title: JV-15-LPSUroA50-3: LPS + Urolithin A, 50uM, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
fastq files were generated using the Illumina GenerateFASTQWorker workflow v2.6.17.15 using bcl2fastq
QA/QC of raw fastq files was performed using FastQC v 0.10.1
Raw fastq sequences were aligned to the hg38 genome using tophat2 v2.0.13 using the Ensembl gtf with the parameters –p 4 -G Homo_sapiens.GRCh38.82.chrAdded.gtf --no-coverage-search –-library-type fr-firststrand
Differentially expressed genes were determined using cuffdiff2 v2.2.1 with the parameters –p 5 –library-type fr-firststrand Homo_sapiens.GRCh38.82.chrAdded.gtf
Genome_build: hg38
Supplementary_files_format_and_content: genes.fpkm_table represents normalized FPKM values using cuffnorm v2.2.1

source_name: HT29 cells treated with LPS and 50 uM UroA for 24 hr

growth_protocol: The HT29 cells (human colon carcinoma cell lines) were maintained in DMEM-high glucose supplemented with 10% fetal bovine serum, 1X penicillin-streptomycin solution (100 U/ml penicillin, and 100 µg/ml streptomycin; Sigma Aldrich) in a humidified atmosphere (5% CO2, 95% air, 37°C).

extract_protocol:
Total RNA was isolated from HT29 cells treated with vehicle and UroA (50 μM) (n=3) for 24 h and RNA was isolated using Trizol based lysis followed by Qiagen RNeasy kits.  The isolated RNA was checked for integrity (RIN>9.5) using the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA) and quantified using a Qubit fluorometric assay (Thermo Fisher Scientific, Waltham, MA).
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) with poly-A enrichment. 1ug of samples (in a volume of 50 µl) were treated with RNA Purification Beads and denatured for 5 minutes at 65oC. Then the supernatant was discarded and the beads were washed with bead wash buffer. Captured polyadenylated RNA was eluted using Elution buffer at 80°C for 2 min. mRNA is further purified in a second bead clean-up, as well as fragmented and primed during elution by adding 19.5 µl of Elute, Prime, Fragment High Mix to the beads and incubating the samples for 8 minutes at 94oC. After fragmentation, 17ul of supernatant is removed from the beads and we proceeded immediately to synthesize first strand cDNA. Following the protocol, 8 µl of First Strand Synthesis Mix Act D and SuperScript II mix was added to each sample and heated on a thermocycler using preprogrammed thermal conditions. Once the reaction finished and reached 4oC, we immediately proceeded for second strand cDNA synthesis.  Diluted end repair control and Second Strand Marking Mix were added, mixed well and incubated in a pre-heated thermocycler at 16oC for one hour. Then the DNA was purified using Agencourt AMPure XP Beads. Finally samples were eluted with Resuspension Buffer and 15 µl of elute was collected and stored at -20oC. A-Tailing Control and A-Tailing Mix were added to the purified samples from step c and the samples were incubated on the preprogrammed thermal cycler. Once the incubation is done, we proceeded immediately to ligate adapters.  Diluted ligation control, Ligation Mix and barcodes were added and incubated in a pre-heated thermocycler at 30oC for 10 minutes. Stop Ligation Buffer was immediately added to each sample and mixed well.  Then the ligated samples were purified using Agencourt AMPure XP Beads. We eluted with 50 µl of Resuspension Buffer and the elute was again purified for a second time using Agencourt AMPure XP Beads. Afterwards, the final elution, consisting of 20 µl of the elute was collected and used for DNA enrichment. Samples were barcoded with Illumina TruSeq Adapters.

treatment_protocol: HT29 cells (80% confluence) were treated with UroA (50 uM) or Vehicle (DMSO-0.01%) for 24 hr.

value: Colorectal cancer -Epithelial

tag: treatment time

value: 24 hrs

tag: truseq adapter number


title: Taihe Silkies-SK_S27

status: Public on Oct 07 2019

type: genomic

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

country: China

institute: China Agricultural University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

label: biotin

molecule: genomic DNA

organism: Gallus gallus

source_name: Taihe Silkies

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: chickens were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: tissue

value: Blood


title: 5726: Treg WT 2

type: SRA

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

library_source: transcriptomic

data_processing:
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with Kallisto (v0.44) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

molecule: total RNA

organism: Mus musculus

source_name: VAT Treg

extract_protocol:
Mice were perfused with PBS and cells were isolated by enzymatic digestion with Collagenase and DNAse prior to FACS sorting in medium+FCS and stored in TRIZOL (invitrogen). RNA was isolated by Rneasy Microkits (Quiagen) following the manufacturers’ protocol and quality was assessed.
10ng of total RNA was converted into cDNA libraries using the SmartSeq2 protocol (Picelli et al., 2013). cDNA was subsequently sequenced in the NextSeq 500 system and demultiplexed using bcl2fastq2 v2.20

tag: strain

tag: line

value: Hpgd fl; Foxp3-YFP-Cre; Treg cell specific deletion of Hpgd

value: VAT

tag: age

value: 12 weeks


title: Taihe Silkies-SK_S38


title: Taihe Silkies-SK_S26


title: JV-14-LPSUroA50-2: LPS + Urolithin A, 50uM, replicate 2

country: USA

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: ctrl_RNA_m1

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

description:
deseq.norm.count.pitx2endel.csv
sample name
ctrlm1

data_processing:
Alignment: We used STAR (version 2.5.2b) to align raw reads to mouse genome (Gencode, GRCm38) and annotated transcripts and genes using Gencode mouse genome gtf file (vM10). Read abundance was quantified by STAR quantification mode '--quantMode GeneCounts'
Gene filtering: Raw read counts were loaded in R statistical environment and created a deseq object using DESeq2 package (R version 3.5.1, DESeq2 version 1.20.0). Read counts for individual samples were compiled by genes, low read count genes (total read count ≤ number of biological samples) were removed from downstream analyses. Mitochondrial genes and ribosomal genes were also removed.
Read normalization: Raw read counts were then normalized using DESeq2 command 'counts(deseq.df, normalized = T)'.
Genome_build: mm10
Supplementary_files_format_and_content: readcount in csv format, representing normalized read count

source_name: left ventricle

extract_protocol:
Left atrial tissue was isolated from 3-month-old mice and preserved in RNALater Solution (Ambion, AM7021). Disruption and homogenization of the tissue was performed using a cordless pestle motor (VWR, 47747-370) and 1.5 mL microtube disposable pestles (VWR, 47747-362) and the subsequent RNA isolation was performed using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA concentration was measured using the Qubit RNA HS Assay Kit (Invitrogen, Q32855) with the Qubit 2.0 Fluorometer (ThermoFisher, Q32866).
600 ng of RNA from each sample was used an input for RNA Sequencing library preparation using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) for Illumina Platforms (Roche, KK8483). Multiplexing of the libraries was performed using the KAPA Dual-Indexed Adapter Kit for Illumina Platforms (Roche, KK8722). Concentrations of primers (280 nM), fragmentation protocol (6 minutes at 94 °C), and number of amplification cycles (9 cycles) were all selected following kit recommendations. Following library preparation, library concentration was measured using the AATI Fragment Analyzer with the NGS Fragment Kit (1-6000 bp) (Agilent, DNF-473-0500). Libraries were sequenced on the Illumina NextSeq 500 with the NextSeq 500/550 High Output Reagent Cartridge V2 (Illumina, Illumina, 15057931).

value: FVB

value: left ventricle

tag: developmental stage

value: 3 month old adult

tag: genotype

value: control

tag: gender

value: male


title: JV-13-LPSUroA50-1: LPS + Urolithin A, 50uM, replicate 1


title: JV-12-LPS-3: Lipopolysaccaride, replicate 3

source_name: HT29 cells treated with LPS for 24 hr


title: Taihe Silkies-SK_S25


title: Taihe Silkies-SK_S33


title: Taihe Silkies-SK_S24


title: Taihe Silkies-SK_S23


title: JV-11-LPS-2: Lipopolysaccaride, replicate 2


title: JV-09-UroA50-3: Urolithin A, 50uM, replicate 3

source_name: HT29 cells treated with 50 uM UroA for 24 hr


title: Taihe Silkies-SK_S21


title: Taihe Silkies-SK_S32


title: JV-08-UroA50-2: Urolithin A, 50uM, replicate 2


title: Taihe Silkies-SK_S20


title: JV-07-UroA50-1: Urolithin A, 50uM, replicate 1


title: Taihe Silkies-SK_S18


title: Taihe Silkies-SK_S17


title: Taihe Silkies-SK_S16


title: JV-04-UroA25-1: Urolithin A, 25uM, replicate 1

source_name: HT29 cells treated with 25 uM UroA for 24 hr


title: JV-05-UroA25-2: Urolithin A, 25uM, replicate 2


title: JV-06-UroA25-3: Urolithin A, 25uM, replicate 3


title: JV-03-Control-3: DMSO (0.01%), replicate 3

source_name: HT29 cells treated with Vehicle for 24 hr


title: Taihe Silkies-SK_S15


title: Taihe Silkies-SK_S13


title: JV-02-Control-2: DMSO (0.01%), replicate 2


title: JV-01-Control-1: DMSO (0.01%), replicate 1


title: Taihe Silkies-SK_S14


title: Taihe Silkies-SK_S12


title: Taihe Silkies-SK_S22


title: meth_donor5_unenriched

city: Utrecht

first: Aditya

last: Barve

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Each tube contains 1000 cells

library_source: genomic

data_processing:
In transcriptome libraries, first read contains UMI (6 first nucleotides) and cell barcode (from 7 to 14 nucleotides) and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell-specific barcode file is added as a part of processed data files. For methylation data (scBS-seq), Bismark was used to map reads. Both reads contain methylation information.
Genome_build: All zebrafish transcriptome libraries were mapped to Danio rerio assembly Zv9, ensemble 74, extended with ERCC92, while human transcriptome and methylation libraries were mapped to human assembly hg19.
Supplementary_files_format_and_content: Tabular separated files, with transcript count (rows) per cell (columns). Cells in each file are labeled according to barcode ID. The cell-specific barcode file is added as a part of processed data files. The bulk scBS-seq protocol after processing resulted in bismark output tabular separated coverage (.cov) files.
Supplementary_files_format_and_content: celseq2_bc.csv: 1st column represents index of the cell specific barcode, and the second column is the barcode

source_name: pancreas

extract_protocol:
After organ isolation, for transcriptome, live single cells are sorted into 384 well plates containing mineral oil, uniquely barcoded cell specific primers for mRNA detection, Spike-in controls and and RNAse inhibitor.  For bisulfite sequencing, cells were collected in tubes containing RLT buffer.
SORT-seq for transcriptome, Bulk scBS-seq for methylation

