title: Untreated_OVCAR8_Day4

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

description: CRISPR amplicon

data_processing:
Library strategy: custom (CRISPR amplicon)
Base calls were performed by the HiSeq instrument control software and further processed using the Offline Base Caller (Illumina) v. 1.9.4.
The reverse complement of the first 20 nucleotides of each fastq read was searched against a file of reference sgRNA referene sequences (available on Addgene: Human Activity-Optimized CRISPR Knockout Library # 1000000100) and each match was counted.
Supplementary_files_format_and_content: counts

growth_protocol: OVCAR-8 cells (obtained from the laboratory of Joan Brugge; Harvard Medical School), were cultured in growth media composed of 1:1 MCDB 105 media (Sigma) / Medium 199 Eagles media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Sigma), in a humidified incubator at 37 °C with 5% CO2. Human cell line authentication (CLA) analysis of OVCAR-8 cells were performed prior to screening by Duke University DNA Analysis facility. Cells tested negative for mycoplasma contamination.

extract_protocol:
Genomic DNA was isolated using a QiAmp DNA blood extraction kit.
Libraries were prepared as in: Wang T, Lander ES, & Sabatini DM (2016) Viral Packaging and Cell Culture for CRISPR-based Screens. Cold Spring Harb Protoc 2016(3): pdb.prot090811 PMID: 26933250, with the following exceptions: Forward PCR primer: AATGATACGGCGACCACCGAGATCTACACGAATACTGCCATTTGTCTCAAGATCTA  DNA Polymerase: ExTaq (Takara)  Genomic DNA/50 μL PCR reaction: 6 μg  Amplification cycles: 28

treatment_protocol: 315×10^6 OVCAR8 cells were transduced with a pooled genome-wide lentiviral sgRNA library in a Cas9-containing vector34–36 (Addgene #1000000100) at MOI < 1. Stably transduced cells were selected with 2 μg/ml puromycin, and 240×10^6 cells were passaged every 48-72 hours at a density of 3×10^6 cells/15 cm dish in Ovcar8 growth medium for the duration of the screen. At 6 weeks post-puromycin selection, 360×10^6 cells were treated with escalating doses of RSL3 (Selleckchem) for 4 days each: 0.5 μM, 1 μM, and 2μM. 1×10^7 cells each were collected from the surviving population of RSL3-treated cells and an endpoint-matched untreated population for sequencing analysis.

value: untreated


title: RSL3_OVCAR8_Day4

status: Public on Sep 16 2020

type: SRA

city: Hangzhou

country: China

description: CRISPR amplicon

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: treatment

tag: cell line


title: NSP003-RM01

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

country: Germany

institute: University Heidelberg

data_processing:
Reads were trimmed using the Trimgalore
Genome alignment was done using Bowtie2 with standard parameter
Duplicates were removed as well as reads mapping multiple times
Input and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite
Peaks were called using the callpeak mode in MACS
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing H3K27ac signal intensity

source_name: Neuroblastoma primary samples

extract_protocol:
For cell lysis, cross-linked samples were incubated 30 min on ice in 950 µL RIPA I (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.2 % SDS, 0.1 % DOC) supplemented with protease inhibitors. Sonication was performed using Bioruptor Plus sonication device (30-60 min each with 30s on and 30s off intervals). After centrifugation (20.000g, 10min and 4°C), supernatant was used for immunoprecipitation.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. This includes the steps of end repair, a-base addition, adapter ligation and amplification. Finally, samples were mixed in equal molar ratios and sequenced on an Illumina sequencing platform.

tag: tissue

value: Neuroblastoma primary samples

tag: type

value: Metastasis

tag: relapse

value: Yes

tag: gender

value: M

value: Amp

tag: Stage


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E11_ad004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age

tag: strain


title: NSP002-PT01

value: Tumor

value: No

value: F


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E11_ad001


title: RSL3_OVCAR8_Day8

description: CRISPR amplicon


title: peripheral blood buffy coat, S0199

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition] chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

source_name: peripheral blood buffy coat

label_protocol: Standard Illumina Protocol

extract_protocol: QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: peripheral blood buffy coat

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad012


title: peripheral blood buffy coat, S0197


title: NSP001-PT01

value: NonAmp


title: Untreated_OVCAR8_Day8

description: CRISPR amplicon


title: peripheral blood buffy coat, S0196


title: RSL3_OVCAR8_Day12

description: CRISPR amplicon


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E2_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad008


title: SY5Y

source_name: Neuroblastoma cell line

extract_protocol: No information provided

value: Neuroblastoma cell line


title: peripheral blood buffy coat, S0195


title: peripheral blood buffy coat, S0200


title: Untreated_OVCAR8_Day12

description: CRISPR amplicon


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad007


title: SMS-KCNR

value: SMS-KCNR


title: peripheral blood buffy coat, S0194


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad004


title: peripheral blood buffy coat, S0193


title: peripheral blood buffy coat, S0192


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E10_ad002


title: peripheral blood buffy coat, S0191


title: SkMuscle_DU_12mo_rep6

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

library_source: transcriptomic

data_processing:
Serial filtering was applied to raw reads to first remove reads containing adaptor sequences, then removing reads containing >10% N, and finally reads with greater than 50% low quality bases were excluded from subsequent analyses.
Paired-end reads for mRNA were mapped to the Rnor_6.0 rat reference genome using HISAT2 (v2.0.5).
Counts for RefSeq genes were obtained using FeatureCounts (v1.5.0-p3) and genes with normalized counts greater than 30 in at least 5 samples were retained for further analysis.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Gastrocnemius muscle

growth_protocol: Male Sprague–Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol:
Total RNA was isolated from gastrocnemius muscle using TRIzol® reagent (Invitrogen, Carlsbad, CA) following manufacturer’s protocol. For each metal and time point, three Affymetrix chips (Clariom S Rats) were used with 250 ng of total RNA derived from a pooled sample from 2-3 animals.
Library preparation and sequencing were performed by Novogene Bioinformatics Technology Corporation. Briefly, RNA sequencing libraries were constructed with TruSeq Stranded Total RNA Sample Prep Kits (Illumina, San Diego, CA) using 1000 ng of total RNA. Samples were indexed with adaptors and submitted for paired-end 2 × 100-bp sequencing using an Illumina HiSeq 2000 instrument. Sequencing was performed on ten RNA samples in each lane of the flow cell, following the manufacturer’s instructions.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: DU

tag: time


title: SkMuscle_DU_12mo_rep7

tag: treatment


title: SK-N-FI

tag: cell line

value: SK-N-FI


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad012


title: SkMuscle_DU_12mo_rep8

tag: tissue


title: TR14


title: SH-EP

value: SH-EP


title: SkMuscle_DU_12mo_rep4


title: peripheral blood buffy coat, S0190


title: peripheral blood buffy coat, S0189


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad006


title: SK-N-AS

value: SK-N-AS


title: SkMuscle_DU_12mo_rep3


title: P4


title: peripheral blood buffy coat, S0188


title: SkMuscle_DU_12mo_rep2


title: P5


title: SK-N-DZ

value: SK-N-DZ


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad004

value: DG


title: NMB

value: NMB


title: SkMuscle_DU_12mo_rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad002

value: male


title: peripheral blood buffy coat, S0185


title: SkMuscle_DU_12mo_rep5


title: NGP

value: NGP


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad010


title: SkMuscle_DU_6mo_rep8


title: NBL-S

value: NBL-S


title: SkMuscle_DU_6mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_E1_ad001


title: peripheral blood buffy coat, S0183

value: peripheral blood buffy coat


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad012


title: NB69


title: peripheral blood buffy coat, S0184


title: SkMuscle_DU_6mo_rep6


title: peripheral blood buffy coat, S0182


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad010


title: LAN6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad008


title: SkMuscle_DU_6mo_rep5


title: peripheral blood buffy coat, S0181


title: LAN2


title: peripheral blood buffy coat, S0187


title: SkMuscle_DU_6mo_rep4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad007


title: peripheral blood buffy coat, S0180


title: KELLY

value: KELLY


title: SkMuscle_DU_6mo_rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad004


title: IMR575

value: Neuroblastoma cell line


title: peripheral blood buffy coat, S0178


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D9_ad002


title: IMR32


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad010


title: SkMuscle_DU_6mo_rep1


title: peripheral blood buffy coat, S0177


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad008


title: GI-ME-N

value: GI-ME-N


title: peripheral blood buffy coat, S0175


title: SkMuscle_DU_3mo_rep7

value: Male


title: CLB-GA

value: CLB-GA


title: SkMuscle_DU_3mo_rep6

value: Sprague-Dawley

value: Skeletal Muscle


title: CHLA90


title: peripheral blood buffy coat, S0172


title: SkMuscle_DU_3mo_rep5

value: DU


title: peripheral blood buffy coat, S0223


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad004


title: peripheral blood buffy coat, S0179


title: peripheral blood buffy coat, S0171


title: CHLA20


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad002


title: SkMuscle_DU_6mo_rep2


title: CHLA15


title: SkMuscle_DU_3mo_rep4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad001


title: HD-N-33


title: SkMuscle_DU_3mo_rep3


title: SkMuscle_DU_3mo_rep8


title: peripheral blood buffy coat, S0169


title: SkMuscle_DU_3mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad010


title: peripheral blood buffy coat, S0174


title: Tumor KO-2 [KO27Tumor]

city: BEIJING

first: Qingren

last: Meng

address: BEIJINGCHAOYANG

institute: BIG

data_processing:
the quality control process was confirmed by Seqtk
map the reads to mm9 genome by TopHat
Htseq software was used to count the gene
DEGs were produced by edgeR package in R,
FPKM was calculated by formula with in-house perl scripts
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM  for every gene and every sample by excel format

source_name: IRF3-/-_colon tumor

extract_protocol:
Colon and tumor tissue were removed, flash frozen in liquid nitrogen, and Total RNA was isolated using RNeasy mini kit (Qiagen,Germany).
Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.

