title: WTd70repD

city: Philadelphia

first: Rafael

middle: Jesus

last: Fernandez

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Pseudoalignment: Salmon
Gene-level sumarization: tximport
Genome_build: Genome GRCh38, transcriptome Gencode v34
Supplementary_files_format_and_content: tab-delimited text containing raw counts per gene per sample

source_name: Sorted iPS Derived SFTPC+

growth_protocol: A modified version of the protocol described in (Jacob et al., 2017) was used to generate SFTPC expressing iAT2 cells. In brief, iPS cells were seeded at 500,000 cells per well on a 6-well plate with ROCK inhibitor for 24 hours and incubated at 5% O2 | 5% CO2 | 90% N2. Definitive endoderm was induced using the StemDiff Definitive Endoderm kit for 3 days. Next, the cells were split at a ratio of 1:3 onto fresh Matrigel plates and anteriorized using dorsomorphin (2 µM) and SB431542 (10 µM) in complete Serum Free Differentiation Media (cSFDM) for three days. Cells were then differentiated into NKX2.1+ progenitors by incubating in CBRa media (cSFDM containing CHIR99021 (3 µM), BMP4 (10 ng/mL), and retinoic acid (100 nM)) for 7 days changing media every 2 days at first and then increasing to every day media changes when the media became more acidic. On day 15 or 16, NKX2.1+ progenitors were isolated using a FACSJazz sorter using the endogenous NKX2.1::GFP reporter.    NKX2.1+ sorted cells were replated at a density of 400,000 cells/mL in 90% Matrigel supplemented with 10% of CK+DCI+TZV media (cSFDM containing 3 µM CHIR99021, 10 ng/mL KGF, 100 nM dexamethasone, 100µM 8Br-cAMP and 100 µM IBMX and 2 µM TZV) (from now on referred to as 90/10 Matrigel). The Matrigel droplets were allowed to cure at 37 °C for 20-30 minutes and then overlaid with an appropriate amount of CK+DCI+TZV Media. These alveolosphere containing matrigel droplets were incubated at 37˚C at 20% O2 | 5% CO2 | 75% N2 (room air) for 14 days changing with fresh media every other day. On Day 28, the iAT2 containing alveolospheres were sorted on a FACSJazz sorter for SFTPC+ cells using the endogenous SFTPC::TdTomato reporter. These sorted SFTPC+ cells were replated at a concentration of 65,000 cells / mL in 90/10 Matrigel drops and grown in K+DCI+TZV at 37˚C in an ambient air incubator supplemented to 5% CO2 for 3 weeks changing media every other day.

extract_protocol:
Zymo Direct-zol Total RNA Micro Kit
Illumina Library Prep, Poly-A Selection

treatment_protocol: All cells were cultured using protocols developed in Jacob et al. 2017,2019. The main difference between samples is the presence of absence of a causal Dyskeratosis congenita mutation, DKC1 A386T.

value: iPS Derived SFTPC+ Cell

value: Male

tag: genotype

value: DKC1 A386

tag: timepoint

tag: rin

tag: barcode

value: AATCCAGC+TTGCTTGC


title: MUTd70repB

status: Public on May 07 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: Sex

value: DKC1 A386T

value: GCAGAAGA+GGTAAGCT


title: MUTd70repC

value: GCAGAAGA+ACTACGGA


title: MUTd70repA

value: GCAGAAGA+AAGCGGAA


title: WTd70repA

value: GCAGAAGA+ACCTGGTT


title: CLL [G70101_GCLL-0065-T-01]

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

country: China

institute: Peking University Third Hospital

description: RRBS

library_source: genomic

data_processing:
Libraries were sequenced and aligned to the bisulfite-converted hg19 reference genome using Bismark v0.15.0 (Krueger et al., 2011) and the original methylation sites were inferred based on cytosine-to-thymine conversion.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Methyl call files are in .txt format.

molecule: genomic DNA

source_name: CLL cells

extract_protocol:
Genomic DNA was isolated and quantified using previously described methods (Boyle et al., 2012).
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

tag: tissue

value: Chronic lymphocytic leukemia

tag: time point

value: Before treatment


title: WTd70repC

value: GCAGAAGA+TGTGGCAT


title: MUTd50repC

value: AACCTACG+GGTAAGCT


title: WTd50repD

value: AACCTACG+TGTGGCAT


title: WTd70repB

value: GCAGAAGA+CGGAACAA


title: N02-Feb

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

data_processing:
Preliminary quality control of raw reads was carried out with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality and adapter trimming of Illumina raw sequences was performed with Trim Galore v0.6.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using a two-step approach, which allowed us to remove two additional bases containing a cytosine, which were artificially introduced in the end-repair step during the library preparation.
Bismark software (version 0.22.1) (Krueger et al. 2011) was used to align each bisulfite-treated read to the bovine reference genome (ARS-UCD1.2) with option -N 1 (maximum number of mismatches allowed). The reference genome was first transformed into a bisulfite-converted version (C-to-T and G-to-A conversions) and then indexed using bowtie2 software (Langmead et al 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A conversions) before they were aligned to similarly converted versions of the genome in a directional manner.
Sequence reads that produced the best unique alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence, and the methylation state of all cytosine positions in the reads was inferred using the Bismark_methylation_extractor function.
Read duplicates were marked and removed using Picard Tools v2.2 (http://broadinstitute.github.io/picard).
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: For each sample were generated a tab-delimited cov file with methylation call for every single position including the following fileds: chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

organism: Bos taurus

source_name: CD4+ lymphocyte cells

extract_protocol:
DNA was extracted from CD4+ cells following the QIAamp DNA Blood Midi Kit (Qiagen) procedures. gDNA concentration was measured with Quant-it Picogreen dsDNA assay and 1 μg input was used in the MSP1 digest. Following overnight incubation at 37°C, digestion reactions were terminated by adding 0.5 M EDTA and purified on a GeneJET PCR purification column.
Libraries were prepared using the NEB Next Ultra DNA library preparation kit for Illumina and methylated adapters. Subsequently, ligated products corresponding to DNA fragments 150–400-bp long were isolated and purified using 2.5% agarose gel electrophoresis. The recovered DNA was bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research). DNA with a known methylation level was used as a spike control, and all conversion rates were >99%, ranging from 99.15 to 99.41% (Supp.Table 2). Fourteen cycles of PCR were performed, and the products were purified using AMPureXP beads. Twenty Reduced Representation Bisulfite Sequencing (RRBS) libraries were used for cluster generation and subsequent sequencing on Illumina HiSeq2500 PE 2 × 50 bp (NXT-Dx Ghent, Belgium, http://www.nxt-dx.com/)

tag: breed

value: Nellore

tag: month

value: February

tag: experimental design

value: Challenge period

tag: treatment

value: Exposed to sun - high Temperature Humidity Index


title: A05-Feb

value: Angus


title: N04-Jun

value: June

value: Recovery period

value: Shadow available


title: N05-Jun


title: N01-Jun


title: N04-Feb


title: N01-Feb


title: N02-Jun


title: N03-Feb


title: MUTd70repD

value: iPS Derived SFTPC+ Cell

value: Male

value: DKC1 A386T

value: AATCCAGC+GAGAGGTT


title: N05-Feb


title: N03-Jun


title: MUTd50repD

value: AACCTACG+ACTACGGA


title: A04-Feb


title: A03-Jun


title: WTd50repC

value: DKC1 A386

value: AACCTACG+CGGAACAA


title: A05-Jun


title: MUTd47repB

value: AACCTACG+AAGCGGAA


title: A04-Jun


title: A03-Feb


title: WTd47repB

value: AACCTACG+ACCTGGTT


title: MUTd47repA

value: AACCTACG+GAGAGGTT


title: CON rep4

city: Shanghai

first: Bo

last: Xu

state: Shanghai

address: 1665 Kongjiang Road

department: Department of Anesthesiology and SICU

institute: Xinhua Hospital, Shanghai Jiaotong University, School of Medicine

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.2.0 mapping to reference genome
count counting
Genome_build: GRCm38（mm10）
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Mus musculus

source_name: Lung

growth_protocol: Mice were housed in a temperature controlled room (22±2°C) with 12 h dark /12 h light cycle and given ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: After intraperitoneal anesthesia with ketamine at 100 mg/kg, mice were fixed in a supine position, then endotracheal intubation was performed, and the tube was connected to a rodent ventilator. Ventilation was performed at tidal volume of 30 ml/kg and respiratory rate of 70 breaths/min for 4 h. Mice in sham group underwent intubation but breathed freely. At the end of experiment, animals were sacrificed by anesthetic overdose, and the lung tissues were harvested for further detections.

tag: strain

value: ICR

tag: age

value: 7-9 weeks

tag: genotype/variation:

value: control


title: WTd47repA

value: AACCTACG+TTGCTTGC


title: CON rep3


title: CON rep5


title: A01-Jun

value: Angus

value: June


title: A01-Feb

value: February

value: Challenge period

value: Exposed to sun - high Temperature Humidity Index


title: A02-Jun

value: Recovery period

value: Shadow available


title: A02-Feb


title: MUTd30repC

value: iPS Derived SFTPC+ Cell

value: Male

value: DKC1 A386T

value: CGGCTATG+ACTACGGA


title: CON rep2


title: CON rep1


title: Jowoon 60 DAH endosperm rep2

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

country: South Korea

institute: Seoul National University

data_processing:
Base calling: Illumina HiSeq 2000 base calling software
Quality check: fastqc
Trimming: Trimmomatic
Alignment: Hisat2
Differentially expression gene: edgeR
Genome_build: IRGSPv1.0

organism: Oryza sativa

source_name: Rice seed

growth_protocol: All plant materials were cultivated in the experimental field of Seoul National University, Suwon, South Korea.

extract_protocol:
Total RNA was harvested using Trizol reagent. SENSE mRNA-Seq Library Prep Kit V2 for Illumina platforms (Cat. No. 001.96)  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina platform.