value: pancreas

tag: protocol

value: Bulk scBS-seq

tag: sampleID


title: JV-10-LPS-1: Lipopolysaccaride, replicate 1


title: Taihe Silkies-SK_S9


title: Taihe Silkies-SK_S11


title: meth_donor5_beta1

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S10


title: meth_donor5_alpha1

description: Each tube contains 1000 cells


title: meth_donor4_unenriched

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S19


title: meth_donor4_beta2

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S7


title: Taihe Silkies-SK_S6


title: meth_donor5_alpha2

description: Each tube contains 1000 cells


title: meth_donor4_beta1

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S5


title: Taihe Silkies-SK_S4


title: meth_donor4_alpha2

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S2


title: tr_donor4_unenriched2

description: each plate contains 384 sorted cells

value: Sort-seq


title: meth_donor4_alpha1

description: Each tube contains 1000 cells


title: Taihe Silkies-SK_S3


title: Taihe Silkies-SK_S1


title: Rhode Island Red-RIR310

source_name: Rhode Island Red


title: meth_donor5_beta2

description: Each tube contains 1000 cells


title: Rhode Island Red-RIR309


title: tr_donor4_beta2

description: each plate contains 384 sorted cells. sorted using GateID normalization method 2


title: Rhode Island Red-RIR308


title: tr_donor4_unenriched1

description: each plate contains 384 sorted cells


title: tr_donor4_beta1

description: each plate contains 384 sorted cells. sorted using GateID normalization method 1


title: Taihe Silkies-SK_S8


title: tr_donor4_alpha1


title: Rhode Island Red-RIR306


title: Rhode Island Red-RIR307


title: tr_donor4_alpha2


title: tr_donor3_unenriched2

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR305


title: tr_donor3_unenriched1

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR304


title: tr_donor3_beta2

description: each plate contains 384 sorted cells. Cells specfic barcodes 1-192 were sorted using GateID normalization method 1, and barcodes 193-384 were used to sort cells using normalization method 2


title: Rhode Island Red-RIR303


title: tr_donor2_unenriched2

description: each plate contains 384 sorted cells


title: tr_donor3_beta1


title: tr_donor2_unenriched1

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR301


title: Rhode Island Red-RIR299


title: Rhode Island Red-RIR300


title: tr_donor2_beta

description: each plate contains 384 sorted cells, Cell specific barcodes 1-192 were used to sort gateID enriched beta cells


title: Rhode Island Red-RIR298


title: tr_td2_unenriched10

description: each plate contains 384 sorted cells


title: tr_td2_unenriched9

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR297


title: Rhode Island Red-RIR296


title: tr_td2_unenriched7

description: each plate contains 384 sorted cells


title: tr_td2_unenriched6

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR294


title: Rhode Island Red-RIR295


title: Rhode Island Red-RIR293


title: Rhode Island Red-RIR292


title: Rhode Island Red-RIR291


title: tr_td2_unenriched3

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR290


title: tr_td2_unenriched2

description: each plate contains 384 sorted cells


title: tr_td2_unenriched1

description: each plate contains 384 sorted cells


title: tr_donor1_unenriched

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR287


title: tr_donor1_beta


title: tr_donor1_alpha

description: each plate contains 384 sorted cells, Cell specific barcodes 193-384 were used to sort gateID enriched alpha cells


title: Rhode Island Red-RIR286


title: Non inflamed mucosa from UC patient 8

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  4

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: Intestinal mucosal biopsies

label_protocol: Fifty nanograms of total RNA were amplified as directed in the NuGEN Ovation Pico WTA System and 5 μg of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

extract_protocol: Total RNA for microarrays was obtained using Mirvana microRNA Kit (Life Technologies Carlsbad, CA) according to manufacturer instructions, and RNA integrity was evaluated with the High Sensitivity RNA Analysis Kit (Advanced Analytical Technologies Ankeny, IA).

treatment_protocol: Human biopsies taken from colonoscopy procedures were placed in RNA Later solution and then stored in -80ºC freezer until RNA extraction.

tag: diagnosis

value: Ulcerative Colitis

value: Intestinal mucosal biopsies

tag: inflammation

value: Non Inflamed

tag: mayo score


title: Rhode Island Red-RIR285


title: Rhode Island Red-RIR284


title: tr_td2_unenriched4

description: each plate contains 384 sorted cells


title: Inflamed mucosa from UC patient 8

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  4

value: Inflamed


title: Inflamed mucosa from UC patient 7

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  3


title: Rhode Island Red-RIR283


title: Non inflamed mucosa from UC patient 7

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  3


title: Rhode Island Red-RIR282


title: tr_td2_unenriched5

description: each plate contains 384 sorted cells


title: Rhode Island Red-RIR281


title: Non inflamed mucosa from UC patient 6

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  2


title: Rhode Island Red-RIR280


title: Non inflamed mucosa from UC patient 5

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  1


title: Inflamed mucosa from UC patient 5

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  1


title: Non inflamed mucosa from UC patient 4

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   4


title: Rhode Island Red-RIR278


title: Rhode Island Red-RIR289


title: Inflamed mucosa from UC patient 4

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  4


title: Rhode Island Red-RIR279


title: Rhode Island Red-RIR277


title: Rhode Island Red-RIR275


title: Non inflamed mucosa from UC patient 3

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   3


title: Inflamed mucosa from UC patient 3

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  3


title: Rhode Island Red-RIR274


title: Rhode Island Red-RIR273


title: Inflamed mucosa from UC patient 2

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  2


title: Non inflamed mucosa from UC patient 1

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)  1


title: Rhode Island Red-RIR271


title: Rhode Island Red-RIR272


title: Inflamed mucosa from UC patient 1

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  1


title: Rhode Island Red-RIR269


title: Inflamed mucosa from UC patient 6

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  2


title: Veh_2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC hg19 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: HMC3 cells

growth_protocol: HMC3 cells (ATCC CRL-3304, Manassas, VA, USA) were cultured in EMEM media (Cellgro, Manassas, VA, USA) supplemented with 10% FBS (Atlanta Biologicals, Flowery Branch, GA, USA).

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA).
RNA-seq libraries were prepared with Ovation RNA-seq system v2 kit (NuGEN)

treatment_protocol: HMC3 cells (passages about 4-6) were seeding in a 6-well plate (1.5x10^6 cells/plate) and treated with vehicle, 0.1nM Estradiol (E2), 400nM ketamine, 400nM (2R,6R)-HNK, 400nM (2S,6S)-HNK, 0.1nM E2+400nM ketamine, 0.1nM E2+ 400nM (2R,6R)-HNK, and 0.1nM E2+ 400nM (2S,6S)-HNK.

tag: treatment

value: vehicle

value: a human microglial cell line


title: Rhode Island Red-RIR268

value: Blood


title: K_2

value: ketamine


title: Veh_1


title: K_1


title: Rhode Island Red-RIR276


title: E2_2S6S_1

value: estradiol + 2S6S-HNK


title: E2_2R6R_2

value: estradiol + 2R6R-HNK


title: Rhode Island Red-RIR266


title: Rhode Island Red-RIR267


title: Rhode Island Red-RIR263


title: Rhode Island Red-RIR261


title: Non inflamed mucosa from UC patient 2

description:
Gene expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   2


title: Rhode Island Red-RIR264


title: E2_K_2

value: estradiol + ketamine


title: Rhode Island Red-RIR260


title: Rhode Island Red-RIR259


title: tr_td2_unenriched8

description: each plate contains 384 sorted cells


title: E2_K_1


title: E2_2R6R_1


title: Rhode Island Red-RIR270


title: Rhode Island Red-RIR258


title: Rhode Island Red-RIR256


title: E2_2

value: estradiol


title: Rhode Island Red-RIR255


title: Rhode Island Red-RIR254


title: 2S6S_2


title: E2_2S6S_2


title: Rhode Island Red-RIR253


title: Rhode Island Red-RIR252


title: Rhode Island Red-RIR250


title: 2R6R_2


title: 2R6R_1


title: Rhode Island Red-RIR249


title: Rhode Island Red-RIR247


title: D25_3GF_CD49f+_CD34-_3

city: NEW YORK

first: MICHAEL

last: DANIEL

state: NY

address: 1 GUSTAVE L LEVY PL # 1496

institute: ICAHN SCHOOL OF MEDICINE OF MOUNT S

data_processing:
Alignment with RNA Star
Gene counting with featureCounts
Normalization and differential gene expression with DESeq2
Pathway analysis with GAGA
Genome_build: GRch37.75
Supplementary_files_format_and_content: Comparative analyses compiled with Biojupies or R; read counts derived from DESeq2

source_name: adult human dermal fibroblast

extract_protocol:
Cells were sorted by FACS and bulk RNA was then isolated using the NucleoSpin RNA XS extraction kit
Illumina Nextera XT DNA Library Preparation Kit was used with 0.1-0.3ng of cDNA for the construction of sequencing libraries

value: HDF

value: adult human dermal fibroblast

value: wild type

tag: cell markers

tag: time after transduction

value: day 25


title: D25_3GF_CD49f+_CD34+_3


title: D25_3GF_CD49f+_CD34+_1


title: Rhode Island Red-RIR248

tag: tissue


title: D25_3GF_CD49f+_CD34+_2


title: Rhode Island Red-RIR245


title: D25_3GF_CD49f+_CD34-_2


title: Rhode Island Red-RIR244


title: Rhode Island Red-RIR242


title: E2_1


title: 2S6S_1


title: D15_3GF_CD49f+_CD34+_1

value: day 15


title: D15_3GF_CD49f+_CD34+_2


title: Rhode Island Red-RIR243


title: D25_3GF_CD49f+_CD34-_1


title: D15_3GF_CD49f+_CD34-_3


title: Beijing You -BY368

source_name: Beijing You


title: D15_3GF_CD49f+_CD34-_2


title: Beijing You -BY367


title: Beijing You -BY366


title: Beijing You -BY365


title: Beijing You -BY364


title: D15_3GF_CD49f+_CD34-_1


title: Adult Parotid Gland Rep2

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

description:
Whole Tissue
Salivary Gland GEO data.xlsx

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.20.0) was used to normalize the read counts, and TPM values were calculated by normalising read counts were further normalised by gene length and total counts to generate Transcript Per Million (TPM) values.
Supplementary_files_format_and_content: TPM values were generated by normalizing raw counts for both library size and gene length.

source_name: Adult Parotid Gland

extract_protocol:
Mouse submandibular and Parotid salivary gland epithelial cells were isolated from adult and Post-natal daty 18 mice  and RNA was extracted using the Direct-zol RNA Mini-Prep kit.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit protocol. 1 ug of total RNA from each sample was used in the the construction of sequencing libraries.