treatment_protocol: Mice were used at the age of six weeks, and then were injected intraperitoneally with 10 mg of azoxymethane (AOM, A5486, Sigma) per kg body weight. Five days later, 2.5% dextran sulfate sodium (DSS, MP Biologicals) was given in the drinking water for 5 days followed by regular drinking water for 2 weeks. This cycle was repeated twice with 2.5% DSS, and mice were sacrificed on day 90.

tag: strain background

tag: genotype/variation

value: colon tumor


title: peripheral blood buffy coat, S0168


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D8_ad007


title: BE-2C


title: Colon KO-2 [KO27colon]

value: colon


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad008


title: peripheral blood buffy coat, S0166


title: SkMuscle_DU_3mo_rep1

tag: gender


title: SkMuscle_DU_1mo_rep8


title: Tumor KO-1 [KO13Tumor]


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad006


title: peripheral blood buffy coat, S0170


title: peripheral blood buffy coat, S0163


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad007


title: peripheral blood buffy coat, S0164


title: SkMuscle_DU_1mo_rep6


title: Colon KO-1 [KO13colon]


title: peripheral blood buffy coat, S0161


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad004


title: Tumor WT-2 [WT16Tumor]

source_name: WT_colon tumor

value: WT


title: peripheral blood buffy coat, S0160


title: SkMuscle_DU_1mo_rep5


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad002

value: DG


title: SkMuscle_DU_1mo_rep4


title: Colon WT-2 [WT16colon]


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D7_ad001


title: peripheral blood buffy coat, S0159


title: peripheral blood buffy coat, S0158


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D6_ad012


title: SkMuscle_DU_1mo_rep2


title: peripheral blood buffy coat, S0157


title: Colon WT-1 [WT4colon]


title: N8-191216

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina Real Time Analysis software (RTA) software was used for base calling.
Sequencing data were demultiplexed using the bcl2fastq Conversion Software (v. 2.20, Illumina; San Diego, California, USA).
Single 100 nucleotide long reads were mapped to mouse genome build mm10 using HISAT2 (v 2.0.3beta) aligner.
Counts obtained obtained with FeatureCounts (v 1.4.4) were normalized for library size using TMM method from EdgeR and voom from limma.
Differential expression was computed with limma, after filtering out genes with average TPM (transcripts per kilobase million) < 1.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID

source_name: FACS sorted neutrophils

growth_protocol: K14HPV16/H2b mice or their FVBN/H2b littermates were used. The K14HPV16/H2b line was generated by crossing K14HPV16/FVBN (H2q) mice with C57BL/6 (H2b) mice to introduce the H2b locus. F1 mice were backcrossed for 11 generations to FVBN, selecting for the H2b locus in every generation. This genetic configuration allows K14HPV16/H2b mice to present E7-derived peptides on MHCI molecules while maintaining the FVBN background that is permissive for squamous carcinogenesis.

extract_protocol:
Total RNA was isolated with the miRNeasy micro kit (Qiagen)
Double stranded cDNA for RNA-seq library preparation was generated using SMART-Seq v4 Ultra Low Input RNA reagents (Catalog Number 634888, Clontech, Mountain View, California, USA) according to the protocol provided with the reagents beginning with 4ng of total RNA and using 9 cycles of PCR. 300 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (Catalog Number 15032354, Illumina, San Diego, California, USA) using the single cell RNA-seq library preparation protocol developed for the Fluidigm C1 (Fluidigm, South San Francisco, California, USA).

treatment_protocol: Live CD11b+Ly6G+Ly6C- neutrophils were FACS sorted from mouse spleen.

value: female

value: 6 months

value: Spleen

tag: cell type

value: CD11b+ Ly6G+

tag: group

value: HPV-

tag: replicate


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D6_ad010

tag: brain region

tag: Sex

value: male

tag: age


title: SkMuscle_DU_1mo_rep3

tag: strain


title: SkMuscle_DU_1mo_rep1


title: SkMuscle_DU_1mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D6_ad007


title: peripheral blood buffy coat, S0156

value: peripheral blood buffy coat

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D6_ad002


title: peripheral blood buffy coat, S0155

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: SkMuscle_P_12mo_rep8

tag: treatment

value: P

tag: time


title: SkMuscle_P_12mo_rep7

value: Male

tag: tissue


title: N2-191216

value: HPV+


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D6_ad001


title: SkMuscle_P_12mo_rep6

value: Sprague-Dawley


title: N5-1912916


title: peripheral blood buffy coat, S0153


title: Tumor WT-1 [WT4Tumor]

tag: strain background

tag: genotype/variation


title: N13-220317

tag: gender

tag: cell type


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad012


title: SkMuscle_P_12mo_rep5

value: Skeletal Muscle


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad008


title: peripheral blood buffy coat, S0152


title: SkMuscle_P_12mo_rep4


title: N12-220317

tag: group

tag: replicate


title: peripheral blood buffy coat, S0151


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad007

tag: brain region

tag: Sex


title: N11-220317

tag: strain

tag: age


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad006


title: SkMuscle_P_12mo_rep3


title: N10-220317


title: SkMuscle_P_12mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad004


title: peripheral blood buffy coat, S0149

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: N4-191216


title: peripheral blood buffy coat, S0150

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: SkMuscle_P_12mo_rep1

tag: treatment


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D5_ad001


title: 20140606.X-4DAF_MM06_OVT

city: Zurich

first: Weihong

last: Qi

address: Winterthurerstr. 190

department: FGCZ

institute: ETHZ

description:
qc-pass
keep

data_processing:
STAR for genome mapping
Threshold for data analysis were chosen to be p<0.001 and RNA-seq reads higher than 10. For a pair-wise comparison, gene expression level change higher than 2-fold and p-value<0.05 were chosen.
Differential expression was assessed with the Bioconductor packages edgeR
Genes were considered as differentially expressed if the p-value was below 0.01 and the expression fold-change was greater than 2
Genome_build: Rice: IRGSP1.0
Supplementary_files_format_and_content: raw counts

organism: Oryza sativa Japonica Group

source_name: developing seeds

growth_protocol: Rice plants (Oryza sativa cv. Nipponbare) were grown in hydroponic solutions at 28°C. Solutions for the hydroponic system were prepared as previously described (Wang et al. 2013).

extract_protocol:
The RNA extraction was done with the Qiagen RNeasy Micro Kit following manufacturer’s instruction manual. All RNA samples were adjusted to a concentration of 100 pg/µl prior to pre-amplification. Pre-amplification for the Illumina sequencing was done using the Clonetech SMARTer Ultra Low kit following the user’s manual with small modifications. In brief, the RNA samples were subjected to first strand cDNA synthesis, followed by 15 cycles of Long Distance (LD) PCR. The PCR amplified cDNA was subsequently purified by immobilizaiton on AMPure XP beads for 15 min at RT, resuspended in 15 µl nuclease-free water and stored at -20°C for further experiments and library preparation.
The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT.  Sequencing were performed on the Illumina HiSeq 2500 single end 126 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

treatment_protocol: Rice grains were collected at 04, 08 and 16 days after flowering (DAF), de-husked and immediately frozen by placing the collection tubes in liquid nitrogen. Five sub-regions of the rice grains, including CC, NE, OVT, EN and AL were dissected for further analysis (see below). The time points were selected based on the reported differentiation of the main cell types (Krishnan and Dayanandan 2003). NE is differentiated into a single layer cell at around 4 DAF, while the enlarged cells and thickenings of NE are noticed at 8 DAF (Krishnan and Dayanandan 2003). CC are visible as greenish cell layer from 4 DAF to 16 DAF. OVT locates in the ventral side of the endosperm, in conjunction with NE (Krishnan and Dayanandan 2003). EN cells are gradually developing and enlarging through 4 to 16 DAF, and the outer layer of EN cells differentiate into AL at about 16 DAF.

tag: cultivar

value: Nipponbare

value: seeds

tag: tissue subregion

value: Ovular vascular trace

tag: day


title: peripheral blood buffy coat, S0154

tag: tissue

tag: pre-pregnancy bmi (kg/m^2)


title: 20140606.X-4DAF_MM13_CC

description:
qc-pass
keep

value: Cross cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad012

value: DG


title: peripheral blood buffy coat, S0146


title: peripheral blood buffy coat, S0145


title: SkMuscle_P_6mo_rep7

tag: gender

tag: time


title: 20140606.X-4DAF_MM05_OVT

description:
qc-pass
keep


title: 20140606.X-4DAF_MM06_NE

description:
qc-pass
keep

value: Nucellar Epidermis


title: peripheral blood buffy coat, S0144


title: SkMuscle_P_6mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad008


title: peripheral blood buffy coat, S0143


title: 20140606.X-4DAF_MM05_NE

description:
qc-pass
keep


title: SkMuscle_P_6mo_rep5


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad010


title: 20140606.X-4DAF_MM05_CC

description:
qc-pass
keep


title: peripheral blood buffy coat, S0142


title: 20140606.B-8DAF_MM22_OVT

description:
qc-pass
keep


title: SkMuscle_P_6mo_rep4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad004


title: SkMuscle_P_6mo_rep3


title: SkMuscle_P_6mo_rep8


title: SkMuscle_P_6mo_rep2


title: peripheral blood buffy coat, S0141


title: peripheral blood buffy coat, S0148


title: 20140606.B-8DAF_MM22_NE

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad002


title: SkMuscle_P_6mo_rep1


title: peripheral blood buffy coat, S0139


title: peripheral blood buffy coat, S0140


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad001


title: 20140606.B-8DAF_MM21_OVT

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D3_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D4_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D3_ad010