value: Endosperm

value: Wild type

tag: maturation stage

value: 60 days after heading

tag: ecotype

value: Jowoon


title: Jowoon 45 DAH embryo rep1

value: Embryo

tag: genotype

value: 45 days after heading


title: Jowoon 45 DAH endosperm rep1


title: Jowoon 45 DAH embryo rep2


title: Gopum 60 DAH endosperm rep1

value: Gopum


title: Jowoon 45 DAH endosperm rep2


title: Jowoon 30 DAH endosperm rep1

value: 30 days after heading


title: Jowoon 60 DAH embryo rep2


title: Jowoon 30 DAH embryo rep1


title: Gopum 60 DAH endosperm rep2


title: Jowoon 60 DAH endosperm rep1


title: Jowoon 30 DAH embryo rep2


title: Jowoon 60 DAH embryo rep1


title: Jowoon 30 DAH endosperm rep2


title: VILI rep5

value: ICR

value: 7-9 weeks

value: VILI


title: Gopum 60 DAH embryo rep2


title: WTd30repC

value: DKC1 A386

tag: timepoint

value: CGGCTATG+TGTGGCAT


title: VILI rep4


title: Gopum 60 DAH embryo rep1


title: VILI rep3


title: MUTd30repB

value: iPS Derived SFTPC+ Cell

tag: rin

value: CGGCTATG+GGTAAGCT


title: Gopum 45 DAH endosperm rep2


title: VILI rep2


title: VILI rep1


title: MUTd30repA

value: Male

value: DKC1 A386T

tag: barcode

value: TCCGCGAA+GAGAGGTT


title: Gopum 45 DAH endosperm rep1

value: Endosperm

value: Wild type


title: WTd30repA

tag: cell type

value: TCCGCGAA+TTGCTTGC


title: TULTWOC1B1

city: Wellesley

first: Andrea

last: Sequeira

state: MA

address: 106 Central St

department: Department of Biological Sciences

institute: Wellesley College

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code TulTwo.
b3_C42i_Simple.csv, b3_C45i_Simple.csv, b3_C67i_low.csv, b3_C39i_Simple.csv

data_processing:
sequencing: paired-end reads from the Illumina HiSeq 2500; fastQC to filter sequences with low quality
reference transcriptome assembly: Trinity/bowtie alignment script, see publication methods for further details
alignment: bowtie to align all transcripts to protein sequences in UniProt, retaining best match for annotation
generation of abundance measurements: RSEM for quantification of transcript abundance and gene expression levels from the Trinity assembly
normalization of gene expression & outlier removal: remove low-expression genes with counts per million of less than 1 in all samples; normalize RNA composition via TMM scaling (edgeR package in R); normalized gene counts transformed to log2 (limma package in R); filter out outliers with low numbers of gene detected, low median expression values, or high % reads from top gene
differential gene expression analysis: use the R package limma for comparisons of expression that contain more than one sample in the groups to be compared; for comparisons with one sample per group, generate a table of log2 fold change, deltaFPKM, and log2FC adjusted by mean expression level for each gene that passed prior QC based on median expression. adjusted log2FC of +/-1 and deltaFPKM of > 1 were considered to be differentially expressed.
gene set enrichment analysis: GSEA
Genome_build: FASTA files with transcript sequences included on series record.
Supplementary_files_format_and_content: .csv file including gene expression raw counts, fold change, and annotated transcript identity for the samples corresponding to that comparison.

molecule: polyA RNA

organism: Naupactus cervinus

source_name: adult abdominal tissue

growth_protocol: Weevils were collected from Argentina in Buenos Aires and Entre Rios Provinces (7 localities) and within the United States in Georgia, Florida, Alabama (6 localities), and California (4 localities) (S1 Table). Adult weevils were maintained in temperature-controlled environmental rooms with 12:12 dark/light cycles at 24-28Â°C and 50% humidity (after Tarrant and McCoy, 1989) for a three-week acclimation period. Each set of weevils was fed their natal host plant. Weevil rearing boxes were checked daily for eggs, and juvenile specimens were separated, allowed to develop for 7-10 days, and frozen before active feeding on plant matter began. Adults were processed three weeks after the acclimation period.

extract_protocol:
Adults and immature (larval) specimens were frozen and preserved in RNAlater (Invitrogen, Carlsbad, CA). RNA extraction was performed using the PureLink RNA Mini Kit (Ambion, Carlsbad, CA). To obtain enough RNA from adult tissues we extracted material from a pool of six weevils for the head and abdomen samples. To extract RNA from immature tissues, between 50 to 100 first instar larvae were pooled, also maintaining the parental host plant and locality of origin. RNA concentration and quality were assessed using a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific, Carlsbad, CA) and a Qubitâ„¢ 4 fluorometer (Invitrogen, Carlsbad, CA).
mRNA sequencing using the standard Illumina Stranded mRNA prep

treatment_protocol: For a set of experimental host switch trials, individual adults were randomly assigned to continue consuming their natal host or to switch to a novel host plant after the three-week acclimation period and processed after an additional three weeks.

tag: experimental host switch

value: no host switch

tag: life stage

value: adult


title: TULTWOC1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code TulTwo.
b3_C66i_low.csv, b3_C38i_Simple.csv, b3_C41i_Simple.csv, b3_C44i_Simple.csv

source_name: adult head tissue


title: Young Sham 2

city: Columbus

first: Emily

last: Nordquist

state: OH

address: 575 Children's Crossroad

department: Department of Cardiovascular Research

institute: Nationwide Children's Hospital

description:
aortic heart valve from 1 individual mouse
CA7610710

data_processing:
Raw FASTQs were split into files containing 4,000,000 reads and checked for quality using the FASTX-Toolkit
The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (3 nucleotides at the left end of the R1 reads and 1nt at the left end of the R2 reads)
Sequence alignment was performed using TopHat v2.1.0 to the mm10 genome.
Exon and gene level counting were performed using the easyRNASeq version 2.4.7 package. A binary annotation file, built using the annotation file generation function of EasyRNASeq, was used for this analysis; the Ensembl release 83 GTF file was used as input.
Filtering of the reads per kilobase million (RPKM) values was performed to retain a list of genes with a minimum of approximately 50 mapped reads in 25% or more samples
To avoid reporting large fold changes due to random variation of counts from low abundance mRNA, RPKM values equivalent to a count of <= 10 reads per gene were replaced with the average RPKM value equivalent to 10 reads/gene across all the samples in the experiment.
Genome_build: mm10
Supplementary_files_format_and_content: 2019-09-09-Lincoln_MCW_Anno_genes_raw copy.txt, 2019-09-09-Lincoln_MCW_Anno_genes_rpkm_nomit_filtered copy.txt

source_name: wild type, aortic heart valve

growth_protocol: Wild type mice were aged to 3-4 months of age for the young timepoint or 16-18 months of age for the aging timepoint

extract_protocol:
Mice were euthanized 48 hours after surgery and aortic valves were isolated on cold 1xPBS, then flash frozen in liquid nitrogen and stored at -80.Total RNA was isolated from the tissue samples using TRI Reagent according to the manufacturer’s user manual (Molecular Research Center #TR118). Following isolation, RNA was quantified by O.D. measurement, digested with RNase free DNase I (Epicentre #D9905K), and re-purified using RNA Clean XP magnetic beads (Beckman Coulter #A63987).  The newly digested RNA samples were then assessed by denaturing gel electrophoresis using a 1% agarose – 2 % formaldehyde gel.
Amplified cDNA libraries suitable for sequencing were prepared from 200 nanograms (ng) of DNA-free total RNA using the Universal Plus mRNA-Seq Library Prep Kit (NuGEN Technologies, Inc.; Part # 0508-96). The quality and size distribution of the amplified libraries were determined by chip-based capillary electrophoresis on Agilent 2100 Bioanalyzer High Sensitivity DNA assays (Agilent Technologies; Part # 5067-4626). Libraries were quantified using the Takara Library Quantification Kit (Part # 638324). The libraries were pooled at equimolar concentrations and diluted prior to loading onto a flow-cell on an Illumina cBot. The libraries were extended, and bridge amplified to create sequence clusters. The flow cell was transferred to the HiSeq 4000 instrument and sequenced using 150 nt paired-end reads plus a single index read.

treatment_protocol: Murine aortic valves were subjected to in vivo wire injury surgery to damage the endothelial layer of the aortic valve, or in vivo sham surgery as a control procedure.

tag: tissue

value: aortic valve

value: 3-4 months

tag: surgery

value: Sham


title: Young Injury 2

description:
aortic heart valve from 1 individual mouse
CA7610709

value: Injured


title: Gopum 30 DAH endosperm rep2

value: 30 days after heading

value: Gopum


title: Gopum 45 DAH embryo rep2

value: Embryo

value: 45 days after heading


title: Gopum 45 DAH embryo rep1


title: Young Injury 3

description:
aortic heart valve from 1 individual mouse
CA7610711


title: WTd30repB

value: iPS Derived SFTPC+ Cell

tag: Sex

value: DKC1 A386

value: CGGCTATG+CGGAACAA


title: TULTHREEC6(2)I2

description:
Immature tissue prep 2 of Naupactus cervinus from locality code TulThree (host switch experiment).
b3_C71i_Simple.csv

source_name: immature larval tissue

value: immature


title: Gopum 30 DAH embryo rep2


title: TULTHREEC6(2)B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code TulThree (host switch experiment).
b3_C71i_Simple.csv


title: Young Sham 1

description:
aortic heart valve from 1 individual mouse
CA7610717


title: Gopum 30 DAH embryo rep1


title: Gopum 30 DAH endosperm rep1

value: Endosperm


title: Young Injury 1

description:
aortic heart valve from 1 individual mouse
CA7610707


title: IF/TA_Pt22

type: RNA

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

label: biotin

source_name: Kidney biopsies

label_protocol: RNA was amplified and labeled using the SensationPlus™ Kit (Affymetrix, Santa Clara, CA, USA) per manufacturer instructions.

extract_protocol: Total RNA was isolated using the High Pure RNA Paraffin Kit (Roche, IN, USA) per manufacturer instructions.

tag: cell line name

value: FFPE Tissue

tag: sample type

value: pediatric transplant recipients with histological diagnosis of interstitial fibrosis/tubular atrophy (IF/TA)


title: TULTHREEC6(2)A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code TulThree (host switch experiment).
b3_C70i_Simple.csv

value: no host switch


title: AR_Pt17

value: pediatric transplant recipients with histological diagnosis of Acute Rejection (AR)


title: IF/TA_Pt21


title: IF/TA_Pt20


title: IF/TA_Pt23


title: IF/TA_Pt24


title: AR_Pt18


title: WT-rB_CpG [SC21]

city: New York

first: Shukti

last: Chakravarti

state: New York

address: 430 E 29th St

department: Department of Ophthalmology and Pathology

institute: NYU Langone Medical Center

data_processing:
The raw read (FASTQ) files were checked for contaminations, adaptor sequences, or other over-represented sequences using FastQC0.11.7; no contaminating sequences were found in the samples.
Transcript expression was quantified using kallisto 0.44.0 with default parameters and prebuilt indices for ensemble mouse GRCm38.96 (https://github.com/pachterlab/kallisto-transcriptome-indices/releases/download/ensembl-96/mus_musculus.tar.gz) (Bray et al, 2016; Nature Biotechnology). Transcript levels were expressed as total reads per million (tpm).
Sequencing control software-HCS v2.2.38
Illumina Hiseq generates raw images utilizing HCS v2.2.28 for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. V1.18.61.0). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4)
In order to verify the integrity of files, md5sum is used.
Supplementary_files_format_and_content: TPM

growth_protocol: Peritoneal lavage was collected from un-elicited Wt/Lum-/- (LKO)/Bgn-/0, -/- (BKO) mice (n=10) by flushing the peritoneal cavity with 6ml of ice-cold PBS. CD11b+ cells were then purified by using CD11b+ selection kit (Stemcell Technology). CD11b+ cells were then suspended in DMEM-F12 (1% charcoal stripped serum) and incubated in 12 well plate (2 x 106 cells/well) for ON at 5% CO2/37OC.

extract_protocol:
Cells were then washed 2x with ice-cold PBS and then lysed directly with RLT buffer and stored in -80oC for RNA extraction on next day using QIAGEN RNA extraction kit with DNAse I treatment.
Library preparation (TruSeq stranded RNA library kit) and sequencing was performed by Macrogen Inc. using an Illumina HiSeq. 2500 platform.
TrueSeq Standard RNA library

treatment_protocol: After overnight incubation cells were washed 2 times with warm PBS w/o Ca2+/Mg2+ and then replaced with serum-free fresh DMEM-F12 media. Cells were then treated with different stimuli as mentioned below: 1) Treated with LPS only 100ng/mL for 6h    OR  2) Treated with 1uM CpG for 6h      OR  3) Pre-treated for 1h with 10ug/mL of recombinant lumican or biglycan followed by LPS or CpG treatment for 6h.