value: Adult (12wk)

value: Parotid Gland


title: Adult Parotid Gland Rep1


title: Adult Parotid Gland Rep3


title: Beijing You -BY363


title: Beijing You -BY362


title: Beijing You -BY360


title: Rhode Island Red-RIR246


title: Dev. Sub-Mandibular Rep2

source_name: Developing Submandibular Gland

value: Post-natal day 18 (P18)

value: Submandibular Salivary Gland


title: Dev. Sub-Mandibular Rep1


title: D15_3GF_CD49f+_CD34+_3


title: Beijing You -BY361


title: Dev. Parotid Gland Rep2

source_name: Developing Parotid Gland


title: Rhode Island Red-RIR241


title: OPC rep. 2

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: MNase-seq OPC rep. 2

data_processing:
Sequences were aligned to the mouse genome (mm10) using Bowtie2 with default settings.
Mono-nucleosomal reads were size selected, and we kept all reads with the lengths between 120-180 bp.
Genome-wide coverage profiles were computed in MATLAB by stacking all reads and counting the number of reads that cover each bp.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files containing the occupancy profiles, for the IGV genome browser

source_name: OPC

growth_protocol: OPCs were isolated and purified from the cortices of postnatal mice (P6-P9) of either sex and cultured for 6-7 days. Astrocytes were isolated from the cortices of postnatal mice (P1-P3) of either sex and cultured for approximately 21 days until confluent. DRG neurons were isolated from the dorsal root ganglia of embryonic mice (E13.5) and cultured for approximately 2 weeks.

extract_protocol:
Nuclei were prepared and digested with microccoccal nuclease (MNase). Purified DNA from samples with about 80% mono-nucleosomes was repaired using the New England Biolabs PreCR repair kit (M0309).
Paired-end libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs E7370) according to the manufacturer’s instructions for < 100 ng input DNA.

tag: sample type

value: purified primary cultures


title: Beijing You -BY357


title: OPC rep. 1

description: MNase-seq OPC rep. 1


title: Beijing You -BY356


title: DRG rep. 2

description: MNase-seq DRG rep. 2

source_name: DRG


title: Beijing You -BY358


title: DRG rep. 1

description: MNase-seq DRG rep. 1


title: Astrocytes rep. 2

description: MNase-seq Astrocytes rep. 2

source_name: Astrocytes


title: Beijing You -BY355


title: Beijing You -BY354


title: Astrocytes rep. 1

description: MNase-seq Astrocytes rep. 1


title: Beijing You -BY353


title: Beijing You -BY351


title: OPC rep. 3 (RNA-seq)

description: OPC rep. 3

data_processing:
Reads were aligned with tophat2 and the reads corresponding to each transcript were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing the HTSeq counts corresponding to each transcript

extract_protocol:
RNA was extracted from cells with 1 ml TRIzol reagent (standard protocol).
Illumina TruSeq stranded mRNA kit

value: OPC


title: Beijing You -BY352

value: Blood


title: OPC rep. 2 (RNA-seq)

description: OPC rep. 2


title: Beijing You -BY350


title: Rhode Island Red-RIR240


title: Beijing You -BY349


title: OPC rep. 1 (RNA-seq)

description: OPC rep. 1


title: DRG rep. 1 (RNA-seq)

description: DRG rep. 1

value: DRG


title: Astrocytes rep. 3 (RNA-seq)

description: Astrocytes rep. 3

value: Astrocytes


title: DRG rep. 3 (RNA-seq)

description: DRG rep. 3


title: Beijing You -BY347


title: Beijing You -BY359


title: Beijing You -BY348


title: Dev. Parotid Gland Rep1


title: Astrocytes rep. 1 (RNA-seq)

description: Astrocytes rep. 1


title: DRG rep. 2 (RNA-seq)

description: DRG rep. 2


title: Rhode Island Red-RIR302


title: Astrocytes rep. 2 (RNA-seq)

description: Astrocytes rep. 2


title: Beijing You -BY343


title: Rhode Island Red-RIR239


title: Beijing You -BY342


title: Rhode Island Red-RIR238


title: Rhode Island Red-RIR237


title: Rhode Island Red-RIR236


title: Beijing You -BY346


title: Rhode Island Red-RIR235


title: Rhode Island Red-RIR234


title: Rhode Island Red-RIR231


title: Rhode Island Red-RIR233


title: Rhode Island Red-RIR232


title: Rhode Island Red-RIR229


title: Rhode Island Red-RIR227


title: Rhode Island Red-RIR224


title: Rhode Island Red-RIR223


title: Rhode Island Red-RIR226


title: Rhode Island Red-RIR225


title: Beijing You -BY344


title: Rhode Island Red-RIR222


title: Beijing You -BY345


title: Rhode Island Red-RIR221


title: Rhode Island Red-RIR218


title: Rhode Island Red-RIR220


title: Rhode Island Red-RIR219


title: Rhode Island Red-RIR216


title: Rhode Island Red-RIR217


title: Rhode Island Red-RIR215


title: Rhode Island Red-RIR214


title: Rhode Island Red-RIR212


title: Rhode Island Red-RIR210


title: Rhode Island Red-RIR213


title: Rhode Island Red-RIR211


title: Rhode Island Red-RIR209


title: Rhode Island Red-RIR230


title: Rhode Island Red-RIR208


title: Rhode Island Red-RIR228


title: Rhode Island Red-RIR207


title: Rhode Island Red-RIR206


title: Rhode Island Red-RIR201


title: Rhode Island Red-RIR203


title: K36M-rep2-input

city: Boston

first: Bradley

middle: E

last: Bernstein

state: MA

address: 185 Cambridge Street

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to mm9 using BWA 0.7.4, and multi-mapped reads and PCR duplicates were removed (Picard Tools).
Peak calling was performed using the Homer package (HOMER v4.8) with matched inputs.
Genome_build: mm9
Supplementary_files_format_and_content: peak files (bedGraph) generated by findpeaks (Homer)

source_name: hematopoietic stem and progenitor cells (Lin-, cKit+ bone marrow cells)

growth_protocol: Mice used in this study were housed and bred in Specific Pathogen Free (SPF) rooms located in the AAALAC-accredited Center for Comparative Medicine vivarium at Massachusetts General Hospital. Mice were housed in ventilated cages on a standard 12:12 light cycle. All procedures involving mice adhered to the guidelines of the approved Massachusetts General Hospital Institutional Animal Care and Use Committee (IACUC) protocol no. 2006N000104.

extract_protocol:
Sheered and fixed samples were lysed and immunoprecipitated. Antibody bound DNA was captured by beads, washed, eluted, reverse-crosslinked and treated with Rnase-A followed by Proteinase-K.
ChIP-seq libraries were prepared by end repair, A base addition and ligation of barcoded sequencing adapters (KAPA HyperPrep kit, Roche).

treatment_protocol: Both male and females were used in this study at 6-8 weeks of age and were induced by adding 2 mg/ml doxycycline to drinking water.

tag: strain

value: C57B6/129 hybrid

value: Bone marrow

tag: chip antibody


title: Rhode Island Red-RIR202


title: K36M-rep2-H3K36me3

value: hematopoietic stem and progenitor cells (Lin-, cKit+ bone marrow cells)

value: H3K36me3 (Abcam, ab9050)


title: K36M-rep1-H3K36me3


title: Rhode Island Red-RIR200


title: Rhode Island Red-RIR199


title: K36M-rep2-H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: K36M-rep1-H3K27me3


title: K9M-rep2-input


title: Rhode Island Red-RIR198


title: K36M-rep1-input


title: Rhode Island Red-RIR197


title: Rhode Island Red-RIR196


title: K9M-rep1-input


title: K9M-rep1-H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: K9M-rep2-H3K9me3


title: WT-rep2-H3K36me3

value: WT H3


title: Rhode Island Red-RIR195


title: Rhode Island Red-RIR204


title: Rhode Island Red-RIR191


title: Rhode Island Red-RIR192


title: WT-rep2-H3K9me3


title: Rhode Island Red-RIR190


title: WT-rep1-input


title: WT-rep1-H3K36me3


title: WT-rep1-H3K27me3


title: Rhode Island Red-RIR188


title: Beijing You -BY294


title: Rhode Island Red-RIR193


title: RRBS_K9M_rep2

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw demultiplexed fastq reads were trimmed to remove Illumina adapters using cutadapt (--quality-cutoff 20 --overlap 3 --minimum-length 25), then using nugen "trimRRBSdiversityAdaptCustomers.py".
Trimmed reads were then aligned to the mm9 genome using bsmap (-v 0.1 -s 12 -q 20 -w 100 -S 1 -u  -R).
Methylation calling was performed using mcall with standard parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file. Columns: chr, start, end, methylation (0 to 1), total reads

source_name: HSCs

growth_protocol: Cells were sorted from mouse peripheral blood.

extract_protocol:
DNA was extracted from cell pellets (100k cells) using the Zymo Quick-DNA Universal Kit following the manufacturer's instructions
10-50ng of each sample was made into an RRBS library using the NuGen Ovation RRBS Methyl-seq kit,  following the manufacturer's instructions but using only half the recommended reaction volumes. Bisulfite conversion was carried out with a Qiagen Epitect Fast kit.  The samples underwent 12 cycles of amplification post-conversion, and a 1x SPRI cleanup.

treatment_protocol: For K36M and K9M, mice were induced by adding 2 mg/ml doxycycline to drinking water

tag: genotype/variation

value: expressing dominant negative mutant H3.3 at lysine 9 (K9M)


title: WT-rep2-input

tag: cell type


title: WT-rep2-H3K27me3


title: Beijing You -BY291


title: Beijing You -BY293


title: Rhode Island Red-RIR187


title: RRBS_K36M_rep1

value: dominant negative H3.3 at lysine 36


title: Beijing You -BY292


title: E7-5-P-IP-K27ac_rep2

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

description: processed data file: E7-5-P-K27ac.tagAlign.fc.signal.bw

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample.

source_name: mouse embryos

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; genomic DNA from embryo samples were separated and extracted by modified microChIPseq; RNA from in vitro culture bulk cells were extracted by using Trizol and precipitated by isopropanol.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of bulk RNA seq were prepared by using NEBNext RNAseq library kit.

treatment_protocol: For Enh9E KO sample, the cells were generated by using CRISPR-Cas9 system to delete the target enhancer region in E14 mouse embryonic stem cells. For mouse neural differentiation assay, we take advantage of the protocol published previously (DOI:10.1016/j.stemcr.2015.09.010).