title: SkMuscle_P_3mo_rep8


title: 20140606.B-8DAF_MM20_NE

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D3_ad006


title: 20140606.B-8DAF_MM21_NE

description:
qc-pass
keep


title: 20140606.B-4DAF_MM13_OVT

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D3_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D3_ad002


title: 20140606.B-8DAF_MM21_CC

description:
qc-pass
keep


title: 20140606.B-4DAF_MM13_NE

description:
qc-pass
keep


title: peripheral blood buffy coat, S0138


title: peripheral blood buffy coat, S0135


title: peripheral blood buffy coat, S0133


title: 20140606.B-16DAF_MM18_NE

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad012


title: SkMuscle_P_3mo_rep7


title: SkMuscle_P_3mo_rep4


title: SkMuscle_P_3mo_rep5


title: peripheral blood buffy coat, S0136


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad010


title: SkMuscle_P_3mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad008


title: peripheral blood buffy coat, S0137


title: SkMuscle_P_3mo_rep6


title: peripheral blood buffy coat, S0132


title: 20140606.B-16DAF_MM18_CC

description:
qc-pass
keep


title: SkMuscle_P_3mo_rep3


title: SkMuscle_P_3mo_rep1


title: peripheral blood buffy coat, S0131


title: 20140606.B-16DAF_MM17_OVT

description:
qc-pass
keep


title: 20140606.B-16DAF_MM18_AL

description:
qc-pass
keep

value: Alurone layer


title: peripheral blood buffy coat, S0128


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad006


title: SkMuscle_P_1mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad002


title: peripheral blood buffy coat, S0127


title: SkMuscle_P_1mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad007


title: SkMuscle_P_1mo_rep8


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D12_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D2_ad001


title: SkMuscle_P_1mo_rep5


title: 20140606.B-16DAF_MM18_EN

description:
qc-pass
keep

value: Endosperm


title: 20140606.B-16DAF_MM17_NE

description:
qc-pass
keep


title: 20140606.B-16DAF_MM17_EN

description:
qc-pass
keep


title: peripheral blood buffy coat, S0124


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D12_ad002


title: peripheral blood buffy coat, S0125


title: SkMuscle_P_1mo_rep4


title: 20140606.B-16DAF_MM17_AL

description:
qc-pass
keep


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D12_ad001


title: 20140606.B-16DAF_MM04_NE

description:
qc-pass
keep


title: SkMuscle_P_1mo_rep2


title: 20140606.B-16DAF_MM04_AL

description:
qc-pass
keep


title: peripheral blood buffy coat, S0130


title: peripheral blood buffy coat, S0122


title: SkMuscle_P_1mo_rep1


title: peripheral blood buffy coat, S0120


title: SkMuscle_P_1mo_rep3


title: peripheral blood buffy coat, S0121


title: SkMuscle_Co_12mo_rep7

value: Co


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D11_ad008


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D11_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D11_ad006


title: 20140606.B-08DAF_MM22_EN

description:
qc-pass
keep


title: peripheral blood buffy coat, S0129


title: 20140606.B-08DAF_MM20_EN

description:
qc-pass
keep


title: 20140606.B-16DAF_MM17_CC

description:
qc-pass
keep


title: peripheral blood buffy coat, S0126


title: peripheral blood buffy coat, S0119


title: 20140606.B-04DAF_MM13_EN

description:
qc-pass
keep


title: SkMuscle_Co_12mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D11_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D11_ad010


title: SkMuscle_Co_12mo_rep5


title: peripheral blood buffy coat, S0115


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad012


title: peripheral blood buffy coat, S0112


title: peripheral blood buffy coat, S0110


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad008


title: SkMuscle_Co_12mo_rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad007


title: peripheral blood buffy coat, S0109


title: peripheral blood buffy coat, S0116


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad006


title: peripheral blood buffy coat, S0108


title: SkMuscle_Co_6mo_rep6


title: SkMuscle_Co_12mo_rep4


title: SkMuscle_Co_12mo_rep8


title: peripheral blood buffy coat, S0106


title: SkMuscle_Co_6mo_rep7


title: SkMuscle_Co_6mo_rep5


title: SkMuscle_Co_12mo_rep1


title: peripheral blood buffy coat, S0107


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad002


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad012


title: Pre-Tfh from FL3

type: RNA

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Transcriptome Array 2.0 (Affymetrix)

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels

label: Biotin

source_name: Ex-vivo pre-Tfh cells

label_protocol: Biotinylated double strand cDNA targets were prepared with the NuGEN Ovation PicoSL WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kitaccording to manufacturer recommendations

extract_protocol: RNA was extracted using AllPrep ARN/ADN kit (Qiagen, Valencia, CA)

value: Lymph node

tag: pathology

value: Follicular lymphoma

tag: cell type

value: pre-Tfh cells


title: SkMuscle_Co_6mo_rep3


title: Pre-Tfh from TONS 3

value: Tonsil

value: Non malignant


title: Pre-Tfh from FL2


title: Pre-Tfh from TONS 1


title: GC-Tfh from FL3

source_name: Ex-vivo GC-Tfh cells

value: germinal center T follicular helper (GC-Tfh) cells


title: GC-Tfh from FL2


title: peripheral blood buffy coat, S0103

value: peripheral blood buffy coat


title: peripheral blood buffy coat, S0104


title: peripheral blood buffy coat, S0105


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D10_ad001

tag: brain region

tag: Sex

value: male


title: SkMuscle_Co_6mo_rep4

value: Male

tag: strain

value: Sprague-Dawley

value: Skeletal Muscle


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad010

tag: age


title: peripheral blood buffy coat, S0102

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: SkMuscle_Co_6mo_rep2


title: SkMuscle_Co_3mo_rep8


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad006


title: SkMuscle_Co_6mo_rep1


title: Pre-Tfh from FL1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad007


title: Toledo_OTX015_Rep2

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
For each gene, the counts per millions have been normalized (TMM normalization, edgeR) and logged (base 2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2 counts per million (CPM) for every gene and every sample

growth_protocol: All cell lines were cultured according to the recommended conditions. All media were supplemented with foetal bovine serum, penicillin-streptomycin-neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/mL, Sigma) and L-glutamine (1%). Cell line identity was authenticated by short tandem repeat (STR) DNA profiling.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells treated for 6 hours and 14 days with DMSO, vorinostat or pracinostat

tag: cell line

value: Toledo

tag: time point

value: 6 hrs


title: SkMuscle_Co_3mo_rep7

tag: treatment


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad008

value: DG


title: SkMuscle_Co_3mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad002


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad004


title: peripheral blood buffy coat, S0099

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)


title: peripheral blood buffy coat, S0098

tag: tissue


title: peripheral blood buffy coat, S0097

tag: pre-pregnancy bmi (kg/m^2)


title: peripheral blood buffy coat, S0101


title: SkMuscle_Co_3mo_rep5

tag: gender


title: CEMBA190625_10F_1_CEMBA190625_10F_2_D1_ad001


title: GC-Tfh from TONS 3


title: Toledo_OTX015_Rep3


title: TMD8_OTX015_Rep3


title: Toledo_OTX015_Rep1


title: GC-Tfh from FL1


title: Pre-Tfh from TONS 2


title: GC-Tfh from TONS 1


title: GC-Tfh from TONS 2


title: TMD8_OTX015_Rep2


title: peripheral blood buffy coat, S0094


title: peripheral blood buffy coat, S0093


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad010


title: OCILy10_OTX015_Rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad012


title: TMD8_OTX015_Rep1


title: SkMuscle_Co_3mo_rep3

tag: time


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad008


title: peripheral blood buffy coat, S0091


title: SkMuscle_Co_3mo_rep1


title: SkMuscle_Co_3mo_rep2


title: peripheral blood buffy coat, S0090


title: OCILy10_OTX015_Rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad007


title: OCILy10_OTX015_Rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad006


title: peripheral blood buffy coat, S0087


title: SkMuscle_Co_3mo_rep4


title: SkMuscle_Co_1mo_rep8


title: SkMuscle_Co_1mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad004


title: peripheral blood buffy coat, S0089


title: peripheral blood buffy coat, S0086


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad002


title: DOHH2_OTX015_Rep3


title: DOHH2_OTX015_Rep1


title: SkMuscle_Co_1mo_rep6


title: Toledo_NEO2734_Rep2


title: Toledo_NEO2734_Rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad012