tag: strain background

tag: genotype/variation

value: WT

value: CD11b+ cells

tag: treatment

tag: size (bp)

tag: conc. ng/ml


title: Aging Sham 3

description:
aortic heart valve from 1 individual mouse
CA7610706

value: aortic valve

tag: age

value: 16-18 months

value: Sham


title: AR_Pt16


title: IF/TA_Pt25


title: TULTHREEC6(1)I2

description:
Immature tissue prep 2 of Naupactus cervinus from locality code TulThree (host swap experiment).
b3_C70i_Simple.csv

value: host switch


title: WT-rB [SC20]

value: rB


title: TULTHREEC6(1)B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code TulThree (host switch experiment)
b3_C69i_Simple.csv

value: adult


title: WT-rL [SC19]

value: rL


title: IF/TA_Pt19


title: Aging Sham 2

description:
aortic heart valve from 1 individual mouse
CA7610705


title: TULTHREEC6(1)A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code TulThree (host switch experiment).
b3_C69i_Simple.csv


title: AR_Pt14


title: WT-rB-LPS [SC18]

value: rB-LPS


title: Aging Injury 1

description:
aortic heart valve from 1 individual mouse
CA7610715

value: Injured


title: Aging Injury 2

description:
aortic heart valve from 1 individual mouse
CA7610716


title: WT-rL_CpG [SC17]


title: TULTHREEC4I2

description:
Immature tissue prep 2 of Naupactus cervinus from locality code TulThree (host 4).
b3_C68i_Simple.csv, b3_C49i_Simple.csv, b3_C43i_Simple.csv, b3_C55i_Simple.csv

value: immature


title: TULTHREEC4B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code TulThree (host 4).
b3_C48i_Simple.csv, b3_C54i_Simple.csv, b3_C42i_Simple.csv, b3_C67i_low.csv


title: Aging Sham 1

description:
aortic heart valve from 1 individual mouse
CA7610701


title: WT-rL-LPS [SC16]

value: rL-LPS


title: AR_Pt15

value: FFPE Tissue


title: TULTHREEC4A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code TulThree (host 4).
b3_C47i_Simple.csv, b3_C53i_Simple.csv, b3_C41i_Simple.csv, b3_C66i_low.csv


title: AR_Pt12


title: AR_Pt13


title: SA_SD

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description: mRNA from single cells

data_processing:
Transcripts from mice were mapped to the reference genome (GRCm38.93/mm10) using Cell Ranger Version 3.0.2
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Analysis of all data sets was performed using Seurat (Version 3.0.0)
Genome_build: mm10
Genome_build: GRCm38.39
Supplementary_files_format_and_content: Seurat output

source_name: SA_SD_dorsal skin

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Single cells were isolated as previously described (Guerrero-Juarez, et al. Nat Commun. 2019)
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at the UCI Genomics High Throughput Facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics

tag: strain

value: male

value: 48 hours post-S. aureus-infection

tag: diet

value: Standard diet

value: Dorsal skin


title: WT-CpG [SC15]

value: WT

value: CD11b+ cells

value: CpG


title: SA_HFD

description: mRNA from single cells

source_name: SA_HFD_dorsal skin

value: 60% high fat diet


title: WT-LPS [SC14]

value: LPS


title: PBS_SD

description: mRNA from single cells

source_name: PBS_SD_dorsal skin

value: 48 hours post-mock-infection


title: Tala81C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Tala81.
b2_Ncerv_DEG.csv

value: no host switch

value: adult


title: Normal_Case12

source_name: Normal allografts

value: normal


title: WT-Untreated [SC13]

value: Untreated


title: Normal_Case11


title: PBS_HFD

description: mRNA from single cells

source_name: PBS_HFD_dorsal skin


title: Tala81C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Tala81.
b2_C25in.csv, b2_Ncerv_DEG.csv


title: BKO-rB [SC12]

source_name: Bgn-/-

value: Bgn-/-

value: rB


title: 200 nM 48 h

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Typically, base call quality diminishes toward the end of a read. This is characteristic to first- and second-generation sequencing technologies (Sanger, Illumina, SOLiD, 454)
SOAPnuke, a filtering software independently developed by BGI, is used for filtering.
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts or in FPKM (fragments per thousand nucleotides per million mapped reads).
Genome_build: hg19_ucsc
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: breast cancer cell

growth_protocol: MDA-MB-231 cells were cultured in a humidified incubator equilibrated with 5% CO2 at 37 °C. The media (Dulbecco Modified Eagle Medium (DMEM)) was supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 24h or 48h in adherent conditions with 100 nM and 200 nM PCI-24781 or DMSO.

tag: cell line

tag: treatment duration

tag: dose


title: Normal_Case10

value: FFPE Tissue


title: Normal_Case09


title: BKO-rB-CpG [SC11]

tag: cell type

value: rB-CpG


title: BKO-rB-LPS [SC10]

value: rB-LPS


title: 200 nM 24 h


title: TULONETWOC1I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code TulOne/Two.
b3_C43i_Simple.csv, b3_C46i_Simple.csv, b3_C68i_Simple.csv, b3_C40i_Simple.csv

tag: experimental host switch

tag: life stage

value: immature


title: Normal_Case08


title: 100 nM 24 h


title: BKO-CpG [SC9]


title: Quin71C1(2)B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Quin71 (host swap experiment)
b1_Ncerv_DEG.csv


title: Quin71C1(1)B1

value: host switch


title: BKO-LPS [SC8]


title: Normal_Case05


title: DMSO 48 h

value: DMSO


title: Normal_Case06


title: Ros77C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Ros77.
b2_Ncerv_DEG.csv


title: Normal_Case03


title: BKO-Untreated [SC7]

value: CD11b+ cells


title: DMSO 24 h


title: Quin71C1(1)A1

description:
Adult head tissue prep 1 of Naupactus cervinus from locality code Quin71 (host swap experiment)
b1_Ncerv_DEG.csv


title: Normal_Case04


title: LKO-rL [SC6]

source_name: Lum-/-

value: Lum-/-

value: rL


title: QUIN71C4I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code Quin71 (host 4).
b3_C58i_Simple.csv


title: LKO-rL-CpG [SC5]

value: rL-CpG


title: Young Sham 3

description:
aortic heart valve from 1 individual mouse
CA7610712

tag: tissue

value: aortic valve

value: 3-4 months

tag: surgery

value: Sham


title: 100 nM 48 h


title: N2_F3_embs_NaCl_6A

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: poly(A) RNA

data_processing:
Quality controlled and adapter trimming of RNA reads were performed using fastp-v0.20.0
Next, reads were aligned using STAR-2.7.1a
Read counts were obtained using subread-2.0.0
Genome_build: C. elegans WS275, C. briggsae WS275, C. tropicalis WS275 and the C kamaaina
Supplementary_files_format_and_content: feature Counts or HTSeq-count, raw counts.

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: All samples of all species were grown from embryo to young adulthood on E. coli HB101 as a food source. Young adults were transferred to plates seeded with different stressful bacteria or 300 mM NaCl plates for 24 hours.

extract_protocol:
Samples were frozen and thawed 5 times and then refrozen. Beijing Genomics perfomed extracts from trizol using a standard phenol cholorform extraction approach.
DNB-Seq standardized library construction was performed by Beijing Genomics using their proprietary technology. DNB-Seq - PE100

treatment_protocol: Embryos collected from control and stressed parents were snap frozen in trizol using liquid nitrogen.

value: Whole organism

tag: accession

tag: developmental stage

value: Embryo

value: F3 animals from NaCl stress


title: N2_F3_embs_NaCl_5A

description: poly(A) RNA


title: Normal_Case01

tag: cell line name

tag: sample type

value: normal


title: QUIN71C2I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code Quin71 (host 2).
b3_C57i_Simple.csv

value: no host switch


title: N2_F3_embs_NaCl_4A

description: poly(A) RNA

tag: treatment


title: Post70C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Post70.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv, b3_C67i_low.csv

value: adult


title: LKO-CpG [SC3]

tag: strain background

tag: genotype/variation

value: CpG

tag: size (bp)

tag: conc. ng/ml


title: N2_F3_embs_BIGb446_9A

description: poly(A) RNA

value: F3 animals from P. vranovensis BIGb0446


title: Quin71C1(2)A1


title: Post70C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Post70.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv, b2_C25in.csv, b3_C66i_low.csv


title: Ros77C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Ros77.
b2_Ncerv_DEG.csv


title: LKO-LPS [SC2]

value: LPS


title: Normal_Case02

value: FFPE Tissue


title: CNIT_Pt11

value: pediatric transplant recipients with histological diagnosis of calcineurin inhibitor toxicity (CNIT)


title: N2_F3_embs_BIGb446_8A

description: poly(A) RNA


title: Per76C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Per76.
b2_Ncerv_DEG.csv


title: N2_F3_embs_BIGb446_7A

description: poly(A) RNA


title: CNIT_Pt10


title: LKO-Untreated [SC1]

value: Lum-/-

value: CD11b+ cells

value: Untreated


title: IRF4-ChIP-seq from mouse cDC2

city: Saint Louis

first: Sunkyung

last: Kim

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using  Bowtie 1.1.1.
Tag directories were made using makeTagDirectory program of the Homer Software package.
Peak calling was performed by ‘findPeaks’ of the Homer Software package.
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH were made using makeUCSCfile program of the Homer Software package.

source_name: cDC cultured with Flt3 ligand derived from bone marrow

growth_protocol: Bones were isolated and crushed using mortar and pestle. After red blood cell lysis, whole bone marrow progenitors were cultured with 100 ng/mL Flt3 ligand for 9 days.  CD11c+ MHC II+ CD24- CD172a+ BST2- CD45RA- cDC2s were sort-purified ( >95% purity) using FACS AriaFusion

extract_protocol:
Cells were crosslinked with 1% formaldehyde, quenched with 1.25M Glycine, washed twice with PBS. The chromatin was sonicated to shear DNA size from 140 to 500 bp. Chromatin fragments were immunoprecipitated with anti-IRF4 antibodies (sc-6059x, Santa Cruz Biotechnology) and Dynabeads Protein G overnight at 4 °C. ChIPed DNA was eluted and reverse-crosslinked for 6 hr. DNA was purified with phenol:chloroform extraction followed by ethanol precipitation. Processes for DNA isolation, library construction, and sequencing are performed the same way with GSE66899 dataset. Detailed methods were described in Nature Immunology (2015)_Grajales-Reyes and Murphy (PMID: 26054719)
Libraries for ChIP-seq were prepared using ThruPLEX-FD kit (Rubicon Genomics) and sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.