value: ICR

tag: devlopmental stage

value: 7.5 dpc


title: E7-5-ExE-IP-K27ac_rep2

description: processed data file: E7-5-ExE-K27ac.tagAlign.fc.signal.bw


title: WT-rep1-H3K9me3

tag: genotype


title: Beijing You -BY289


title: RRBS_K9M_rep1


title: E7-5-AM-IP-K27ac_rep2

description: processed data file: E7-5-AM-K27ac.tagAlign.fc.signal.bw


title: RRBS_WT_rep1

value: wildtype


title: Beijing You -BY288


title: E7-5-A-IP-K27ac_rep2

description: processed data file: E7-5-A-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR189


title: Beijing You -BY286


title: E7-0-P-IP-K27ac_rep2

description: processed data file: E7-0-P-K27ac.tagAlign.fc.signal.bw

value: 7.0 dpc


title: Beijing You -BY287


title: Beijing You -BY295


title: Beijing You -BY285


title: Beijing You -BY290


title: Beijing You -BY284


title: E7-0-A-IP-K27ac_rep2

description: processed data file: E7-0-A-K27ac.tagAlign.fc.signal.bw


title: Beijing You -BY283


title: Beijing You -BY280


title: E6-5-ExE-IP-K27ac_rep2

description: processed data file: E6-5-ExE-K27ac.tagAlign.fc.signal.bw

value: 6.5 dpc


title: Rhode Island Red-RIR186

value: Blood


title: 20w WT

city: Goettingen

first: Laura

middle: C

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

institute: University Medical Center, Goettingen

description:
This Sample represents 3 replicates: 20wWT1, 20wWT2, 20wWT3
processed data file: DESeq2_normalized_counts.xlsx

data_processing:
cDNA libraries were amplified and sequenced by using the cBot and HiSeq4000 from Illumina (SR; 1x50 bp; 51 cycles with single indexing; 6 GB ca. 30- 35 million reads per sample).
Sequence reads were aligned to the mouse reference assembly (UCSC version mm9) using Bowtie 2.0.
For each gene, the number of mapped reads was counted using htseqcount and DESeq2 was used to analyze the differential expression.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: DESeq2_normalized_counts.xlsx: Excel file containing the output from DESeq2: normalized counts of the raw data.

source_name: Cardiac ventricles

growth_protocol: Mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
RNA was isolated from mice cardiac tissue using NucleoSpin RNA kit from Macherey-Nagel (Cat no: 740955.10). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: WT

tag: age

value: 20 weeks

value: Cardiac ventricles


title: E7-5-P-IP-K9ac_rep2

description: processed data file: E7-5-P-K9ac.tagAlign.fc.signal.bw


title: RRBS_K36M_rep2


title: Beijing You -BY282


title: Beijing You -BY277


title: E7-5-ExE-IP-K9ac_rep2

description: processed data file: E7-5-ExE-K9ac.tagAlign.fc.signal.bw


title: 4w KO

description:
This Sample represents 3 replicates: 4wKO1, 4wKO2, 4wKO3
processed data file: DESeq2_normalized_counts.xlsx

value: Klf15 KO

value: 4 weeks


title: 4w WT

description:
This Sample represents 3 replicates: 4wWT1, 4wWT2, 4wWT3
processed data file: DESeq2_normalized_counts.xlsx


title: Beijing You -BY276


title: Beijing You -BY278


title: P10 KO

description:
This Sample represents 3 replicates: P10KO1, P10KO2, P10KO3
processed data file: DESeq2_normalized_counts.xlsx

value: Postnatal day10


title: E7-5-AM-IP-K9ac_rep2

description: processed data file: E7-5-AM-K9ac.tagAlign.fc.signal.bw


title: Beijing You -BY279


title: Beijing You -BY273


title: Beijing You -BY275


title: E7-5-A-IP-K9ac_rep2

description: processed data file: E7-5-A-K9ac.tagAlign.fc.signal.bw


title: P10 WT

description:
This Sample represents 3 replicates: P10WT1, P10WT2, P10WT3.
processed data file: DESeq2_normalized_counts.xlsx


title: Beijing You -BY274


title: 20w KO

description:
This Sample represents 3 replicates: 20wKO1, 20wKO2, 20wKO3
processed data file: DESeq2_normalized_counts.xlsx


title: Rhode Island Red-RIR185


title: E7-0-ExE-IP-K27ac_rep2

description: processed data file: E7-0-ExE-K27ac.tagAlign.fc.signal.bw


title: E7-0-P-IP-K9ac_rep2

description: processed data file: E7-0-P-K9ac.tagAlign.fc.signal.bw


title: E6-5-Epi-IP-K27ac_rep2

description: processed data file: E6-5-Epi-K27ac.tagAlign.fc.signal.bw


title: Beijing You -BY281


title: Beijing You -BY270


title: Beijing You -BY271


title: Pe infection, chipped DNA

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
Base-calls performed using CASAVA version 1.4
Genome_build: Dm3

organism: Drosophila melanogaster

source_name: Adult fly gut

growth_protocol: Female adult flies (2-3 days post-eclosion) were reared at 25 degrees C. two days prior to treatment, they were transferred at 29 degrees C

extract_protocol:
For each condition, 100 guts were dissected from w1118 adult female flies. Flies were kept in liquid nitrogen and batches of 20  Guts were dissected on ice, frozen in liquid nitrogen and stored at -80°C. On the day of the experiments, guts were homogenized in NE Buffer (15mM HEPES, 10mM KCl, 0.1mM EDTA, 0.5 mM EGTA, 350mM Sucrose, 0.1% Tween-20, 5mM MgCl2, 1mM DTT, 1mM PMSF, protease inhibitor tablet) supplemented with 1% formaldehyde using a douncer and pestle. After 10 minutes, crosslinking was quenched by the addition of Glycine for a final concentration of 0.125M.  Samples were cleared by centrifuging for 4 min at 4000 rpm and 4°C. Samples were washed twice with ice-cold NE buffer and twice with ice-cold RIPA buffer (25mM Tris-HCl pH7.6, 150mM NaCl, 0.5% Na-deoxycholate, 0.5mM DTT, 0.1% SDS, 1% NP-40, protease inhibitor tablet). Finally, samples were resuspended in 130 μl RIPA buffer and sonicated in Covaris E-220 (30 seconds, Intensity: 175, Cycles per burst 200, Duty 20%, Water level: 10). Samples were then cleared by centrifugation for 10 min, 4°C max speed. At this point, 1% of the total volume was separated as input and stored at 4°C, then, the remaining amount was diluted 1:5 in IP Dilution buffer (2.8 ml H2O, 3 μl 10% SDS, 7.2 μl 0.5M EDTA, 33 μl Triton X-100, 50.1 μl Tris-HCl pH 8.1, 100.2 μl 5M NaCl). We then added 1 μg of antibody (Abcam ab5408) and incubated the sample overnight at 4°C on a rotating platform. The next day, the sample was transferred to a tube containing 50 μl of magnetic beads (M-280 Sheep Anti-Mouse IgG) blocked overnight in Beads Blocking Buffer (8.77ml PBS 1x, 1 ml BSA 1%, 10 μl Triton X-100, 220 μl 45% Fish Gelatin) and the mixture was incubated for 2 hours at 4°C on a magnetic platform. Using a magnetic racks, beads were washed once with Low Salt Buffer (20mM Tris-HCl pH 8.1, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), twice with High Salt Buffer (20mM Tris-HCl pH 8.1, 500 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), LiCl Buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1mM EDTA, 1% NP-40, 1% NA-deoxycholate) and TE-NaCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). In between each wash, beads were incubated 10 min at 4°C on a rotating platform. After the last wash, beads are resuspended in 500 μl of Elution Buffer (3.24 mL H2O, 50 μl Tris-HCl pH 7.5 1M, 10 μl EDTA 0.5M, 1 mL NaHCO3 0.5M, 500 μl 10% SDS, 200 μl NaCl 5M) and the input sample was supplemented with the same amount. From then on, both the input and the IP were treated similarly. We first incubated them at 37°C for 30 min with 900 rpm shaking in the presence of 7.5 μl RNAse A 20 mg/ml. We then added 10 μl of Proteinase K and incubated the sample at 55°C overnight. The next day, we added 10 μl of Proteinase K and incubated for 1h at 45°C.  Samples were then spin down for 5 min at room temperature and 2000 rpm, finally, we used 500 μl of samples as starting material for Qiagen PCR purification kit, following the manufacturer instructions. We eluted the the IP and the input in 30 μl. We used the Qubit dsDNA HS kit to measure the DNA load.
10 ng of DNA were transferred to a low binding tube and completed to 55.5 μl with H2O. We added 3 μl of NEBNext Ultra End Repair / dA-Tailing Module Enzyme mix and 6.5 μl of Reaction buffer and incubated each tube at 20°C for 30 min, then 65°C for 30 min. The product of the reaction was purified using the Qiagen MinElute PCR Purification Kit, elution was made in 12.5 μl of Elution Buffer. For each tube, an adapter with a different barcode was selected. We used the DNA Quick ligase kit, using 15 μl of 2x buffer, 1.5 μl of DNA quick ligase and 1 μl of adapter hybrid primer. Mixture was incubated at 22°C for 30 min. The reaction was purified using the Qiagen MinElute PCR Purification Kit, elution was made in 50 μl of Elution Buffer. Samples were purified using AMPure beads in a 1:1 ratio, washed twice with 80% EtOH and resuspended in 20 μl of Elution Buffer. Using 1 μl, we perfrom a qPCR using the KAPA SYBR green kit 50 μl total volume to determine the number of cycle for each samples. We then amplify each sample by PCR using the KAPA master mix. We then perform a size selection using AMPure beads, first using a 0.6.1 ratio and excluding the bound fraction followed by a 1:1 ratio selection, washing twice with 80% EtOH and resuspending in 20 μl Elution Buffer. We used in 1 μl to measure the DNA load with Qubit dsDNA HS assay and 1 μl to assess the fragment profile using the Agilent Bio-analyzer DNA 12000 kit.

treatment_protocol: Flies were starved for 2 hours at 29 degrees, then were either fed 1.5X sucrose, Pseudomonas entomophila OD100, or Erwinia carotovora carotovora 15 at OD100. The treatment lasted 4 hours. The flies were then killed by submerging them in liquid nitrogen and stored at -80°C