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C9_ad001


title: SkMuscle_Co_1mo_rep5


title: SkMuscle_Co_1mo_rep4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad008


title: peripheral blood buffy coat, S0082


title: peripheral blood buffy coat, S0084


title: Toledo_NEO2734_Rep1


title: TMD8_NEO2734_Rep3


title: peripheral blood buffy coat, S0081


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad006


title: peripheral blood buffy coat, S0088


title: SkMuscle_Co_1mo_rep2


title: SkMuscle_Co_12mo_rep2


title: DOHH2_OTX015_Rep2


title: SkMuscle_Co_1mo_rep1


title: peripheral blood buffy coat, S0085


title: TMD8_NEO2734_Rep2


title: SkMuscle_Ni_6mo_rep8

value: Ni


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad002


title: peripheral blood buffy coat, S0077


title: peripheral blood buffy coat, S0080


title: SkMuscle_Ni_6mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad004


title: TMD8_NEO2734_Rep1


title: peripheral blood buffy coat, S0076


title: SkMuscle_Co_1mo_rep3


title: peripheral blood buffy coat, S0075


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C8_ad001


title: OCILy10_NEO2734_Rep3


title: SkMuscle_Ni_6mo_rep6


title: OCILy10_NEO2734_Rep1


title: peripheral blood buffy coat, S0074


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad007


title: DOHH2_NEO2734_Rep3


title: peripheral blood buffy coat, S0073


title: SkMuscle_Ni_6mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad002


title: peripheral blood buffy coat, S0072


title: peripheral blood buffy coat, S0068


title: OCILy10_CB103_Rep3


title: peripheral blood buffy coat, S0070


title: OCILy10_NEO2734_Rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad012


title: peripheral blood buffy coat, S0067


title: SkMuscle_Ni_6mo_rep5


title: DOHH2_NEO2734_Rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad008


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad008


title: SkMuscle_Ni_6mo_rep3


title: SkMuscle_Ni_3mo_rep7


title: SkMuscle_Ni_6mo_rep1


title: SkMuscle_Ni_3mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C7_ad001


title: SkMuscle_Ni_3mo_rep8


title: OCILy10_CB103_Rep2


title: SkMuscle_Ni_6mo_rep4


title: peripheral blood buffy coat, S0066


title: peripheral blood buffy coat, S0065


title: Toledo_DMSO_Rep3

value: DMSO


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad007


title: SkMuscle_Ni_3mo_rep5


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad006


title: peripheral blood buffy coat, S0064


title: Toledo_DMSO_Rep2


title: DOHH2_NEO2734_Rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad004


title: Toledo_DMSO_Rep1


title: OCILy10_CB103_Rep1


title: peripheral blood buffy coat, S0060


title: TMD8_DMSO_Rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad002


title: peripheral blood buffy coat, S0059


title: TMD8_DMSO_Rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C6_ad001


title: TMD8_DMSO_Rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad012


title: peripheral blood buffy coat, S0058


title: SkMuscle_Ni_3mo_rep2


title: OCILy10_DMSO_Rep3


title: peripheral blood buffy coat, S0057


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad010


title: SkMuscle_Ni_1mo_rep7


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad006


title: SkMuscle_Ni_1mo_rep8


title: peripheral blood buffy coat, S0056


title: SkMuscle_Ni_1mo_rep6


title: OCILy10_DMSO_Rep2


title: peripheral blood buffy coat, S0061


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad004


title: SkMuscle_Ni_3mo_rep4


title: SkMuscle_Ni_3mo_rep3


title: peripheral blood buffy coat, S0055


title: OCILy10_DMSO_Rep1


title: SkMuscle_Ni_1mo_rep5


title: peripheral blood buffy coat, S0054


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad002


title: SkMuscle_Ni_1mo_rep4


title: DOHH2_DMSO_Rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C5_ad001


title: peripheral blood buffy coat, S0053


title: DOHH2_DMSO_Rep2


title: SkMuscle_Ni_1mo_rep3


title: peripheral blood buffy coat, S0050


title: SkMuscle_Ni_1mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad012


title: SW480 shRBMS1 sample

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: RNA-seq

data_processing:
STAR (v2.5) was used to map the reads to the human transcriptome (build hg38).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Cuffdiff was used to compare transcipt expressions
RefSeq IDs were used to report differential expression data
Genome_build: hg38
Supplementary_files_format_and_content: Cufflinks tracking output file for genes, and processed gene expression log-fold changes for RefSeqs using cuffdiff

growth_protocol: Cells were grown in McCoy's media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
RNA samples were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on an Illumina NextSeq 500.

treatment_protocol: Cells were transduced with shRNAs, either shControls or shRBMS1 (TRCN0000074936, Sigma)

tag: replicate

tag: shRNA


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad008

tag: brain region


title: SkMuscle_Ni_1mo_rep1


title: SW480 shControl sample rep 2

description: RNA-seq

value: shControl


title: SkMuscle_Ta_12mo_rep8

value: Ta


title: SW480 shControl sample rep 1

description: RNA-seq


title: peripheral blood buffy coat, S0046


title: peripheral blood buffy coat, S0048


title: SkMuscle_Ta_12mo_rep7


title: peripheral blood buffy coat, S0044


title: DFU Patient P2#21

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Demultiplex and convert to FastQ (Casava 1.8.2)
Map to hg19 (Tophat 2.1.1)
Calculate RPKM (Partek GS 6.16.0812)
ANOVA comparison (Partek GS 6.16.0812)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM and anova comparison

source_name: Diabetic foot Ulcer

extract_protocol:
Discarded, unidentified, diabetic foot ulcer samples were obtained from consenting patients receiving standard care and considered as non-human subject research by the University of Miami Intuitional Review Board
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ulcer

value: Nonhealer


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad004

tag: Sex


title: SkMuscle_Ta_12mo_rep6

tag: strain


title: SkMuscle_Ni_3mo_rep1


title: DFU Patient P2#03


title: SkMuscle_Ta_12mo_rep5


title: DOHH2_DMSO_Rep1


title: SkMuscle_Ta_12mo_rep4


title: peripheral blood buffy coat, S0052


title: peripheral blood buffy coat, S0041


title: peripheral blood buffy coat, S0043


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad010

tag: age


title: DFU Patient P2#01


title: SkMuscle_Ta_12mo_rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad007


title: DFU Patient UM#31W4


title: SkMuscle_Ta_12mo_rep2


title: peripheral blood buffy coat, S0037

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad007


title: SkMuscle_Ta_12mo_rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad006


title: SkMuscle_Ta_6mo_rep8


title: peripheral blood buffy coat, S0036

tag: maternal age at delivery (years)


title: DFU Patient P2#13

value: Healer


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad012


title: SkMuscle_Ta_6mo_rep7


title: peripheral blood buffy coat, S0035


title: DFU Patient UM#24W0


title: peripheral blood buffy coat, S0034


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad001


title: DFU Patient UM#30W4


title: SkMuscle_Ta_6mo_rep6


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad012


title: DFU Patient UM#23W0


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad008


title: peripheral blood buffy coat, S0033


title: SkMuscle_Ta_6mo_rep5


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad010


title: peripheral blood buffy coat, S0032


title: DFU Patient UM#15W0


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad007


title: SkMuscle_Ta_6mo_rep4


title: peripheral blood buffy coat, S0030


title: peripheral blood buffy coat, S0039


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad006


title: peripheral blood buffy coat, S0029


title: SkMuscle_Ta_6mo_rep2


title: peripheral blood buffy coat, S0028


title: Diabetic Foot Skin Donor #39

source_name: Diabetic foot skin

value: Skin


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad004


title: SkMuscle_Ta_6mo_rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad002


title: peripheral blood buffy coat, S0027


title: Diabetic Foot Skin Donor #34


title: Diabetic Foot Skin Donor #37


title: peripheral blood buffy coat, S0026


title: SkMuscle_Ta_3mo_rep8


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C2_ad001


title: SkMuscle_Ta_3mo_rep7


title: peripheral blood buffy coat, S0025


title: DFU Patient UM#8W4


title: Diabetic Foot Skin Donor #32


title: SkMuscle_Ta_6mo_rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C12_ad006


title: Diabetic Foot Skin Donor #31


title: peripheral blood buffy coat, S0024


title: DFU Patient UM#7W4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C12_ad004


title: SkMuscle_Ta_3mo_rep5


title: Diabetic Foot Skin Donor #21


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C12_ad002


title: peripheral blood buffy coat, S0023


title: SkMuscle_Ta_3mo_rep4


title: Diabetic Foot Skin Donor #20


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C12_ad001


title: peripheral blood buffy coat, S0021


title: SkMuscle_Ta_3mo_rep3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C11_ad012


title: peripheral blood buffy coat, S0020


title: peripheral blood buffy coat, S0019


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C11_ad008


title: SkMuscle_Ta_3mo_rep6


title: SkMuscle_Ta_3mo_rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C11_ad006


title: peripheral blood buffy coat, S0016


title: peripheral blood buffy coat, S0015


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C11_ad002


title: SkMuscle_Ta_1mo_rep8


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax16

city: Gainesville

first: Jose

last: Solbiati

state: Florida

address: 1395 Center Drive

department: Oral biology

institute: University of Florida

data_processing:
We used the PATRIC annotation for genome ID 431947.7 of P. gingivalis sequences 33277  for our analysis. Low-quality sequences were removed from the query files using Trimmomatic .
Cleaned files were aligned against the P. gingivalis ATCC 33277 genome database using bowtie2 .
Eukaryotic sequences, human and G. mellonella, were aligned against genome release 33 (GRCh38.p13) in GenCode (https://www.gencodegenes.org/) and RefSeq assembly accession GCF_003640425.2, respectively. Alignment for eukaryotic sequences was performed using STAR . Read counts from the BAM files were obtained using featureCounts.
In the case of THP-1 infection experiments, differential expression analysis was performed using NOISeqBio (102). After exploratory analysis with NOISeqBio, we selected RPKM normalization for THP-1 cells data, tmm normalization with length correction for P. gingivalis intracellular transcriptome, and tmm normalization without length correction for was P. gingivalis planktonic transcriptome. Only with significant differential expression and log changes > 2 were used in posterior analyses.
Genome_build: human:  release 33 (GRCh38.p13), Porphyromonas gingivalis genome ID 431947.7 of P. gingivalis sequences 33277 , galleria mellonella: GCF_003640425.2.
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Galleria mellonella

source_name: larvae

growth_protocol:
Bacterial growth conditions. Porphyromonas gingivalis ATCC 33277 was cultured anaerobically at 37°C. Cells maintained on BHI-Blood agar plates supplemented with 5 μg/ml hemin, and 1 μg/ml menadione (vitamin K). Two different liquid growth media were used in the experiments. For the construction of the mutant and the infection experiments, we used TSB broth supplemented with 1 mg/ml yeast extract, 5 μg/ml hemin, and 1 μg/ml menadione. For the transcriptome experiments, we grew P. gingivalis in 20% heat-inactivated human serum (Sigma-Aldrich H3667-20ML) supplemented with 5 μg/ml hemin as describe in Grenier et al.
THP-1 cells culture. The human monocyte/macrophage cell line THP-1 (ATCC®, TIB-202) was cultured at 37°C in a 5% CO2 incubator in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, L-glutamine (2 mM), penicillin/streptomycin (100 U/100 µg/ml), HEPES (10 mM), sodium pyruvate (1 mM), glucose (4.5 mg/ml), sodium bicarbonate (1.5 mg/ml) and 2-mercaptoethanol (0.05 mM; Sigma-Aldrich, St. Louis, MO). Cells were adjusted to 5x105 viable cells/ml and, in order to induce differentiation into a macrophage-like state, THP-1 cells were placed into fresh medium containing 100 ng/ml phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, St. Louis, MO) and 1 ml of THP-1 cells were added to each well of 24-well cell culture plates. After 48 hrs of incubation, the cell culture medium was replaced by antibiotic-free medium, and cells were used in challenge studies.
Galleria mellonella: G. mellonella larvae were purchased from SWorm Ltd., South Korea, and were used within five days of receipt. For the G. mellonella killing assays, insects in the final instar larval stage were purchased from Vanderhorst, Inc. (St. Marys, OH), stored at 4°C in the dark.