tag: strain

value: Bone marrow

value: bone marrow-derived conventional dendritic cell 2 (cDC2)

tag: chip antibody

value: Anti-IRF4 (M-17), sc-6059x, Santa Cruz Biotechnology


title: CNIT_Pt08


title: LKO-rL-LPS [SC4]

value: rL-LPS


title: CNIT_Pt09


title: Per76C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Per76.
b2_Ncerv_DEG.csv


title: RH4 Ent6 p300

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.
Spike in normalization was done by dividing the number of human reads in each bin according to million mapped dm3 reads.
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Cells were grown to 80% confluence, treated with either DMSO (0.05% by volume) or HDAC inhibitor Entinostat (final concentration 1 uM) for 1 or 6 hours. Samples were then harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen). Spike in of drosophila chromatin was performed using the Active Motif components (cat # 61686, cat # 53083).

tag: antibody

value: p300 Antibody (C-20):sc-585 - Santa Cruz Biotechnology

tag: enrichment target

tag: target function

value: Histone modification

value: Entinostat 1 microM


title: N2_cntrl_2A

description: poly(A) RNA

value: Whole organism

value: Embryo

value: F3 animals from E. coli HB101


title: Otta78C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Otta78.
b2_Ncerv_DEG.csv

tag: experimental host switch

value: no host switch

tag: life stage

value: adult


title: CNIT_Pt06

value: FFPE Tissue


title: RH4 D6 p300

value: DMSO


title: N2_cntrl_1A

description: poly(A) RNA

tag: tissue


title: CNIT_Pt07

value: pediatric transplant recipients with histological diagnosis of calcineurin inhibitor toxicity (CNIT)


title: Otta78C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Otta78.
b2_C25in.csv, b2_Ncerv_DEG.csv


title: POST70C1I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code Post70.
b3_Ncerv_DEG.csv, b3_C57i_Simple.csv, b3_C58i_Simple.csv, b3_C68i_Simple.csv

value: immature


title: N2_15446_3A

description: poly(A) RNA

tag: accession

value: NaCl and P. vranovensis concurrently


title: CNIT_Pt04


title: 20231-007_S7

first: Whitney

last: England

state: CA

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

description: RNA from extracellular vesicles

data_processing:
Reads containing ambiguous bases or with a mean quality score < 30 were removed from analysis using Prinseq.
UMIs were identified and extracted from the remaining reads using UMI-Tools
Reads were aligned to all human mature miRNAs or pre-miRNAs from miRBase v22 using bowtie2 with "very sensitive" parameters and a seed length of 8bp with no mismatches allowed in the seed. Primary mappings >= 16bp in length were retained for further analysis.
Mapped reads were deduplicated with UMI-Tools using the unique grouping method, considering each unique UMI an individual miRNA.
Read counts for each miRNA were determined using samtools.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv: Sample x miRNA matrix of raw read counts

source_name: cerebrospinal fluid

extract_protocol:
CSF samples were acquired by lumbar puncture. RNA was isolated from 4mL CSF using the exoRNeasy Serum/Plasma Maxi Kit per the manufacturer’s instructions.
Library preparation was performed using the QIAseq miRNA Library Kit.

value: cerebrospinal fluid

tag: disease state

value: HD


title: 20231-010_S10

description: RNA from extracellular vesicles


title: Oleary72C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Oleary72.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv


title: Oleary72C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Oleary72.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv


title: N2_15446_2A

description: poly(A) RNA

tag: developmental stage


title: N2_cntrl_3A

description: poly(A) RNA


title: FBS42

description: poly(A) RNA

value: Aeromonas sp. BIGb0469


title: OLEAR72C1I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code Oleary72.
b3_C56i_Simple.csv


title: 20231-003_S3

description: RNA from extracellular vesicles


title: 20231-005_S5

description: RNA from extracellular vesicles


title: Nan79C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Nan79.
b2_Ncerv_DEG.csv


title: Normal_Case07

tag: cell line name

tag: sample type

value: normal


title: CNIT_Pt03


title: Sel1l KO DN3 cells rep2

city: Houston

first: Fanglue

last: Peng

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence,  and then map to mouse transcriptome GRCm38 using STAR 2.5.2b with parameter --outFilterMultimapNmax 10  --outFilterMultimapScoreRange 1 --alignSJDBoverhangMin 1  --sjdbScore 2 --alignIntronMin 20 --alignSJoverhangMin 8.
HTseq 2.7  was used to generate raw read counts for each gene
htseq count tables of all samples were then imported to DEseq2. We filtered out the genes with less than 1 read count and performed differential gene expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Table with RPKM for every gene and every sample

source_name: DN3 cells

extract_protocol:
DN3 thymocytes were directly sorted into TRIzol LS (ThermoFisher, cat. 10296028) and RNA was extracted following the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Sel1l-f/f hCD2cre+

tag: age

value: 6 weeks


title: CNIT_Pt05


title: Sel1l KO DN3 cells rep3


title: 20231-002_S2

description: RNA from extracellular vesicles


title: CNIT_Pt01


title: Sel1l KO DN3 cells rep4


title: Nan79C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Nan79.
b2_C25in.csv, b2_Ncerv_DEG.csv


title: CNIT_Pt02


title: FBS41

description: poly(A) RNA

tag: treatment


title: Sel1l KO DN3 cells rep1


title: KERTWOC2I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code KerTwo.
b3_C68i_Simple.csv, b3_C40i_Simple.csv, b3_C49i_Simple.csv, b3_C52i_Simple.csv


title: FBS40

description: poly(A) RNA


title: 108-60_S14

description: RNA from extracellular vesicles


title: WT DN3 cells rep4


title: FBS39

description: poly(A) RNA

value: P. vranovensis BIGb427


title: KERONEC1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code KerOne.
b3_C39i_Simple.csv, b3_C48i_Simple.csv, b3_C51i_Simple.csv, b3_C67i_low.csv

source_name: adult abdominal tissue


title: 108-59_S13

description: RNA from extracellular vesicles


title: WT DN3 cells rep3


title: N2_15446_1A

description: poly(A) RNA

value: Whole organism


title: FBS38

description: poly(A) RNA

value: Embryo


title: KERONEC1A1

description:
Adult head tissue prep 1 of Naupactus cervinus from locality code KerOne.
b3_C38i_Simple.csv, b3_C47i_Simple.csv, b3_C50i_Simple.csv, b3_C66i_low.csv

source_name: adult head tissue


title: 108-51_S12

description: RNA from extracellular vesicles


title: WT DN3 cells rep2


title: FBS37

description: poly(A) RNA


title: 108-102_S6

description: RNA from extracellular vesicles


title: 108-88_S17

description: RNA from extracellular vesicles


title: For67C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code For67.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv, b3_C67i_low.csv


title: FBS35

description: poly(A) RNA

value: S. plymuthica


title: 20231-009_S9

description: RNA from extracellular vesicles

value: Ctrl


title: WT DN3 cells rep1


title: For67C1A1

description:
Adult head tissue prep 1 of Naupactus cervinus from locality code For67.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv, b3_C66i_low.csv

value: no host switch

value: adult


title: Byr68C1B1

description:
Adult abdomen tissue prep 1 of Naupactus cervinus from locality code Byr68.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv


title: Byr68C1A1

description:
Adult head tissue prep1 of Naupactus cervinus from locality code Byr68.
b1_Ncerv_DEG.csv, b2_Ncerv_DEG.csv


title: WT R2 erythrocytes, WT2

city: TianJin

first: Changlu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Clean reads were aligned the mouse genome sequence using HISAT2
StringTie was used to quantify gene and transcript isoform expression based on the aligned reads.
DEGs were identified by DESeq2 package with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene count and FPKM for each sample

source_name: Mouse  erythrocytes

extract_protocol: Total RNA was extracted using TRIzol(Invitrogen, Cat# 15596026). Library construction and data processing were performed by Novogene (Beijing, China),sequenced with an Illumina HiSeq platform that generate 150 bp paired-end reads.

tag: cell type

value: erythrocytes

tag: development stage

value: WT


title: WT R2 erythrocytes, WT1


title: 20231-008_S8

description: RNA from extracellular vesicles


title: FBS33

description: poly(A) RNA

value: E. coli HB101


title: WT R2 erythrocytes, WT3


title: FBS34

description: poly(A) RNA


title: 20231-006_S6

description: RNA from extracellular vesicles


title: 20231-004_S4

description: RNA from extracellular vesicles


title: FBS36

description: poly(A) RNA


title: Fundc1 deficiency  R2 erythrocytes, KO3

value: Fundc1 deficient


title: BYR68C1I1

description:
Immature tissue prep 1 of Naupactus cervinus from locality code Byr68.
b3_C56i_Simple.csv

source_name: immature larval tissue

value: immature


title: 20231-001_S1

description: RNA from extracellular vesicles

value: cerebrospinal fluid


title: FBS31

description: poly(A) RNA


title: FBS32

description: poly(A) RNA


title: Fundc1 deficiency  R2 erythrocytes, KO2


title: Atria_DKO_Male_M26

first: Gregory

middle: Robert

last: Grant

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
Raw RNA-seq reads were aligned to the GRCm38 build of the mouse genome by STAR v2.7.6a, with the following command line parameters: --outSAMunmapped Within KeepPairs--outFilterMismatchNmax33--seedSearchStartLmax33--alignSJoverhangMin 8. Additionally, STAR was provided with the gene models (Ensembl v91) in GTF format during alignments.
Data were normalized and quantified at both gene and exon-intron level, using a downsampling strategy implemented in the PORT pipeline (github.com/itmat/Normalization -v0.8.45e-beta).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files contain PORT-normalized/quantified gene-level read counts from uniquely-aligned reads that map to single genes.

source_name: heart atria

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
Heart atria and kidney medulla were collected from animals perfused with ice-cold PBS dissolved in UltraPure DEPC-treated water to minimize degradation of RNA. The tissues were immediately stored separately in RNAlater solution at 4ºC. After 24h, the tissue samples were transferred to -80ºC for storage until analyses. RNA was extracted using TRIzol Reagent and RNeasy Kit following the manufacturer’s protocol.
RNA integrity was checked on an Agilent Technologies 2100 Bioanalyzer. RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA Library Prep Kit.

treatment_protocol: Mice of both genders were fed a high salt diet (HSD, 8% NaCl, TD.92012, Harlan Teklad, Madison, WI) and saline containing 0.9% NaCl (Hospira, Lake Forest, IL) from 8-10 weeks of age for two weeks. Mice were weighed before and after the HSD feeding.

value: heart atria

value: Ipr/Ldlr DKO

tag: gender

value: male

tag: library barcode

value: ACGCACCT-GGTGAAGG


title: 108-82_S16

description: RNA from extracellular vesicles


title: Fundc1 deficiency  R2 erythrocytes, KO1


title: FB380_3_24

description: poly(A) RNA

value: Bacterial isolate 16H8


title: 108-81_S15

description: RNA from extracellular vesicles


title: FB380_3_23

description: poly(A) RNA

value: Whole organism


title: Atria_DKO_Male_M22

value: GACGTCTT-GGTTCACC


title: Atria_DKO_Male_M18

value: CCTTCACC-GACGCTCC


title: Cadherin-11 KD 48 hours replicate 4

city: Cleveland

first: Jiannan

last: Li

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
Paired-ended 100 base pair reads were trimmed with Trim Galore! (v.0.4.4) and checked for quality with FastQC (v0.11.7) (http://www.bioinformatics.babraham.ac.uk/projects) before alignment to the human genome (GRCh38.p13).
Reads were aligned using HISAT2 (v2.1.0). Output SAM files were then sorted and converted to BAM files and indexed in Samtools. Gene counts were determined by the number of uniquely aligned, unambiguous reads (Subread: featureCounts, v1.5.2) and annotated (GRCH38, Ensembl 99 release).
Raw counts were loaded into R (v3.6.2) and filtered to exclude transcripts that were lowly expressed (counts per million reads mapped [CPM] < 1) before performing differential expression (DE) analysis with DESeq2.
Genome_build: GRCh38.p13

source_name: Intestinal Myofibroblasts

growth_protocol: All HIMF were cultured in DMEM supplemented with 10% FBS, 2% L-Glut, 1% PSF, and 2.5% HEPES at 37 degree, 5% CO2 incubator.