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody [4H8] (Abcam ab5408)

tag: infection

value: Pseudomonas entomophila

tag: developmental stage

value: adult


title: E7-0-ExE-IP-K9ac_rep2

description: processed data file: E7-0-ExE-K9ac.tagAlign.fc.signal.bw


title: Beijing You -BY268


title: Beijing You -BY267


title: Ecc15 infection, input DNA

value: Erwinia carotovora carotovora 15


title: E7-0-A-IP-K9ac_rep2

description: processed data file: E7-0-A-K9ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR184


title: Beijing You -BY269


title: E6-5-ExE-IP-K9ac_rep2

description: processed data file: E6-5-ExE-K9ac.tagAlign.fc.signal.bw


title: Unchallenged, input DNA

value: Control


title: Ecc15 infection, chipped DNA


title: E6-5-Epi-IP-K9ac_rep2

description: processed data file: E6-5-Epi-K9ac.tagAlign.fc.signal.bw

value: ICR


title: Beijing You -BY266


title: Pe infection, input DNA


title: Rhode Island Red-RIR182


title: Unchallenged, chipped DNA


title: Rhode Island Red-RIR181


title: E7-5-P-IP-K4me1_rep2

description: processed data file: E7-5-P-K4me1.tagAlign.fc.signal.bw

value: 7.5 dpc


title: DGRP-229_Infected

data_processing:
Base-calls performed using CASAVA version 1.4
Sequencing reads were mapped to individualized genomes generated using the Dm3 genome sequence and the DGRP freeze 2 genotyping data.
The Ensemble GTF file from BDGP5.25 was used as a starting file for annotations. We used the genotype data, namely indels from the DGRP freeze 2 genotypes to generate individualized GTF files using offsetGTF from the mmseq package.
STAR aligner version 2.3.0 was used to map the reads to individualized genomes.
Htseq-count version 0.5.4p3 was for generating the count tables.
Genome_build: Dm3
Supplementary_files_format_and_content: count table

growth_protocol: Female adult flies (2-3 days post-eclosion) were reared at 25 degrees C until treatment.

extract_protocol:
For each condition, guts from 30 adult female flies were collected in PBS four hours post treatment and directly homogenized in trizol (Invitrogen) using a bead-beater. A standard protocol for RNA extraction was performed.
Illumina stranded Truseq libraries

treatment_protocol: Flies were starved for 2 hours at 29 degrees, then were either fed 1.5X sucrose (control) or Pseudomonas entomophila OD600nm = 100 (infected)

value: fly gut


title: Rhode Island Red-RIR178


title: Rhode Island Red-RIR180


title: Rhode Island Red-RIR179


title: DGRP-040_Infected


title: Rhode Island Red-RIR177


title: E7-5-AM-IP-K4me1_rep2

description: processed data file: E7-5-AM-K4me1.tagAlign.fc.signal.bw


title: E7-5-ExE-IP-K4me1_rep2

description: processed data file: E7-5-ExE-K4me1.tagAlign.fc.signal.bw


title: DGRP-085_Infected


title: Rhode Island Red-RIR176


title: Rhode Island Red-RIR173


title: Rhode Island Red-RIR174


title: E7-5-A-IP-K4me1_rep2

description: processed data file: E7-5-A-IP-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR172


title: DGRP-908_Infected


title: Rhode Island Red-RIR171


title: E7-0-P-IP-K4me1_rep2

description: processed data file: E7-0-P-K4me1.tagAlign.fc.signal.bw

value: 7.0 dpc


title: DGRP-907_Infected


title: Rhode Island Red-RIR170


title: Rhode Island Red-RIR183


title: E7-0-ExE-IP-K4me1_rep2

description: processed data file: E7-0-ExE-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR169


title: Rhode Island Red-RIR168


title: Rhode Island Red-RIR165


title: Rhode Island Red-RIR167


title: Rhode Island Red-RIR166


title: E6-5-ExE-IP-K4me1_rep2

description: processed data file: E6-5-ExE-K4me1.tagAlign.fc.signal.bw

value: 6.5 dpc


title: DGRP-882_Infected


title: Rhode Island Red-RIR163

value: Blood


title: E6-5-Epi-IP-K4me1_rep2

description: processed data file: E6-5-Epi-K4me1.tagAlign.fc.signal.bw


title: DGRP-890_Infected


title: Rhode Island Red-RIR164


title: DGRP-818_Infected


title: Rhode Island Red-RIR161


title: Rhode Island Red-RIR160


title: DGRP-802_Infected


title: NPC-K27ac

description: processed data file: micro_ChIP

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
For the integrated HMM_state_15.enhancerRegion processed data, we show genome-wide 200bp tiles of ChromHMM results for enhancers. Only 4 types of enhancers identified by ChromHMM were annotated, 1 for bivalent, 2 for poised, 3 for active and 4 for double acylated enhancers. Other types were annotated as 0.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files for RRBS data include the DNA methylation level of each single CpG site. The tagAlign files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample.The bigwig files for  ChIP-Seq show the genome wide coverge minus the input. The "HMM_state_15.enhancerRegion.kmeans.subKmeans.mergeAll.xls.gz" file includes the integrated analysis of all the sequenced epigenetic markers of this project.

source_name: neural progenitor cells derived from Epiblast stem cell line

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.  Epiblast stem cells were maintained on fetal bovine serum coated dishes in chemical defined medium (CDM) supplemented with Activin A (20ng/mL) and bFGF (10ng/mL). To derive neural progenitor cells, Epiblast stem cells were dissociated as single cells by 0.05% Trypsin, and cultured in 5% KSR neural differentiation medium (DMEM, 5% KSR, NEAA, Glutamax, b-Mercaptoethanol)  with a density of 10,000/3.5 cm petri dish.

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; genomic DNA from embryo samples were separated and extracted by modified microChIP or single cell based bisulfite seq.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of single cell based bisulfite seq were constructed according to the protocol described in (H Guo et al,2015).

value: neural progenitor cells

tag: antibody


title: DGRP-897_Infected


title: DGRP-738_Infected


title: NPC-INPUT

description: processed data file: genomic input sequencing


title: DGRP-721_Infected


title: Rhode Island Red-RIR156

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

source_name: Rhode Island Red

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.


title: Rhode Island Red-RIR158


title: Rhode Island Red-RIR157


title: E7.5_P_rep1_RNA

description: processed data file: merge.dexseq_clean_refseq.gene.all.xls

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
For the integrated HMM_state_15.enhancerRegion processed data, we show genome-wide 200bp tiles of ChromHMM results for enhancers. Only 4 types of enhancers identified by ChromHMM were annotated, 1 for bivalent, 2 for poised, 3 for active and 4 for double acylated enhancers. Other types were annotated as 0.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files for RRBS data include the DNA methylation level of each single CpG site. The tagAlign files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample. The bigwig files for  ChIP-Seq show the genome wide coverge minus the input. The "HMM_state_15.enhancerRegion.kmeans.subKmeans.mergeAll.xls.gz" file includes the integrated analysis of all the sequenced epigenetic markers of this project.


title: E7.5_P_rep2_RNA


title: Rhode Island Red-RIR154


title: DGRP-535_Infected


title: Rhode Island Red-RIR155


title: Rhode Island Red-RIR153


title: DGRP-502_Infected


title: DGRP-441_Infected


title: Rhode Island Red-RIR162


title: E7.5_A_rep2_RNA


title: Rhode Island Red-RIR149


title: E7.5_ExE_rep1_RNA


title: DGRP-426_Infected


title: Rhode Island Red-RIR152


title: Rhode Island Red-RIR151


title: Rhode Island Red-RIR148


title: Rhode Island Red-RIR147


title: E7.5_A_rep1_RNA


title: Rhode Island Red-RIR159


title: DGRP-386_Infected


title: Rhode Island Red-RIR146


title: Rhode Island Red-RIR143


title: Rhode Island Red-RIR144


title: E7.5_AM_rep2_RNA


title: E7.5_AM_rep1_RNA


title: DGRP-332_Infected


title: Rhode Island Red-RIR142


title: E7.0_P_rep2_RNA


title: DGRP-287_Infected


title: Rhode Island Red-RIR141


title: DGRP-280_Infected


title: E7.5_ExE_rep2_RNA


title: Rhode Island Red-RIR140


title: Rhode Island Red-RIR150


title: E7.0_P_rep1_RNA


title: Rhode Island Red-RIR139


title: DGRP-237_Infected


title: Rhode Island Red-RIR138


title: Rhode Island Red-RIR137


title: E7.0_ExE_rep2_RNA


title: DGRP-217_Infected


title: Rhode Island Red-RIR135


title: Rhode Island Red-RIR134


title: DGRP-142_Infected


title: E7.0_A_rep2_RNA


title: Rhode Island Red-RIR133


title: DGRP-129_Infected


title: Rhode Island Red-RIR145


title: Rhode Island Red-RIR132


title: Rhode Island Red-RIR131


title: Rhode Island Red-RIR130


title: E7-0-A-IP-K4me1_rep2

description: processed data file: E7-0-A-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR129


title: E6.5_ExE_rep2_RNA


title: Rhode Island Red-RIR128


title: DGRP-101_Infected


title: E7.0_A_rep1_RNA


title: DGRP-038_Infected


title: E6.5_ExE_rep1_RNA


title: Rhode Island Red-RIR127


title: Rhode Island Red-RIR126


title: Rhode Island Red-RIR125


title: DGRP-714_Infected


title: Rhode Island Red-RIR136


title: E6.5_Epi_rep2_RNA


title: Rhode Island Red-RIR123


title: DGRP-774_Infected


title: E7.0_ExE_rep1_RNA


title: DGRP-707_Infected


title: E6.5_Epi_rep1_RNA


title: Rhode Island Red-RIR122


title: Rhode Island Red-RIR120


title: DGRP-639_Infected


title: Rhode Island Red-RIR119


title: E7-5-P-IP-K27ac

description: processed data file: E7-5-P-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR118


title: DGRP-486_Infected


title: Rhode Island Red-RIR117


title: E7-5-AM-IP-K27ac

description: processed data file: E7-5-AM-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR115


title: Rhode Island Red-RIR116


title: DGRP-379_Infected


title: Rhode Island Red-RIR114


title: DGRP-360_Infected


title: E7-0-P-IP-K27ac

description: processed data file: E7-0-P-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR113


title: DGRP-335_Infected


title: Rhode Island Red-RIR124


title: Rhode Island Red-RIR112


title: Rhode Island Red-RIR111


title: E7-0-ExE-IP-K27ac

description: processed data file: E7-0-ExE-K27ac.tagAlign.fc.signal.bw


title: DGRP-313_Infected


title: Rhode Island Red-RIR110


title: Rhode Island Red-RIR109


title: Rhode Island Red-RIR121


title: E7-5-ExE-IP-K27ac

description: processed data file: E7-5-ExE-K27ac.tagAlign.fc.signal.bw


title: E7-0-A-IP-K27ac

description: processed data file: E7-0-A-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR108


title: Rhode Island Red-RIR107


title: E6-5-ExE-IP-K27ac

description: processed data file: E6-5-ExE-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR106