extract_protocol:
RNA Extraction. Total RNA was extracted from those samples using the mirVana RNA Isolation Kit (Life Technologies, Grand Island, NY). Samples were bead-beaten for 1 min at maximum speed with 300 μl of 0.1-mm zirconia-silica beads (BioSpec Products, Bartlesville, Okla.) in the mirVana lysis buffer. Bacterial ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kits (Bacteria) (Epicentre, Madison, WI) following the manufacturer's protocol. For RNA processing for eukaryotic analysis, we used Dynabeads mRNA Purification Kit to isolate eukaryotic mRNA for transcriptome analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols. For RNA sequencing, Illumina adapter-specific primers were used to amplify and selectively enrich for the cDNA generated from enriched mRNA. Quantified libraries were pooled and sequenced using a HiSeq 2500 machine, 2x100 Flow-cell (Illumina). The Nextera XT kit was used to generate libraries from amplified DNA.

treatment_protocol:
Bacterial infection experiments. P. gingivalis wild-type and Δcas3 mutant were harvested from the broth culture by centrifugation, bacteria were washed 3x in RPMI-1640 medium and adjusted to OD660 1.0 (approximately 1x109 CFU/ml) and added to PMA-activated THP-1 cells at a multiplicity of infection of 100, in the antibiotic-free medium, and after 2h of infection, THP-1 cells were washed to remove non-adherent bacteria. After 2hr incubation, THP-1 cells were treated for 1 hr with metronidazole (200 μg/ml)/gentamicin (300 μg/ml) to kill extracellular bacteria (94), were washed to remove antibiotics, then were lysed with sterile water, followed by addition of an equal volume of 2x PBS, and serial 10-fold dilutions of each lysate were plated on blood agar plates. CFU/ml of P. gingivalis was calculated. In separate experiments, THP-1 cells were cultured with P. gingivalis wild-type or the mutant, and both cell culture supernatant fluids, and RNA were harvested for measurement of cytokine expression and dual transcription, respectively.
Galleria mellonella infection model. Seven groups of 15 larvae, ranging from 200 to 300 mg, and with no signs of melanization, were randomly chosen and used for subsequent infection. A 25-μl Hamilton syringe was used to inject 5-μl aliquots of bacterial inoculum into each larva's hemocoel via the last left proleg (96). Two groups received wild-type P.gingivalis (7.7x108, and 7.7x107 CFUs per larvae), two groups received the cas3 mutant (4.3x108 and 4.3x107 CFUs per larvae). Three control groups included THSB medium alone, THSB + P. gingivalis wild-type heat-killed (10 min at 75oC), and THSB + Δcas3 mutant heat-killed (10 min at 75oC). After injection, larvae were incubated at 37°C, and the appearance of melanization and survival were recorded at 0.5, 1, 1.5, 2, 3, 3.75, 4.25, 6.25, 22, 24, 28 and 42 hours. After injection, larvae were incubated at 37°C, and appearance (signs of melanization) and survival were recorded at selected intervals. Larvae were scored as dead when they displayed no movement in response to touch. Kaplan-Meier killing curves were plotted, and estimations of differences in survival were compared using a log-rank test. A P value of ≤0.05 was considered significant. All data were analyzed with GraphPad Prism,


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax15


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax14


title: SkMuscle_Ta_1mo_rep6


title: peripheral blood buffy coat, S0014


title: peripheral blood buffy coat, S0040


title: Diabetic Foot Skin Donor #11


title: peripheral blood buffy coat, S0013


title: SkMuscle_Ta_3mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C11_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad012


title: SkMuscle_Ta_1mo_rep5


title: SkMuscle_Ta_1mo_rep4


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax13


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax12


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad010


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax11


title: SkMuscle_Ta_1mo_rep3


title: peripheral blood buffy coat, S0012


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad008


title: peripheral blood buffy coat, S0011


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax10


title: SkMuscle_Ta_1mo_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad007


title: peripheral blood buffy coat, S0010


title: SkMuscle_Ta_1mo_rep1


title: G.mellonella injected with Cas3KO Porphyromonas gingivalis Wax9


title: peripheral blood buffy coat, S0009


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad006


title: G.mellonela injected with WT Porphyromonas gingivalis Wax8


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad004


title: erf13-3-3

city: Qingdao

first: bingsheng

last: lv

state: shan dong

address: Jimo Binhai Lu 72

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The seedlings grew on 1/2 MS medium for 9 days, the roots of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Roots

tag: genotype

value: ERF13 SRDX line


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C4_ad002

value: male


title: peripheral blood buffy coat, S0008

value: peripheral blood buffy coat


title: peripheral blood buffy coat, S0007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C10_ad002


title: erf13-3-2


title: G.mellonela injected with WT Porphyromonas gingivalis Wax6

tag: treatment


title: erf13-3-1


title: G.mellonela injected with WT Porphyromonas gingivalis Wax7


title: 35S ERF13 MYC-3

value: ERF13 over expression line


title: peripheral blood buffy coat, S0005

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: G.mellonela injected with WT Porphyromonas gingivalis Wax5


title: 35S ERF13 MYC-2


title: peripheral blood buffy coat, S0004

tag: child sex (male = 0; female = 1)


title: G.mellonela injected with WT Porphyromonas gingivalis Wax4


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad008


title: peripheral blood buffy coat, S0003

tag: tissue


title: G.mellonela injected with WT Porphyromonas gingivalis Wax3


title: peripheral blood buffy coat, S0001

tag: pre-pregnancy bmi (kg/m^2)


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad007


title: WT-3

value: wild type


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad012


title: WT-1


title: EHEC Term-seq 2

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: RNA 3' ends

data_processing:
trimming ->flexbar; Dodt et al Biology (Basel) 2012
alignment ->novoalign; http://www.novocraft.com/products/novoalign/
mapping ->pyReadCounters (pyCRAC package); https://bitbucket.org/sgrann/pycrac/src/default/
Genome_build: Escherichia coli O157H7 03/29/2000 Assembly (eschColi_O157H7); http://microbes.ucsc.edu/cgi-bin/hgTracks?db=eschColi_O157H7&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr%3A10001%2D35000&hgsid=3141099_gK4Oe4AymM112WpWcC3Jj6rgOKtz
Supplementary_files_format_and_content: Bedgraph and SGR format files containing chromosome, position and read depth. A separate file is provided for each strand - indicated plus or minus in the file name

organism: Escherichia coli O157:H7 str. Sakai

source_name: whole cell culture

growth_protocol: Samples were inoculated 1/100 from overnight LB cultures into MEM-HEPES media supplemented with 0.1% glucose and 250nM FeNO3. The culture was growth to OD600=0.8 and harvested using RNAlater and a Qiagen RNEasy kit as per manufactures instructions.

extract_protocol:
Rna was extracted using RNAlater and a Qiagen RNEasy kit as per the manufacturers instructions
Total RNA sequence sampels were processed at the Ramaciotti Centre for Genomics at the University of New South Wales using standard protcols. dRNA-seq and Term-seq libraries were prepared by Veritis Biotechnologies (Freiberg,  Germany) using protcols adapted from (Sharma CM et al. 2010. Nature 464:250-255) and (Dar et al Nature 2016) respectively.

treatment_protocol: Cells were not additionally treated

tag: experiment

value: Term-Seq


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C1_ad002


title: THP1_LPS_4

city: Stanford

first: Jesse

middle: M

last: Engreitz

address: Biomedical Innovation Building Rm 3700

institute: Stanford University

description: HyPR-seq probes against innate immune response genes

data_processing:
Library strategy: HyPR-seq
Filter reads with fastp
Extract cell barcodes with UMI-Tools
Map reads to custom index with Bowtie
Convert to bam files with SAMTools
Generate count tables with UMI-Tools
Genome_build: hg19
Supplementary_files_format_and_content: HyPR-seq: count tables (cells by probes or cells by genes) for all cells that passed QC

molecule: other

source_name: THP1 monocytic cell line

growth_protocol:
K562: The immortalized myelogenous leukemia K562 cell line was obtained from ATCC (ATCC, CCL-243). Cells were maintained in RPMI 1640 Medium (Corning, 10-040-CM) supplemented with 10% fetal bovine serum (Life Technologies, 16140071) and 1% penicillin-streptomycin (Life Technologies, 15140163). Cell lines were cultured at 37°C with 5% CO₂ and were subcultured twice a week by aspirating off all cell culture medium except 0.5 ml in a T-75 flask and 1 ml in a T-175 flask, and refreshing the flasks with 13 ml and 49 ml of medium respectively.
THP1: The human monocyte THP1 cell line was obtained from ATCC (ATCC, TIB-202). Cells were maintained in RPMI 1640 Medium (Corning, 10-040-CM) supplemented with 10% fetal bovine serum (Life Technologies, 16140071) and 1% penicillin-streptomycin (Life Technologies Inc., 15140163). Cell lines were cultured at 37°C with 5% CO₂ and were subcultured twice a week by aspirating off all cell culture medium except 0.5 ml in a T-75 flask and 1 ml in a T-175 flask, and refreshing the flasks with 13 ml and 49 ml of medium respectively.