extract_protocol:
RNA was isolated from HIMF using the Qiagen Mini RNeasy Kit
RNA-SEQ libraries were generated using Illumina TruSEQ kits following the manufacturer’s protocol

treatment_protocol: HIMF were treated with Cadherin-11 siRNA or scramble siRNA for 8 hour and waited for 48 hours, respectively

value: Crohn's disease stricturedl colon

tag: passages

value: passage 8-10

value: Cadherin-11 siRNA


title: 108-11_S7

description: RNA from extracellular vesicles

value: Ctrl


title: Atria_DKO_Male_M14

city: Philadelphia

value: AGCTCGCT-GCAGAATC


title: FB380_3_22

description: poly(A) RNA

value: Embryo


title: Cadherin-11 KD 48 hours replicate 3


title: 108-07_S5

description: RNA from extracellular vesicles


title: Cadherin-11 KD 48 hours replicate 2


title: FB380_3_21

description: poly(A) RNA

value: E. coli HB101


title: Atria_DKO_Male_M10

value: GGTGAACC-GCGTTGGA


title: Atria_DKO_Male_M6

value: GGAGCGTC-GTCCGTGC


title: 108-04_S1

description: RNA from extracellular vesicles

value: cerebrospinal fluid


title: SMART-Seq_MONO_R848_20h_D3

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using kallisto
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analysed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Genome_build: Ensembl human transcriptome (version 96)
Supplementary_files_format_and_content: File includes sample specific read counts per gene in FPKM

source_name: human CD14+ monocytes

growth_protocol: Granulocytes were isolated from buffy coats of healthy donors and manipulated under endotoxin-free conditions. After Ficoll-Plaque gradient centrifugation, followed by dextran sedimentation and hypotonic lysis of erythrocytes, neutrophils were isolated to reach 99.7 ± 0.2 % purity, by positively removing any eventual contaminating cells using the EasySep neutrophil enrichment kit (StemCell Technology, Vancouver, Canada). Human monocytes were isolated from PBMCs by anti-CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) to reach > 98 % purity. Neutrophils and monocytes were then suspend at 5x106/ml in RPMI 1640 medium supplemented with 10 % low endotoxin FBS (< 0.5 EU/ml; from Sigma, Saint Louis, MO, USA),

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

treatment_protocol: Neutrophils and monocytes were treated or not with  5 µM R848, seated either in 6/24-well tissue culture plates or in polystyrene flasks (Greiner Bio-One, Kremsmüster, Austria), and cultured at 37°, 5 % CO2 atmosphere.

tag: time

value: CD14+ monocytes


title: Cadherin-11 KD 48 hours replicate 1


title: Atria_DKO_Male_M4

value: heart atria

value: Ipr/Ldlr DKO

value: male

value: GATTCTGC-GACGAGAG


title: FB380_3_20

description: poly(A) RNA

value: Whole organism


title: Atria_DKO_Male_M24

value: TCATCCTT-AGCGAGCT


title: Untreated 48 hours replicate 4

value: Crohn's disease stricturedl colon

value: scramble siRNA


title: FB380_3_19

description: poly(A) RNA


title: SMART-Seq_MONO_R848_20h_D2


title: Untreated 48 hours replicate 2

value: passage 8-10


title: Untreated 48 hours replicate 3


title: FB380_3_17

description: poly(A) RNA

value: Adult


title: Untreated 48 hours replicate 1


title: FB380_3_16

description: poly(A) RNA


title: SMART-Seq_MONO_UT_20h_D3

value: no treatment


title: SMART-Seq_MONO_UT_20h_D2


title: Atria_LdlrKO_Male_M23

value: Ldlr KO

value: CTCTCGTC-TATAACCT


title: SMART-Seq_MONO_UT_20h_D1


title: FB380_3_14

description: poly(A) RNA

value: Bacterial isolate 8D12


title: Atria_LdlrKO_Male_M21

value: AAGTCCAA-TATGAGTA


title: Atria_LdlrKO_Male_M17

value: GTATGTTC-AACAGGAA


title: Atria_LdlrKO_Male_M13

value: CTGCTTCC-GATAGATC


title: FB380_3_18

description: poly(A) RNA

value: E. coli HB101


title: Atria_DKO_Male_M2

value: heart atria

value: Ipr/Ldlr DKO

value: TCCAACGC-TTGGACTT


title: SMART-Seq_MONO_R848_6h_D1

value: 6 h

value: CD14+ monocytes


title: SMART-Seq_MONO_R848_6h_D2


title: Atria_LdlrKO_Male_M9

value: male

value: AGTACTCC-AACCTGTT


title: FB380_3_12

description: poly(A) RNA

value: Whole organism

value: Bacterial isolate16E12


title: FB380_3_10

description: poly(A) RNA

value: Adult


title: SMART-Seq_MONO_R848_20h_D1


title: SMART-Seq_MONO_UT_6h_D3

value: no treatment


title: SMART-Seq_MONO_UT_6h_D2


title: FB380_3_11

description: poly(A) RNA


title: FB380_3_09

description: poly(A) RNA

value: Bacterial isolate 16B11


title: Atria_LdlrKO_Male_M25

value: Ldlr KO

value: GCACGGAC-GTCTCGCA


title: SMART-Seq_MONO_UT_6h_D1


title: Atria_LdlrKO_Male_M1

value: AACAGGTT-ATACCAAG


title: FB380_3_15

description: poly(A) RNA

value: Bacterial isolate 8D12


title: FB380_3_08

description: poly(A) RNA


title: Atria_DKO_Female_F18

value: female

value: AAGATACT-ACTTACAT


title: SMART-Seq_MONO_R848_6h_D3


title: FB380_3_07

description: poly(A) RNA


title: Atria_DKO_Female_F16

value: heart atria

value: Ipr/Ldlr DKO

value: AGCCTCAT-AGTAGAGA


title: SMART-Seq_PMN_R848_20h_D2

source_name: human neutrophil

value: neutrophil


title: Atria_LdlrKO_Male_M5

value: male

value: TTCCTGTT-AGTATCTT


title: FB380_3_13

description: poly(A) RNA

value: Whole organism


title: SMART-Seq_PMN_R848_20h_D3


title: Atria_LdlrKO_Male_M3

value: GATCTATC-ATGAGGCT


title: Atria_DKO_Female_F12

value: ATGTAAGT-ACTCTATG


title: FB380_3_04

description: poly(A) RNA

value: Adult

value: Bacterial isolate 15F11


title: SMART-Seq_PMN_UT_20h_D3

value: no treatment


title: Atria_DKO_Female_F10

value: TCTCTACT-CGCGGTTC


title: Atria_DKO_Female_F8

value: GGACTTGG-CGCAGACG


title: FB380_3_02

description: poly(A) RNA

value: E. coli HB101


title: Atria_DKO_Female_F6

value: female

value: CGCTATGT-TCCGACAC


title: SMART-Seq_PMN_UT_20h_D1


title: SMART-Seq_PMN_R848_6h_D3

value: 6 h


title: SMART-Seq_PMN_UT_20h_D2


title: Atria_DKO_Female_F4

value: heart atria

value: Ipr/Ldlr DKO

value: GGTCACGA-GTATTATG


title: FB380_2_S42

description: poly(A) RNA

value: Bacterial isolate S16


title: SMART-Seq_PMN_R848_6h_D2

value: neutrophil


title: Atria_DKO_Female_F2

value: TGGCCGGT-TAGAGCGC


title: SMART-Seq_PMN_R848_6h_D1


title: Atria_DKO_Female_F14

value: CTTGGTAT-CCAAGTCC


title: Atria_LdlrKO_Female_F17

value: Ldlr KO

value: GTGTCGGA-GCTTGCGC


title: FB380_2_S40

description: poly(A) RNA

value: Whole organism

value: Adult


title: FB380_3_06

description: poly(A) RNA

value: Bacterial isolate 15F11


title: Atria_LdlrKO_Female_F15

value: CATAATAC-TTCTAACG


title: FB380_2_S39

description: poly(A) RNA

value: E. coli HB101


title: Atria_LdlrKO_Female_F13

value: female

value: GCGCTCTA-GCTCCGAC


title: FB380_3_03

description: poly(A) RNA


title: SMART-Seq_PMN_UT_6h_D2

value: no treatment

value: 6 h


title: FB380_3_05

description: poly(A) RNA


title: SMART-Seq_PMN_UT_6h_D1


title: FB380_2_S38

description: poly(A) RNA


title: SMART-Seq-HL60_siOCT2_R848_R4

source_name: granulocytic-differentiated HL-60 cell line

growth_protocol: HL-60 cells were cultured at 37°C, 5 % CO2 atmosphere, in RPMI 1640 containing 10 % FCS. To induce granulocytic differentiation, HL-60 cells were cultured in 1.25 % DMSO-containing culture medium for 5 days

treatment_protocol: Transfection of siRNA was performed by electroporation using Ingenio Electroporation Solution (Myrus), and the Amaxa Nucleofector II device (Lonza). Briefly, at the fourth day of culture in DMSO, 107 HL-60 cells were suspended in 100 l of Ingenio solution containing either 150 pmol of ONTARGET plus Human POU2F2 (5452) siRNA pool, or ON-TARGET plus nontargeting siRNA pool (GE Healthcare Dharmacon, Lafayette, CO, USA), and then transferred to a nucleoporation cuvette. Electroporation was performed using the T019 program of the Nucleofector II device. Transfected cells were plated in RPMI 1640 containing 10 % FCS for 24 h and, after medium replacement, were incubated with or without 5 M R848 for further 6 h.