title: DGRP-303_Infected


title: Rhode Island Red-RIR105


title: E6-5-Epi-IP-K27ac

description: processed data file: E6-5-Epi-K27ac.tagAlign.fc.signal.bw


title: DGRP-301_Infected


title: E7-5-P-IP-K9ac

description: processed data file: E7-5-P-K9ac.tagAlign.fc.signal.bw


title: DGRP-229_Control


title: Rhode Island Red-RIR101


title: E7-5-A-IP-K27ac

description: processed data file: E7-5-A-K27ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR102


title: DGRP-208_Infected


title: Rhode Island Red-RIR100


title: DGRP-040_Control


title: E7-5-AM-IP-K9ac

description: processed data file: E7-5-AM-K9ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR99


title: Rhode Island Red-RIR98


title: E7-5-A-IP-K9ac

description: processed data file: E7-5-A-K9ac.tagAlign.fc.signal.bw


title: DGRP-085_Control


title: Rhode Island Red-RIR96


title: Rhode Island Red-RIR97


title: Rhode Island Red-RIR95


title: Rhode Island Red-RIR94


title: DGRP-908_Control


title: DGRP-907_Control


title: Rhode Island Red-RIR93


title: E7-0-ExE-IP-K9ac

description: processed data file: E7-0-ExE-K9ac.tagAlign.fc.signal.bw


title: DGRP-897_Control


title: Rhode Island Red-RIR92


title: E7-0-P-IP-K9ac

description: processed data file: E7-0-P-K9ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR104


title: E7-0-A-IP-K9ac

description: processed data file: E7-0-A-K9ac.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR91


title: Rhode Island Red-RIR90


title: DGRP-890_Control


title: E6-5-ExE-IP-K9ac

description: processed data file: E6-5-ExE-K9ac.tagAlign.fc.signal.bw


title: E7-5-ExE-IP-K9ac

description: processed data file: E7-5-ExE-K9ac.tagAlign.fc.signal.bw


title: E6-5-Epi-IP-K9ac

description: processed data file: E6-5-Epi-K9ac.tagAlign.fc.signal.bw


title: DGRP-882_Control


title: Rhode Island Red-RIR86


title: E7-5-P-IP-K4me1

description: processed data file: E7-5-P-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR88


title: Rhode Island Red-RIR85


title: DGRP-818_Control


title: Rhode Island Red-RIR87


title: DGRP-802_Control


title: Rhode Island Red-RIR83


title: E7-5-ExE-IP-K4me1

description: processed data file: E7-5-ExE-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR82


title: DGRP-738_Control


title: Rhode Island Red-RIR81


title: E7-5-AM-IP-K4me1

description: processed data file: E7-5-AM-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR80


title: Rhode Island Red-RIR79


title: DGRP-721_Control


title: E7-5-A-IP-K4me1

description: processed data file: E7-5-A-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR78


title: Rhode Island Red-RIR77


title: E7-0-P-IP-K4me1

description: processed data file: E7-0-P-K4me1.tagAlign.fc.signal.bw


title: DGRP-535_Control


title: Rhode Island Red-RIR89


title: DGRP-502_Control


title: Rhode Island Red-RIR76


title: Rhode Island Red-RIR75


title: E7-0-ExE-IP-K4me1

description: processed data file: E7-0-ExE-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR73


title: Rhode Island Red-RIR72


title: E7-0-A-IP-K4me1

description: processed data file: E7-0-A-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR84


title: Rhode Island Red-RIR71


title: Rhode Island Red-RIR70


title: E6-5-ExE-IP-K4me1

description: processed data file: E6-5-ExE-K4me1.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR69


title: DGRP-386_Control


title: Rhode Island Red-RIR68


title: E6-5-Epi-IP-K4me1

description: processed data file: E6-5-Epi-K4me1.tagAlign.fc.signal.bw


title: DGRP-332_Control


title: Rhode Island Red-RIR66


title: E7-5-P-IP-K4M3_rep2

description: processed data file: E7-5-P-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR67


title: Rhode Island Red-RIR65


title: Rhode Island Red-RIR64


title: DGRP-280_Control


title: E7-5-ExE-IP-K4M3_rep2

description: processed data file: E7-5-ExE-K4M3.tagAlign.fc.signal.bw


title: E7-5-P-IP-K4M3_rep1


title: Rhode Island Red-RIR61


title: DGRP-441_Control


title: Rhode Island Red-RIR60


title: E7-5-ExE-IP-K4M3_rep1


title: DGRP-217_Control


title: DGRP-426_Control


title: Rhode Island Red-RIR57


title: Rhode Island Red-RIR55


title: DGRP-142_Control


title: E7-5-AM-IP-K4M3_rep2

description: processed data file: E7-5-AM-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR56


title: Rhode Island Red-RIR54


title: E7-5-AM-IP-K4M3_rep1


title: DGRP-287_Control


title: Rhode Island Red-RIR52


title: E7-5-A-IP-K4M3_rep2

description: processed data file: E7-5-A-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR63


title: Rhode Island Red-RIR49


title: DGRP-101_Control


title: DGRP-038_Control


title: DGRP-237_Control


title: E7-5-A-IP-K4M3_rep1


title: E7-0-P-IP-K4M3_rep2

description: processed data file: E7-0-P-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR47


title: Rhode Island Red-RIR48


title: DGRP-714_Control


title: Rhode Island Red-RIR59


title: E7-0-P-IP-K4M3_rep1


title: Rhode Island Red-RIR45


title: Rhode Island Red-RIR46


title: DGRP-774_Control


title: Rhode Island Red-RIR44


title: Rhode Island Red-RIR43


title: E7-0-ExE-IP-K4M3_rep2

description: processed data file: E7-0-ExE-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR42


title: DGRP-129_Control


title: E7-0-ExE-IP-K4M3_rep1


title: Rhode Island Red-RIR53


title: Rhode Island Red-RIR41


title: DGRP-639_Control


title: Rhode Island Red-RIR51


title: DGRP-486_Control


title: Rhode Island Red-RIR39


title: Rhode Island Red-RIR35


title: Rhode Island Red-RIR34


title: E6-5-ExE-IP-K4M3_rep2

description: processed data file: E6-5-ExE-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR32


title: E6-5-ExE-IP-K4M3_rep1


title: Rhode Island Red-RIR30


title: Rhode Island Red-RIR31


title: Rhode Island Red-RIR33


title: Rhode Island Red-RIR29


title: E6-5-Epi-IP-K4M3_rep2

description: processed data file: E6-5-Epi-K4M3.tagAlign.fc.signal.bw


title: DGRP-335_Control


title: Rhode Island Red-RIR28


title: E6-5-Epi-IP-K4M3_rep1


title: DGRP-313_Control


title: Rhode Island Red-RIR27


title: Rhode Island Red-RIR26


title: DGRP-303_Control


title: Rhode Island Red-RIR25


title: DGRP-379_Control


title: DGRP-301_Control


title: Rhode Island Red-RIR37


title: E7-0-A-IP-K4M3_rep1

description: processed data file: E7-0-A-K4M3.tagAlign.fc.signal.bw


title: Rhode Island Red-RIR24


title: DGRP-360_Control


title: Rhode Island Red-RIR23


title: E7-5-P-INPUT


title: DGRP-208_Control


title: Patient 2009

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Library strategy: FFPEcap-seq
Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 and the following arguments: bowtie -S --chunkmbs 512 -m 1 -t --best -q -l 32 -e 80 -n 2. Reads were also aligned to a refSeq reference using Bowtie V 1.1.2 and the following arguments: bowtie -S -n 2 -a -m 10 -S --chunkmbs 512.
Unique Molecular Index and additional sequences were trimmed off of the 5' end of the read.  Indexes were added to the read name and reads with the same position and index were collapsed into a single read.
Genome aligned reads mapping to hg19 UCSC knownGene gene models were counted using featureCounts from the SubRead package. Normalized counts were generated using DESeq2.
Genome_build: hg19, refSeq
Supplementary_files_format_and_content: BigWig files contain pileups of reads mapped to the hg19 human genome build or a refseq reference. Reads have been collapsed, which removes duplicate molecules that contained identical unique molecular indexes and mapped to identical locations.
Supplementary_files_format_and_content: Tab file contains a matrix of normalized gene counts for matched FFPE derived RNA and freshly derived RNA FFPEcap-seq, and standard RNA-seq from GSE109892.

source_name: Endometrial Carcinoma Grade 2

growth_protocol: Ishikawa cells (Sigma Aldrich), were maintained at 37°C with 5% CO2 in RPMI-1640 media containing 10% fetal bovine serum, 50 U/mL penicillin, and 50 mg/mL streptomycin.