extract_protocol:
For HyPR-Seq, cells are harvested in 1X phosphate buffered saline (PBS) at 350g for 5 mins at 4°C in a swinging bucket rotor. Cells were fixed in 4% Formaldehyde solution (4% formaldehyde in 1XPBS and 0.1% Tween 20) for one hour at room temperature at a concentration of 1 million cells per ml. The fixed cells are then washed twice with of 1X PBS containing 0.2% Tween 20 (1X PBST) at 850g for 5 mins at 4°C. The washed cells were then permeabilized in 70% ice cold ethanol at a concentration of 1 million cells per ml and stored at 4°C for 10 mins. The permeabilized cells are then harvested and washed twice with 1XPBST (850g for 5 mins). The cells were then transferred to 2ml V-bottom tubes for subsequent probe hybridization with up to 5 million (cells per hybridization reaction. The cells were resuspended in 0.5mls of probe hybridization buffer (5X SSC, 30% formamide, 0.1% Tween 20) and was incubated at 37°C for 5 min. Probes mix was prepared at a concentration of 20nM per probe in 2mls of probe hybridization buffer. The prehybridized cells are harvested at 850g for 5 mins at room temperature, resuspended in the probes mix and incubated overnight at 37°C in a hybridization oven (VWR Cat# 10055-006). The probe hybridized cells were harvested (850g for 5 mins) and washed with probe hybridization buffer with a 10min incubation of cells in buffer at 37oC before the spin. These wash and incubation steps were done a total of four times. After the last spin, the cells were incubated in a 75nM H1 hairpin mix. To prepare the H1 hairpin mix for one hybridization reaction, 5ul of 3uM H1 hairpin was snap cooled (heat at 95°C for 90 seconds and cooled to room temperature for 30 min) and resuspended in 200ul of 5XSSCT buffer (5XSSC and 0.1% Tween 20). The cells were resuspended in 200ul of H1 hairpin mix was incubated at 37°C for one hour in the hybridization oven. After the H1 hairpin hybridization, the cells are washed twice with 5XSSCT at room temperature (850g for 5 mins). The cells are then resuspended in a 75nM “readout” oligo mix. To prepare the “readout” mix for one hybridization reaction, 5ul of 3uM of “readout” oligo was snap cooled as detailed above and resuspended in 200ul of 5XSSCT buffer. The cells are resuspended in the oligo mix and incubated 37°C for one hour. After oligo incubation, the cells were harvested and washed in 5X SSCT three times (850g for 5 mins). After the last spin the cells were suspended in and washed 1X T4 Ligase reaction buffer (NEB #B0202S). Finally, the cells were resuspended in Ligase buffer (1X T4 ligase buffer, 1:50 dilution of T4 DNA ligase NEB #M0202S) and incubated at room temperature for one hour. Following this final incubation, cells were washed three times in 1XPBST and filtered through a 20micron filter (20um pluriStrainer cat. 43-0020-01). The cells were then counted using a hemocytometer (Fisher Scientific SKU#DHCF015) and checked for single cell suspension before proceeding to droplet generation. For long term storage of the cells, add RNase inhibitor to the cell suspension (NEB M0314S).
To generate emulsions, we first combined 2X Evagreen supermix (Biorad cat 186-4033), 500nM indexing primer (Table S3), 2,000 cells and 20,000 barcoded beads (Chemgenes) in a total of 20ul per reaction. Once the PCR mix is made, emulsions were generated using QX200 Digital Droplet Generator (BioRad #1864002) as per manufacturer’s instructions. Briefly, the droplet generation cartridge (Biorad #186-4007) was inserted into the holder (Biorad 186-3051) and 20ul of the prepared PCR mix was added to the middle sample wells as per instructions. 70ul of the droplet generating oil (Biorad, 186-4005) was added into the bottom row and the gasket (Biorad 186-4007) was placed over the filled cartridge and placed in the droplet generator. Once the droplets were formed, the cartridge containing the emulsions was placed under the UV lamp (6.5 J/cm2 at 365 nm) about 3-8cms away from the bulb for 5min. After UV exposure, ~50ul of droplets per well were transferred to 96 well plates (Eppendorf 951020362) and sealed with foil (Biorad #181-4040) using a plate sealer (PX1 Plate Sealer 181-4000) for droplet PCR amplification (Eppendorf Mastercycler Pro E90030010). The following cycling conditions were used: Denaturation: 94°C for 30 sec; Cycling: 30 cycles of 94°C for 5 sec, 64°C for 30 sec, and 72°C for 30 sec; Final extension: 72°C for 5 min. All PCR cycling steps were performed with 50% ramp rate (2°C/min). To break the emulsions, one to four PCR wells were combined in a tube and equal volumes of 100% PFO were added (~150l). The tubes were vortexed for 5 sec to ensure complete emulsion breakage and spun at 1000g for 1min. The top aqueous layer was carefully removed and cleaned with 1.8X SPRI beads according to manufacturer’s instructions. The amplicon libraries were loaded on a gel to determine size (206bp) and to ensure no primer dimers remained. The libraries were quantified by Qubit before proceeding to sequencing.

treatment_protocol: THP1 cells were stimulated using cell culture medium with LPS at a final concentration of 0.5 µg/ml, diluted from a 5 mg/ml LPS stock (Millipore Sigma, L3024), for 20 hours.

tag: data source

value: cell line

tag: cell type

tag: timepoint

tag: stimulation

value: LPS +

tag: probe number


title: EHEC Term-seq 3

description: RNA 3' ends


title: THP1_LPS_3


title: EHEC Term-seq 1

description: RNA 3' ends


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad012

tag: brain region

value: DG

tag: Sex

tag: strain


title: THP1_NoLPS_4

value: LPS -


title: EHEC dRNA-seq TEX-

description: RNA 5' ends

value: dRNA-Seq


title: 35S ERF13 MYC-1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad010

tag: age


title: G.mellonela injected with WT Porphyromonas gingivalis Wax2


title: THP1_NoLPS_3


title: EHEC dRNA-seq TEX+

description: RNA 5' ends


title: THP1_LPS_2


title: G.mellonela injected with WT Porphyromonas gingivalis Wax1


title: mock fed, rep. 1

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

description:
background
mock_1

data_processing:
Sequence data were trimmed using Trimmomatic prior to mapping to the Drosophila melanogaster cDNA transcriptome (BDGP6) using kallisto.
Genome_build: BDGP6
Supplementary_files_format_and_content: tpm

organism: Drosophila melanogaster

source_name: mock 1

growth_protocol: larvae were cultured on standard growth medium at 25C.

extract_protocol:
Total RNA was extracted using Trizol.  RNA biotinylation and purification was performed using the Click IT Nascent RNA Capture Kit (ThermoFisher)
NuGen Ovation Universal RNA-Seq with AnyDeplete ribosomal RNA removal

treatment_protocol: 5EUd and 5EC feeding was performed for 12 hours in standard media.

value: all carcass cells

value: mock fed

value: early L3


title: 109(2)80_CD:UPRT, EC fed, rep. 1

value: md neurons

value: EC fed


title: mock fed, rep. 2

description:
background
mock_2

source_name: mock 2


title: EHEC total RNA-seq 3

description: total RNA

value: RNA-Seq


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad004


title: WT-2

tag: seedling age

value: Roots


title: THP1_LPS_1

tag: genotype


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad002

value: male


title: EHEC total RNA-seq 2

description: total RNA


title: reference, Eud fed, replicate 2

source_name: reference tag Eud 2

tag: treatment

value: Eud fed


title: reference, Eud fed, replicate 1

source_name: reference tag Eud 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B9_ad001


title: THP1_NoLPS_1


title: 109(2)80_CD:UPRT, EC fed, rep. 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad012


title: K562_mixing

description: HyPR-seq probes against detection barcodes for mixing experiment

source_name: K562 immortalised myelogenous leukemia cell line


title: EHEC total RNA-seq 1

description: total RNA


title: 50_LPS

city: Juiz de Fora

first: Raquel

middle: Morais de Paiva

last: Daibert

address: Av. Eugenio do Nascimento, 610

country: Brazil

institute: Embrapa Dairy Cattle

data_processing:
RNA-seq reads quality avaliation by Fastqc
Reads were aligned to Bos taurus whole genome (UMD3.1.94) using STAR v.2.6.0c
The transcripts abundance were estimated by HTSeq-count v0.10.0 for each sample
Gene expression was calculated by EdgeR package version 3.8 using contrasted transcript abundance files between divergent phenotypes to each cell cultured treatment (unstimulated and LPS)
Genome_build: UMD3.1.94
Supplementary_files_format_and_content: tab-delimited text files include Ensembl gene codes and counts for each Sample

molecule: polyA RNA

organism: Bos taurus

source_name: Peripheral blood

growth_protocol: Monocyte derived macrophages (1x108 cells) from from Taurine and Indicine bovines were grown in RPMI medium containing 10% FBS, and supplemented with 10.000 units/ml penicillin, 10 mg/m streptomycin and 25 μg/ml amphotericin B, 2mM L-glutamin, 10mM Sodium Piruvate and 1% Non-essential amino acids for 11 days. Then, 100 ng/ml LPS was added to medium for 48h in treated samples.