tag: cell line

value: R848 (5mM) for 6 h

tag: silencing


title: SMART-Seq-HL60_siOCT2_R848_R3

value: granulocytic-differentiated HL-60 cell line


title: Atria_LdlrKO_Female_F11

tag: tissue

value: heart atria

value: GCGCAAGC-TCACGCCG


title: FB380_2_S37

description: poly(A) RNA

tag: accession


title: SMART-Seq-HL60_siOCT2_R848_R2


title: Atria_LdlrKO_Female_F7

value: GTCGGAGC-GGTTATAA


title: FB380_2_S36

description: poly(A) RNA

value: Embryo

value: Pseudomonas sp. 15C5


title: FB380_2_S35

description: poly(A) RNA


title: Atria_LdlrKO_Female_F5

value: Ldlr KO

value: CGGCGTGA-GCGCCTGT


title: FB380_3_01

description: poly(A) RNA

value: Whole organism

value: Adult


title: Atria_LdlrKO_Female_F3

value: AGGTTATA-CAGTTCCG


title: FB380_2_S41

description: poly(A) RNA

value: Bacterial isolate S16


title: FB380_2_S34

description: poly(A) RNA


title: FB380_2_S33

description: poly(A) RNA

organism: Caenorhabditis tropicalis

value: P. vranovensis BIGb446


title: SMART-Seq-HL60_siOCT2_R848_R1


title: SMART-Seq-HL60_siOCT2_UT_R4


title: FB380_2_S06

description: poly(A) RNA

value: 300 mM NaCl


title: Atria_LdlrKO_Female_F1

value: female

value: TTATAACC-GATATCGA


title: FB380_2_S32

description: poly(A) RNA


title: SMART-Seq_PMN_UT_6h_D3

value: no treatment

value: 6 h

value: neutrophil


title: SMART-Seq_PMN_R848_20h_D1


title: SMART-Seq-HL60_siOCT2_UT_R3

value: granulocytic-differentiated HL-60 cell line


title: Atria_LdlrKO_Female_F9

value: heart atria

value: CGTTAGAA-TTCAGGTC


title: FB380_2_S04

description: poly(A) RNA

value: Embryo


title: FB380_2_S31

description: poly(A) RNA


title: SMART-Seq-HL60_siOCT2_UT_R2


title: FB380_2_S30

description: poly(A) RNA


title: FB380_2_S03

description: poly(A) RNA

value: E. coli HB101


title: PK-2

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

data_processing:
Raw reads of 150 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the mouse genome (mm10) using hisat2
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.2.1.

source_name: mouse lung cancer cells

growth_protocol: RPMI-1640 (Hyclone) with 10% FBS

extract_protocol:
Total RNA of SPK and SPK model cells was extracted using RNeasy kit (Qiagen, Valencia, CA) and quantified with NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA).
The cDNA sequencing libraries were prepared using Illumina's TruSeq Sample Preparation Kit (San Diego, CA) and the sequencing was performed using Illumina Genome Analyzer.

treatment_protocol: No treatment

value: lung tumors

tag: disease model

value: PK

tag: genotype (knockout)

tag: genotype (overexpression)


title: PK-3


title: PK-1


title: FB380_2_S29

description: poly(A) RNA

value: Whole organism

tag: developmental stage


title: SMART-Seq-HL60_siOCT2_UT_R1


title: SMART-Seq-HL60_siC_R848_R4

value: R848 (5mM) for 6 h

value: si-CTRL


title: FB380_2_S01

description: poly(A) RNA


title: SMART-Seq-HL60_siC_R848_R3


title: FB380_2_S02

description: poly(A) RNA


title: SPK-3

value: SPK

value: Smad4 and p53


title: FB380_2_S27

description: poly(A) RNA


title: FB380_2_S28

description: poly(A) RNA

value: 300 mM NaCl


title: QG122_F3_embs_NaCl_6A

description: poly(A) RNA

organism: Caenorhabditis kamaaina

value: F3 animals from NaCl stress


title: SPK-1


title: SPK-2


title: FB380_2_S26

description: poly(A) RNA


title: QG122_F3_embs_NaCl_5A

description: poly(A) RNA


title: SMART-Seq-HL60_siC_UT_R4

value: no treatment


title: SMART-Seq-HL60_siC_R848_R2


title: SMART-Seq-HL60_siC_UT_R3


title: FB380_2_S25

description: poly(A) RNA


title: QG122_F3_embs_BIGb446_9A

description: poly(A) RNA

value: F3 animals from P. vranovensis BIGb0446


title: QG122_F3_embs_NaCl_4A

description: poly(A) RNA


title: SMART-Seq-HL60_siC_UT_R2


title: FB380_2_S48

description: poly(A) RNA

organism: Caenorhabditis briggsae

value: Adult

value: P. vranovensis BIGb446


title: C2 36 t10

city: Tours

first: Charlotte

last: Lécureuil

address: Parc de Grammont

country: France

institute: University Tours

data_processing:
control quality with FastQC software
alignment with TopHat2 software (version 2.1.0) on annotated exons
counting with featureCounts software (version 1.6.3)
differentially expressed gene analysis using SARTools-DESeq2 R package (Varet et al, 2016, PloS one, 11(6):e0157022)
Genome_build: Genome Reference Consortium Nasonia vitripennis (Nvit_2.1) - Rago et al. BMC Genomics (2016) 17:678
Supplementary_files_format_and_content: featureCounts matrix table

organism: Nasonia vitripennis

extract_protocol:
Total RNA was isolated from frozen tissues using Macherey-Nagel Nucleo-Spin® RNA XS kit according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded library mRNA sample prep kit
RNA-seq experiments (paired-end read length of 2x100 pb) have been performed on an Illumina HiSeq 2500

tag: strain

value: AsymC

value: pool of 60 testes

tag: Stage

value: white nymphae


title: A4 36 t24

value: white nymphae with red eyes


title: QG122_F3_embs_BIGb446_8A

description: poly(A) RNA

value: Embryo

tag: treatment


title: B4 36 t24


title: FB380_2_S47

description: poly(A) RNA


title: B2 36 t10


title: FB380_2_S46

description: poly(A) RNA


title: QG122_F3_embs_BIGb446_7A

description: poly(A) RNA


title: SMART-Seq-HL60_siC_UT_R1

value: granulocytic-differentiated HL-60 cell line


title: hMONO_R848_20h_ChIP_OCT2_D2

data_processing:
Reads were quality-filtered according the Illumina pipeline
To avoid effects derived from different reads lengths, reads were truncated to 51bp using fastx_trimmer from the FASTX-toolkit. Trimmed reads were mapped to the human genome using Bowtie2 v2.3.5.1 with default parameters, and deduplication was performed with markdup of Sambamba v0.6.7. Only reads mapping to the nuclear genome were kept for downstream analyses.
PU.1, C/EBPb and OCT2 peaks were identified using MACS2 v2.2.6 with the following parameters –gsize hs -p 1e-4 –fix-bimodal –call-summits, peaks that overlap with ENCODE blacklist regions were removed with bedtools v2.26.0. ChIP-seq biological with the following parameters -r biological -s 1E-10 -w 1E-6 -m Highest -c 2 replicates peaks were then combined using MSPC
H3K27Ac-enriched regions were identified by MACS2 with parameters –gsize hs  --broad –broad-cutoff 0.1 –nomodel –extsize 146. Peaks overlapping ENCODE blacklist regions were removed and biological replicates were combined by MSPC to construct consensus peaks. Consensus H3K27Ac coordinates were re-centered to the best nucleosome free regions (NFR) within a 200 bp window, using the command “getPeakTags –nfr”, and then resized to 2 kb
Differential H3K27ac occupancy and TFs binding (|log2[fold change]|>1)  and false discovery rare < 0.01 was performed using Bioconductor/R DiffBind v2.14.
Genome_build: Genome Reference Consortium GRCh38, Dec/2013
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated using HOMER

growth_protocol: Granulocytes were isolated from buffy coats of healthy donors and manipulated under endotoxin-free conditions. After Ficoll-Plaque gradient centrifugation, followed by dextran sedimentation and hypotonic lysis of erythrocytes, neutrophils were isolated to reach 99.7 ± 0.2 % purity, by positively removing any eventual contaminating cells using the EasySep neutrophil enrichment kit (StemCell Technology, Vancouver, Canada). Neutrophils were then suspend at 5x106/ml in RPMI 1640 medium supplemented with 10 % low endotoxin FBS (< 0.5 EU/ml; from Sigma, Saint Louis, MO, USA),

extract_protocol:
Protein-DNA cross-linking was achieved by incubating 2.5x106 (for histone modification ChIP), or 107 (for TF ChIP), neutrophils with 1 % formaldehyde for 10 min at room T, under gentle agitation. Cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM, and incubating cells at room T for five more minutes. After fixation, cells were washed with ice-cold PBS, collected by scraping, and finally pelleted by centrifugation (5 min, 300xg, 4°C). Pellets were suspended in 900 l L1 lysis buffer (50 mM Tris, pH 8.0, 2 mM EDTA, 0.1 % IGEPAL, 10 % glycerol) containing protease inhibitors. Nuclei were pelleted at 1000xg at 4°C and resuspended in 300 l L2 lysis buffer (50 mM Tris, pH 8.0, 1 % SDS, 5 mM EDTA) including protease inhibitors. Chromatin was sheared to an average DNA size of 300-400 bp by sonication on wet ice [6 pulses of 15 seconds at the 50 % maximum potency, with 15 second pauses, using a BANDELIN SONOPLUS ultrasonic homogenizers HD 2070 (Bandelin, Berlin, Germany)]. Lysates were then cleared by centrifugation to remove debris (10 min, 13000xg, 12°C), and diluted 10x in dilution buffer (50 mM Tris, 5 mM EDTA, 200 mM, 0.5 % IGEPAL). Immunoprecipitations were carried out overnight at 4°C using 5 µg/ml antibodies. Immune complexes were then collected by adding 15 µl of protein A sepharose-coupled magnetics beads (GE Healthcare, Piscataway, NJ, USA) for 1 h at 4°C under gentle rotation. Beads were then immobilized on a magnetic support and washed three times in washing buffer (20 mM Tris, pH 8.0, 0.1 % SDS, 2 mM EDTA, 1% IGEPAL, 500 mM NaCl) and once in TE. The resulting protein complexes were then eluted in TE containing 2 % SDS, and reversed crosslinked by an overnight incubation at 65°C. The DNA was purified by QiaQuick PCR purification kit (Qiagen) according to the manufacturer’s instructions, and eluted in 50-100 µl.
ChIP DNA was prepared for HiSeq2000 and NextSeq 500 sequencing following TruSeq DNA sample preparation guide (Illumina, Cambridge, UK). In brief, 10-50 ng purified DNA from chromatin immunoprecipitation were adapter-ligated and PCR-amplified according to the manufacturer’s protocol (Illumina).

treatment_protocol: Neutrophils were treated or not with  5 µM R848, seated either in 6/24-well tissue culture plates or in polystyrene flasks (Greiner Bio-One, Kremsmüster, Austria), and cultured at 37°, 5 % CO2 atmosphere.