extract_protocol:
Fresh RNA was extracted with the Quick-RNA Miniprep kit.  For FFPE RNA, four 20 μm scrolls were collected from these samples and RNA was extracted using the RNeasy FFPE kit (Qiagen).
A detailed FFPEcap-seq protocol can be found in the supplemental protocol. RNA concentration was measured using a Qubit 2.0 with the RNA high sensitivity or RNA broad range assay (ThermoFisher), depending on the concentration.  Enzyme pre-treatment was performed using 1 μL (1 unit) Terminator Nuclease (Lucigen), 2 μL T4 Polynucleotide Kinase (New England Biolabs), 2 μL 10x Terminator Buffer A, 2 μL 10 mM ATP, 1 μL SUPERase In (ThermoFisher), input RNA, and water in a 20 μL reaction. Samples were incubated for 45 minutes at 30°C before being cleaned up with the RNA Clean and Concentration kit (Zymo Research). RNA was eluted using 6 μL of water, with 5 μL being collected after centrifugation. 1 μL of eluted RNA was used for quantification with the Qubit 2.0 RNA high sensitivity kit (ThermoFisher). For enzymatic treatment controls, the above procedure was followed except Terminator and T4 Polynucleotide Kinase were replaced with water. When polyphosphatase was tested, 1 μL (20 units) RNA 5’ polyphosphatase (Lucigen) was included in the reaction.  To begin the modified nanoCAGE library preparation, trehalose-sorbitol solution was made by adding 5 mL of a saturated trehalose solution (Sigma) to 10 mL of 1.28 g/mL sorbitol solution (Sigma). 1 g of celex 100 (Sigma) was added to the solution and vortexed vigorously and allowed to sit for 3 hours at room temperature.  The tube was then centrifuged for 10 minutes at 600xg and the supernatant was aliquoted and stored at -30°C.  Oligo master mix was made by combining 8 μL of Trehalose-Sorbitol solution with 1 μL 1 mM Template switching oligo, and 1 μL 100 μM reverse transcriptase oligo (see Table S1 for all oligo sequences).  All oligonucleotides were ordered from Integrated DNA technologies.  1 μL of the oligo master mix was combined with the remaining 4 μL of RNA and incubated at 65°C for 10 minutes, then immediately moved to ice for 2 minutes. The template switching reaction contained 1 μL Prime Script Reverse Transcriptase (Takara), 2 μL 5x Prime Script buffer, 1.5 μL 5M Betaine, 0.5 μL 200 mM DTT, and 0.625 μL 10 mM dNTP mixture. The template switching reaction mixture was combined with the RNA oligo mixture and heated to 22°C for 10 minutes, 40°C for 30 minutes, and then 75°C for 15 minutes.  The sample was then cleaned up using Ampure XP beads (Beckman Coulter) with a ratio of 1.5:1 of bead volume to sample volume.  The cDNA was eluted in 40 μL water. For second strand synthesis, 7.5 μL purified cDNA was added to 25 μL Phusion HF master mix (New England Biolabs), with 2.5 μL 10 μM 2nd strand forward primer, 2.5 μL of 10 μM 2nd strand reverse primer, and 12.5 μL of water. The reaction was heated at 95°C for 1 minute, followed by 24 cycles of 95°C for 15 seconds, 65°C for 10 seconds, and 68°C for 2 minutes.  This reaction was purified using Ampure XP beads (Beckman Coulter) with a 0.8:1 ratio of bead volume to sample volume and eluted in 30 μL water. The final library was created by taking 40 ng of purified double stranded cDNA and mixing it with 25 μL 2x Phusion HF master mix (New England Biolabs), 1.25 μL 10 μM library forward primer, 1.25 μL 10 μM library reverse primer (containing a sample index), and water to a total volume of 50 μL. Samples were heated to 95°C for 1 minute, followed by 2 cycles of 95°C for 15 seconds, 55°C for 10 seconds, and 68°C for 2 minutes, then followed by 8 cycles of 95°C for 15 seconds, 65°C for 10 seconds, and 68°C for 2 minutes. This reaction was purified using Ampure XP beads (Beckman Coulter) with a 0.8:1 ratio of bead volume to sample volume and eluted in 30 μL water.

treatment_protocol: Cells were transferred to hormone depleted media five days prior to RNA harvest in order to match previously performed RNA-seq experiments. Hormone depleted media consisted of phenol red-free RPMI-1640, 10% charcoal-dextran treated fetal bovine serum (Sigma Aldrich), 50 U/mL penicillin, and 50 mg/mL streptomycin.

tag: experiment group

value: Patient Sample


title: Rhode Island Red-RIR22


title: E7-5-ExE-INPUT_rep2


title: Patient 2005


title: Rhode Island Red-RIR21


title: E7-5-ExE-INPUT


title: Cytokines3

city: Baltimore

first: Dax

last: Fu

state: MD

address: 733 N Broadway st

institute: JHU

data_processing:
Reads were demultiplexed using Illumina’s bcl2fastq2
Read quality was checked for each sample using FastQC v0.10.1.
Reads were then imported into STAR version  2.5.2b   for alignment into BAM files.
The aligned reads were assembled with CLASS v.2.1.7, for each sample,  to create transcript models (transfrags).
The resulted gtf files were fed to Stringtie –merge (v1.3.6) to create  a non-redundant set of transcripts. This file will be used later on,  in the differential expression step.
Cuffdiff v2.2.1 was run on each sample in order to obtain FPKM values found in the FPKM_matrix.xlsx file.
Cuffdiff and DESeq were used to look for  significant changes in transcript expression.
Genome_build: Hg38 and gencodev22.gff;
Supplementary_files_format_and_content: DESeq output was split in 2 files , containing the transfrags that were annotated ( DESeq_results_gn.csv) and the ones that could not be assigned to a known gene (DESeq_results_no_gn.csv ). Columns are : baseMean =  is a just the average of the normalized count values, dividing by size factors, taken over all samples; log2FoldChange = is the effect size estimate. It tells us how much the gene's expression seems to have changed due to treatment in comparison to control;  lfcSE =  the standard error estimate for the log2 fold change estimate; stat = also express the uncertainty of a particular effect size estimate as the result of a statistical test;  pvalue = a hypothesis test to see whether evidence is sufficient to decide against the null hypothesis that there is no effect of the treatment on the gene and that the observed difference  between treatment and control was merely caused by experimental variability.
Supplementary_files_format_and_content: Cuffdiff_*_exp.diff.txt files were generated with Cuffdiff (these tab delimited files contain the feature_id,  gene name,  locus,  test_status (OK=test successful, NOTEST=not enough alignments for testing, LOWDATA=too complex or shallowly sequenced, HIDATA=too many fragments in locus, or FAIL=when an ill-conditioned covariance matrix or other numerical exception prevents testing), FPKM values for each gene or transcript in both samples, value of test statistics used to compute significance of the observed change in FPKM, p-value and q-values=The FDR-adjusted p-value of the test statistic. Last column states if the feature is significantly differentially expressed or not.
Supplementary_files_format_and_content: FPKM_matrix.xlsx  =  normalized abundance matrix containing the FPKMs for each gene in each sample and the stdev for each set (control and condition);

source_name: EndoC-betaH1_after cytokine exposure

growth_protocol: EndoC-βH1 cells from Univercell-Biosolutions were detached from culture flasks using 0.05% trypsin and 0.53 mM EDTA, and then reseeded at 75,000 cells/well at 70% confluence in a 96-well TPP plate coated with Matrigel-fibronectin matrix. The cells were subcultured at 37 oC in a 5% CO2 humidified atmosphere, and grown in a serum-free culture medium containing 11 mM glucose Dulbecco’s modified Eagle’s medium, 10% BSA faction V, 10mM nicotinamide, 50uM 2-mercaptoethanol, 5.5ug/ml transferrin, 6.7 ng/ml sodium selenite, 100 U/ml Penicillin and 100ug/ml streptomycin.

extract_protocol:
EndoC cells were treated with or without 1 x Cytokines for 24h. Cells were collected, washed by PBS. Cells were lysed and RNA were extracted using RNeasy Mini Kit (QIAGEN, Cat. # 74104).
NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7765) were used to generate libraries.  The BioAnalyzer is used for quality control of the libraries to ensure adequate concentration and appropriate fragment size.  The resulting library insert size is 200bp-500bp with a median size around 300bp. Libraries were uniquely barcoded and pooled for sequencing.

treatment_protocol: A cytokine cocktail was prepared in the culture medium containing 5 ng/ml IL-1β, 10 ng/ml TNF-α 50 ng/ml IFN-γ and 100 ng/ml IL-17. All cytokines were provided by R&D Systems. The subcultured EndoC-βH cells were allowed to adhere for 24 hr prior to addition of the cytokine cocktail.

tag: cell line

value: pancreatic beta cells

tag: treatment

value: after cytokine exposure


title: E7-5-P-INPUT_rep2


title: Rhode Island Red-RIR20


title: Cytokines2


title: E7-5-AM-INPUT_rep2


title: Rhode Island Red-RIR19


title: E7-5-AM-INPUT


title: Cytokines1


title: Control2

source_name: EndoC-betaH1_before cytokine exposure

value: before cytokine exposure


title: E7-5-A-INPUT_rep2


title: Rhode Island Red-RIR18


title: E7-5-A-INPUT


title: Control1


title: Rhode Island Red-RIR17


title: Rhode Island Red-RIR16


title: E7-0-P-INPUT_rep2


title: DGRP-707_Control


title: DMSO_rep3_batch2

city: London

first: Liisi

last: Laaniste

address: 160 Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
BCL files generated by Illumina sequencing systems to standard FASTQ using Bcl2Fastq v2.20
Data quality was assesed by FastQC
Sequenced reads were mapped to hg38 whole genome and quantified using STAR v2.5.0a with parameters --quantMode GeneCounts
Column #4 of STAR output count matrix was used, as the data are reverse stranded
Genome_build: hg38
Supplementary_files_format_and_content: files with comma separated values for each experiment include raw counts for all samples

source_name: anaplastic astrocytoma cell culture

growth_protocol: Primary Astrocytoma WHO grade III culture (TB98) was established from fresh tumors and maintained in DMEM/F12 (1:1) supplemented with 10% foetal bovine serum (Complete medium, CM). Fresh tumor samples were washed in DMEM/F12 (1:1) and minced through a cell strainer to obtain a single-cell suspension. Contaminating red blood cells were removed by pelleting cells by centrifugation at 12k rpm for 5 minutes and re-suspending in 1mL of sterile H2O for 30 seconds followed by the addition of 5 mL of CM. After a further round of centrifugation and removal of supernantant, fresh CM was added to the cells and the cell suspension transferred to culture flasks and incubated at 37oC to allow for growth. Cells were passaged 4 times before plating them for the experiment.

extract_protocol:
Total RNA using the RNasey Mini kit according to the manufacturer’s instructions.
mRNA was isolated from total RNA using oligo dT beads. After fragmentation the sample was converted to double stranded DNA and ligated to Illumina adapters. The second strand cDNA was then degraded by the UNG enzyme providing directional information to the library. Indexing of each sample was performed by PCR.