extract_protocol:
200 ng of total RNA was subjected to library synthesis using the HiSeq SBS Kit v4. 200 ng of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end-repaired (100 bp), adenylated, and ligated with Illumina indexes by PCR. Sequencing was pair-end performed using HiSeq Flow Cell v4.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peripheral blood mononuclear cells were isolated from Taurine and Indicine bovines  with Ficoll Paque PLUS reagent and incubated for 11 days at 37°C in 5% CO2 in supplemented RPMI medium and followed by successive washes to eliminate non-adherent cells. Resulted monocyte derived macrophages were treated with LPS or left with medium only (not treated) for 48h.

tag: breed

value: Taurine

value: Monocyte-derived macrophages

value: LPS


title: 50_CTRL

value: Unstimulated


title: K562_timecourse_20hr_3

description: HyPR-seq probes against GATA1 locus genes and introns, timecourse

value: cell line


title: 3_LPS


title: K562_timecourse_20hr_1


title: K562_timecourse_20hr_2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad008

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: DG


title: 3_CTRL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad006


title: THP1_NoLPS_2

value: LPS -


title: ΔaphB(AphB+) 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Delta phy Reconst IIA

hyb_protocol: Cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Images were Scanned using Agilent Technologies G2600D

data_processing: Images were quantified using Feature Extraction software Version 11.5.1.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX Vsoftware from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Xanthomonas oryzae pv. oryzae

source_name: ΔaphB reconstituted with full aphB

label_protocol: Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis). The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity using Nanodrop.

extract_protocol: RNA was prepared using Trizol (Invitrogen,CA,USA) method

treatment_protocol: Peptone sucrose medium grown bacterial secondary culture (mid exponential phase)

tag: strain background

value: Xoo

tag: genotype/variation

value: phytochrome null mutant with full phytochrome reconstituted


title: DFU Patient UM#27W4

value: Ulcer

value: Nonhealer


title: ΔaphB 2

description: Delta aph B IIA

source_name: derivative of Xoo(WT)

value: phytochrome null mutant


title: ΔaphB 1

description: Delta aph B IA


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad002

city: La Jolla

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: ΔaphB(AphB+) 1

description: Delta phyReconst IC


title: 20_CTRL


title: K562_timecourse_6hr_2


title: Xoo(WT) 2

description: XOO IIA

source_name: Indian isolate

value: Xoo wild type


title: K562_timecourse_6hr_3


title: 20_LPS


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_C3_ad002


title: K562_timecourse_6hr_1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad012


title: DFU Patient UM#28W4


title: 1_CTRL


title: 7_LPS

value: Indicine


title: 7_CTRL


title: Xoo(WT) 1

description: XOO ID


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B8_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad008


title: K562_timecourse_5.5hr_3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad006


title: K562_timecourse_5hr_3


title: 6_CTRL


title: 1_LPS


title: 5_LPS


title: K562_timecourse_5.5hr_1


title: K562_timecourse_5hr_2


title: 5_CTRL


title: Muscle_W_12mo_rep3

hyb_protocol: Standard Affyemtrix protocol

scan_protocol: Standard Affyemtrix protocol

data_processing: Raw signal intensity data was background corrected, log2 transformed and normalized with robust multi-array average (RMA) from the Affymetrix data bank using the “oligo” package in R v4.0.1 (8). Each Affymetrix chip contains 25,117 probesets, including 2163 control and unmapped probesets.

label: biotin

source_name: gastrocnemius, W, 12 months, replicate 3

label_protocol: Standard Affyemtrix protocol

growth_protocol: Male Sprague-Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol: Total RNA was isolated from gastrocnemius muscle using TRIzol® reagent (Invitrogen, Carlsbad, CA) following manufacturer’s protocol. For each metal and time point, three Affymetrix chips (Clariom S Rats) were used with 250 ng of total RNA derived from a pooled sample from 2-3 animals.

tag: gender

value: Male

value: Sprague-Dawley

tag: tissue

value: Skeletal Muscle

value: W

tag: time


title: Muscle_W_06mo_rep3

source_name: gastrocnemius, W, 6 months, replicate 3


title: Muscle_W_03mo_rep3

source_name: gastrocnemius, W, 3 months, replicate 3


title: Muscle_W_12mo_rep2

source_name: gastrocnemius, W, 12 months, replicate 2


title: 2_LPS

tag: cell type

value: Monocyte-derived macrophages


title: Muscle_W_06mo_rep2

source_name: gastrocnemius, W, 6 months, replicate 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad012

value: male


title: K562_timecourse_4.5hr_2

tag: data source

tag: timepoint


title: 6_LPS

value: LPS


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad002


title: K562_timecourse_5.5hr_2

value: cell line

tag: stimulation

tag: probe number


title: K562_timecourse_4.5hr_3


title: 2_CTRL

value: Unstimulated


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B7_ad001

tag: brain region

value: DG

tag: Sex


title: Muscle_W_03mo_rep2

source_name: gastrocnemius, W, 3 months, replicate 2

tag: strain


title: K562_timecourse_4.5hr_1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad010

tag: age


title: K562_timecourse_4hr_3

tag: genotype


title: K562_timecourse_5hr_1


title: Muscle_W_01mo_rep3

source_name: gastrocnemius, W, 1 month, replicate 3

tag: treatment


title: Muscle_W_01mo_rep2

source_name: gastrocnemius, W, 1 month, replicate 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad008


title: SW480 shRBMS1 9hr rep 2

description: RNA-seq

data_processing:
STAR (v2.5) was used to map the reads to the human transcriptome (build hg38).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Cuffdiff was used to compare transcipt expressions with and without amanitin treatment for shControl and shRBMS1 samples.
RNA stability changes were then reported by normalizing log fold-change values in shRBMS1 cells to control cells for RefSeq ID.
Genome_build: hg38
Supplementary_files_format_and_content: Cufflinks tracking output file for genes, and processed gene expression log-fold changes (with and without 9hr amanitin) for RefSeqs using cuffdiff

extract_protocol:
RNA samples were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on an Illumina HiSeq 4000.

treatment_protocol: Cells were transduced with shRNAs, either shControls or shRBMS1 (TRCN0000074936, Sigma). They were also treated with amanitin for 9hr or not (0hr).

tag: replicate

tag: time point

tag: agent

value: amanitin

tag: cell line

tag: shRNA


title: Muscle_W_06mo_rep1

source_name: gastrocnemius, W, 6 months, replicate 1

tag: gender

tag: tissue

tag: time


title: Muscle_W_12mo_rep1

source_name: gastrocnemius, W, 12 months, replicate 1


title: SW480 shRBMS1 9hr rep 1

description: RNA-seq


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad007


title: K562_timecourse_4hr_2

tag: data source

tag: cell type

tag: timepoint


title: SW480 shRBMS1 0hr rep 1

description: RNA-seq


title: SW480 shControl 9hr rep 2

description: RNA-seq

value: shControl


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad004

tag: brain region


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad002

tag: Sex


title: K562_timecourse_3.5hr_2

tag: stimulation

tag: probe number


title: K562_timecourse_3.5hr_3

tag: genotype


title: Muscle_Ta_12mo_rep3

source_name: gastrocnemius, tantalum, 12 months, replicate 3

tag: strain

tag: treatment

value: Ta


title: SW480 shControl 9hr rep 1

description: RNA-seq

tag: replicate

tag: time point


title: SW480 shControl 0hr rep 2

description: RNA-seq

tag: agent

tag: cell line


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B6_ad001

tag: age


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad012


title: K562_timecourse_3hr_3

source_name: K562 immortalised myelogenous leukemia cell line


title: SW480 shControl 0hr rep 1

description: RNA-seq

tag: shRNA


title: Muscle_W_03mo_rep1

source_name: gastrocnemius, W, 3 months, replicate 1

tag: gender

tag: tissue

tag: time


title: SW480 shRBMS1 0hr rep 2

description: RNA-seq


title: K562_timecourse_4hr_1

tag: data source

tag: cell type

tag: timepoint


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad010

tag: brain region

tag: Sex


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad008


title: shAKAP12 sample rep 3

description: RNA-seq

data_processing:
STAR (v2.7) was used to map the reads to the human transcriptome (build hg38).
featureCounts (v1.6) was used to count reads that map to each gene.
DESeq2 (v1.22) was used to compare transcipt expressions
Genome_build: hg38
Supplementary_files_format_and_content: featureCount output files for genes, and processed gene expression log-fold changes for genes using DESeq2

extract_protocol:
RNA samples were extracted 48 hours after seeding using total RNA isolation kit (Norgen Biotek).
Libraries were generated using QuantSeq FWD kit and run on an Illumina HiSeq 4000.

treatment_protocol: CRISPRi-ready cells (expressign dCas9-KRAB) were transduced with sgRNAs, either sgControls or sgAKAP12.