tag: chip antibody

value: Anti-OCT2 (Abcam # ab179808)

tag: cell type

value: monocyte


title: FB380_2_S45

description: poly(A) RNA

value: Whole organism

value: E. coli HB101


title: SMART-Seq-HL60_siC_R848_R1

value: R848 (5mM) for 6 h

value: si-CTRL


title: QG122_cntrl_3A

description: poly(A) RNA

value: F3 animals from E. coli HB101


title: hMONO_UT_20h_ChIP_OCT2_D2

value: no treatment


title: C4 36 t24


title: A2 36 t10


title: QG122_cntrl_2A

description: poly(A) RNA


title: C5 25 t24


title: FB380_2_S43

description: poly(A) RNA


title: hPMN_R848_20h_ChIP_OCT2_D2

value: neutrophil


title: FB380_2_S44

description: poly(A) RNA

value: Adult


title: QG122_cntrl_1A

description: poly(A) RNA


title: FB380_2_S15

description: poly(A) RNA

value: P. vranovensis BIGb446


title: hPMN_UT_20h_ChIP_OCT2_D2


title: B5 25 t24

value: AsymC


title: A5 25 t24

value: pool of 60 testes


title: hPMN_R848_20h_ChIP_PU.1_D2


title: FB380_2_S23

description: poly(A) RNA


title: FB380_2_S24

description: poly(A) RNA


title: FB380_2_S14

description: poly(A) RNA


title: C3 25 t10

value: white nymphae


title: B3 25 t10


title: FB380_2_S22

description: poly(A) RNA


title: FB380_2_S11

description: poly(A) RNA

value: 300 mM NaCl


title: hPMN_R848_20h_ChIP_CEBPb_D2

value: Anti-C/EBPβ (sc-150)


title: C1 Control t0


title: hPMN_UT_20h_ChIP_CEBPB_D2


title: hPMN_R848_20h_ChIP_H3K27ac_D2

value: Anti-H3K27Ac (Abcam # ab4729)


title: A3 25 t10


title: FB380_2_S13

description: poly(A) RNA

value: Embryo


title: FB380_2_S21

description: poly(A) RNA


title: FB380_2_S20

description: poly(A) RNA


title: FB380_2_S10

description: poly(A) RNA


title: FB380_2_S09

description: poly(A) RNA


title: hPMN_UT_20h_ChIP_H3K27ac_D2


title: FB380_2_S18

description: poly(A) RNA


title: B1 Control t0


title: A1 Control t0


title: FB380_2_S19

description: poly(A) RNA


title: hPMN_R848_6h_ChIP_H3K27ac_D2

value: 6 h


title: FB380_2_S08

description: poly(A) RNA

value: Whole organism


title: FB380_2_S17

description: poly(A) RNA

value: E. coli HB101


title: FB380_2_S07

description: poly(A) RNA


title: KO-CREB1 HCT116

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
RNA-sequencing reads were trimmed for adaptor sequences, low-quality and un-paired reads  by using Cutadapt(v2.0.dev0).
The RNA-seq clean data were aligned to the GENCODE V19 using STAR (v2.4.2a) and RSEM (v1.2.26).
The gene expression difference analysis was performed by using EBseq (1.22.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected values for each sample.

source_name: HCT116 cells

growth_protocol: HCT116 and KO-CREB1 cell lines were maintained at 37℃ and 5% CO2 in DMEM media supplemented with 10% fetal bovine serum, 100 I.U./ml Penicillin, 100 μg/ml Streptomycin.

extract_protocol:
RNA isolated using RNAzol
Ribosomal RNA was depleted from HCT116 wild-type and KO-CREB1 cells by using a Ribo-Zero rRNA Removal Kit (Epicentre). Then, the RNA was used as input for the Illumina TruSeq® Stranded Total RNA HT/LT Sample Prep Kit (Illumina). Libraries were pooled and sequenced on an Illumina Hiseq 3000 PE150 platform.

treatment_protocol: HCT116 wild-type CREB1 cells were subjected to PX461 plasmid that contains CRISPR/nCas9 and sgRNAs targeting CREB1. Following selection, the single clone cell that showed a complete  absence of CREB1 was refered as KO-CREB1 cells.

tag: genotype

value: CREB1 knockout


title: hPMN_UT_6h_ChIP_H3K27ac_D2


title: FB380_2_S16

description: poly(A) RNA


title: hPMN_UT_20h_ChIP_PU.1_D2


title: FB380_2_S12

description: poly(A) RNA


title: dzur_rep1

status: Public on May 06 2021

city: Ithaca

first: Tobias

last: Doerr

state: NY

address: 525 N Campus Rd

department: Microbiology

institute: Cornell University

data_processing:
Sequencing and Analysis was performed y GENEWIZ, LLC (South Plainfield, NJ, USA)
Libraries were sequenced on Illumina HiSeq instrument (2x150 bp paired end high output)
Reads were evaluated for sequence quality and trimmed of adapter sequences
Genome_build: SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression (Varet et al., PLOS ONE, 2016; Love et al., Genome Biology, 2014) using the following parameters: fitType parametric, cooksCutoff TRUE, independentFiltering TRUE, alpha 0.05, pAdjustMethod BH, typeTrans VST, locfunc median
DESeq2 was used to generate normalized counts and statistical analysis of differential gene expression (Love et al., Genome Biology, 2014)
Supplementary_files_format_and_content:
tab-delimited text files include FPKM values for each sample
Combined matrix table with raw gene counts for every gene and every sample
Combined matrix table with normalized gene counts for every gene and every sample
Matrix table with differential expression values and p-values for each gene

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: N16961 dzur mutant at mid-log phase in LB medium

growth_protocol: Overnight cultures were diluted 1:100 and grown shaking in LB broth at 37oC until cultures reached mid-log phase (optical density at 600 nm = 0.5)

extract_protocol:
Cells were harvested via centrifguation, resuspended in 1X phosphate buffered solution, and treated with RNA protect (Qiagen). mirVana™ miRNA Isolation Kit (Ambion) was used according to manufacturer instructions. Total RNA was treated with DNAfree (Ambion) and precipitated with ethanol and ammonium acetate.
Libraries were prepared using standard Illumina protocols for RNA and small RNA by GENEWIZ, LLC. (South Plainfield, NJ, USA). Workflow included ribosomal RNA depletion, RNA fragmentation and random priming, first and second strand cDNA synthesis, end repair, 5'phosphorylation, and dA-Tailing, Adapter ligation, PCR enrichment, and sequencing.

value: N16961 dzur

tag: sample type

value: bacteria harvested from broth culture

tag: growth phase

value: mid-log phase in LB medium


title: dzur_rep2


title: wild-type_rep3

source_name: wild-type N16961 at mid-log phase in LB medium


title: dzur_rep3


title: wildtype_rep2


title: wildtype_rep1


title: HCT116

value: CREB1 wild-type


title: Plagl1+/-pat #5

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

data_processing:
Initial sequencing library quality control: FastQC 0.11.8
Reads were mapped to mouse genome (Ensembl, GRCm38) using hisat2 v.2.1.0
SAM files generated by hisat2 were converted to BAM, sorted and indexed using samtools 1.9
Reads mapping to genes were counted using featureCounts version 1.6.1
Differentially expressed genes were detected using DESeq2 1.24.0
Over-represented gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa and Goto, 2000) pathways were detected using clusterProfiler 3.12.0 Bioconductor package
Genome_build: GRCm38 (Ensembl)

source_name: Plagl1+/-pat retina

extract_protocol: NEBNext Ultra II Directional RNA Library Prep Kit

tag: age

value: Post-natal stage (P)7

value: retina


title: Plagl1+/-pat #4


title: Plagl1+/-pat #8


title: Plagl1+/-pat #7


title: Plagl1+/-pat #2


title: Plagl1+/-pat #1


title: Wild-type #4

source_name: Wild-type retina

value: Wild-type


title: FB380_2_S05

description: poly(A) RNA

source_name: Whole organism


title: Plagl1+/-pat #6


title: Wild-type #3


title: Wild_type_1737-Mn-rep2

city: Silver Spring

first: Michael

last: Schmitt

address: 10903 New Hampshire Ave

institute: US Food and Drug Administration

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity > 30 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 m in a reaction volume of 25 µl. An equal volume (25 µl) of 2x Hi-RPM Hybridization Buffer was added to stop the fragmentation reaction. 40 µl of each sample was hybridized to Agilent Custom Microarrays designed using the Corynebacterium diphtheriae strain NCTC 13129 for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 m at room temperature with Gene Expression Wash Buffer 1 and 1 m at 37°C using Gene Expression Wash Buffer 2. Slides were scanned immediately.

scan_protocol: Slides were scanned on the Agilent G2600D SureScan Microarray Scanner using settings recommended by the manufacturer (Dye channel: G (green), Scan region: Scan Area 61 x 21.6 mm, Scan Resolution: 3 µm, and 100% Green PMT gain).

data_processing: The scanned images were analyzed with Feature Extraction Software version 12.0.3.1 (Agilent) using default parameters to obtain gProcessedSignal values. Median gProcessedSignal values were divided by the entire sample set mean and log2 transformed.

organism: Corynebacterium diphtheriae

source_name: Wild type 1737-Mn

label_protocol: Cyanine-3 labeled cRNA was prepared from 0.1 µg RNA using the Low Input Quick Amp WT Labeling Kit (Agilent) following the manufacturer’s instructions. cRNA was purified using the RNAeasy kit (QIAGEN). Dye incorporation and cRNA yield were assessed with the GE NanoVue Plus.

growth_protocol: Wild-type C. diphtheriae or the mntR mutant were grown overnight in the semi-defined medium mPGT supplemented with 1 µM FeCl3. Overnight cultures were diluted 1:1 with fresh media and allowed to grow for 2-3 h. The optical density of cultures was measured (A600) and the cells diluted to an optical density of 0.1 into mPGT supplemented with 0.5 µM FeCl3 (required for growth) and either 0 or 5 µM MnCl2. Cells were harvested by centrifugation at mid-logarithmic growth.

extract_protocol: Cells were lysed in phosphate buffered saline supplemented with 10% ethanol, 0.2% phenol, and 14.3 mM beta-mercaptoethanol in Lysing Matrix B (MP Biomedicals). Appropriate volumes of TriZOL LS reagent (Thermo Fisher Scientific) were added to lysates and samples were briefly vortexed. RNA was purified following the Zymo Direct-zol RNA MiniPrep Plus protocol (Zymo Research Corporation). RNA was treated with Ambion Turbo DNAse I (Invitrogen). The RNA concentration and integrity were assessed by the Agilent Bioanalyzer 2100 following the RNA 6000 Nano protocol.

value: wild type


title: Wild_type_1737-no_Mn-rep3

source_name: Wild type 1737-no Mn


title: Wild_type_1737-Mn-rep3


title: delta_mntR-Mn-rep2

source_name: delta mntR-Mn

value: mntR (dip0619) in frame deletion


title: delta_mntR-Mn-rep3


title: delta_mntR-no_Mn-rep3

source_name: delta mntR-no Mn


title: Wild_type_1737-no_Mn-rep2


title: delta_mntR-Mn-rep1


title: Wild_type_1737-no_Mn-rep1


title: delta_mntR-no_Mn-rep2


title: Wild_type_1737-Mn-rep1


title: Wild-type #2


title: Plagl1+/-pat #3


title: delta_mntR-no_Mn-rep1


title: Arid1aE15D3

city: Ann Arbor

first: Kenneth

middle: Y

last: Kwan

state: MI

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

institute: University of Michigan

data_processing:
Sample barcodes separated with Illumina bcl2fastq v2.17.
UMI extracted into read name with UMI-tools v0.5.3. Command invocation: umi_tools extract --stdin {input} --stdout {output} --extract-method=string --bc-pattern=NNNNNNNN --log {log}
Adapter reads removed with Cutadapt v1.13. Command invocation: cutadapt -o {TRIM_DIR}/{sample}.fastq.gz -b {FULL_PRIMER} --cut 2 --discard-trimmed {input}
Reads aligned to reference genome with STAR v2.5.2a. Command invocation: STAR --genomeDir {input.genome} --readFilesIn {input.reads} --readFilesCommand zcat --outFileNamePrefix {MAP_DIR}/{wildcards.sample} --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --runThreadN {NUM_THREADS}
Reads deduplicated by UMI and position with UMI-tools v0.5.3. Command invocation: umi_tools dedup -I {sorted_bam} -S {dedup_bam}
Gene counts quantified by HTSeq v0.6.1p1. Command invocation: htseq-count --format bam --mode intersection-nonempty --type gene {input} {GTF} > {output}
Gene counts normalized with edgeR v3.20.9.
Genome_build: mm10
Supplementary_files_format_and_content: The tsv files for each sample contain the deduplicated gene counts as Tab-Separated Values (TSV).