treatment_protocol: Pasage 5 cells were seeded on 6-well plates at a desity of  4 × 10E5 cells per well and allowed to adhere for 24h. The cells were then treated with 20uM, 10nM or 2nM resveratrol for 24 hours before harvesting

value: anaplastic astrocytoma cells

value: DMSO

tag: treatment duration

tag: passages

tag: idh1 status in tumor tissue

value: IDH1 mutation

tag: experiment


title: Rhode Island Red-RIR15

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

institute: China Agricultural University

tag: tissue


title: E7-0-P-INPUT

tag: strain


title: Rhode Island Red-RIR14


title: Rhode Island Red-RIR103


title: E7-0-ExE-INPUT_rep2


title: Control3

tag: cell type


title: E7-0-ExE-INPUT

tag: devlopmental stage


title: Rhode Island Red-RIR13


title: DMSO_rep1_batch2


title: Severe_non_cerebral_malaria_PBMC_patient4

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
NCM4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Human GE 8x60k agilent microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: Severe, non, cerebral, malaria, PBMC, patient4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 8-10ml venous peripheral blood from malaria patients were collected at the onset of P. falciparum infection. PBMCs were separeted by Ficoll gradient centrifugation.Total RNA was isolated using the Trizol reagent (Invitrogen) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole blood

tag: disease state

value: Severe anemia

tag: gender

value: M

tag: leucocytes count (giga/l)


title: Severe_non_cerebral_malaria_PBMC_patient3

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
NCM3

source_name: Severe, non, cerebral, malaria, PBMC, patient3

tag: age


title: DMSO_rep2_batch2


title: RSV_2nM_rep3_batch2

value: 2nM resveratrol


title: Rhode Island Red-RIR12


title: Severe_non_cerebral_malaria_PBMC_patient2

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
NCM2

source_name: Severe, non, cerebral, malaria, PBMC, patient2

value: F


title: RSV_2nM_rep2_batch2


title: E7-0-A-INPUT_rep2

value: ICR


title: Mild_malaria_PBMC_patient5

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM5

source_name: Mild, malaria, PBMC, patient5

value: Mild Malaria


title: E7-0-A-INPUT

value: 7.0 dpc


title: Severe_non_cerebral_malaria_PBMC_patient1

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
NCM1

source_name: Severe, non, cerebral, malaria, PBMC, patient1


title: Rhode Island Red-RIR11

value: Blood


title: RSV_2nM_rep1_batch2


title: Mild_malaria_PBMC_patient6

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM6

source_name: Mild, malaria, PBMC, patient6


title: Mild_malaria_PBMC_patient4

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM4

source_name: Mild, malaria, PBMC, patient4


title: Rhode Island Red-RIR10


title: Mild_malaria_PBMC_patient2

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM2

source_name: Mild, malaria, PBMC, patient2


title: E6-5-ExE-INPUT_rep2

source_name: mouse embryos

value: 6.5 dpc


title: Mild_malaria_PBMC_patient3

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM3

source_name: Mild, malaria, PBMC, patient3


title: Rhode Island Red-RIR9


title: Mild_malaria_PBMC_patient1

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
MM1

source_name: Mild, malaria, PBMC, patient1


title: RSV_10nM_rep2_batch2

value: 10nM resveratrol


title: RSV_10nM_rep3_batch2


title: E6-5-Epi-INPUT_rep2


title: Rhode Island Red-RIR8


title: RSV_10nM_rep1_batch2


title: E6-5-Epi-INPUT


title: Rhode Island Red-RIR7


title: Cerebral_malaria_PBMC_patient6

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM6

source_name: Cerebral, malaria, PBMC, patient6

value: Cerebral Malaria


title: DMSO_rep3_batch1

value: 20uM resveratrol


title: Cerebral_malaria_PBMC_patient5

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM5

source_name: Cerebral, malaria, PBMC, patient5


title: Rhode Island Red-RIR5

source_name: Rhode Island Red


title: DMSO_rep2_batch1


title: E6-5-ExE-INPUT


title: Cerebral_malaria_PBMC_patient3

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM3

source_name: Cerebral, malaria, PBMC, patient3


title: Rhode Island Red-RIR4


title: HLH_T4_scRNAseq

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
ScRNA-seq alignment process was completed by cellranger(version 3.0.0)
Seurat V3 workflow
Genome_build: hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts

source_name: Peripheral blood mononuclear cell

extract_protocol:
Preparation: Collect 3ml herprized peripheral blood from patient. Put all regent, 1×ACK, 0.04% PBS-BSA, and sample on ice;Lyse RBCs;Centrifuge at 300g, RT for 3min;Collect the plasma (around 1.5ml) in an EP tube;Add 30ml 1×ACK to resuspend blood by inverting the tube;Put the mixed ACK-sample on ice and lysis for <7min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant;Add 10ml 1×ACK to lysis again;Lysis on ice for <5min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant.;Wash and count (get rid of dead cells);Resuspend cells by 5ml 0.04% PBS-BSA pre-cold buffer;Mix throughout by pipetting;Suck out 10ul for counting (add 10ul Typan Blue);Suck out 2×106 cells into EP tube and put the remaining cells on ice;Centrifuge the EP tube at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 1ml 0.04%PBS-BSA buffer;Centrifuge at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 830ul 0.04%PBS-BSA buffer;Count (both living and dead cells) twice;Keep the density of living cells between 0.7~1.2×106/ml;Freeze the remaining cells
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform
single cell RNA-seq

value: PBMC

tag: treatment time

value: Day 76, T3

value: EBV-HLH


title: 20ng-72h-2

city: Oullins

first: Florian

last: SIMON

address: 165 Chemin du Grand Revoyet

institute: University Lyon 1

data_processing:
The sequencing reads were obtained after demultiplexing the raw sequencing data using bcl2fastq v2.19.1.403 Version v2.15.0 for NextSeq™ 500 (Illumina)
We validated the quality controls of each sample using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then generated alignment files using STAR v2.5.2b in the “2-pass” mode, on the hg19 human genome.
Upon obtaining the final sorted alignment file, the count of reads was performed using GFOLD V1.1.4 (option: count; https://bitbucket.org/feeldead/gfold/)
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM for each samples

source_name: Brain

growth_protocol: 4-5 10^5 cells/cm2 were coated in a 6-well plate on EBM-2 medium supplemented with 5% FBS, penicillin-streptomycin 100 µg/mL, 1.4 µM hydrocortisone, 5 µg/mL acid ascorbic, 10 mM HEPES, 1% chemically defined lipid concentrate and 1 ng/mL bFGF.

extract_protocol:
Extraction was performed using the Maxwell 16 LEV Simply RNA cells kit
RNA libraries were prepared for sequencing using 1 µg of total mRNA with NEB library preparation kit

treatment_protocol: Cells were exposed or not to 20 ng/mL interleukin-6 for 72h. Medium with or without IL-6 was renewed every 24h.

value: 20 ng/mL interleukin-6 for 72h


title: 20ng-72h-3


title: 20ng-72h-1


title: Tneg-3


title: RSV_20uM_rep2_batch1

source_name: anaplastic astrocytoma cell culture

value: anaplastic astrocytoma cells

value: IDH1 mutation


title: Cerebral_malaria_PBMC_patient2

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM2

source_name: Cerebral, malaria, PBMC, patient2

value: whole blood


title: Rhode Island Red-RIR3


title: HLH_T2_scRNAseq

value: Day 7, T1


title: HLH_T3_scRNAseq

value: Day 21, T2


title: Rhode Island Red-RIR2


title: Tneg-2


title: Cerebral_malaria_PBMC_patient4

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM4

source_name: Cerebral, malaria, PBMC, patient4

value: F


title: RSV_20uM_rep1_batch1


title: Tneg-1


title: Rhode Island Red-RIR6


title: HLH_T1_scRNAseq

value: Day 0, T0


title: Rhode Island Red-RIR1


title: Cerebral_malaria_PBMC_patient1

description:
Gene expression profiling of PBMCs from senegalese cerebral and mild malaria patient by agilent technology
CM1

source_name: Cerebral, malaria, PBMC, patient1

value: M


title: DMSO_rep1_batch1


title: RSV_20uM_rep3_batch1


title: Arabidopsis leaf infected by 96-11-17M 48h rep 1

status: Public on Oct 06 2019

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio (V2010.1).
A reference genome sequence data of Arabidopsis thaliana was obtained from Illumina iGenome supporting site (assembly ID: TAIR10; http://support.illumina.com/sequencing/sequencing_software/igenome.html). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with FPFM values

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: pathogen

value: Vibrio vulnificus

tag: pathogen strain

tag: cultivar

value: leaf

tag: infection time

tag: replication number


title: Arabidopsis leaf infected by 96-11-17M 48h rep 2


title: Arabidopsis leaf infected by 96-11-17M 72h rep 2


title: Arabidopsis leaf infected by 96-11-17M 24h rep 2


title: Arabidopsis leaf infected by 96-11-17M 12h rep 2


title: Arabidopsis leaf infected by 96-11-17M 24h rep 1


title: Arabidopsis leaf infected by 96-11-17M 12h rep 1


title: Arabidopsis leaf infected by 96-11-17M 0h rep 1


title: S365_P22_LCP66

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: Set 2 (Illumina HiSeq 4000)

data_processing: Basecalling performed by RTA version 2.4.11. Demultiplexing performed by Bcl2fastq version 2.17. Alignment, tagging, gene and transcript counting performed CellRanger version 2.2.0. Aggregation performed by CellRanger version 3.0.2. Genome_build: GRCh38. Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) sample information (samples.txt).

source_name: Primary liver cancer single-cell

extract_protocol: Libraries were prepared according to 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed and re-suspended in PBS + 0.04% BSA. Sample viability was assessed and a final concentration of 1,200 cells/µl of sample was adjusted. The cDNAs was obtained after the GEM generation and barcoding, followed by GEM RT reaction and cleanup steps. Purified cDNA was amplified for 14 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were then run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as recommended by 10x Genomics V2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For samples preparation on the 10x Genomics platform, the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used.

tag: cancer type

value: Intrahepatic cholangiocarcinoma

tag: cell number


title: Arabidopsis leaf infected by 96-11-17M 0h rep 2


title: S364_P21_LCP65

description: Set 2 (Illumina HiSeq 4000)

value: Hepatocellular carcinoma


title: S300_P02_LCP60

description: Set 2 (Illumina HiSeq 4000)


title: S351_P10_LCP34

description: Set 2 (Illumina HiSeq 4000)


title: S358_P16_LCP46

description: Set 2 (Illumina HiSeq 4000)


title: S355_P13_LCP42

description: Set 2 (Illumina HiSeq 4000)


title: BEAS2B: Y472_1

city: Clevleand

first: Mohamed

middle: E.

last: Abazeed

state: OH

department: Radiation Oncology/Translational Hematology Oncology Research

institute: Cleveland Clinic

description: replicate 1

data_processing:
Reads were aligned to a genome assembly using STAR and aligned reads were assigned.
Gene read counts were normalized within sample, averaged for replicates and log transformed.
Genome_build: hg19

growth_protocol: BEAS2B cells were grown in advanced DMEM-F12 media (ThermoFisher, MA) supplemented with 1% fetal bovine serum and 100 U/mL Penicillin, 100 g/mL of Streptomycin,  292 g/mL L-Glutamine and 1% HEPES. All cultures were maintained at 37o C in a humidified 5% CO2 atmosphere and tested to ensure absence of Mycoplasma.  Cultures were partitioned before >80% confluencey.

extract_protocol:
RNA was isolated using the Rneasy Plus Mini Kit.
Samples were checked using BioA and libraries were prepared using the TruSeq Stranded mRNA kit. Each library was quantified using Qubit and then pooled toether. Library pool was quantified using qPCR. Pool was then diluted to 4 nM and loaded on the HiSeq High Output Mode. Run was performed using a full flow cell (8 lanes) PE 100. 5% PhiX was spiked in to check run qaulity.

tag: cell line

value: immortalized bronchial epitheial cells

tag: passages


title: BEAS2B: Y472_2

description: replicate 2


title: BEAS2B: W450L_1

description: replicate 1


title: BEAS2B: W450L_2

description: replicate 2