title: Muscle_W_01mo_rep1

source_name: gastrocnemius, W, 1 month, replicate 1


title: K562_timecourse_3hr_2

tag: stimulation

tag: genotype

tag: probe number


title: K562_timecourse_3hr_1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad006

tag: strain


title: Muscle_Ta_06mo_rep3

source_name: gastrocnemius, tantalum, 6 months, replicate 3

tag: treatment


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad002


title: shAKAP12 sample rep 1

description: RNA-seq

tag: replicate


title: K562_timecourse_3.5hr_1


title: shControl sample rep 2

description: RNA-seq

tag: cell line


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B5_ad001

tag: age


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad012


title: shControl sample rep 1

description: RNA-seq

tag: shRNA


title: K562_timecourse_2.5hr_3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad010


title: shAKAP12 sample rep 2

description: RNA-seq


title: K562_timecourse_2.5hr_2


title: K562_timecourse_2.5hr_1


title: K562_timecourse_2hr_3


title: Muscle_Ta_12mo_rep2

source_name: gastrocnemius, tantalum, 12 months, replicate 2

tag: gender


title: Muscle_Ta_01mo_rep3

source_name: gastrocnemius, tantalum, 1 month, replicate 3

tag: tissue


title: Liver metastasis from patient 567

description:
RNA-seq
p567_Met_v_Pri.isoforms.fpkm_tracking

data_processing:
Reads were trimmed (-q 15 -u 9 -a AGATCGGAAGAGCACACGTCT) using cutadapt.
STAR (v2.5) was used to map the reads to the human transcriptome (build hg38).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Cuffdiff was used to compare transcipt expressions with and without amanitin treatment for shControl and shRBMS1 samples.
Genome_build: hg38
Supplementary_files_format_and_content: Cufflinks tracking output file for genes, and processed gene expression log-fold changes (with and without 9hr amanitin) for RefSeqs using cuffdiff

source_name: Liver metastasis

extract_protocol:
Cryopreserved tissue from primary and metastatic tumors were thawed on ice and ground with ice-cold mortar and pestle. Total RNA was then extracted from ground tissue using the Nucleospin RNA Plus kit from Machery-Nagel.
Lexogen SENSE total rna-seq kit (FFPE/degraded RNA protocol) was then used to prepare Ribo-cop depleted RNA samples into Illumina compatible fragments.

tag: biopsy location

value: liver

tag: patient id


title: Muscle_Ta_03mo_rep3

source_name: gastrocnemius, tantalum, 3 months, replicate 3

tag: time


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad008


title: Muscle_Ta_06mo_rep2

source_name: gastrocnemius, tantalum, 6 months, replicate 2


title: Muscle_Ta_03mo_rep2

source_name: gastrocnemius, tantalum, 3 months, replicate 2


title: Muscle_Ta_01mo_rep1

source_name: gastrocnemius, tantalum, 1 month, replicate 1


title: Muscle_Ta_01mo_rep2

source_name: gastrocnemius, tantalum, 1 month, replicate 2


title: K562_timecourse_2hr_1

tag: data source

tag: cell type

tag: timepoint


title: Muscle_Ta_03mo_rep1

source_name: gastrocnemius, tantalum, 3 months, replicate 1


title: Primary tumor from patient 1029

description:
RNA-seq
p1029_Met_v_Pri.isoforms.fpkm_tracking

source_name: Primary tumor

value: colon


title: Muscle_Ta_06mo_rep1

source_name: gastrocnemius, tantalum, 6 months, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad007

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: Sex


title: Liver metastasis from patient 1029


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad006


title: K562_timecourse_1.5hr_3

tag: stimulation

tag: genotype

tag: probe number


title: K562_timecourse_2hr_2


title: K562_timecourse_1.5hr_2


title: Muscle_Ta_12mo_rep1

source_name: gastrocnemius, tantalum, 12 months, replicate 1

tag: strain

tag: treatment


title: U87MG-WT-3

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

data_processing:
Reads were mapped to GRCh38 using STAR v2.5.2
Gene quantifications were calculated using Cufflinks v2.2.1 to quantify refGene annotations. Gene read counts calculated using featureCounts v1.6.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read counts per gene for each Sample

growth_protocol: HCT116 (ATCC, CCL-247) and GSTO1 KO cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum. U-87 MG (generously provided by Dr. Alan L. Epstein (University of Southern California, Los Angeles, CA)) Cells were kept at 37 ̊C in a humidified atmosphere of 5% CO2. All cell lines were maintained in culture under 30 passages and tested regularly for Mycoplasma contamination using PlasmoTest.

extract_protocol:
Cells were lysed with TRIzol® Reagent (ThermoFisher Scientific, Waltham, MA) at room temperature. RNA was further purified with DirectZol kit (Zymo Research, Irvine, CA).
RNA quality was assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared with TruSeq Stranded mRNA Library Prep (Illumina) per the supplier’s protocol with 1μg of RNA and 12 cycles of PCR amplification. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (Illumina). The libraries were barcoded, pooled and sequenced using 50bp paired-end 50bp (U-87 MG, University of Michigan DNA Sequencing Core, MI) and single-end 50bp (HCT116, University of Michigan DNA Sequencing Core, MI) sequencing.

treatment_protocol: GSTO1 knockout cancer cell lines were generated using the Edit-R CRISPR-Cas9 system from Dharmacon (GE Healthcare, Lafayette, CO). Edit-R Lentiviral hEF1α-Blast-Cas9 lentiviral particles (generously provided by Phillip L. Palmbos, University of Michigan, MI) were transduced into U-87 MG, HCT116 and A172 cells and stable Cas9 expressing lines were generated by blasticidin selection. Cells were co-transfected with tracrRNA and GSTO1-targeting crRNA (CM-011950-01-0002) specific for exon 2 or non-targeting crRNA control (U-002000-05). Individual colonies were further selected and screened for loss of GSTO1 expression. Targeted mutations were confirmed using Sanger sequencing.

tag: cell line


title: Primary tumor from patient 567


title: U87MG-WT-2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad004

address: 10010 North Torrey Pines Road

tag: age


title: Muscle_Pb_12mo_rep3

city: Lexington

first: Yuan

last: Wen

institute: University of Kentucky

source_name: gastrocnemius, lead, 12 months, replicate 3

tag: gender

value: Pb


title: K562_timecourse_1.5hr_1

source_name: K562 immortalised myelogenous leukemia cell line


title: Muscle_Pb_06mo_rep3

source_name: gastrocnemius, lead, 6 months, replicate 3

tag: tissue


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad012


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B4_ad001


title: K562_timecourse_1hr_3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad010


title: U87MG-WT-1


title: U87MG-KO-3


title: K562_timecourse_1hr_2


title: Muscle_Pb_12mo_rep2

source_name: gastrocnemius, lead, 12 months, replicate 2


title: K562_timecourse_1hr_1


title: K562_timecourse_0.5hr_3


title: U87MG-KO-2


title: K562_timecourse_0.5hr_2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad008


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad007


title: U87MG-KO-1


title: Muscle_Pb_03mo_rep3

source_name: gastrocnemius, lead, 3 months, replicate 3


title: Muscle_Pb_03mo_rep2

source_name: gastrocnemius, lead, 3 months, replicate 2


title: Muscle_Pb_06mo_rep2

source_name: gastrocnemius, lead, 6 months, replicate 2


title: Muscle_Pb_01mo_rep2

source_name: gastrocnemius, lead, 1 month, replicate 2


title: Muscle_Pb_01mo_rep3

source_name: gastrocnemius, lead, 1 month, replicate 3


title: Muscle_Pb_12mo_rep1

source_name: gastrocnemius, lead, 12 months, replicate 1


title: K562_timecourse_0hr_3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad012


title: K562_timecourse_0hr_2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B3_ad001


title: K562_highly_expressed_2

description: HyPR-seq probes against highly expressed genes and introns


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad008


title: Muscle_Ni_06mo_rep3

source_name: gastrocnemius, nickel, 6 months, replicate 3

value: Ni


title: Muscle_Pb_06mo_rep1

source_name: gastrocnemius, lead, 6 months, replicate 1

value: Male


title: Muscle_Pb_01mo_rep1

source_name: gastrocnemius, lead, 1 month, replicate 1

value: Sprague-Dawley


title: THP1_LPS_RNAseq_3

description: PolyA mRNA from THP1 cells

data_processing:
Pseudo-align reads to hg19 transcriptome index using kallisto
Aggregate TPM values over all isoforms for the same gene
Genome_build: hg19
Supplementary_files_format_and_content: Expression level (TPM) for each gene

source_name: monocytic cell line

growth_protocol: The human monocyte THP1 cell line was obtained from ATCC (ATCC, TIB-202). Cells were maintained in RPMI 1640 Medium (Corning, 10-040-CM) supplemented with 10% fetal bovine serum (Life Technologies, 16140071) and 1% penicillin-streptomycin (Life Technologies Inc., 15140163). Cell lines were cultured at 37°C with 5% CO₂ and were subcultured twice a week by aspirating off all cell culture medium except 0.5 ml in a T-75 flask and 1 ml in a T-175 flask, and refreshing the flasks with 13 ml and 49 ml of medium respectively.

extract_protocol:
RNA was extracted from 20 million THP1 cells in thre biological replicates.
RNA-seq libraries were prepared using the Smart-seq2 protocol in bulk

value: LPS +


title: Muscle_Pb_03mo_rep1

source_name: gastrocnemius, lead, 3 months, replicate 1

value: Skeletal Muscle


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: K562_highly_expressed_1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad002


title: Muscle_Ni_01mo_rep3

source_name: gastrocnemius, nickel, 1 month, replicate 3


title: THP1_NoLPS_RNAseq_3

description: PolyA mRNA from THP1 cells

value: LPS -


title: THP1_NoLPS_RNAseq_2

description: PolyA mRNA from THP1 cells


title: THP1_LPS_RNAseq_1

description: PolyA mRNA from THP1 cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B12_ad006

value: male


title: K562_timecourse_0.5hr_1


title: THP1_LPS_RNAseq_2

description: PolyA mRNA from THP1 cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B12_ad002


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad004


title: Muscle_Ni_06mo_rep1

source_name: gastrocnemius, nickel, 6 months, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad001


title: K562_timecourse_0hr_1

source_name: K562 immortalised myelogenous leukemia cell line


title: Muscle_Ni_06mo_rep2

source_name: gastrocnemius, nickel, 6 months, replicate 2


title: Muscle_Ni_03mo_rep2

source_name: gastrocnemius, nickel, 3 months, replicate 2