source_name: Cerebral cortex

extract_protocol:
Total RNA was isolated from freshly micro-dissected embryonic 15.5 cortices using Trizol and RNA Clean & Concentrator Kit. 600ng of total RNA was used for library generation.
The ClickSeq procedure used was previously described (Routh et al. 2017). Briefly, total RNA was extracted using Trizol (Invitrogen) according to manufacturer’s protocol. The RNA was then treated with DNaseI, cleaned and concentrated using RNA Clean and Concentrator Kit (Zymo Research). Ribosomal RNA was removed using NEBNext rRNA Depletion Kit (NEB). Reverse transcription was carried out with SuperScript II (Invitrogen) following manufacturer’s procedures using 1:30 5mM AzdNTP:dNTP and 3’Genomic Adapter-6N RT primer (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN). The reaction was then treated with RNaseH to remove RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The azido-terminated cDNA was diluted with DMSO and click adaptor (/5Hexynyl/NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT). The click reaction was initiated by adding Cu2+ (Lumiprobe) in presence of vitamin C.  The resulting click ligation was purified using DNA Clean and Concentrator Kit (Zymo). The final amplification step was carried out using 2x One Taq Hot Start Mastermix (NEB), using Illumina universal primer (AATGATACGGCGACCACCGAG) and Illumina indexing primer (CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT).  The PCR reaction was cleaned using Ampure XP magnetic beads (Beckman) at 1.25x ratio, which size-selects for product size above 200bp. The resulting library was analyzed using TapeStation (Agilent) to check for proper size distribution and quality of DNA.

value: Emx1-Cre Arid1a conditional mutant

tag: batch

value: cerebral cortex

tag: litter

tag: Sex

value: male


title: Arid1aE15D5

value: control

tag: tissue

value: female


title: Arid1aE15D6


title: Arid1aE15D4


title: Arid1aE15D2


title: Arid1aE15C5


title: Arid1aE15C1


title: Arid1aE15C2


title: Arid1aE15C3


title: Arid1aE15D1


title: ATAC-Seq E15_5

city: Cambridge

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw sequencing data was processed via the Cell Ranger pipeline (10xGenomics, version 2.0.1) to generate a count matrix from the bcl files.
Genome_build: mm10 (GRCm38.84)
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices HDF5

source_name: mouse brain cortex

extract_protocol:
For single cell ATAC seq tissue pieces were transferred to NbActiv1 (BrainBits) immediately after dissection and we followed the nuclei isolation protocol from 10xGenomics. Tissue was dissociated with a 1ml pipette, then centrifuged 500rcf at 4°C for 5min and resuspended in 1 ml NbActiv1. Concentration was determined using a hemocytometer chamber. Cells were centrifuged at 500rcf for 5min at 4°C and resuspended in 100μl chilled diluted Lysis Buffer (Tris-HCl pH 7.4 1mM, NaCl 1mM, MgCl2 0.3mM, Tween-20 0.01%, Nonidet P40 Substitute 0.01%, Digitonin 0.001%, BSA 0.1%) and incubated for 5min at 4°C. We then added 1ml chilled Wash Buffer (Tris-HCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%) to the lysed cells and pipette mixed 5 times. Finally, we centrifuged at 500rcf for 5min at 4°C and resuspended in chilled 1:10 diluted Nuclei Buffer (10xGenomics) to a final concentration of 6000nuclei/ul (based on previous concentration and assuming a loss of 50%). Nuclei concentration was determined once more and then proceeded immediately to the Chromium Single Cell ATAC.
We loaded the chips aiming to recover 7,000 nuclei and proceeded according to instructions. Libraries were quantified in BioAnalyzer and sequenced in NextSeq Illumina platforms.
single cell ATAC, Chromium V1

treatment_protocol: Dissection was performed in Hybernate E (Brainbits). The tissue was then embedded in 3% low melting agarose at 35-37C. Once the agarose solidified, the tissue was sectioned in 250um thick sections in a vibratome in iced Hybernate E. Sections were transferred to another plate and the prospective somatosensory cortex was dissected and meninges removed.

value: somatosensory cortex

tag: chromium single cell atac chemistry


title: Arid1aE15C4


title: ATAC-Seq E18_5


title: ATAC-Seq E13_5


title: crac_Nanos2TAGTAG_5_Rep1_NNNGACTTAGC

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

description:
CRAC, Nanos2TAGTAG, line 5, Rep1, barcode NNNGACTTAGC
OTHER – CRAC-seq
03_AC180516_VMPHGNanos2_G1_comp_flexbar_Aligned.out_fwd.bw
03_AC180516_VMPHGNanos2_G1_comp_flexbar_Aligned.out_rev.bw

data_processing:
sequenced on a NextSeq system; PCR duplicates removed by fastx_collapser (FASTX Toolkit 0.0.14); 5' barcodes removed by pyBarcodeFilter.py v3.0 script from pyCRAC package; reads trimmed by flexbar v3.4.0 to remove 3’-linker sequence.
alignment to mm10 genome with STAR and salmon; also to transcripome with Novoalign; BigWig files were generated using genomecov (bedtools v2.27.0)
peaks called using argrelextrema function of the SciPy python library; peak intensities of replicates averaged to rank peaks
genomic forward and reverse oriented bigwig files

source_name: Spermatogonial stem cell lines (SSCs)

growth_protocol: see sample characteristics

extract_protocol:
After UV-crosslinking, lysates were prepared from SSCs, and protein-RNA complexes were isolated with antibody, protease cleavage and Nickel-affinity purification, under denaturing conditions. RNA-protein complexes were eluted from Nickel-columns and separated by SDS-PAGE and transferred to a membrane. Proteins were digested and RNA was extracted.
Cross-linked RNA molecules were partially digested with RNase A and T1 and subjected to phosphatase treatment. A 3' barcode, which is complementary to the reverse transcription primer, is ligated to RNA. A 5' barcode, which includes the experimental barcode and the UMI, was ligated to RNA. After protein digestion, RNA was extracted and reverse transcribed. cDNA was PCR amplified for 28 cycles using primers compatible with Illumina sequencing. DNA fragments of 130-190 bases were extracted and purified from an agarose gel.


title: crac_Nanos2CTL_Rep2_NNNTAAGC

description:
CRAC, Nanos2CTL, Rep2, barcode NNNTAAGC
OTHER – CRAC-seq
03_AC180516_wt_2_comp_flexbar_Aligned.out_fwd.bw
03_AC180516_wt_2_comp_flexbar_Aligned.out_rev.bw

data_processing:
sequenced on a NextSeq system; PCR duplicates removed by fastx_collapser (FASTX Toolkit 0.0.14); 5' barcodes removed by pyBarcodeFilter.py v3.0 script from pyCRAC package; reads trimmed by flexbar v3.4.0 to remove 3’-linker sequence.
alignment to mm10 genome with STAR and salmon; also to transcripome with Novoalign
genomic forward and reverse oriented bigwig files


title: crac_Nanos2CTL_Rep1_NNNTGGAGC

description:
CRAC, Nanos2CTL, Rep1, barcode NNNTGGAGC
OTHER – CRAC-seq
03_AC180516_wt_1_comp_flexbar_Aligned.out_fwd.bw
03_AC180516_wt_1_comp_flexbar_Aligned.out_rev.bw


title: E10.5_Enhancer_capture_rep3

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
Distal_Element_Interacting.txt

data_processing:
Library strategy: Capture-C
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 1 maintaining strict read order, mm9
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Promoter_Interacting.txt: Custom combined data format (chrom \t start \t stop \t sample_gene \t sample_gene \t etc...)
Supplementary_files_format_and_content: Distal_Element_Interacting.txt: Custom combined data format (chrom \t start \t stop \t sample_gene \t sample_gene \t etc...)

source_name: Primitive Erythroid

growth_protocol: Primary Primitive Erythroblasts: Primary primitive erythroblasts were derived from yolk sacs at embryonic day 10.5 (E10.5). A total of ~1x106 erythroblasts were obtained from each single embryo. Definitive Erythroid Cells: Definitive erythroid cells were obtained from a well-established fetal liver culture system (Drissen et al. 2005). Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cell suspension was expanded for 5–7 d in Stempro (Invitrogen) supplemented with Epo (1 U/ml), SCF (50 ng/ml) and dexamethasone (1 μM). After expansion of the cultures, mature red blood cells were removed by negative selection for Ter119 using anti-Ter119 magnetic beads (Miltenyi Biotec), to obtain a population of erythroid precursors, which was then purified by CD44 positive cell sorting before being placed into expansion media to recover for 6 hours.  mES Cell line: ES cell lines were maintained in BHK-21 GMEM (Invitrogen) supplemented with 10% foetal calf serum (Gibco), 100 U/ml Penicillin/Streptomycin (Invitrogen), 2mM Glutamine (Invitrogen), 1mM Sodium Pyruvate (Invitrogen), 1x MEM Non-essential amino acids (Invitrogen). 0.1mM 2-mercaptoethanol (Invitrogen) 1000U/ml LIF (ESGRO) on 0.1% gelatin coated plates. Cells were passaged every 2 days.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
1-5ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

treatment_protocol: Definitive Erythroid Cells: Cultures were switched to medium containing a high Epo concentration (5 U/ml) to induce differentiation into mature erythroid cells and harvested after 24 hours. mES Cell line: Cells were resuspended by treatment with 0.05% trypsin/EDTA (Invitrogen) for 2 minutes at 37ºC, before washing with growth media and fixation.

value: Erythrocytes from E10.5 mice

tag: genes analysed


title: E10.5_Promoter_capture_rep1

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
Promoter_Interacting.txt


title: E10.5_Enhancer_capture_rep1


title: E10.5_Promoter_capture_rep2


title: FL_Enhancer_capture_rep1

source_name: Fetal Liver

value: Cultured fetal liver cells


title: FL_Enhancer_capture_rep2


title: Arid1aE15C6


title: E10.5_Promoter_capture_rep3


title: Embryonic Stem Cell_Promoter_capture_rep2

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell


title: E10.5_Enhancer_capture_rep2


title: FL_Promoter_capture_rep2


title: Embryonic Stem Cell_Promoter_capture_rep3


title: FL_Promoter_capture_rep1


title: FL_Promoter_capture_rep3


title: Embryonic Stem Cell_Promoter_capture_rep1


title: Wild-type #1


title: crac_Nanos2TAGTAG_5_Rep2_NNNACTCAGC

description:
CRAC, Nanos2TAGTAG, line 5, Rep2, barcode NNNACTCAGC
OTHER – CRAC-seq
03_AC180516_VMPHGNanos2_G2_comp_flexbar_Aligned.out_fwd.bw
03_AC180516_VMPHGNanos2_G2_comp_flexbar_Aligned.out_rev.bw