing:
Reads were aligned to mouse reference genome mm10 using STAR and uniquely mapped reads were included in further analysis
The output file was subsequently converted into BigWig file by homemade scripts and uploaded to UCSC genome browser to visualize
Meanwhile, generated BAM file was used to calculate Fragments Per Kilobase per Million reads (FPKM) of genes with RSEM
supplementary_files_format_and_content:BigWig files were generated by STAR v2.5.3a and UCSC utilites; Scores represent RPM signal for piled up genomic alignments

extract_protocol:
Total RNA were extracted using Rneasy Mini Kit (Qiagen) according to manufacturer protocols.
RNA-seq libraries were prepared by Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme) and QIAseq Stranded RNA Library Kits (Qiagen) according to manufacturer protocols.

value: control


title: ChIPseq_H3K27ac_TT2_paired_end


title: IR rep 1

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequence reads were aligned to the mouse transcriptome using TopHat.
Cufflinks package was used to quantify transcript levels
DEG analysis was performed using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: whole genome FPKM matrix

source_name: Brain

extract_protocol:
At 30 days post-IR, mice were perfused with PBS and brains were dissected out. Total RNA was extracted from dissected whole brains using TRIzol (Invitrogen) according to the manufacturer's instructions. RNA quantity was then determined using a Qubit fluorometer (Thermo Fisher), and RNA quality was analyzed with an RNA tape on the 4200 TapeStation (Agilent).
TruSeq Stranded Total RNA Ribo-Zero kit (Illumina) was used to prepare sequencing libraries from 2 μg total RNA.
Sequencing was performed on the NextSeq500 using 75 nucleotide single end SBS chemistry, with ~30‐40 Million reads for each sample.

treatment_protocol: Mice were mock-irradiated or cranially irradiated AP (anterior-posterior) with an X-ray device (X-RAD 320, Precision X-ray; 250 kV, 15 mA, 1.65 mm Al filter, at 5 cm) fitted with a specifically designed collimator providing a 10.08 mm-diameter field size iso-dose exposure (total dose of 10 Gy).

value: brain

tag: treatment

value: irradiated (10 Gy), 30 days


title: IR rep 2


title: IR rep 3


title: Mock-IR rep 3

value: mock-irradiated, 30 days


title: Mock-IR rep 2


title: Mock-IR, rep1


title: D3839 EBd7 CD71+ CTCF 2

city: Oxford

first: Mira

middle: Tony

last: Kassouf

state: England

address: John Radcliffe Hospital, Headly way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated mutant mES cells deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5), ChIPed for CTCF, sample 2
Genome-wide library of ChIPed chromatin

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates;
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: E14TG2a.IV mES derived Erythroid cells

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ChIP-Seq as in Hay D et al, Nature Genetics, 2016.
Cells were fixed with 1% Formaldehyde, lysed, sonicated and immunoprecipitated with the antibody of interest (CTCF: Merck Millipore 07-729 at 5ug/ml, H3K27ac: Abcam ab4729 at 0.5ug/ml, H3K4me1: Abcam ab8895 at 0.3ug/ml, H3K4me3: Abcam ab8580 at 2.5ug/ml). Libraries were prepared using the NEB Ultra II library preparation kit according to manufacturer’s instructions. Samples were sequenced using 40 bp paired end reads on the NextSeq platform
The strategy was to characterise the chromatin state of the CD71+ erythroid cells (WT and mutant) derived from mESC-EB in vitro differentitation system by isolating and analysing DNA regions bound by the antibodies of interest, genome-wide.

value: E14TG2a.IV mES derived Erythroid cells

tag: chip antibody

value: CTCF:Merck Millipore 07-729 at 5ug/ml


title: WT EBd7 CD71+ H3K4me3 2

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for H3K4me3, sample 2
Genome-wide library of ChIPed chromatin

value: H3K4me3:Abcam ab8580 at 2.5ug/ml


title: WT EBd7 CD71+ H3K27ac 2

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for H3K27ac, sample 2
Genome-wide library of ChIPed chromatin

value: H3K27ac:Abcam ab4729 at 0.5ug/ml